US20150132313A1 - Interferon alpha-induced pharmacodynamic markers - Google Patents

Interferon alpha-induced pharmacodynamic markers Download PDF

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US20150132313A1
US20150132313A1 US14/494,439 US201414494439A US2015132313A1 US 20150132313 A1 US20150132313 A1 US 20150132313A1 US 201414494439 A US201414494439 A US 201414494439A US 2015132313 A1 US2015132313 A1 US 2015132313A1
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ifi6
rsad2
ifi44
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Yihong Yao
Bahija Jallal
Ricardo Ciboti
Anthony Coyle
Peter Kiener
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MedImmune LLC
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MedImmune LLC
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Priority claimed from PCT/US2007/024941 external-priority patent/WO2008070135A2/en
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Assigned to MEDIMMUNE, LLC reassignment MEDIMMUNE, LLC ASSIGNMENT OF ASSIGNORS INTEREST (SEE DOCUMENT FOR DETAILS). Assignors: CIBOTTI, RICARDO, JALLAL, BAHIJA, KIENER, PETER, COYLE, ANTHONY, YAO, YIHONG
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Definitions

  • the present invention relates to pharmacodynamic (PD) markers inducible by interferon (IFN) alpha, probes and kits that detect the PD markers, and methods employing the same.
  • PD pharmacodynamic
  • IFN interferon
  • the present invention encompasses PD markers that are induced by IFN ⁇ .
  • the PD markers can be used in methods of treating patients with a therapeutic agent that binds to and modulates IFN ⁇ activity, methods that identify patients as candidates for a therapeutic agent that binds to and modulates IFN ⁇ activity, methods of diagnosing a patient as having a disorder associated with increased IFN ⁇ levels, methods of monitoring disease progression of a patient receiving treatment with a therapeutic agent that binds to and modulates IFN ⁇ activity, and methods of identifying a candidate therapeutic for treating IFN ⁇ -mediated disorders.
  • One embodiment of the invention encompasses a method of identifying a patient as a candidate for a therapeutic agent that binds to and modulates IFN ⁇ activity. Presence or absence of an IFN ⁇ -inducible PD marker expression profile is detected in a sample from the patient.
  • Another embodiment of the invention encompasses a method of treating a patient having a type I IFN or IFN ⁇ -mediated disease or disorder.
  • An agent that binds to and modulates type I IFN or IFN ⁇ activity is administered to the patient.
  • the agent neutralizes a type I IFN or IFN ⁇ -inducible PD marker expression profile of the patient.
  • Yet another embodiment of the invention encompasses a method of treating an autoimmune disease patient comprising a moderate or strong type I IFN or an IFN ⁇ PD marker profile.
  • An agent that binds to and modulates type I IFN or IFN ⁇ activity is administered to the patient.
  • the agent neutralizes the type I IFN or IFN ⁇ -inducible PD marker expression profile of the patient.
  • a further embodiment of the invention encompasses a method of neutralizing a type I IFN or IFN ⁇ -inducible PD marker expression profile in a patient in need thereof.
  • An agent that binds to and modulates type I IFN or IFN ⁇ activity is administered to the patient.
  • the agent neutralizes the type I IFN or IFN ⁇ -inducible PD marker expression profile of the patient.
  • Another embodiment of the invention encompasses a method of diagnosing a patient as having a disorder associated with increased IFN ⁇ levels. Presence or absence of an IFN ⁇ -inducible PD marker expression profile is detected in a sample from the patient.
  • a further embodiment of the invention encompasses a method of monitoring disease progression of a patient receiving treatment with a therapeutic agent that binds to and modulates IFN ⁇ activity.
  • a first IFN ⁇ -inducible PD marker expression profile is obtained in a first sample from the patient.
  • a therapeutic agent that binds to and modulates IFN ⁇ activity is administered to the patient.
  • a second IFN ⁇ -inducible PD marker expression profile is obtained from a second sample from the patient. The first and the second IFN ⁇ -inducible PD marker expression profiles are compared.
  • Yet another embodiment of the invention encompasses a method of identifying a candidate therapeutic for treating IFN ⁇ -mediated disorders.
  • Cells comprising an IFN ⁇ -inducible PD marker expression profile are contacted with an agent. Presence or absence of a change in the IFN ⁇ -induced PD marker expression profile of the cells is detected.
  • a further embodiment of the invention encompasses a set of probes.
  • kits that comprise the probes.
  • Another embodiment of the invention encompasses a method of detecting IFN activity in a sample.
  • Cells comprising a polynucleotide sequence comprising a reporter gene under the control of an IFN-stimulated response element are incubated with a sample. Expression of the reporter gene is detected.
  • FIG. 1 TAQMAN qPCR IFI44 gene expression analysis of IFN ⁇ -stimulated whole blood of healthy donors.
  • FIG. 2 TAQMAN qPCR IRF2 gene expression analysis of IFN ⁇ -stimulated whole blood of healthy donors.
  • FIG. 3 TAQMAN qPCR RSAD2 gene expression analysis of IFN ⁇ -stimulated whole blood of healthy donors.
  • FIG. 4 TAQMAN qPCR G1P3 gene expression analysis of IFN ⁇ -stimulated whole blood of healthy donors.
  • FIG. 5 TAQMAN qPCR HERC5 gene expression analysis of IFN ⁇ -stimulated whole blood of healthy donors.
  • FIG. 6 MEDI-545 neutralization of RAB8B gene expression induced by IFN- ⁇ in whole blood of healthy donors.
  • FIG. 7 MEDI-545 neutralization of IRF7 gene expression induced by IFN- ⁇ in whole blood of healthy donors.
  • FIG. 8 MEDI-545 neutralization of MARCKS gene expression induced by IFN- ⁇ in whole blood of healthy donors.
  • FIG. 9 MEDI-545 neutralization of IL6ST gene expression induced by IFN- ⁇ in whole blood of healthy donors.
  • FIG. 10 MEDI-545 neutralization of Ly6E gene expression induced by IFN- ⁇ in whole blood of healthy donors.
  • FIG. 11 MEDI-545 neutralization of IFIT3 gene expression induced by IFN- ⁇ in whole blood of healthy donors.
  • FIG. 12 MEDI-545 neutralization of IFIT1 gene expression induced by IFN- ⁇ in whole blood of healthy donors.
  • FIG. 13 MEDI-545 neutralization of HERC5 gene expression induced by IFN- ⁇ in whole blood of healthy donors.
  • FIG. 14 MEDI-545 neutralization of OAS1 gene expression induced by IFN- ⁇ in whole blood of healthy donors.
  • FIG. 15 MEDI-545 neutralization of OAS3 gene expression induced by IFN- ⁇ in whole blood of healthy donors.
  • FIG. 16 MEDI-545 neutralization of RSAD2 gene expression induced by IFN- ⁇ in whole blood of healthy donors.
  • FIG. 17 Ex vivo stimulation in whole blood identifies genes inducible by type I IFN.
  • FIG. 18 MEDI-545 neutralization of top 25 type I IFN inducible genes in individual lupus patients' whole blood.
  • FIG. 19 Heatmap of target modulation and PCA plot using top 25 up-regulated type I IFN inducible probe sets in whole blood of patient 1541 before and after MEDI-545 treatment.
  • FIG. 20 Heatmap of target modulation and PCA plot based on 25 most up-regulated type I IFN inducible genes in whole blood of patient 1449 before and after MEDI-545 treatment.
  • FIG. 21 Heatmap of target modulation calculated based on 165 type I IFN inducible genes up-regulated in whole blood of one patient treated with 0.3 mg/kg MEDI-545.
  • FIG. 22 PCA using 169 probe sets that are type I IFN inducible-24/35 SLE patients have statistically significant type I IFN signature in whole blood.
  • FIG. 23 MEDI-545 neutralizes the top 25 most upregulated type I IFN inducible probe sets of lupus patients.
  • Target neutralization of the top 25 most upregulated type I IFN inducible genes was measured at days 1, 4, 7, 14, 28, and 84 for each patient. Dose range was from 1 (placebo) to 3 mg/kg MedI 545.
  • FIG. 24 MEDI-545 neutralizes the top 25 most upregulated type I IFN inducible probe sets of lupus patients.
  • Target neutralization of the top 25 most upregulated type I IFN inducible genes was measured at days 1, 4, 7, 14, and 28 for each patient. Dose range was from 0 (placebo) to 30 mg/kg MEDI-545.
  • FIGS. 25 a and 25 b Heatmap (a) and PCA (b) showing neutralization of the top 25 type I IFN inducible probe sets in whole blood of a SLE patient treated with 30 mg/kg MEDI-545 at 0, 1, 4, 7, and 14 days post-dosing.
  • FIGS. 26 a and 26 b PCA plots of lupus patient before (a) and after (b) dosing with placebo control show no trend in the change of type I IFN inducible gene signature.
  • the 25 most upregulated type I IFN inducible probe sets were used to perform the PCA analysis.
  • FIG. 27 Type-I IFN ⁇ subtypes are upregulated in the whole blood of individual lupus patients.
  • FIG. 28 Distribution of average fold-change of top 25 type I IFN inducible probe sets in whole blood of individual lupus patients.
  • FIG. 29 a - 29 c Pair-wise fold change ranking test proves MEDI-545 neutralizes type I IFN genes in a clinical trial. Top genes neutralized are shown for (a) SLE patients having a type I IFN gene signature at 14 days following MEDI-545 treatment; ( FIG. 29 a discloses “DEAD (Asp-Glu-Ala-Asp)” as SEQ ID NO: 1) (b) SLE patients not having a type I IFN gene signature at 14 days following MEDI-545 treatment; and (c) SLE patients 14 days following treatment with placebo. Genes highlighted in yellow are genes identified as having a type-I IFN signature.
  • FIG. 30 Hierarchical clustering of 1384 probe sets differentially regulated by IFN ⁇ subtypes, IFN ⁇ , IFN ⁇ , and TNF ⁇ in ex vivo stimulated whole blood. Each row corresponds to a single probe set, while each column corresponds to a single sample.
  • the branch lengths indicate the correlation with which probe sets/samples are joined, with a longer branch indicating a weaker correlation.
  • Color represents relative expression level of individual probe sets as compared to the average expression of the no treatment controls. Red indicates up-regulation versus control; green indicates down-regulation versus control; black indicates no change.
  • FIG. 31 a - 31 b a. Hierarchical clustering of the relative expression of the top 25 most overexpressed type-I IFN inducible probe sets in whole blood ex vivo challenged with a variety of IFN ⁇ subtypes, IFN ⁇ , IFN ⁇ , and TNF ⁇ .
  • b Heatmap of the relative expression of the same 25 probe sets compared to no-treatment control in keratinocyte ex vivo challenged with IFN ⁇ 2a, IFN ⁇ , IFN ⁇ , and TNF ⁇ . Red indicates upregulated gene expression relative to no treatment control, green indicates downregulated gene expression relative to no treatment control, black indicates no significant change in gene expression of challenged samples relative to control.
  • FIG. 32 a - 32 c The distribution of the average (a) and median (b) fold change of the top 25 most overexpressed type-I IFN inducible probe sets in 26 pairs of lesional skin compared to non-lesional skin. (c) the average of the average and median fold change of the top 25 most overexpressed type-I IFN inducible probe sets in 26 pairs of lesional and non-lesional skin.
  • FIG. 33 a - 33 d Relative expression of selected type-I IFN inducible genes ((a) HPSE, (b) OASL, and (c) HERC6) and non type-IFN inducible genes ((d) SERPINB4) in lesional skin (LS) compared to non-lesional skin (NS), and non-lesional skin compared to normal skin (NN) in psoriatic patients based on microarray data. The fold change of these genes in LS is compared to its paired NS, while NS is compared to the average of 21 normal skin controls.
  • selected type-I IFN inducible genes ((a) HPSE, (b) OASL, and (c) HERC6) and non type-IFN inducible genes ((d) SERPINB4) in lesional skin (LS) compared to non-lesional skin (NS), and non-lesional skin compared to normal skin (NN) in psoriatic patients based on microarray data.
  • the p value for HPSE, OASL, HERC6, and SERPINB4 is a comparison between NS and NN, between LS and NS are (listed in pairs): 0.468, ⁇ 0.00001; 0.376, ⁇ 0.00001; 0.03, ⁇ 0.00001; 0.0002, ⁇ 0.00001.
  • FIG. 34 a - 34 b (a) Hierarchical clustering of all psoriasis samples profiled (21 normal (blue bars)) 26 paired non lesional (black bars) and lesional skin (red bars) from 24 psoriatic patients, and 3 lesional skin (red bars) from 3 psoriatic patients whose paired non lesional skin either did not yield sufficient cRNA for hybridization or scanned arrays had scaling factors that were more than 3 times the average) using the 164 upregulated type-I IFN inducible probe sets in lesional skin compared to those in mostly paired non-lesional skin. Each row corresponds to a single probe set, while each column corresponds to a single sample.
  • the branch lengths indicate the degree of correlation with which samples are joined, with a longer branch indicating a weaker correlation.
  • Color represents relative expression level of individual probe set as compared to the average expression of the 21 normals. Red represents upregulation vs. control and green represents downregulation vs. control.
  • FIG. 35 Overexpression of selected type-I IFN inducible genes in 18 pairs of lesional and non-lesional skin from 18 psoriatic patients based on TAQMAN QRT-PCR assays using Fluidigm's BIOMARKTM 48.48 dynamic array.
  • FIG. 36 a - 36 b Correlation coefficient distribution of overexpressed genes in lesional skin of psoriatic patients between TAQMAN and array results. The genes are grouped based on correlation coefficient between TAQMAN QRT-PCR and microarray measurement. (a) correlation coefficient distribution of all 40 upregulated genes in lesional skin that are validated by TAQMAN QRT-PCR; (b) correlation coefficient distribution of 29 type-IFN inducible genes.
  • FIG. 37 a - 37 d Comparison of TAQMAN QRT-PCR based assay using BIOMARKTM48.48 dynamic array and Affymetrix® GENECHIP microarray results for selected type-I IFN inducible genes ISG 15 and MX1.
  • FIG. 38 TAQMAN QRT-PCR validation of Affymetrix® GENECHIP microarray results of overexpression of type-I IFN inducible genes IFI27 and CXCL10.
  • FIG. 39 a - 39 f Ex vivo stimulation of normal keratinocytes with leukocyte IFN and IFN ⁇ 2a and dose-dependent neutralization of type-I IFN induced genes by IFN ⁇ antibody.
  • Each dose titration curve is generated on three technical replicates.
  • FIG. 40 a - 40 c Relative expression of mRNA and median fold changes of type-I IFN ⁇ subtypes ( FIG. 40 a ), other members of the type-I IFNs ( FIG. 40 b ), and IFN ⁇ receptors ( FIG. 40 c ) in the lesional skin (LS) or the non-lesional skin (NS) compared to skin from healthy normal controls (NN).
  • the averages of the relative mRNA levels of these cytokines and their receptors in the normal skin of two healthy donors were scaled to be 1 based on TAQMAN QRT-PCR assays using TLDA from Applied Biosciences.
  • Black the relative fold change of mRNA in the non-lesional skin compared to normal skin (NS/NN); Red: the relative fold change of mRNA in the lesional skin compared to normal skin (LS/NS).
  • the p values for the overexpression of these individual genes in the non-lesional skin or lesional skin compared to healthy normal skin are as follows: IFN ⁇ 1, 0.303, ⁇ 0.001; IFN ⁇ 2, 0.389, 0.072; IFN ⁇ 5, ⁇ 0.001, 0.002; IFN ⁇ 6, 0.664, 0.093; IFN ⁇ 7, 0.586, 0.077; IFN ⁇ 8, 0.430, 0.049; IFN ⁇ 14, 0.224, 0.049; IFN ⁇ 17, 0.552, 0.0203; IFN ⁇ 21, 0.113, 0.003; IFN ⁇ 3, 0.255, 0.022; IFN ⁇ , 0.03, ⁇ 0.001; IFN ⁇ , 0.516, 0.049; IFNAR1, 0.192, ⁇ 0.001; IFNAR2, ⁇ 0.001,
  • FIG. 41 Relative expression of mRNA and median fold changes of IFN ⁇ , TNF ⁇ , and IFN ⁇ receptors in the lesional skin (LS), or the non-lesional skin (NS) compared to skin from healthy normal controls (NN).
  • the averages of the relative mRNA levels of these cytokines and their receptors in the normal skin of two healthy donors were scaled to be 1 based on TAQMAN QRT-PCR assays using TLDA from Applied Biosciences.
  • Black the relative fold change of mRNA in the non-lesional skin compared to normal skin
  • Red the relative fold change of mRNA in the lesional skin compared to normal skin.
  • the p values for the overexpression of these individual genes in the non-lesional skin or lesional skin compared to healthy normal skin are as follows: IFN ⁇ , 0.02, ⁇ 0.001; IFNGR1, ⁇ 0.001, ⁇ 0.001; IFNGR2, ⁇ 0.001, ⁇ 0.001; TNF ⁇ , ⁇ 0.001, ⁇ 0.001, respectively.
  • FIG. 42 A Venn diagram illustrating both the number of probe sets that are altered by type I IFN, IFN ⁇ , and TNF ⁇ during ex vivo stimulation, and probe sets that are altered in the lesional skin compared to non-lesional skin.
  • Red numbers probe sets that show increased expression with cytokine treatment or compared to non-lesional skin baseline;
  • Green numbers probe sets that show decreased expression with cytokine treatment or compared to non-lesional skin baseline.
  • the intersecting regions represent the probe sets that are common to both comparisons.
  • FIGS. 43 a and 43 b Co-overexpression type-I IFN, type-II IFN, and TNF-inducible genes in lesional/non-lesional skin of psoriatic patients based on Affymetrix GENECHIP® microarray results.
  • the type-I IFN, type-II IFN, and TNF ⁇ inducible genes were selected based on ex vivo stimulation experiments (Examples 10 and 16). A probe set with an at least 2-fold change from non-lesional to lesion skin was considered overexpressed.
  • FIG. 44 Immunohistochemical analysis of biopsies from psoriatic skin, non-lesional skin and skin from normal donors.
  • BDCA2 is a specific marker for pDCs which are present at greater numbers in lesional skin compared to non-lesional skin, and not at all in normal skin.
  • CD83 is a marker for mDCs
  • CD4 is present on T cells and dendritic cells.
  • STAT1 protein staining was observed in the epidermis of lesional skin (both nuclear and cytoplasmic) and dermal mononuclear inflammatory cells, but not in non-lesional or normal skin.
  • ISG15 protein increase was observed in psoriatic skin and to a lesser extent in non-lesional skin, but was not detected in normal skin.
  • FIG. 45 A Venn diagram illustrating the number of probe sets that show altered expression at mRNA level in the lesional skin compared to non-lesional skin, or in the non-lesional skin compared to normal skin of psoriatic patients. Values shaded in red indicate the number of probe sets significantly upregulated while those values shaded in green indicate the number of probe sets significantly downregulated.
  • the intersecting region represents probe sets that are common to both comparisons.
  • FIG. 46 Graphic representation of type-IFN signaling pathway that is activated in the lesional skin of psoriatic patients. Pathway image was generated with GeneGo's MetaCore integrated software suite. Individual symbols within the image represent well characterized proteins or protein complexes. Arrows linking the proteins represent the stimulatory, inhibitory, or interactive effect of the protein on the target protein. Thermometers adjacent to the individual symbols represent relative expression levels (red indicates overexpression, while green indicates underexpression) of transcripts that comprise the protein (or protein complex) within the particular pathway.
  • FIGS. 47 a and 47 b Table providing fold change (fc; log 2 transformed) and q value (calculated by FDR) of the top 100 probe sets upregulated in the lesional skin compared to non-lesional skin in psoriasis. Also listed are the log 2 transformed fold change and q values of these genes when comparing non-lesional skin with healthy normal skin controls. Type I IFN inducible genes are listed in bold font.
  • FIG. 48 Distinctive separation of the lesional skin from non-lesional skin and normal skin—hierarchical clustering of all samples using transcript profiles of all genes on a whole genome (Affymetrix whole genome U133 plus v2.0 array) array.
  • FIG. 49 a - 49 d Probe sets identified as IFN ⁇ inducible by overlap in FIG. 42 .
  • FIG. 49 b discloses “DEAD (Asp-Glu-Ala-Asp)” as SEQ ID NO: 1.
  • FIG. 50 a - 50 b Probe sets identified as TNF ⁇ inducible by overlap in FIG. 42 .
  • FIG. 51 a - 51 g Probe sets identified as type I IFN inducible by overlap in FIG. 42 .
  • FIG. 51 c discloses “DEAD (Asp-Glu-Ala-Asp)” as SEQ ID NO: 1.
  • FIG. 52 Immunohistochemical analysis of biopsies from skin lesions of a placebo-treated SLE patient to detect pDC, mDC, and T cell infiltrates.
  • FIG. 53 Immunohistochemical analysis of biopsies from skin lesions of a placebo-treated SLE patient to detect HERC5, ISG15, and IP10 proteins, proteins expressed from type I IFN-induced genes.
  • FIG. 54 Immunohistochemical analysis of biopsies from skin lesions of an SLE patient treated with 10 mg/kg MEDI-545 to detect pDC, mDC, and T cell infiltrates.
  • FIG. 55 Immunohistochemical analysis of biopsies from skin lesions of an SLE patient treated with 10 mg/kg MEDI-545 to detect HERC5, ISG15, and IP10 proteins, proteins expressed from type I IFN-induced genes.
  • FIG. 56 Immunohistochemical analysis of biopsies from skin lesions of an SLE patient treated with 10 mg/kg MEDI-545 to detect pDC, mDC, and T cell infiltrates.
  • FIG. 57 Immunohistochemical analysis of biopsies from skin lesions of an SLE patient treated with 10 mg/kg MEDI-545 to detect HERC5, ISG15, and IP10 proteins, proteins expressed from type I IFN-induced genes.
  • FIGS. 58 a and 58 b Heatmap (a) and PCA (b) showing neutralization of the top 25 type I IFN inducible genes in a skin biopsy of an SLE patient treated with 10 mg/kg MEDI-545 at 0 and 7 days post-dosing.
  • FIG. 59 a - d Detection of type I and type II IFN activity in an IFN bioassay.
  • FIGS. 60 a and 60 b Detection of MEDI-545 (a) and MEDI-546 (b)-mediated neutralization of IFN ⁇ activity in the IFN bioassay.
  • FIG. 61 Detection of anti-IFN ⁇ -mediated neutralization of IFN ⁇ activity in the IFN bioassay.
  • FIG. 62 Detection of anti-IFN ⁇ -mediated neutralization of IFN ⁇ activity in the IFN bioassay.
  • FIG. 63 Detection of anti-IFN ⁇ -mediated neutralization of IFN ⁇ activity in the IFN bioassay.
  • FIG. 64 Heat map showing modulation of gene expression in whole blood from healthy donors ex vivo stimulated with IFN ⁇ , TNF ⁇ , or IFN ⁇ / ⁇ . Negative control (NT).
  • FIG. 65 Type I IFN-inducible genes were among the most upregulated genes in whole blood of SLE patients.
  • FIG. 66 IFN ⁇ , IFN ⁇ , IFNAR1 and IFNAR2 mRNAs are upregulated in whole blood of lupus patients.
  • FIG. 67 Heat map showing modulation of gene expression in healthy donor PBMCs ex vivo stimulated with lupus patient serum.
  • FIGS. 68 a and 68 b (A) PCA plot showing lupus patients having a strong/moderate type I IFN inducible signature (approximately 66% in this sampling) cluster together. (b) Table providing the 25 genes used for PCA analysis.
  • FIG. 69 Confirmation of overexpression of selected type-I IFN inducible genes in lupus patients based on TAQMAN QRT-PCR assays using Fluidigm's BIOMARKTM48.48 dynamic array.
  • FIGS. 70 a and 70 b (a) Ability of four different SLE patient serum samples to induce type I IFN activity in a reporter gene assay. (b) Number of transcripts induced at least 3-fold in healthy human PBMCs by each of the four different SLE patient serum samples following 4 hour co-incubation.
  • FIGS. 71 a and 71 b The majority of genes neutralized by an anti-IFN ⁇ Ab 4 hours post co-incubation of SLE patient serum and healthy human PBMCs are type I IFN genes, while the majority of genes neutralized by the anti-IFN ⁇ Ab 18 hours post co-incubation of SLE patient serum and healthy human PBMCs are non-type I IFN genes as shown by (a) heatmap analysis and represented (b) in bar graphs.
  • FIGS. 72 a and 72 b Provides the (a) type I IFN genes and (b) non-type I IFN genes that were upregulated and neutralized by an anti-IFN ⁇ Ab 18 hours post co-incubation of SLE patient serum and healthy human PBMCs, but that were not upregulated 4 hours post co-incubation of SLE patient serum and healthy human PBMCs.
  • FIG. 73 Provides pathways and cell processes neutralized by an anti-IFN ⁇ Ab 18 hours following co-incubation of SLE patient serum and healthy human PBMCs.
  • FIGS. 74 a and 74 b Detection of (a) increased and (b) decreased levels of specific proteins in serum of lupus patients.
  • FIG. 75 QuantiGenePlex 1.0 analysis of IFN-inducible gene signatures from whole blood of 5 healthy donors stimulated with 20 IU/mL IFN ⁇ 2b.
  • FIG. 76 Dose-dependent changes in gene expression in blood from a single healthy donor treated with multiple concentrations of IFN ⁇ 2b.
  • FIG. 77 Detection of IFN-inducible transcripts in PAXgene-preserved whole blood samples from SLE subjects with and without detectable serum IFN ⁇ activity.
  • FIGS. 78 a and 78 b Correlation between QuantiGenePlex and Fluidigm technologies in SLE PAXgene-preserved whole blood samples.
  • FIGS. 79 a and 79 b Longitudinal testing of SLE samples following administration of an anti-IFN ⁇ monoclonal antibody: comparison of QuantiGenePlex 2.0 and Fluidigm technologies.
  • FIG. 81 a - 81 c Type I IFN-inducible genes in whole blood of SLE patients can be used to separate SLE patients with a type I IFN gene signature from healthy normal controls.
  • FIG. 83 a - 83 c TAQMAN QRT-PCR confirmed the overexpression of type I IFN-inducible genes in whole blood of SLE patients.
  • FIG. 84 Magnitude of overexpression of type I IFN gene signature in whole blood of SLE patients as measured by the median fold change of the 25 most overexpressed type I IFN-inducible genes or type I IFN gene signature score in individual SLE patients. The horizontal bars represent the median values. Patients whose type I IFN gene signature score was ⁇ 10 were considered to have strong type I IFN gene signatures; those with scores between 4 and 10 were considered to have moderate type I IFN gene signatures, whereas those with scores ⁇ 4 were considered to have weak type I IFN gene signatures.
  • FIG. 85 a - 85 c Stratification of 35 SLE patients into groups of low (a; green), moderate (b; gray), and high (c; red) type I IFN gene signature based on median fold change across the 21-gene panel of type I IFN-inducible genes. Densities for each SLE patient are calculated and graphed using the fold change for each of the 21 genes from each SLE patient on the log 2 scale to provide a representation of the distribution of 21 genes fold change values.
  • FIG. 86 Dose-dependent neutralization of 21 upregulated IFN- ⁇ / ⁇ -inducible genes in SLE patients by MEDI-545.
  • FIGS. 87 a and 87 b Heatmap (a) and PCA (b) showing neutralization of 21 upregulated IFN- ⁇ / ⁇ -inducible genes in whole blood of an SLE patient treated with 30 mg/kg MEDI-545 (0, 1, 4, 7, and 14 days post-dose).
  • FIGS. 88 a and 88 b PCA plots prepared using the 21 upregulated IFN- ⁇ / ⁇ -inducible probe sets do not show IFN signature neutralization in placebo-treated patients.
  • FIG. 89 Neutralization of the 21 upregulated IFN- ⁇ / ⁇ -inducible probe sets in patients treated with 0.3, 1.0, 3.0, 10.0, and 30.0 mg/kg MEDI-545.
  • FIG. 90 Methodology for calculating target neutralization for FIG. 89 .
  • the invention encompasses methods of identifying, diagnosing, treating, and monitoring disease progression in patients.
  • Patients include any animal having a type I IFN or an IFN ⁇ -inducible disease, disorder, or condition.
  • the patient may have the disease, disorder, or condition as a result of experimental research, e.g., it may be an experimental model developed for the disease, disorder, or condition. Alternatively, the patient may have the disease, disorder, or condition in the absence of experimental manipulation.
  • Patients include humans, mice, rats, horses, pigs, cats, dogs, and any animal used for research.
  • the patient may comprise a type I IFN or IFN ⁇ -inducible PD marker expression profile.
  • the type I IFN or IFN ⁇ -inducible PD marker expression profile may be a strong profile, a moderate profile, or a weak profile.
  • the type I IFN or IFN ⁇ -inducible PD marker expression profile can readily be designated as strong, moderate, or weak by determining the fold dysregulation of the type I IFN or IFN ⁇ -inducible PD marker expression profile of the patient, (e.g., the fold increase in expression of upregulated type I IFN or IFN ⁇ -inducible PD markers in the patient), relative to a control sample(s) or control patient(s) and comparing the patient's fold dysregulation to that of other patients having a type I IFN or IFN ⁇ -inducible PD marker expression profile.
  • Fold dysregulation can be calculated by well known methods in the art as can the comparing. See, e.g., Example 8.
  • the type I IFN or IFN ⁇ -inducible PD marker expression profile may comprise upregulation of any group of genes or group of genes detected by the probes identified in Tables 19, 20, 21, 22, 23, 24, 26, 28, or 30.
  • the group of genes or group of genes detected by the probes identified in Tables 19, 20, 21, 22, 23, 24, 26, 28 or 30 may include any at least 2, any at least 3, any at least 4, any at least 5, any at least 6, any at least 7, any at least 8, any at least 9, any at least 10, any at least 11, any at least 12, any at least 13, any at least 14, any at least 15, any at least 16, any at least 17, any at least 18, any at least 19, any at least 20, any at least 21, any at least 22, any at least 23, any at least 24, any at least 25, any at least 26, any at least 27, any at least 28, any at least 29, any at least 30, any at least 40, or any at least 50 of the genes or genes detected by the probes identified in the Tables.
  • the group of genes that may be included in the type I IFN or IFN ⁇ -inducible PD marker expression profile of the patient may be MX1, LY6E, IFI27, OAS1, IFIT1, IFI6, IFI44L, ISG15, LAMP3, OASL, RASD2, and IFI44.
  • the genes or genes detected by the probes may include IFI44, IFI27, IFI44L, DNAPTP6, LAMP3, LY6E, RSAD2, HERC5, IFI6, ISG15, OAS3, SIGLEC1, OAS2, USP18, RTP4, IFIT1, MX1, OAS1, EPSTI1, PLSCR1, and IFRG28.
  • the genes may include any at least 2, any at least 3, any at least 4, any at least 5, any at least 6, any at least 7, any at least 8, any at least 9, any at least 10, or any at least 11, or any at least 12, or any at least 13, or any at least 14, or any at least 15, or any at least 16, or any at least 17, or any at least 18, or any at least 19, or at least 20, or any at least 21, or any at least 22, or any at least 23, or any at least 24, or any least 25, or any at least 26, or any at least 27, or any at least 28, or any at least 29, or any at least 30 of LAMP3, DNAPTP6, FLJ31033, HERC6, SERPING1, EPST11, RTP4, OASL, FBXO6, IFIT2, IFI44, OAS3, BATF2, ISG15, IRF7, RSAD2, IFI35, OAS1, LAP3, IFIT1, IFIT5, PLSCR1, IFI44L, MS4A4A, GALM, UBE2L6, TOR1B, SAMD9L, HERC5,
  • the type I IFN or IFN ⁇ -inducible PD marker expression profile may contain upregulation of the entire group of genes or group of genes detected by the probes identified in one of Table 19, or Table 20, or Table 21, or Table 22, or Table 23, or Table 24, or Table 26, or Table 28, or Table 30 or may be any one or more of the genes identified in FIG. 72 .
  • the type I IFN or IFN ⁇ -inducible PD marker expression profile may include upregulation of all the genes identified in Table 24.
  • the type I IFN or IFN ⁇ -inducible PD marker expression profile may include upregulation of the genes identified in FIG. 72 A or FIG. 72 b , or FIG. 72 a and FIG. 72 b.
  • the patient comprising the type I IFN or IFN ⁇ -inducible PD marker expression profile may further comprise downregulated type I IFN or IFN ⁇ PD marker(s).
  • the downregulated PD markers may include any one, any two, any three, any four, any five, any six, any seven, any eight, any nine, any ten, any 15, any 20, any 25, any 30, any 35, any 40, any 45, or any 50 of the genes in Table 31 or any of CYP1B1, TGST1, RRAGD, IRS2, MGST1, TGFBR3, and RGS2.
  • the patient comprising the type I IFN or IFN ⁇ -inducible PD marker expression profile may further comprise upregulation of expression of any number of IFN ⁇ or type-I IFN subtypes.
  • the IFN ⁇ or type-I IFN subtypes may include any more than one, more than two, more than three, more than four, more than five, more than six, more than seven, more than eight, more than nine, or more than ten IFN ⁇ or type-I IFN subtypes. These subtypes may include IFN ⁇ 1, IFN ⁇ 2, IFN ⁇ 4, IFN ⁇ 5, IFN ⁇ 6, IFN ⁇ 7, IFN ⁇ 8, IFN ⁇ 10, IFN ⁇ 14, IFN ⁇ 17, IFN ⁇ 21, IFN ⁇ , or IFN ⁇ .
  • the patient may comprise upregulation of expression of IFN subtypes IFN ⁇ 1, IFN ⁇ 2, IFN ⁇ 8, and IFN ⁇ 14.
  • a patient treated in the methods encompassed by the invention may simply be one identified as comprising a gene expression profile with upregulation of expression of any number of IFN ⁇ or type-I IFN subtypes.
  • the IFN ⁇ or type-I IFN subtypes may include any more than one, more than two, more than three, more than four, more than five, more than six, more than seven, more than eight, more than nine, or more than ten IFN ⁇ or type-I IFN subtypes. These subtypes may include IFN ⁇ 1, IFN ⁇ 2, IFN ⁇ 4, IFN ⁇ 5, IFN ⁇ 6, IFN ⁇ 7, IFN ⁇ 8, IFN ⁇ 10, IFN ⁇ 14, IFN ⁇ 17, IFN ⁇ 21, IFN ⁇ , or IFN ⁇ . These subtypes may include IFN ⁇ 1, IFN ⁇ 2, IFN ⁇ 8, and IFN ⁇ 14.
  • the patient comprising the type I IFN or IFN ⁇ -inducible PD marker expression profile may further comprise upregulation of expression of IFN ⁇ receptors, either IFNAR1 or IFNAR2, or both, or TNF ⁇ , or IFN ⁇ , or IFN ⁇ receptors (either IFNGR1, IFNGR2, or both IFNGR1 and IFNGR2).
  • the patient may simply be identified as one who comprises upregulation of expression of IFN ⁇ receptors, either IFNAR1 or IFNAR2, or both, or TNF ⁇ , or IFN ⁇ , or IFN ⁇ receptors (either IFNGR1, IFNGR2, or both IFNGR1 and IFNGR2).
  • the upregulation or downregulation of the type I IFN or IFN ⁇ -inducible PD markers in the patient's expression profile may be by any degree relative to that of a sample from a control (which may be from a sample that is not disease tissue of the patient (e.g., non-lesional skin of a psoriasis patient) or from a healthy person not afflicted with the disease or disorder).
  • a control which may be from a sample that is not disease tissue of the patient (e.g., non-lesional skin of a psoriasis patient) or from a healthy person not afflicted with the disease or disorder).
  • the degree upregulation or downregulation may be at least 10%, at least 15%, at least 20%, at least 25%, at least 30%, at least 40%, at least 50%, at least 60%, at least 70%, at least 75%, at least 80%, at least 90%, at least 100%, at least 125%, at least 150%, or at least 200%, or at least 300%, or at least 400%, or at least 500% that of the control or control sample.
  • the patient may overexpress or have a tissue that overexpresses a type I IFN subtype at least 10%, at least 15%, at least 20%, at least 25%, at least 30%, at least 40%, at least 50%, at least 60%, at least 70%, at least 75%, at least 80%, at least 90%, at least 100%, at least 125%, at least 150%, or at least 200%, or at least 300%, or at least 400%, or at least 500% that of the control.
  • the type I IFN subtype may be any one of IFN ⁇ 1, IFN ⁇ 2, IFN ⁇ 4, IFN ⁇ 5, IFN ⁇ 6, IFN ⁇ 7, IFN ⁇ 8, IFN ⁇ 10, IFN ⁇ 14, IFN ⁇ 17, IFN ⁇ 21, IFN ⁇ , or IFN ⁇ .
  • the type I IFN subtypes may include all of IFN ⁇ 1, IFN ⁇ 2, IFN ⁇ 8, and IFN ⁇ 14.
  • the patient may further comprise or alternatively comprise alterations in levels of proteins in serum.
  • the patient may have increased serum levels of proteins such as adiponectin, alpha-fetoprotein, apolipoprotein CIII, beta-2 microglobulin, cancer antigen 125, cancer antigen 19-9, eotaxin, FABP, factor VII, ferritin, IL-10, IL-12p70, IL-16, IL-18, IL-1ra, IL-3, MCP-1, MMP-3, myoglobin, SGOT, tissue factor, TIMP-1, TNF RII, TNF-alpha, VCAM-1, or vWF.
  • proteins such as adiponectin, alpha-fetoprotein, apolipoprotein CIII, beta-2 microglobulin, cancer antigen 125, cancer antigen 19-9, eotaxin, FABP, factor VII, ferritin, IL-10, IL-12p70, IL-16, IL-18, IL-1ra, IL
  • the patient may have increased serum levels of any 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13 14, 15, 16, 17, 18, 19, 20, 21, o 22, 23, 24, 25, or 26 of these proteins in serum.
  • the increased level may be at least 10%, at least 15%, at least 20%, at least 25%, at least 30%, at least 40%, at least 50%, at least 60%, at least 70%, at least 75%, at least 80%, at least 90%, at least 100%, at least 125%, at least 150%, or at least 200%, or at least 300%, or at least 400%, or at least 500% that of a control, e.g., a healthy subject.
  • the alteration may be a decrease in serum levels of proteins such as BDNK, complement 3, CD40 ligand, EGF, ENA-78, EN-RAGE, IGF-1, MDC, myeloperoxidase, RANTES, or thrombopoietin
  • the patient may have decreased serum levels of any 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or 11 or these proteins.
  • the decreased level may be at least 10%, at least 15%, at least 20%, at least 25%, at least 30%, at least 40%, at least 50%, at least 60%, at least 70%, at least 75%, at least 80%, at least 90%, or at least 100% that of a control, e.g., a healthy subject.
  • the PD marker profile may comprise one or more of these increased or decreased serum levels of proteins.
  • the patient may further comprise auto-antibodies that bind to any one of the following auto-antigens: (a) Myxovirus (influenza virus) resistance 1, interferon-inducible protein p78; (b) surfeit 5, transcript variant c; (c) proteasome (posome, macropain) activator subunit 3 (PA28 gamma; Ki) transc; (d) retinoic acid receptor, alpha; (e) Heat shock 10 kDa protein 1 (chaperonin 10); (f) tropomyosin 3; (g) pleckstrin homology-like domain, family A, member 1; (h) cytoskeleton-associated protein 1; (i) Sjogren syndrome antigen A2 (60 kDa, ribonucleoprotein auto-antigen SS-A/Ro); (j) NADH dehydrogenase (ubiquinone) 1, alpha/beta subcomplex 1, 8 kDa; (k) NudE nuclear distribution gene E homo
  • nidulans (l) MutL homolog 1, colon cancer, nonpolyposis type 2 ( E. coli ); (m) leucine rich repeat (in FLII) interacting protein 2; (n) tropomyosin 1 (alpha); (o) spastic paraplegia 20, spartin (Troyer syndrome); (p) preimplantation protein, transcript variant 1; (r) mitochondrial ribosomal protein L45; (s) Lin-28 homolog ( C. elegans ); (t) heat shock 90 kDa protein 1, alpha; (u) dom-3 homolog Z ( C.
  • elegans dynein, cytoplasmic, light intermediate polypeptide 2; (w) Ras-related C3 botulinum toxin substrate 1 (rho family, small GTP binding protein); (x) synovial sarcoma, X breakpoint 2, transcript variant 2; (y) moesin; (z) homer homolog ( Drosophila ), transcript variant 1; (aa) GCN5 general control of amino-acid synthesis 5-like 2 (yeast); (bb) eukaryotic translation elongation factor 1 gamma; (cc) eukaryotic translation elongation factor 1, delta; (dd) DNA-damage-inducible transcript 3; (ee) CCAAT/enhancer binding protein (C/EBP) gamma; and any other auto-antigen described in provisional application entitled “Auto-antibody markers of autoimmune disease” filed May 3, 2007 or in provisional application entitled “Auto-antibody markers of autoimmune disease” to be filed Nov.
  • the patient may comprise auto-antibodies that bind to any number of these auto-antigens, e.g., any at least 2, at least 3, at least 4, at least 5, at least 6, at least 7, at least 8, at least 9 at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 20, at least 25.
  • auto-antibodies that bind to any number of these auto-antigens, e.g., any at least 2, at least 3, at least 4, at least 5, at least 6, at least 7, at least 8, at least 9 at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 20, at least 25.
  • a type I IFN or an IFN ⁇ -inducible disease, disorder, or condition is any that exhibits a type I IFN or an IFN ⁇ PD marker expression profile or gene signature.
  • a PD marker expression profile and a gene signature will be understood to be equivalent.
  • These diseases, disorders, or conditions include those with an autoimmune component such as systemic lupus erythematosus, insulin dependent diabetes mellitus, inflammatory bowel disease (including Crohn's disease, ulcerative colitis, and Celiac's disease), multiple sclerosis, psoriasis, autoimmune thyroiditis, rheumatoid arthritis, glomerulonephritis, idiopathic inflammatory myositis, Sjogren's syndrome, vasculitis, dermatomyositis, polymyositis, and sarcoidosis.
  • Other diseases, disorders, or conditions include graft versus host disease and transplant rejection.
  • the patients may also exhibit any of a number of symptoms as discussed in, e.g., provisional patent application Methods of Treating Systemic Lupus Erythematosis filed Apr. 16, 2007, or may have a clinical SLEDAI score or BILAG score as discussed in the same. These symptoms may include fatigue, organ damage, malar rash, and alopecia.
  • the patient may be scored using a known clinical scoring system, e.g., SLEDAI which is an index of SLE disease activity as measured and evaluated within the last 10 days (Bombardier C, Gladman D D, Urowitz M B, Caron D, Chang C H and the Committee on Prognosis Studies in SLE: Derivation of the SLEDAI for Lupus Patients.
  • BILAG index is an activity index of SLE that is based on specific clinical manifestations in eight organ systems: general, mucocutaneous, neurological, musculoskeletal, cardiovascular, respiratory, renal, and hematology results. Scoring is based on a letter system, but weighted numerical scores can also be assigned to each letter, making it possible to calculate a BILAG score in the range of 0-72. (Griffiths, et al., Assessment of Patients with Systemic Lupus Erythematosus and the use of Lupus Disease Activity Indices). Other scoring indices include the PGA score, the composite responder index (CRI), and the ANAM4TM test.
  • the methods described herein, e.g., of treating an autoimmune disorder may be used for any subject identified as having any activity level of disease activity as measured by any classification methodology known in the art, e.g., mild, moderate, high, or very high.
  • the methods described herein, e.g., of treating an autoimmune disorder may result in a decrease in a patient's symptoms or may result in an improvement in a score of disease for the patient's type I IFN or an IFN ⁇ -inducible disease, disorder, or condition.
  • a therapeutic agent may be administered to a patient or a patient may be identified as a candidate for administration of an agent or a therapeutic agent.
  • a therapeutic agent is any molecule that binds to and modulates type I IFN or IFN ⁇ activity.
  • the therapeutic agent may be a small molecule or a biological agent. If the therapeutic agent is a small molecule it may be synthesized or identified and isolated from a natural source.
  • the therapeutic agent may be an antibody specific for any subtype(s) of type I IFN or IFN ⁇ .
  • the antibody may be specific for any one of IFN ⁇ 1, IFN ⁇ 2, IFN ⁇ 4, IFN ⁇ 5, IFN ⁇ 6, IFN ⁇ 7, IFN ⁇ 8, IFN ⁇ 10, IFN ⁇ 14, IFN ⁇ 17, IFN ⁇ 21, IFN ⁇ , or IFN ⁇ .
  • the antibody may be specific for any two, any three, any four, any five, any six, any seven, any eight, any nine, any ten, any eleven, any twelve type I IFN of IFN ⁇ subtypes.
  • the antibody may be specific for IFN ⁇ 1, IFN ⁇ 2, IFN ⁇ 4, IFN ⁇ 5, IFN ⁇ 8, IFN ⁇ 10, and IFN ⁇ 21; or it may be specific for IFN ⁇ 1, IFN ⁇ 2, IFN ⁇ 4, IFN ⁇ 5, IFN ⁇ 8, and IFN ⁇ 10; or it may be specific for IFN ⁇ 1, IFN ⁇ 2, IFN ⁇ 4, IFN ⁇ 5, IFN ⁇ 8, and IFN ⁇ 21; or it may be specific for IFN ⁇ 1, IFN ⁇ 2, IFN ⁇ 4, IFN ⁇ 5, IFN ⁇ 10, and IFN ⁇ 21.
  • Antibodies specific for type I IFN or IFN ⁇ include MEDI-545, any biologic or antibody other than MEDI-545, antibodies described in U.S.
  • the antibody may be a synthetic antibody, a monoclonal antibody, polyclonal antibodies, a recombinantly produced antibody, an intrabody, a multispecific antibody (including bi-specific antibodies), a human antibody, a humanized antibody, a chimeric antibody, a single-chain Fv (scFv) (including bi-specific scFv), a BiTE molecule, a single chain antibody, a Fab fragments, a F(ab′) fragment, a disulfide-linked Fv (sdFv), or an epitope-binding fragment of any of the above.
  • the antibody may be any of an immunoglobulin molecule or immunologically active portion of an immunoglobulin molecule.
  • the antibody may be of any isotype.
  • it may be any of isotypes IgG1, IgG2, IgG3 or IgG4.
  • the antibody may be a full-length antibody comprising variable and constant regions, or an antigen-binding fragment thereof, such as a single chain antibody, or a Fab or Fab′2 fragment.
  • the antibody may also be conjugated or linked to a therapeutic agent, such as a cytotoxin or a radioactive isotope.
  • Second agents include, but are not limited to non-steroidal anti-inflammatory drugs such as ibuprofen, naproxen, sulindac, diclofenac, piroxicam, ketoprofen, diflunisal, nabumetone, etodolac, and oxaprozin, indomethacin; anti-malarial drugs such as hydroxychloroquine; corticosteroid hormones, such as prednisone, hydrocortisone, methylprednisolone, and dexamethasone; methotrexate; immunosuppressive agents, such as azathioprine and cyclophosphamide; and biologic agents that, e.g., target T cells such as Alefacept and Efalizumab, or target TNF ⁇ , such as, Enbrel, Remicade, and Humira.
  • target T cells such as Alefacept and Efalizumab
  • target TNF ⁇ such as, Enbrel, Remi
  • Treatment with the agent may result in neutralization of the type I IFN or IFN ⁇ -inducible profile. Treatment with the agent may result in a decrease in one or more symptoms of the type I IFN or an IFN ⁇ -mediated disease or disorder. Treatment with the agent may result in fewer flare-ups related to the type I IFN or an IFN ⁇ -mediated disease or disorder. Treatment with the agent may result in improved prognosis for the patient having the type I IFN or an IFN ⁇ -mediated disease or disorder. Treatment with the agent may result in a higher quality of life for the patient. Treatment with the agent may alleviate the need to co-administer second agents or may lessen the dosage of administration of the second agent to the patient. Treatment with the agent may reduce the number of hospitalizations of the patient that are related to the type I IFN or an IFN ⁇ -mediated disease or disorder.
  • the agent that binds to and modulates type I IFN or IFN ⁇ activity may neutralize a type I IFN or IFN ⁇ -inducible profile.
  • Neutralization of the type I IFN or IFN ⁇ -inducible profile may be a reduction in at least one, at least two, at least three, at least five, at least seven, at least eight, at least ten, at least twelve, at least fifteen, at least twenty, at least twenty five, at least thirty, at least thirty five, at least forty, at least forty five, or at least fifty genes up-regulated by type I IFN or IFN ⁇ .
  • the genes upregulated by type I IFN or IFN ⁇ may be any group of genes in Tables 19, 20, 21, 22, 23, 24, 26, 28, or 30 as discussed above.
  • Neutralization of the type I IFN or IFN ⁇ -inducible profile is a reduction of at least 2%, at least 3%, at least 4%, at least 5%, at least 7%, at least 8%, at least 10%, at least 15%, at least 25%, at least 30%, at least 35%, at least 40%, at least 45%, at least 50%, at least 60%, at least 70%, at least 75%, at least 80%, or at least 90% of any of the at least one, at least two, at least three, at least five, at least seven, at least eight, at least ten, at least twelve, at least fifteen, at least twenty, at least twenty five, at least thirty, at least thirty five, at least forty, at least forty five, or at least fifty genes up-regulated in any type I IFN or IFN ⁇ -inducible profile.
  • neutralization of the type I IFN or IFN ⁇ -inducible profile refers to a reduction of expression of up-regulated type I IFN or IFN ⁇ -inducible genes that is within at most 50%, at most 45%, at most 40%, at most 35%, at most 30%, at most 25%, at most 20%, at most 15%, at most 10%, at most 5%, at most 4%, at most 3%, at most 2%, or at most 1% of expression levels of those type I IFN or IFN ⁇ -inducible genes in a control sample.
  • the agent that binds to and modulates type I IFN or IFN ⁇ activity is a biologic agent, such as an antibody
  • the agent may neutralize the type I IFN or IFN ⁇ profile at doses of 0.3 to 30 mg/kg, 0.3 to 10 mg/kg, 0.3 to 3 mg/kg, 0.3 to 1 mg/kg, 1 to 30 mg/kg, 3 to 30 mg/kg, 5 to 30 mg/kg, 10 to 30 mg/kg, 1 to 10 mg/kg, 3 to 10 mg/kg, or 1 to 5 mg/kg.
  • Neutralization of the type I IFN or IFN ⁇ -inducible profile may be increased expression of at least one, at least two, at least three, at least five, at least seven, at least eight, at least ten, at least twelve, at least fifteen, at least twenty, at least twenty five, at least thirty, at least thirty five, at least forty, at least forty five, or at least fifty genes whose expression is reduced by type I IFN or IFN ⁇ .
  • the genes whose expression is reduced by type I IFN or IFN ⁇ may be any group of genes in Table 30.
  • Neutralization of down-regulated genes in a type I IFN or IFN ⁇ -inducible profile is an increase of at least 2%, at least 3%, at least 4%, at least 5%, at least 7%, at least 8%, at least 10%, at least 15%, at least 25%, at least 30%, at least 35%, at least 40%, at least 45%, at least 50%, at least 60%, at least 70%, at least 75%, at least 80%, or at least 90%, or at least 100%, or at least 125%, or at least 130%, or at least 140%, or at least 150%, or at least 175%, or at least 200%, or at least 250%, or at least 300%, or at least 500% of any of the at least one, at least two, at least three, at least five, at least seven, at least eight, at least ten, at least twelve, at least fifteen, at least twenty, or at least twenty five genes whose expression is downregulated in any type I IFN or IFN ⁇ -inducible profile.
  • neutralization of the type I IFN or IFN ⁇ -inducible profile refers to an increase in expression of type I IFN or IFN ⁇ -inducible genes to within at most 50%, at most 45%, at most 40%, at most 35%, at most 30%, at most 25%, at most 20%, at most 15%, at most 10%, at most 5%, at most 4%, at most 3%, at most 2%, or at most 1% of expression levels of those type I IFN or IFN ⁇ -inducible (downregulated) genes in a control sample.
  • the agent that binds to and modulates type I IFN or IFN ⁇ activity is a biologic agent, such as an antibody
  • the agent may neutralize the type I IFN or IFN ⁇ profile at doses of 0.3 to 30 mg/kg, 0.3 to 10 mg/kg, 0.3 to 3 mg/kg, 0.3 to 1 mg/kg, 1 to 30 mg/kg, 3 to 30 mg/kg, 5 to 30 mg/kg, 10 to 30 mg/kg, 1 to 10 mg/kg, 3 to 10 mg/kg, or 1 to 5 mg/kg.
  • the agent that binds to and modulates type I IFN or IFN ⁇ activity may further or alternatively neutralize expression of one or more type I IFN or IFN ⁇ subtypes.
  • the IFN ⁇ or type-I IFN subtypes may include any more than one, more than two, more than three, more than four, more than five, more than six, more than seven, more than eight, more than nine, or more than ten IFN ⁇ or type-I IFN subtypes. These subtypes may include IFN ⁇ 1, IFN ⁇ 2, IFN ⁇ 4, IFN ⁇ 5, IFN ⁇ 6, IFN ⁇ 7, IFN ⁇ 8, IFN ⁇ 10, IFN ⁇ 14, IFN ⁇ 17, IFN ⁇ 21, IFN ⁇ , or IFN ⁇ .
  • subtypes may include all of IFN ⁇ 1, IFN ⁇ 2, IFN ⁇ 8, and IFN ⁇ 14.
  • these subtypes may include IFN ⁇ 1, IFN ⁇ 2, IFN ⁇ 4, IFN ⁇ 5, IFN ⁇ 8, IFN ⁇ 10, IFN ⁇ 21.
  • Neutralization of the IFN ⁇ or type-I IFN subtypes may be a reduction of at least 2%, at least 3%, at least 4%, at least 5%, at least 7%, at least 8%, at least 10%, at least 15%, at least 25%, at least 30%, at least 35%, at least 40%, at least 45%, at least 50%, at least 60%, at least 70%, at least 75%, at least 80%, or at least 90% of any of the at least one, at least two, at least three, at least five, at least seven, at least eight, or at least ten of the subtypes.
  • Neutralization of the IFN ⁇ or type-I IFN subtypes may be a reduction in expression of IFN ⁇ or type-I IFN subtype genes that is within at most 50%, at most 45%, at most 40%, at most 35%, at most 30%, at most 25%, at most 20%, at most 15%, at most 10%, at most 5%, at most 4%, at most 3%, at most 2%, or at most 1% of expression levels of those IFN ⁇ or type I IFN subtypes in a control sample.
  • the agent that binds to and modulates IFN ⁇ activity or type I IFN activity is a biologic agent, such as an antibody
  • the agent may neutralize the IFN ⁇ or type I IFN subtypes at doses of 0.3 to 30 mg/kg, 0.3 to 10 mg/kg, 0.3 to 3 mg/kg, 0.3 to 1 mg/kg, 1 to 30 mg/kg, 3 to 30 mg/kg, 5 to 30 mg/kg, 10 to 30 mg/kg, 1 to 10 mg/kg, 3 to 10 mg/kg, or 1 to 5 mg/kg.
  • the agent that binds to and modulates type I IFN or IFN ⁇ activity may further or alternatively neutralize expression of IFN ⁇ receptors, either IFNAR1 or IFNAR2, or both, or TNF ⁇ , or IFN ⁇ , or IFN ⁇ receptors (either IFNGR1, IFNGR2, or both IFNGR1 and IFNGR2).
  • Neutralization of expression of IFN ⁇ receptors may be a reduction of at least 2%, at least 3%, at least 4%, at least 5%, at least 7%, at least 8%, at least 10%, at least 15%, at least 25%, at least 30%, at least 35%, at least 40%, at least 45%, at least 50%, at least 60%, at least 70%, at least 75%, at least 80%, or at least 90% of any of the at least one, at least two, at least three, at least five, or at least six of these genes.
  • IFN ⁇ receptors either IFNAR1 or IFNAR2, or TNF ⁇ , or IFN ⁇ , or IFN ⁇ receptors (either IFNGR1, IFNGR2, or both IFNGR1 and IFNGR2) is a reduction of expression of at most 50%, at most 45%, at most 40%, at most 35%, at most 30%, at most 25%, at most 20%, at most 15%, at most 10%, at most 5%, at most 4%, at most 3%, at most 2%, or at most 1% of expression levels of these genes in a control sample.
  • the agent that binds to and modulates type I IFN or IFN ⁇ activity is a biologic agent, such as an antibody
  • the agent may neutralize expression of IFN ⁇ receptors IFNAR1 or IFNAR2, or TNF ⁇ , or IFN ⁇ , or IFN ⁇ receptors IFNGR1 or IFNGR2 at doses of 0.3 to 30 mg/kg, 0.3 to 10 mg/kg, 0.3 to 3 mg/kg, 0.3 to 1 mg/kg, 1 to 30 mg/kg, 3 to 30 mg/kg, 5 to 30 mg/kg, 10 to 30 mg/kg, 1 to 10 mg/kg, 3 to 10 mg/kg, or 1 to 5 mg/kg.
  • the agent that binds to and modulates type I IFN or IFN ⁇ activity may further or alternatively neutralize alterations of levels of proteins in serum, e.g., increase levels of those proteins whose serum levels are downregulated or decrease levels of those proteins whose serum levels are upregulated to levels closer to those of control subjects.
  • Neutralization of expression of proteins in serum may be by bringing the level of at least one, at least two, at least three, at least five, at least six, at least seven, at least eight, at least nine, at least ten, at least twelve, at least fifteen, at least twenty proteins in serum, such as adiponectin, alpha-fetoprotein, apolipoprotein CIII, beta-2 microglobulin, cancer antigen 125, cancer antigen 19-9, eotaxin, FABP, factor VII, ferritin, IL-10, IL-12p70, IL-16, IL-18, IL-1ra, IL-3, MCP-1, MMP-3, myoglobin, SGOT, tissue factor, TIMP-1, TNF RII, TNF-alpha, VCAM-1, vWF, BDNK, complement 3, CD40 ligand, EGF, ENA-78, EN-RAGE, IGF-1, MDC, myeloperoxidase, RANTES, or thrombopo
  • the agent that binds to and modulates type I IFN or IFN ⁇ activity is a biologic agent, such as an antibody
  • the agent may neutralize levels of the serum proteins, e.g., adiponectin, alpha-fetoprotein, apolipoprotein CIII, beta-2 microglobulin, cancer antigen 125, cancer antigen 19-9, eotaxin, FABP, factor VII, ferritin, IL-10, IL-12p70, IL-16, IL-18, IL-1ra, IL-3, MCP-1, MMP-3, myoglobin, SGOT, tissue factor, TIMP-1, TNF RII, TNF-alpha, VCAM-1, vWF, BDNK, complement 3, CD40 ligand, EGF, ENA-78, EN-RAGE, IGF-1, MDC, myeloperoxidase, RANTES, or thrombopoietin, at doses of 0.3 to 30 mg/kg, 0.3 to 10 mg/
  • the agent that binds to and modulates type I IFN or IFN ⁇ activity may further or alternatively reduce number or level of auto-antibodies that bind to any one, any at least 2, any at least 3, any at least 4, any at least 5, any at least 6, any at least 7, any at least 8, any at least 9, any at least 10, any at least 15, or any at least 20 of the following auto-antigens: (a) Myxovirus (influenza virus) resistance 1, interferon-inducible protein p78; (b) surfeit 5, transcript variant c; (c) proteasome (posome, macropain) activator subunit 3 (PA28 gamma; Ki) transc; (d) retinoic acid receptor, alpha; (e) Heat shock 10 kDa protein 1 (chaperonin 10); (f) tropomyosin 3; (g) pleckstrin homology-like domain, family A, member 1; (h) cytoskeleton-associated protein 1; (i) Sjogren syndrome antigen A2 (
  • nidulans (l) MutL homolog 1, colon cancer, nonpolyposis type 2 ( E. coli ); (m) leucine rich repeat (in FLII) interacting protein 2; (n) tropomyosin 1 (alpha); (o) spastic paraplegia 20, spartin (Troyer syndrome); (p) preimplantation protein, transcript variant 1; (r) mitochondrial ribosomal protein LA5; (s) Lin-28 homolog ( C. elegans ); (t) heat shock 90 kDa protein 1, alpha; (u) dom-3 homolog Z ( C.
  • Reduction in level of auto-antibody may be a reduction of at least 2%, at least 3%, at least 4%, at least 5%, at least 7%, at least 8%, at least 10%, at least 15%, at least 25%, at least 30%, at least 35%, at least 40%, at least 45%, at least 50%, at least 60%, at least 70%, at least 75%, at least 80%, or at least 90% in presence of any of the auto-antibodies.
  • the agent that binds to and modulates type I IFN or IFN ⁇ activity is a biologic agent, such as an antibody
  • the agent may reduce number or level or auto-antibodies at doses of 0.3 to 30 mg/kg, 0.3 to 10 mg/kg, 0.3 to 3 mg/kg, 0.3 to 1 mg/kg, 1 to 30 mg/kg, 3 to 30 mg/kg, 5 to 30 mg/kg, 10 to 30 mg/kg, 1 to 10 mg/kg, 3 to 10 mg/kg, or 1 to 5 mg/kg.
  • the agent that binds to and modulates type I IFN or IFN ⁇ activity may not neutralize expression of genes that are not included in an interferon-inducible signature or PD marker profile.
  • Samples may also be obtained from patients in the methods of the invention. Samples include any biological fluid or tissue, such as whole blood, saliva, urine, synovial fluid, bone marrow, cerebrospinal fluid, nasal secretions, sputum, amniotic fluid, bronchoalveolar lavage fluid, peripheral blood mononuclear cells, total white blood cells, lymph node cells, spleen cells, tonsil cells, or skin.
  • biological fluid or tissue such as whole blood, saliva, urine, synovial fluid, bone marrow, cerebrospinal fluid, nasal secretions, sputum, amniotic fluid, bronchoalveolar lavage fluid, peripheral blood mononuclear cells, total white blood cells, lymph node cells, spleen cells, tonsil cells, or skin.
  • the samples may be obtained by any means known in the art.
  • IFN ⁇ -inducible PD marker expression profiles may include up-regulated expression or activity of genes in cells exposed to elevated IFN ⁇ levels relative to baseline.
  • Up-regulated expression or activity of genes includes an increase in expression of mRNA from a gene, an increase in expression of a protein encoded by a gene, or an increase in activity of a protein encoded by a gene.
  • the expression or activity of the genes may be up-regulated as a direct or indirect response to IFN ⁇ .
  • the up-regulated expression or activity of any gene detected in a sample, by probes, or by probes in kits in an IFN ⁇ -inducible PD marker expression profile may be at least 1.2-fold, at least 1.25-fold, at least 1.3-fold, at least 1.4-fold, at least 1.5-fold, at least 2.0-fold, at least 2.25-fold, at least 2.5-fold, at least 2.75-fold, at least 3.0-fold, at least 3.5-fold, at least 4.0-fold, at least 4.5-fold, at least 5.0-fold, at least 6.0-fold, at least 7.0-fold, at least 8.0-fold, at least 9.0-fold, at least 10.0-fold, at least 15.0-fold, at least 20.0-fold, at least 25.0-fold, or at least 50.0-fold relative to baseline levels of control cells, e.g., cells of healthy volunteers or cells of control animals or cells not exposed to IFN ⁇ in culture. All of the genes in the IFN ⁇ -inducible PD marker expression profile may have up-regulated expression
  • the down-regulated expression or activity of any gene detected in a sample, by probes, or by probes in kits in an IFN ⁇ -inducible PD marker expression profile may be at least 5%, at least 10%, at least 15%, at least 20%, at least 25%, at least 30%, at least 35%, at least 40%, at least 45%, at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% relative to baseline levels of control cells, e.g., cells of healthy volunteers or cells of control animals or cells not exposed to IFN ⁇ in culture. All of the genes in the IFN ⁇ -inducible PD marker expression profile may have down-regulated expression or activity at the same fold decrease. Alternatively, the genes in the PD marker expression profile may have varying levels of down-regulated expression or activity.
  • the number of genes included in IFN ⁇ -inducible PD marker expression profile may be at least 2, at least 3, at least 4, at least 5, at least 10, at least 20, at least 25 at least 30, at least 50, at least 75, at least 100, at least 150, at least 200, at least 250, at least 300, at least 400, at least 500, at least 750, at least 1000, at least 1500, at least 2000, at least 2500, at least 5000, at least 10000, or at least 15000 genes.
  • These genes may include those listed in Tables 19 and/or 20 and/or 21 and/or 22 and/or 23 and/or 24 and/or 26 and/or 28 and/or 30 and/or 31 and/or any of the genes identified in FIG. 72 , 74 , 75 , or 77 .
  • the genes included in IFN ⁇ -inducible PD marker expression profile may be up-regulated genes, down-regulated genes, or a combination of up- and down-regulated genes.
  • the genes included in the IFN ⁇ -inducible PD marker expression profile may be the genes provided in Tables 19 and/or 20 and/or 21 and/or 22 and/or 23 and/or 24 and/or 26 and/or 28 and/or 30 and/or 31 and/or any of the genes identified in FIG. 72 , 74 , 75 , or 77 .
  • the genes included in the IFN ⁇ -inducible PD marker expression profile may consist of or comprise at least 10%, at least 20%, at least 25%, at least 30%, at least 40%, at least 50%, at least 60%, at least 75%, at least 80%, at least 85% at least 90%, at least 95%, or at least 100% of the genes provided in Tables 19 and/or 20 and/or 21 and/or 22 and/or 23 and/or 24 and/or 26 and/or 28 and/or 30 and/or 31 and/or any of the genes identified in FIG. 72 , 74 , 75 , or 77 .
  • the IFN ⁇ -inducible PD markers in an expression profile may include any at least 5 genes such as, for example: MX1, LLY6E, IFI27, OAS1, IFIT1; or MX1, LLY6E, IFI27, OAS1, IFI6; or MX1, LLY6E, IFI27, OAS1, IFI44L; or MX1, LLY6E, IFI27, OAS1, ISG15; or MX1, LLY6E, IFI27, OAS1, LAMP3; or MX1, LLY6E, IFI27, OAS1, OASL; or MX1, LLY6E, IFI27, OAS1, RSAD2; or MX1, LLY6E, IFI27, OAS1, IFI44; or MX1, LLY6E, IFI27, OAS1, IFIT2; or MX1, LLY6E, IFI27, OAS1, OAS3; or MX1, LLY6E, IFI27, OAS1, USP18; or MX1, L
  • the IFN ⁇ -inducible PD markers in an expression profile may include any at least 6 genes such as, for example: MX1, LLY6E, IFI27, OAS1, IFIT1, IFI6; or MX1, LLY6E, IFI27, OAS1, IFIT1, IFI44L; or MX1, LLY6E, IFI27, OAS1, IFIT1, ISG15; or MX1, LLY6E, IFI27, OAS1, IFIT1, LAMP3; or MX1, LLY6E, IFI27, OAS1, IFIT1, OASL; or MX1, LLY6E, IFI27, OAS1, IFIT1, RSAD2; or MX1, LLY6E, IFI27, OAS1, IFIT1, IFI44; or MX1, LLY6E, IFI27, OAS1, IFIT1, IFIT2; or MX1, LLY6E, IFI27, OAS1, IFIT1, OAS3; or MX1, LLY6E, IFI27, OAS1, IFIT
  • the IFN ⁇ -inducible PD markers in an expression profile may include any at least 7 genes such as, for example: MX1, LLY6E, IFI27, OAS1, IFIT1, IFI6, IFI44L; or MX1, LLY6E, IFI27, OAS1, IFIT1, IFI6, ISG15; or MX1, LLY6E, IFI27, OAS1, IFIT1, IFI6, LAMP3; or MX1, LLY6E, IFI27, OAS1, IFIT1, IFI6, OASL; or MX1, LLY6E, IFI27, OAS1, IFIT1, IFI6, RSAD2; or MX1, LLY6E, IFI27, OAS1, IFIT1, IFI6, IFI44; or MX1, LLY6E, IFI27, OAS1, IFIT1, IFI6, IFIT2; or MX1, LLY6E, IFI27, OAS1, IFIT1, IFI6, OAS3; or MX1, LLY6E, IFI27, OAS1, I
  • the IFN ⁇ -inducible PD markers in an expression profile may include any at least 8 genes such as, for example: MX1, LLY6E, IFI27, OAS1, IFIT1, IFI6, IFI44L, ISG15; or MX1, LLY6E, IFI27, OAS1, IFIT1, IFI6, IFI44L, LAMP3; or MX1, LLY6E, IFI27, OAS1, IFIT1, IFI6, IFI44L, OASL; or MX1, LLY6E, IFI27, OAS1, IFIT1, IFI6, IFI44L, RSAD2; or MX1, LLY6E, IFI27, OAS1, IFIT1, IFI6, IFI44L, IFI44; or MX1, LLY6E, IFI27, OAS1, IFIT1, IFI6, IFI44L, IFIT2; or MX1, LLY6E, IFI27, OAS1, IFIT1, IFI6, IFI44L, OAS3; or MX1, LLY6E,
  • the IFN ⁇ -inducible PD markers in an expression profile may include any at least 12 genes such as, for example: MX1, LLY6E, IFI27, OAS1, IFIT1, IFI6, IFI44L, ISG15, LAMP3, OASL, RSAD2, IFI44; or MX1, LLY6E, IFI27, OAS1, IFIT1, IFI6, IFI44L, ISG15, LAMP3, OASL, RSAD2, IFIT2; or MX1, LLY6E, IFI27, OAS1, IFIT1, IFI6, IFI44L, ISG15, LAMP3, OASL, RSAD2, OAS3; or MX1, LLY6E, IFI27, OAS1, IFIT1, IFI6, IFI44L, ISG15, LAMP3, OASL, RSAD2, USP18; or MX1, LLY6E, IFI27, OAS1, IFIT1, IFI6, IFI44L, ISG15, LAMP3, OASL, RSAD2, US
  • the IFN ⁇ -inducible PD markers in an expression profile may include any at least 8 genes such as, for example: IFI44, IFI6, SAMD9L, GBP1, OAS1, BIRC4BP, SRGAP2, and RSAD2.
  • the IFN ⁇ -inducible PD markers in such an expression profile may further include at least one or more gene listed in Tables 19 and/or 20 and/or 21 and/or 22 and/or 23 and/or 24 and/or 26 and/or 28 and/or 30.
  • the IFN ⁇ -inducible PD markers in an expression profile may include any at least 7 genes such as, for example: IFI44, SAMD9L, GBP1, OAS1, BIRC4BP, SRGAP2, and RSAD2; or IFI44, IFI6, GBP1, OAS1, BIRC4BP, SRGAP2, and RSAD2; or IFI44, IFI6, SAMD9L, OAS1, BIRC4BP, SRGAP2, and RSAD2; or IFI44, IFI6, SAMD9L, GBP1, BIRC4BP, SRGAP2, and RSAD2; or IFI44, IFI6, SAMD9L, GBP1, OAS1, SRGAP2, and RSAD2; or IFI44, IFI6, SAMD9L, GBP1, OAS1, BIRC4BP, and RSAD2.
  • the IFN ⁇ -inducible PD markers in such an expression profile may further include at least one or more gene listed in Tables 19 and/or 20 and/or 21 and/
  • the IFN ⁇ -inducible PD markers in an expression profile may include any at least 6 genes such as, for example: IFI44, IFI6, SAMD9L, GBP1, OAS1, and BIRC4BP; or IFI6, SAMD9L, GBP1, OAS1, BIRC4BP, and SRGAP2; or SAMD9L, GBP1, OAS1, BIRC4BP, SRGAP2, and RSAD2; or IFI44, GBP1, OAS1, BIRC4BP, SRGAP2, and RSAD2; or IFI44, IFI6, OAS1, BIRC4BP, SRGAP2, and RSAD2; or IFI44, IFI6, SAMD9L, BIRC4BP, SRGAP2, and RSAD2; or IFI44, IFI6, SAMD9L, GBP1, SRGAP2, and RSAD2; or IFI44, IFI6, SAMD9L, GBP1, SRGAP2, and RSAD2; or IFI44, IFI6, SAMD9
  • the IFN ⁇ -inducible PD markers in an expression profile may include any at least 5 genes such as, for example: GBP1, OAS1, BIRC4BP, SRGAP2, and RSAD2; or IFI44, OAS1, BIRC4BP, SRGAP2, and RSAD2; or IFI44, IFI6, BIRC4BP, SRGAP2, and RSAD2; or IFI44, IFI6, SAMD9L, SRGAP2, and RSAD2; or IFI44, IFI6, SAMD9L, GBP1, and RSAD2; or IFI44, IFI6, SAMD9L, GBP1, and OAS1; or SAMD9L, OAS1, BIRC4BP, SRGAP2, and RSAD2; or SAMD9L, GBP1, BIRC4BP, SRGAP2, and RSAD2; or SAMD9L, GBP1, BIRC4BP, SRGAP2, and RSAD2; or SAMD9L, GBP1, OAS1, SRGAP
  • the IFN ⁇ -inducible PD markers in an expression profile may include any at least 4 genes selected from the group consisting of: IFI44, IFI6, SAMD9L, GBP1, OAS1, BIRC4BP, SRGAP2, and RSAD2.
  • the IFN ⁇ -inducible PD markers in such an expression profile may further include at least one or more gene listed in Tables 19 and/or 20 and/or 21 and/or 22 and/or 23 and/or 24 and/or 26 and/or 28 and/or 30.
  • the IFN ⁇ -inducible PD markers in an expression profile may include any at least 3 genes selected from the group consisting of: IFI44, IFI6, SAMD9L, GBP1, OAS1, BIRC4BP, SRGAP2, and RSAD2.
  • the IFN ⁇ -inducible PD markers in such an expression profile may further include at least one or more gene listed in Tables 19 and/or 20 and/or 21 and/or 22 and/or 23 and/or 24 and/or 26 and/or 28 and/or 30.
  • the IFN ⁇ -inducible PD markers in an expression profile may include any at least 2 genes selected from the group consisting of: IFI44, IFI6, SAMD9L, GBP1, OAS1, BIRC4BP, SRGAP2, and RSAD2.
  • the IFN ⁇ -inducible PD markers in such an expression profile may further include at least one or more gene listed in Tables 19 and/or 20 and/or 21 and/or 22 and/or 23 and/or 24 and/or 26 and/or 28 and/or 30.
  • the IFN ⁇ -inducible PD markers in an expression profile may include at least genes IFI27, SIGLEC1, RSAD2, IFI6, IFI44L, IFI44, USP18, IFIT2, SAMD9L, BIRC4BP, DNAPTP6, OAS3, LY6E, IFIT1, LIPA, LOC129607, ISG15, PARP14, MX1, OAS2, OASL, CCL2, HERC5, OAS1.
  • the IFN ⁇ -inducible PD markers in such an expression profile may further include at least one or more gene listed in Table 19 and/or 20 and/or 21, and/or 22, and/or 23, and/or 24, and/or 26, and/or 28, and/or 30.
  • the IFN ⁇ -inducible PD markers in an expression profile may include at least genes IFIT1, IFIT3, IRF7, IFI6, IL6ST, IRF2, LY6E, MARCKS, MX1, MX2, OAS1, EIF2AK2, ISG15, STAT2, OAS3, IFI44, IFI44L, HERC5, RAB8B, LILRA5, RSAD2, and FCHO2.
  • the IFN ⁇ -inducible PD markers in such an expression profile may further include at least one or more gene listed in Table 19 and/or 20 and/or 21, and/or 22, and/or 23, and/or 24, and/or 26, and/or 28 and/or 30.
  • the IFN ⁇ -inducible PD markers in an expression profile may include at least genes SERPING1, IFIT2, IFIT3, IFI6, LY6E, MX1, OAS1, ISG15, IFI27, OAS3, IFI44, LAMP3, DNAPTP6, ETV7, HERC5, OAS2, USP18, XAF1, RTP4, SIGLEC1, and EPSTI1.
  • the IFN ⁇ -inducible PD markers in such an expression profile may further include at least one or more gene listed in Table 19 and/or 20 and/or 21, and/or 22, and/or 23, and/or 24, and/or 26, and/or 28 and/or 30.
  • the IFN ⁇ -inducible PD markers in an expression profile may include at least genes SERPING1, IFIT2, IFIT3, IFI6, LY6E, MX1, OAS1, ISG15, IFI27, OAS3, IFI44, LAMP3, DNAPTP6, ETV7, HERC5, OAS2, USP18, XAF1, RTP4, SIGLEC1, EPSTI1, and RSAD2.
  • the IFN ⁇ -inducible PD markers in such an expression profile may further include at least one or more gene listed in Table 19 and/or 20 and/or 21, and/or 22, and/or 23, and/or 24, and/or 26, and/or 28 and/or 30.
  • the IFN ⁇ -inducible PD markers in an expression profile may include at least genes BCL2, BAK1, BAD, BAX, and BCL2L1.
  • the IFN ⁇ -inducible PD markers in such an expression profile may further include at least one or more gene listed in Table 19 and/or 20 and/or 21, and/or 22, and/or 23, and/or 24, and/or 26, and/or 28 and/or 30.
  • the IFN ⁇ -inducible PD markers in an expression profile may include at least genes RTP4, RSAD2, HERC5, SIGLEC1, USP18, LY6E, ETV7, SERPING1, IFIT3, OAS1, HSXIAPAF1, G1P3, MX1, OAS3, IFI27, DNAPTP6, LAMP3, EPSTI1, IFI44, OAS2, IFIT2, and ISG15.
  • the IFN ⁇ -inducible PD markers in such an expression profile may further include at least one or more gene listed in Table 19 and/or 20 and/or 21, and/or 22, and/or 23, and/or 24, and/or 26, and/or 28 and/or 30.
  • the IFN ⁇ -inducible PD markers in an expression profile may include at least genes LAMP3, SIGLEC1, DNAPTP6, IFIT2, ETV7, RTP4, SERPING1, HERC5, XAF1, MX1, EPSTI1, OAS2, OAS1, OAS3, IFIT3, IFI6, USP18, RSAD2, IFI44, LY6E, ISG15, and IFI27.
  • the IFN ⁇ -inducible PD markers in such an expression profile may further include at least one or more gene listed in Table 19 and/or 20 and/or 21, and/or 22, and/or 23, and/or 24, and/or 26, and/or 28 and/or 30.
  • the IFN ⁇ -inducible PD markers in an expression profile may include at least genes DNAPTP6, EPSTI1, HERC5, IFI27, IFI44, IFI44L, IFI6, IFIT1, IFIT3, ISG15, LAMP3, LY6E, MX1, OAS1, OAS2, OAS3, PLSCR1, RSAD2, RTP4, SIGLEC1, and USP18.
  • the IFN ⁇ -inducible PD markers in such an expression profile may further include at least one or more gene listed in Table 19 and/or 20 and/or 21, and/or 22, and/or 23, and/or 24, and/or 26, and/or 28 and/or 30.
  • the IFN ⁇ -inducible PD markers in an expression profile may include at least genes SAMD9L, IFI6, IFI44, IFIT2, ZC3HAV1, ETV6, DAPP1, IL1RN, CEACAM1, OAS1, IFI27, OAS3, IFI44L, HERC5, IFIT1, EPSTI1, ISG15, SERPING1, OASL, GBP1, and MX1.
  • the IFN ⁇ -inducible PD markers in such an expression profile may further include at least one or more gene listed in Table 19 and/or 20 and/or 21, and/or 22, and/or 23, and/or 24, and/or 26, and/or 28 and/or 30.
  • the IFN ⁇ -inducible PD markers in an expression profile may include at least genes IFI6, RSAD2, IFI44, IFI44L, IFI27, MX1, IFIT1, ISG15, LAMP3, OAS3, OAS1, EPSTI1, IFIT3, OAS2, SIGLEC1, and USP18.
  • the IFN ⁇ -inducible PD markers in such an expression profile may further include at least one or more gene listed in Table 19 and/or 20 and/or 21, and/or 22, and/or 23, and/or 24, and/or 26, and/or 28 and/or 30.
  • the IFN ⁇ -inducible PD markers in an expression profile may include at least genes IFI6, RSAD2, IFI44, IFI44L, IFI27, MX1, IFIT1, HERC5, ISG15, LAMP3, OAS3, OAS1, EPSTI1, IFIT3, OAS2, LY6E, SIGLEC1, and USP18.
  • the IFN ⁇ -inducible PD markers in such an expression profile may further include at least one or more gene listed in Table 19 and/or 20 and/or 21, and/or 22, and/or 23, and/or 24, and/or 26, and/or 28 and/or 30.
  • the IFN ⁇ -inducible PD markers in an expression profile may include at least genes IFI6, RSAD2, IFI44, IFI44L, IFI27, MX1, and IFIT1.
  • the IFN ⁇ -inducible PD markers in such an expression profile may further include at least one or more gene listed in Table 19 and/or 20 and/or 21, and/or 22, and/or 23, and/or 24, and/or 26, and/or 28 and/or 30.
  • the IFN ⁇ -inducible PD markers in an expression profile may include at least genes IFI6, RSAD2, IFI44, IFI44L, and IFI27.
  • the IFN ⁇ -inducible PD markers in such an expression profile may further include at least one or more gene listed in Table 19 and/or 20 and/or 21, and/or 22, and/or 23, and/or 24, and/or 26, and/or 28 and/or 30.
  • the IFN ⁇ -inducible PD markers in an expression profile may include at least genes SAMD9L, IFI6, IFI44, IFIT2, OAS1, IFI27, OAS3, IFI44L, HERC5, IFIT1, EPSTI1, ISG15, SERPING1, OASL, GBP1, and MX1.
  • the IFN ⁇ -inducible PD markers in such an expression profile may further include at least one or more gene listed in Table 19 and/or 20 and/or 21, and/or 22, and/or 23, and/or 24, and/or 26, and/or 28 and/or 30.
  • the IFN ⁇ -inducible PD markers in an expression profile may include at least genes IFI27, IL-121R beta2, IL-15R alpha, IL-15, suppressor of cytokine signaling 1 (SOCS1), janus kinase 2, CXCL11 (T-TAC), TNFSF13B (BAFF), TRAF-type domain 1 (TRAFD1), SERPING1, CD274 (PD1-L), indoleamine 2,3 dioxygenase (INDO), lymphocyte-activation gene 3 (LAG3), and caspase 5.
  • the IFN ⁇ -inducible PD markers in such an expression profile may further include at least one or more gene listed in Table 19 and/or 20 and/or 21, and/or 22, and/or 23, and/or 24, and/or 26, and/or 28 and/or 30.
  • the IFN ⁇ -inducible PD markers in an expression profile may include at least genes complement factor B, insulin-like growth factor (IGF2BP3), cyclin A1, neuropilin 2, complement 1qB, complement 1qC, CD80, CD47, MMP14, toll-like receptor 3 (TLR3), TLR adaptor molecule 2 (TICAM2), macrophage scavenger receptor-1 (MSR1), desmoplakin, PDGR receptor, CCL13 (MCP-4), CXCL13 (BCA-1), CCL19 (CCR7), IL-1 family 5, purinergic receptor P2X7, IRS 1, caspase 3, and cyclin-dependent kinase-like 1 (CDKL1).
  • the IFN ⁇ -inducible PD markers in such an expression profile may further include at least one or more gene listed in Table 19 and/or 20 and/or 21, and/or 22, and/or 23, and/or 24, and/or 26, and/or 28 and/or 30.
  • the IFN ⁇ -inducible PD markers in an expression profile may include alterations in any one or more of serum protein levels of adiponectin, alpha-fetoprotein, apolipoprotein CIII, beta-2 microglobulin, cancer antigen 125, cancer antigen 19-9, eotaxin, FABP, factor VII, ferritin, IL-10, IL-12p70, IL-16, IL-18, IL-1ra, IL-3, MCP-1, MMP-3, myoglobin, SGOT, tissue factor, TIMP-1, TNF RII, TNF-alpha, VCAM-1, vWF, BDNK, complement 3, CD40 ligand, EGF, ENA-78, EN-RAGE, IGF-1, MDC, myeloperoxidase, RANTES, or thrombopoietin.
  • the IFN ⁇ -inducible PD markers in an expression profile may include alterations in any one or more of serum protein levels of adiponectin, alpha-fetoprotein, apolipoprotein CIII, beta-2 microglobulin, cancer antigen 125, cancer antigen 19-9, eotaxin, FABP, factor VII, ferritin, IL-10, IL-12p70, IL-16, IL-18, IL-1ra, IL-3, MCP-1, MMP-3, myoglobin, SGOT, tissue factor, TIMP-1, TNF RII, TNF-alpha, VCAM-1, or vWF.
  • the IFN ⁇ -inducible PD markers in such an expression profile may further include at least one or more gene listed in Table 19 and/or 20 and/or 21, and/or 22, and/or 23, and/or 24, and/or 26, and/or 28 and/or 30.
  • the IFN ⁇ -inducible PD markers in an expression profile may include alterations in any one or more of serum protein levels of BDNK, complement 3, CD40 ligand, EGF, ENA-78, EN-RAGE, IGF-1, MDC, myeloperoxidase, RANTES, or thrombopoietin.
  • the IFN ⁇ -inducible PD markers in such an expression profile may further include at least one or more gene listed in Table 19 and/or 20 and/or 21, and/or 22, and/or 23, and/or 24, and/or 26, and/or 28 and/or 30.
  • An IFN ⁇ -inducible PD marker expression profile may further include genes whose expression or activity is down-regulated in cells exposed to non-baseline IFN ⁇ levels.
  • the genes whose expression or activity is down-regulated may be any of the genes that are identified in Table 31.
  • the genes may include any one or more of SLC4A1, PRSS33, FCER1A, BACH2, KLRB1, D4S234E, T cell receptor alpha locus/l cell receptor delta locus, FEZ1, AFF3, CD160, ABCB1, PTCH1, OR2W3, IGHD, NOG, NR3C2, TNS1, PDZK1IP1, SH2D1B, STRBP, ZMYND11, TMOD1, FCRLA, DKFZp761P0423, EPB42, NR6A1, LOC341333, MS4A1, IGHM, SIGLECP3, KIR2DS2, PKIA, BLR1, C5orf4, MYLK, LOC283663, MAD1L
  • any number of these genes may serve as PD markers in an IFN ⁇ -inducible PD marker expression profile. For example, at least 2, at least 3, at least 4, at least 5, at least 6, at least 7, at least 8, at least 9, at least 10, at least 11, at least 12 at least 15, at least 20, at least 25, at least 30, at least 35, at least 40, at least 45, or at least 50 down-regulated genes may be included in the IFN ⁇ -inducible PD marker expression profile.
  • the IFN ⁇ -inducible PD marker expression profile may further include genes listed in Tables 19 and/or 20 and/or 21 and/or 22 and/or 23 and/or 24 and/or 26 and/or 28.
  • the IFN ⁇ -inducible PD marker expression profile may include gene FEZ1, or may include genes FEZ1 and NOG, or may include gene NOG, or may include genes FEZ1, NOG, and SLC4A1, or may include gene SLC4A1, or may include genes NOG and SLC4A1, or may include genes FEZ1, NOG, SLC4A1, and D4S234E, or may include genes FEZ1, NOG, SLC4A1, D4S234E, and PRSS33.
  • the IFN ⁇ -inducible PD marker expression profile may further include genes listed in Tables 19 and/or 20 and/or 21 and/or 22 and/or 23 and/or 24 and/or 26 and/or 28 and/or 30, and/or 31.
  • Down-regulated genes may have down-regulated expression or activity of at least 5%, at least 10%, at least 15%, at least 20%, at least 25%, at least 30%, at least 35%, at least 40%, at least 45%, at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% that of control cells, e.g., cells of healthy volunteers or cells of control animals or cells not exposed to IFN ⁇ in culture.
  • control cells e.g., cells of healthy volunteers or cells of control animals or cells not exposed to IFN ⁇ in culture.
  • Up- or down-regulation of gene expression or activity of IFN ⁇ -inducible PD markers may be determined by any means known in the art. For example, up- or down-regulation of gene expression may be detected by determining mRNA levels. mRNA expression may be determined by northern blotting, slot blotting, quantitative reverse transcriptase polymerase chain reaction, or gene chip hybridization techniques. See U.S. Pat. Nos. 5,744,305 and 5,143,854 for examples of making nucleic acid arrays for gene chip hybridization techniques.
  • Up- or down-regulation of gene expression or activity of IFN ⁇ -inducible PD markers may be determined by detecting protein levels.
  • the up- or down-regulated gene whose protein levels are detected may be any one, any two, any three, any four, any five, any six, any seven, any eight, any nine, any ten, any twelve, any fifteen, any twenty, any twenty five, any thirty, any thirty five, or more of adiponectin, alpha-fetoprotein, apolipoprotein CIII, beta-2 microglobulin, cancer antigen 125, cancer antigen 19-9, eotaxin, FABP, factor VII, ferritin, IL-10, IL-12p70, IL-16, IL-18, IL-1ra, IL-3, MCP-1, MMP-3, myoglobin, SGOT, tissue factor, TIMP-1, TNF RII, TNF-alpha, VCAM-1, vWF, BDNK, complement 3, CD40 ligand, EGF, ENA-78
  • An IFN ⁇ -inducible PD marker expression profile may comprise a profile of protein activity.
  • Up- or down-regulation of gene expression or activity of IFN ⁇ -inducible PD markers may be determined by detecting activity of proteins including, but not limited to, detectable phosphorylation activity, de-phosphorylation activity, or cleavage activity.
  • up- or down-regulation of gene expression or activity of IFN ⁇ -inducible PD markers may be determined by detecting any combination of these gene expression levels or activities.
  • a candidate therapeutic for treating IFN ⁇ -mediated disorders may be identified by the methods encompassed by the invention.
  • Candidate therapeutics may be any type of molecule including a small molecule or a biological agent.
  • a candidate therapeutic identified by the methods encompassed by the invention may immediately be identified as useful as a therapeutic for a disease, disorder, or condition.
  • a candidate therapeutic identified by the methods encompassed by the invention may need to be further tested and/or modified before selection for treating patients.
  • a candidate therapeutic identified by the methods encompassed by the invention may, after further testing, be de-selected as a molecule for treating patients.
  • cells comprising an IFN ⁇ -inducible PD marker expression profile are contacted with an agent.
  • the cells may be any type of cells, such as commercially available immortalized cell lines that comprise an IFN ⁇ -inducible PD marker expression profile, commercially available immortalized cell lines that have been treated with IFN ⁇ to induce an IFN ⁇ -inducible PD marker expression profile, cells isolated from a patient having an IFN ⁇ -inducible PD marker expression profile, or cells isolated from a healthy patient and treated with IFN ⁇ to induce an IFN ⁇ -inducible PD marker expression profile.
  • Presence or absence of a change in the IFN ⁇ -inducible PD marker expression profile of the cells is detected following contacting the cells with the agent.
  • Presence of change may be any change in IFN ⁇ -inducible PD marker expression profile including at least a 10% decrease in up-regulated expression or activity of at least 1 gene in the IFN ⁇ -inducible PD marker expression profile, at least a 20% decrease of the at least 1 up-regulated gene, at least a 30% decrease of the at least up-regulated 1 gene, at least a 40% decrease of the at least 1 up-regulated gene, at least a 50% decrease of the at least 1 up-regulated gene, at least a 60% decrease of the at least 1 up-regulated gene, at least a 70% decrease of the at least 1 up-regulated gene, at least a 75% decrease of the at least 1 up-regulated gene, at least an 80% decrease of the at least 1 up-regulated gene, at least an 85% decrease of the at least 1 up-regulated gene, at least a 90% decrease of the at least 1 up-regulated gene,
  • presence of change may be any change in IFN ⁇ -inducible PD marker expression profile including at least a 10% increase in expression or activity of at least 1 down-regulated gene in the IFN ⁇ -inducible PD marker expression profile, at least a 20% increase of the at least 1 down-regulated gene, at least a 30% increase of the at least 1 down-regulated gene, at least a 40% increase of the at least 1 down-regulated gene, at least a 50% increase of the at least 1 down-regulated gene, at least a 60% increase of the at least 1 down-regulated gene, at least a 70% increase of the at least 1 down-regulated gene, at least a 75% increase of the at least 1 down-regulated gene, at least an 80% increase of the at least 1 down-regulated gene, at least an 85% increase of the at least 1 down-regulated gene, at least a 90% increase of the at least 1 down-regulated gene, at least a 95% increase of the at least 1 down-regulated gene, at least a 96% increase of the at least 1 down-regulated gene
  • samples from the patient may be obtained before and after administration of an agent, e.g., an agent that binds to and modulates type I IFN or IFN ⁇ activity, or an agent that binds to and does not modulate type I IFN or IFN ⁇ activity, or a combination of agents that may or may not include an agent that binds to and modulates type I IFN or IFN ⁇ activity.
  • an agent e.g., an agent that binds to and modulates type I IFN or IFN ⁇ activity, or an agent that binds to and does not modulate type I IFN or IFN ⁇ activity, or a combination of agents that may or may not include an agent that binds to and modulates type I IFN or IFN ⁇ activity.
  • Type I IFN or IFN ⁇ inducible PD marker expression profiles are obtained in the (before and after agent administration) samples. The type I IFN or IFN ⁇ inducible PD marker expression profiles in the samples are compared.
  • Comparison may be of the number of type I IFN or IFN ⁇ inducible PD markers present in the samples or may be of the quantity of type I IFN or IFN ⁇ inducible PD markers present in the samples, or any combination thereof.
  • Variance indicating efficacy of the therapeutic agent may be indicated if the number or level (or any combination thereof) of up-regulated type I IFN or IFN ⁇ inducible PD markers decreases in the sample obtained after administration of the therapeutic agent relative to the sample obtained before administration of the therapeutic agent.
  • the number of up-regulated type I IFN or IFN ⁇ inducible PD markers may decrease by at least 1, at least 2, at least 3, at least 4, at least 5, at least 6, at least 7, at least 8, at least 9, or at least 10.
  • the level of any given up-regulated type I IFN or IFN ⁇ inducible PD marker may decrease by at least 10%, at least 20%, at least 25%, at least 30%, at least 35%, at least 40%, at least 50%, at least 60%, at least 70%, at least 80%, at least 90%, or at least 95%.
  • the number of up-regulated type I IFN or IFN ⁇ inducible PD markers with decreased levels may be at least 1, at least 2, at least 3, at least 4, at least 5, at least 6, at least 7, at least 8, at least 9, at least 10, at least 15, at least 20, at least 25, at least 30, or at least 35. Any combination of decreased number and decreased level of up-regulated type I IFN or IFN ⁇ inducible PD markers may indicate efficacy.
  • Variance indicating efficacy of the therapeutic agent may be indicated if the number or level (or any combination thereof) of down-regulated type I IFN or IFN ⁇ inducible PD markers decreases in the sample obtained after administration of the therapeutic agent relative to the sample obtained before administration of the therapeutic agent.
  • the number of down-regulated type I IFN or IFN ⁇ inducible PD markers may decrease by at least 1, at least 2, at least 3, at least 4, at least 5, at least 6, at least 7, at least 8, at least 9, or at least 10.
  • the level of any given down-regulated type I IFN or IFN ⁇ inducible PD marker may increase by at least 10%, at least 20%, at least 25%, at least 30%, at least 35%, at least 40%, at least 50%, at least 60%, at least 70%, at least 80%, at least 90%, or at least 95%.
  • the number of down-regulated type I IFN or IFN ⁇ inducible PD markers with increased levels may be at least 1, at least 2, at least 3, at least 4, at least 5, at least 6, at least 7, at least 8, at least 9, at least 10, at least 15, at least 20, at least 25, at least 30, or at least 35. Any combination of decreased number and increased level of down-regulated type I IFN or IFN ⁇ inducible PD markers may indicate efficacy.
  • the sample obtained from the patient may be obtained prior to a first administration of the agent, i.e., the patient is na ⁇ ve to the agent.
  • the sample obtained from the patient may occur after administration of the agent in the course of treatment.
  • the agent may have been administered prior to the initiation of the monitoring protocol.
  • an additional samples may be obtained from the patient and type I IFN or IFN ⁇ inducible PD markers in the samples are compared.
  • the samples may be of the same or different type, e.g., each sample obtained may be a blood sample, or each sample obtained may be a serum sample.
  • the type I IFN or IFN ⁇ inducible PD markers detected in each sample may be the same, may overlap substantially, or may be similar.
  • the samples may be obtained at any time before and after the administration of the therapeutic agent.
  • the sample obtained after administration of the therapeutic agent may be obtained at least 2, at least 3, at least 4, at least 5, at least 6, at least 7, at least 8, at least 9, at least 10, at least 12, or at least 14 days after administration of the therapeutic agent.
  • the sample obtained after administration of the therapeutic agent may be obtained at least 2, at least 3, at least 4, at least 5, at least 6, at least 7, or at least 8 weeks after administration of the therapeutic agent.
  • the sample obtained after administration of the therapeutic agent may be obtained at least 2, at least 3, at least 4, at least 5, or at least 6 months following administration of the therapeutic agent.
  • Additional samples may be obtained from the patient following administration of the therapeutic agent.
  • At least 2, at least 3, at least 4, at least 5, at least 6, at least 7, at least 8, at least 9, at least 10, at least 12, at least 15, at least 20, at least 25 samples may be obtained from the patient to monitor progression or regression of the disease or disorder over time.
  • Disease progression may be monitored over a time period of at least 1 week, at least 2 weeks, at least 3 weeks, at least 4 weeks, at least 5 weeks, at least 6 weeks, at least 7 weeks, at least 2 months, at least 3 months, at least 4 months, at least 5 months, at least 6 months, at least 1 year, at least 2 years, at least 3 years, at least 4 years, at least 5 years, at least 10 years, or over the lifetime of the patient.
  • Additional samples may be obtained from the patient at regular intervals such as at monthly, bi-monthly, once a quarter year, twice a year, or yearly intervals.
  • the samples may be obtained from the patient following administration of the agent at regular intervals. For instance, the samples may be obtained from the patient at one week following each administration of the agent, or at two weeks following each administration of the agent, or at three weeks following each administration of the agent, or at one month following each administration of the agent, or at two months following each administration of the agent.
  • multiple samples may be obtained from the patient following an or each administration of the agent.
  • Disease progression in a patient may similarly be monitored in the absence of administration of an agent.
  • Samples may periodically be obtained from the patient having the disease or disorder.
  • Disease progression may be identified if the number of type I IFN or IFN ⁇ inducible PD markers increases in a later-obtained sample relative to an earlier obtained sample.
  • the number of type I IFN or IFN ⁇ inducible PD markers may increase by at least 1, at least 2, at least 3, at least 4, at least 5, at least 6, at least 7, at least 8, at least 9, or at least 10.
  • Disease progression may be identified if level of any given up-regulated type I IFN or IFN ⁇ inducible PD marker increases by at least 10%, at least 20%, at least 25%, at least 30%, at least 35%, at least 40%, at least 50%, at least 60%, at least 70%, at least 80%, at least 90%, or at least 95%.
  • Disease progression may be identified if level of any given down-regulated type I IFN or IFN ⁇ inducible PD marker decreases by at least 10%, at least 20%, at least 25%, at least 30%, at least 35%, at least 40%, at least 50%, at least 60%, at least 70%, at least 80%, at least 90%, or at least 95%.
  • the number of up-regulated type I IFN or IFN ⁇ inducible PD markers with increased levels may be at least 1, at least 2, at least 3, at least 4, at least 5, at least 6, at least 7, at least 8, at least 9, at least 10, at least 15, at least 20, at least 25, at least 30, or at least 35.
  • the number of down-regulated type I IFN or IFN ⁇ inducible PD markers with decreased levels may be at least 1, at least 2, at least 3, at least 4, at least 5, at least 6, at least 7, at least 8, at least 9, at least 10, at least 15, at least 20, at least 25, at least 30, or at least 35. Any combination of increased number and increased level of up-regulated type I IFN or IFN ⁇ inducible PD marker may indicate disease progression.
  • any combination of decreased number and decreased level of down-regulated type I IFN or IFN ⁇ inducible PD marker may indicate disease progression.
  • Disease regression may also be identified in a patient having a disease or disorder, not treated by an agent. In this instance, regression may be identified if the number of type I IFN or IFN ⁇ inducible PD markers decreases in a later-obtained sample relative to an earlier obtained sample.
  • the number of type I IFN or IFN ⁇ inducible PD markers may decrease by at least 1, at least 2, at least 3, at least 4, at least 5, at least 6, at least 7, at least 8, at least 9, or at least 10.
  • Disease regression may be identified if level of any given up-regulated type I IFN or IFN ⁇ inducible PD marker decreases by at least 10%, at least 20%, at least 25%, at least 30%, at least 35%, at least 40%, at least 50%, at least 60%, at least 70%, at least 80%, at least 90%, or at least 95%.
  • Disease regression may be identified if level of any given down-regulated type I IFN or IFN ⁇ inducible PD marker increases by at least 10%, at least 20%, at least 25%, at least 30%, at least 35%, at least 40%, at least 50%, at least 60%, at least 70%, at least 80%, at least 90%, or at least 95%.
  • the number of up-regulated type I IFN or IFN ⁇ inducible PD markers with decreased levels may be at least 1, at least 2, at least 3, at least 4, at least 5, at least 6, at least 7, at least 8, at least 9, at least 10, at least 15, at least 20, at least 25, at least 30, or at least 35.
  • the number of down-regulated type I IFN or IFN ⁇ inducible PD markers with increased levels may be at least 1, at least 2, at least 3, at least 4, at least 5, at least 6, at least 7, at least 8, at least 9, at least 10, at least 15, at least 20, at least 25, at least 30, or at least 35.
  • Disease progression or disease regression may be monitored by obtaining samples over any period of time and at any interval.
  • Disease progression or disease regression may be monitored by obtaining samples over the course of at least 1 week, at least 2 weeks, at least 3 weeks, at least 4 weeks, at least 5 weeks, at least 6 weeks, at least 7 weeks, at least 2 months, at least 3 months, at least 4 months, at least 5 months, at least 6 months, at least 1 year, at least 2 years, at least 3 years, at least 4 years, at least 5 years, at least 10 years, or over the lifetime of the patient.
  • Disease progression or disease regression may be monitored by obtaining samples at least monthly, bi-monthly, once a quarter year, twice a year, or yearly. The samples need not be obtained at strict intervals.
  • the invention also encompasses kits and probes.
  • the probes may be any molecule that detects any expression or activity of any gene that may be included in an IFN ⁇ -inducible PD marker expression profile.
  • the invention also encompasses methods of detecting IFN activity. These methods may employ cells comprising a polynucleotide sequence comprising a reporter gene under the control of an interferon-stimulated response element.
  • the cells comprising the polynucleotide sequence may be any cells amenable to transfection or transformation with a polynucleotide sequence and that can be maintained in culture. These cells include animal cells, bacterial cells, yeast cells, insect cells, or plant cells. These cells may be adherent or may grow in suspension.
  • the cells are animal cells, they may be from a known cell line such as HeLa, COS, NIH3T3, AGS, 293, CHO, Huh-7, HUVEC, MCF-7, C6, BHK-21, BNL CL 2, C2C12, HepG2, and ATDC5. Countless other cell lines are known and can be obtained by those of skill in the art.
  • the cells may alternatively be primary cells that have or have not been immortalized.
  • the cells may comprise a polynucleotide sequence comprising a reporter gene under the control of an interferon-stimulated response element.
  • the polynucleotide sequence may be stably integrated in the DNA of the cell or may be an extrachomosomal element that is stably or transiently in the cell.
  • the polynucleotide may have been introduced to the cell as a naked polynucleotide molecule, a polynucleotide molecule complexed with lipids or other molecules, or a polynucleotide in a virus particle.
  • the polynucleotide may have been a linear or a circular molecule.
  • Non-limiting examples of circular polynucleotide molecules include plasmids, and artificial chromosomes. These vectors may be cleaved with enzymes, for example, to generate linear polynucleotide molecules.
  • the polynucleotide was introduced as a naked polynucleotide it may have been introduced into the cells by any of many well known techniques in the art. These techniques include, but are not limited to, electroporation, microinjection, and biolistic particle delivery. See, also, e.g., Loeffler and Behr, 1993 , Meth. Enzymol. 217:599-618; Cohen et al., 1993 , Meth. Enzymol. 217:618-644 ; Clin. Pharma. Ther. 29:69-92 (1985), Sambrook, et al. Molecular Cloning: A Laboratory Manual.
  • Lipids or liposomes comprise a mixture of fat particles or lipids which bind to DNA or RNA to provide a hydrophobic coated delivery vehicle.
  • Suitable liposomes may comprise any of the conventional synthetic or natural phospholipid liposome materials including phospholipids from natural sources such as egg, plant or animal sources such as phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol, sphingomyelin, phosphatidylserine or phosphatidylinositol.
  • Synthetic phospholipids also may be used, e.g., dimyristoylphosphatidylcholine, dioleoylphosphatidylcholine, dioleoylphosphatidycholine and corresponding synthetic phosphatidylethanolamines and phosphatidylglycerols.
  • Lipids or liposomes that may be conjugated with the vector are also commercially available to the skilled artisan.
  • lipid or liposome transfection reagents examples include LIPOFECTAMINETM (Invitrogen), GENEJUICE® (Novagen), GENEJAMMER® (Stratagene), FUGENE® HD (Roche), MEGAFECTINTM (Qbiogene), SUPERFECT® (Qiagen), and EFFECTENE® (Qiagen).
  • polynucleotide was introduced as a complex with other molecules it may have been compacted or in a nanosphere.
  • Compacted polynucleotide complexes are described in U.S. Pat. Nos. 5,972,901, 6,008,336, and 6,077,835.
  • Nanospheres are described in U.S. Pat. Nos. 5,718,905 and 6,207,195.
  • These compacted polynucleotide complexes and nanospheres that complex nucleic acids utilize polymeric cations. Typical polymeric cations include gelatin, poly-L-lysine, and chitosan.
  • the polynucleotide may have been complexed with DEAE-dextran, or transfected using techniques such as calcium phosphate coprecipitation, or calcium chloride coprecipitation.
  • the virus may have been any well known suitable virus for polynucleotide delivery.
  • Example viruses that may be used as vectors include adenovirus, adeno-associated virus, lentivirus, retrovirus, herpes virus (e.g. herpes simplex virus), vaccina virus, papovirus, Sendai virus, SV40 virus, respiratory syncytial virus, etc.
  • the polynucleotide sequence may include a reporter gene and an interferon-stimulated response element.
  • the reporter gene may be any one of luciferase, chloramphenicol acetyl transferase, ⁇ -galactosidase, green fluorescent protein, ⁇ -glucuronidase, or secreted placental alkaline phosphatase. Variations of many of these reporter genes, e.g., green fluorescent protein and luceriferase, are known and can be readily identified and/or produced by those of skill in the art. Other reporter genes in addition to those listed will also be known to those of skill in the art and are readily available. Interferon-stimulated response elements are also known to those of skill in the art.
  • the cells employed in the assay may be incubated with a sample.
  • the sample may be obtained from a patient, from a vendor with patient samples, or a control sample used for calibration or as a control. If the sample is obtained from a patient it may be any biological fluid or tissue, such as whole blood, saliva, urine, synovial fluid, bone marrow, cerebrospinal fluid, nasal secretions, sputum, amniotic fluid, bronchoalveolar lavage fluid, peripheral blood mononuclear cells, total white blood cells, lymph node cells, spleen cells, tonsil cells, or skin.
  • biological fluid or tissue such as whole blood, saliva, urine, synovial fluid, bone marrow, cerebrospinal fluid, nasal secretions, sputum, amniotic fluid, bronchoalveolar lavage fluid, peripheral blood mononuclear cells, total white blood cells, lymph node cells, spleen cells, tonsil cells, or skin.
  • Expression of the reporter gene is detected by any well known means in the art. The expression, even if “0” indicates IFN activity in the sample. One of skill in the art may further quantitate any level of expression of the reporter gene which may then correlate to level of IFN activity in the sample.
  • a method of treating a patient having a type I IFN or an IFN ⁇ -mediated disease or disorder comprising:
  • the method of 1 further comprising detecting neutralization of the type I IFN or IFN ⁇ -inducible PD marker expression profile of the patient.
  • the method of embodiment 1 wherein the type I IFN or IFN ⁇ -inducible PD marker expression profile comprises up-regulated expression or activity of genes MX1, LY6E, IFI27, OAS1 IFIT1, IFI6, IFI44L, ISG15, LAMP3, OASL, RSAD2, and IFI44.
  • the method of embodiment 1 wherein the type I IFN or an IFN ⁇ -mediated disease or disorder is one of lupus, psoriasis, vasculitis, sarcoidosis, Sjogren's syndrome, or idiopathic inflammatory myositis.
  • the method of embodiment 1 wherein the type I IFN or IFN ⁇ -inducible PD marker expression profile comprises up-regulated expression or activity of at least IFN ⁇ subtypes 1, 2, 8, and 14.
  • the method of embodiment 1 wherein the type I IFN or IFN ⁇ -inducible PD marker expression profile comprises transcripts of PD marker genes.
  • the method of embodiment 1 wherein the type I IFN or IFN ⁇ -inducible PD marker expression profile comprises polypeptides expressed from PD marker genes.
  • the type I IFN or IFN ⁇ -inducible PD marker expression profile comprises up-regulated expression or activity of genes IFI27, SIGLEC1, RSAD2, IFI6, IFI44L, IFI44, USP18, IFIT2, SAMD9L, BIRC4BP, DNAPTP6, OAS3, LY6E, IFIT1, LIPA, LOC129607, ISG15, PARP14, MX1, OAS2, OASL, CCL2, HERC5, OAS1
  • the type I IFN or IFN ⁇ -inducible PD marker expression profile comprises up-regulated expression or activity of genes IFIT1, IFIT3, IRF7, IFI6, IL6ST, IRF2, LY6E, MARCKS, MX1, MX2, OAS1, EIF2AK2, ISG15, STAT2, OAS3, IFI44, IFI44L, HERC5, RAB8B, LILRA5, RSAD2, and FCHO2
  • the type I IFN or IFN ⁇ -inducible PD marker expression profile comprises up-regulated expression or activity of genes SERPING1, IFIT2, IFIT3, IFI6, LY6E, MX1, OAS1, ISG15, IFI27, OAS3, IFI44, LAMP3, DNAPTP6, ETV7, HERC5, OAS2, USP18, XAF1, RTP4, SIGLEC1, and EPSTI1.
  • the type I IFN or IFN ⁇ -inducible PD marker expression profile comprises up-regulated expression or activity of genes RTP4, RSAD2, HERC5, SIGLEC1, USP18, LY6E, ETV7, SERPING1, IFIT3, OAS1, HSXIAPAF1, G1P3, MX1, OAS3, IFI27, DNAPTP6, LAMP3, EPSTI1, IFI44, OAS2, IFIT2, and ISG15.
  • the type I IFN or IFN ⁇ -inducible PD marker expression profile comprises up-regulated expression or activity of genes LAMP3, SIGLEC1, DNAPTP6, IFIT2, ETV7, RTP4, SERPING1, HERC5, XAF1, MX1, EPSTI1, OAS2, OAS1, OAS3, IFIT3, IFI6, USP18, RSAD2, IFI44, LY6E, ISG15, and IFI27.
  • the method of embodiment 1 wherein the type I IFN or IFN ⁇ -inducible PD marker expression profile comprises up-regulated expression or activity of genes DNAPTP6, EPSTI1, HERC5, IFI27, IFI44, IFI44L, IFI6, IFIT1, IFIT3, ISG15, LAMP3, LY6E, MX1, OAS1, OAS2, OAS3, PLSCR1, RSAD2, RTP4, SIGLEC1, and USP18.
  • the type I IFN or IFN ⁇ -inducible PD marker expression profile comprises up-regulated expression or activity of genes SAMD9L, IFI6, IFI44, IFIT2, ZC3HAV1, ETV6, DAPP1, IL1RN, CEACAM1, OAS1, IFI27, OAS3, IFI44L, HERC5, IFIT1, EPSTI1, ISG15, SERPING1, OASL, GBP1, and MX1.
  • the method of embodiment 1 wherein the type I IFN or IFN ⁇ -inducible PD marker expression profile comprises up-regulated expression or activity of genes SAMD9L, IFI6, IFI44, IFIT2, OAS1, IFI27, OAS3, IFI44L, HERC5, IFIT1, EPSTI1, ISG15, SERPING1, OASL, GBP1, and MX1.
  • the method of embodiment 1 wherein the type I IFN or IFN ⁇ -inducible PD marker expression profile comprises up-regulated expression or activity of genes IFI6, RSAD2, IFI44, IFI44L, IFI27, MX1, IFIT1, ISG15, LAMP3, OAS3, OAS1, EPSTI1, IFIT3, OAS2, SIGLEC1, and USP18.
  • the method of embodiment 1 wherein the type I IFN or IFN ⁇ -inducible PD marker expression profile comprises up-regulated expression or activity of genes IFI6, RSAD2, IFI44, IFI44L, and IFI27.
  • the method of embodiment 32 wherein the type I IFN or IFN ⁇ -inducible PD marker expression profile further comprises up-regulated expression or activity of genes MX1 and IFIT1.
  • the method of embodiment 33 wherein the type I IFN or IFN ⁇ -inducible PD marker expression profile further comprises up-regulated expression or activity of genes OAS2 and OAS1.
  • the type I IFN or IFN ⁇ -inducible PD marker expression profile further comprises down-regulated expression or activity of genes NOG, SLC4A1, PRSS33, and FEZ1.
  • the method of embodiment 1 wherein the type I IFN or IFN ⁇ -inducible PD marker expression profile comprises down-regulated expression or activity of genes NOG, SLC4A1, PRSS33, and FEZ1.
  • polypeptides include cancer antigen 125, ferritin, tissue factor, and MMP-3.
  • polypeptides include EGF, thrombopoietin, and CD40 ligand.
  • a method of treating an autoimmune disease patient comprising a moderate or strong type I IFN or an IFN ⁇ PD marker profile comprising: administering an agent that binds to and modulates type I IFN or IFN ⁇ activity; wherein the agent neutralizes the type I IFN or IFN ⁇ -inducible PD marker expression profile of the patient.
  • the method of 41 further comprising detecting neutralization of the type I IFN or IFN ⁇ -inducible PD marker expression profile of the patient.
  • the method of embodiment 41 wherein the type I IFN or IFN ⁇ -inducible PD marker expression profile comprises up-regulated expression or activity of genes MX1, LY6E, IFI27, OAS1 IFIT1, IFI6, IFI44L, ISG15, LAMP3, OASL, RSAD2, and IFI44.
  • the type I IFN or IFN ⁇ -inducible PD marker expression profile comprises up-regulated expression or activity of genes IFI27, SIGLEC1, RSAD2, IFI6, IFI44L, IFI44, USP18, IFIT2, SAMD9L, BIRC4BP, DNAPTP6, OAS3, LY6E, IFIT1, LIPA, LOC129607, ISG15, PARP14, MX1, OAS2, OASL, CCL2, HERC5, OAS1
  • the type I IFN or IFN ⁇ -inducible PD marker expression profile comprises up-regulated expression or activity of genes IFIT1, IFIT3, IRF7, IFI6, IL6ST, IRF2, LY6E, MARCKS, MX1, MX2, OAS1, EIF2AK2, ISG15, STAT2, OAS3, IFI44, IFI44L, HERC5, RAB8B, LILRA5, RSAD2, and FCHO2
  • the method of embodiment 41 wherein the type I IFN or IFN ⁇ -inducible PD marker expression profile comprises up-regulated expression or activity of genes SERPING1, IFIT2, IFIT3, IFI6, LY6E, MX1, OAS1, ISG15, IFI27, OAS3, IFI44, LAMP3, DNAPTP6, ETV7, HERC5, OAS2, USP18, XAF1, RTP4, SIGLEC1, and EPSTI1.
  • the type I IFN or IFN ⁇ -inducible PD marker expression profile comprises up-regulated expression or activity of genes RTP4, RSAD2, HERC5, SIGLEC1, USP18, LY6E, ETV7, SERPING1, IFIT3, OAS1, HSXIAPAF1, G1P3, MX1, OAS3, IFI27, DNAPTP6, LAMP3, EPSTI1, IFI44, OAS2, IFIT2, and ISG15.
  • the method of embodiment 41 wherein the type I IFN or IFN ⁇ -inducible PD marker expression profile comprises up-regulated expression or activity of genes LAMP3, SIGLEC1, DNAPTP6, IFIT2, ETV7, RTP4, SERPING1, HERC5, XAF1, MX1, EPSTI1, OAS2, OAS1, OAS3, IFIT3, IFI6, USP18, RSAD2, IFI44, LY6E, ISG15, and IFI27.
  • the method of embodiment 41 wherein the type I IFN or IFN ⁇ -inducible PD marker expression profile comprises up-regulated expression or activity of genes DNAPTP6, EPSTI1, HERC5, IFI27, IFI44, IFI44L, IFI6, IFIT1, IFIT3, ISG15, LAMP3, LY6E, MX1, OAS1, OAS2, OAS3, PLSCR1, RSAD2, RTP4, SIGLEC1, and USP18.
  • the type I IFN or IFN ⁇ -inducible PD marker expression profile comprises up-regulated expression or activity of genes SAMD9L, IFI6, IFI44, IFIT2, ZC3HAV1, ETV6, DAPP1, IL1RN, CEACAM1, OAS1, IFI27, OAS3, IFI44L, HERC5, IFIT1, EPSTI1, ISG15, SERPING1, OASL, GBP1, and MX1.
  • the method of embodiment 41 wherein the type I IFN or IFN ⁇ -inducible PD marker expression profile comprises up-regulated expression or activity of genes SAMD9L, IFI6, IFI44, IFIT2, OAS1, IFI27, OAS3, IFI44L, HERC5, IFIT1, EPSTI1, ISG15, SERPING1, OASL, GBP1, and MX1.
  • the method of embodiment 41 wherein the type I IFN or IFN ⁇ -inducible PD marker expression profile comprises up-regulated expression or activity of genes IFI6, RSAD2, IFI44, IFI44L, IFI27, MX1, IFIT1, ISG15, LAMP3, OAS3, OAS1, EPSTI1, IFIT3, OAS2, SIGLEC1, and USP18.
  • the method of embodiment 41 wherein the type I IFN or IFN ⁇ -inducible PD marker expression profile comprises up-regulated expression or activity of genes IFI6, RSAD2, IFI44, and IFI27.
  • the method of embodiment 53 wherein the type I IFN or IFN ⁇ -inducible PD marker expression profile further comprises up-regulated expression or activity of genes MX1 and IFIT1.
  • the method of embodiment 41 wherein the type I IFN or IFN ⁇ -inducible PD marker expression profile comprises up-regulated expression or activity of at least IFN ⁇ subtypes 1, 2, 8, and 14.
  • autoimmune disease patient is a lupus, psoriasis, vasculitis, sarcoidosis, Sjogren's syndrome, or idiopathic inflammatory myositis patient.
  • a method of neutralizing a type I IFN or IFN ⁇ -inducible PD marker expression profile in a patient in need thereof, comprising:
  • the method of 72 further comprising detecting neutralization of the type I IFN or IFN ⁇ -inducible PD marker expression profile of the patient.
  • the method of embodiment 72 wherein the type I IFN or IFN ⁇ -inducible PD marker expression profile comprises up-regulated expression or activity of genes MX1, LY6E, IFI27, OAS1 IFIT1, IFI6, IFI44L, ISG15, LAMP3, OASL, RSAD2, and IFI44.
  • the method of embodiment 72 wherein the type I IFN or IFN ⁇ -inducible PD marker expression profile comprises up-regulated expression or activity of at least IFN ⁇ subtypes 1, 2, 8, and 14.
  • the method of embodiment 72 wherein the type I IFN or IFN ⁇ -inducible PD marker expression profile comprises transcripts of PD marker genes.
  • the method of embodiment 72 wherein the type I IFN or IFN ⁇ -inducible PD marker expression profile comprises polypeptides expressed from PD marker genes.
  • the type I IFN or IFN ⁇ -inducible PD marker expression profile comprises up-regulated expression or activity of genes IFI27, SIGLEC1, RSAD2, IFI6, IFI44L, IFI44, USP18, IFIT2, SAMD9L, BIRC4BP, DNAPTP6, OAS3, LY6E, IFIT1, LIPA, LOC129607, ISG15, PARP14, MX1, OAS2, OASL, CCL2, HERC5, OAS1.
  • the type I IFN or IFN ⁇ -inducible PD marker expression profile comprises up-regulated expression or activity of genes IFIT1, IFIT3, IRF7, IFI6, IL6ST, IRF2, LY6E, MARCKS, MX1, MX2, OAS1, EIF2AK2, ISG15, STAT2, OAS3, IFI44, IFI44L, HERC5, RAB8B, LILRA5, RSAD2, and FCHO2.
  • the method of embodiment 72 wherein the type I IFN or IFN ⁇ -inducible PD marker expression profile comprises up-regulated expression or activity of genes SERPING1, IFIT2, IFIT3, IFI6, LY6E, MX1, OAS1, ISG15, IFI27, OAS3, IFI44, LAMP3, DNAPTP6, ETV7, HERC5, OAS2, USP18, XAF1, RTP4, SIGLEC1, and EPSTI1.
  • the type I IFN or IFN ⁇ -inducible PD marker expression profile comprises up-regulated expression or activity of genes RTP4, RSAD2, HERC5, SIGLEC1, USP18, LY6E, ETV7, SERPING1, IFIT3, OAS1, HSXIAPAF1, G1P3, MX1, OAS3, IFI27, DNAPTP6, LAMP3, EPSTI1, IFI44, OAS2, IFIT2, and ISG15.
  • the method of embodiment 72 wherein the type I IFN or IFN ⁇ -inducible PD marker expression profile comprises up-regulated expression or activity of genes LAMP3, SIGLEC1, DNAPTP6, IFIT2, ETV7, RTP4, SERPING1, HERC5, XAF1, MX1, EPSTI1, OAS2, OAS1, OAS3, IFIT3, IFI6, USP18, RSAD2, IFI44, LY6E, ISG15, and IFI27.
  • the method of embodiment 72 wherein the type I IFN or IFN ⁇ -inducible PD marker expression profile comprises up-regulated expression or activity of genes DNAPTP6, EPSTI1, HERC5, IFI27, IFI44, IFI44L, IFI6, IFIT1, IFIT3, ISG15, LAMP3, LY6E, MX1, OAS1, OAS2, OAS3, PLSCR1, RSAD2, RTP4, SIGLEC1, and USP18.
  • the type I IFN or IFN ⁇ -inducible PD marker expression profile comprises up-regulated expression or activity of genes SAMD9L, IFI6, IFI44, IFIT2, ZC3HAV1, ETV6, DAPP1, IL1RN, CEACAM1, OAS1, IFI27, OAS3, IFI44L, HERC5, IFIT1, EPSTI1, ISG15, SERPING1, OASL, GBP1, and MX1.
  • the method of embodiment 72 wherein the type I IFN or IFN ⁇ -inducible PD marker expression profile comprises up-regulated expression or activity of genes SAMD9L, IFI6, IFI44, IFIT2, OAS1, IFI27, OAS3, IFI44L, HERC5, IFIT1, EPSTI1, ISG15, SERPING1, OASL, GBP1, and MX1.
  • the method of embodiment 72 wherein the type I IFN or IFN ⁇ -inducible PD marker expression profile comprises up-regulated expression or activity of genes IFI6, RSAD2, IFI44, IFI44L, IFI27, MX1, IFIT1, ISG15, LAMP3, OAS3, OAS1, EPSTI1, IFIT3, OAS2, SIGLEC1, and USP18.
  • the method of embodiment 72 wherein the type I IFN or IFN ⁇ -inducible PD marker expression profile comprises up-regulated expression or activity of genes IFI6, RSAD2, IFI44, IFI44L, and IFI27.
  • the method of embodiment 103 wherein the type I IFN or IFN ⁇ -inducible PD marker expression profile further comprises up-regulated expression or activity of genes MX1 and IFIT1.
  • the method of any one of embodiments 74 or 94-104 wherein the type I IFN or IFN ⁇ -inducible PD marker expression profile further comprises down-regulated expression or activity of genes NOG, SLC4A1, PRSS33, and FEZ1.
  • the method of embodiment 72 wherein the type I IFN or IFN ⁇ -inducible PD marker expression profile comprises down-regulated expression or activity of genes NOG, SLC4A1, PRSS33, and FEZ1.
  • polypeptides include cancer antigen 125, ferritin, tissue factor, and MMP-3.
  • polypeptides include EGF, thrombopoietin, and CD40 ligand.
  • a method of monitoring or prognosing autoimmune disease progression of a patient comprising:
  • a method of monitoring disease progression of a patient receiving treatment with a therapeutic agent that binds to and modulates IFN ⁇ activity comprising:
  • the method of embodiment 116 wherein the first IFN ⁇ -inducible PD marker expression profile comprises up-regulated expression or activity of genes MX1, LY6E, IFI27, OAS1, IFIT1, IFI6, IFI44L, ISG15, LAMP3, OASL, RSAD2, and IFI44
  • the first type I IFN or IFN ⁇ -inducible PD marker expression profile comprises up-regulated expression or activity of genes IFI27, SIGLEC1, RSAD2, IFI6, IFI44L, IFI44, USP18, IFIT2, SAMD9L, BIRC4BP, DNAPTP6, OAS3, LY6E, IFIT1, LIPA, LOC129607, ISG15, PARP14, MX1, OAS2, OASL, CCL2, HERC5, OAS1.
  • the first type I IFN or IFN ⁇ -inducible PD marker expression profile comprises up-regulated expression or activity of genes IFIT1, IFIT3, IRF7, IFI6, IL6ST, IRF2, LY6E, MARCKS, MX1, MX2, OAS1, EIF2AK2, ISG15, STAT2, OAS3, IFI44, IFI44L, HERC5, RAB8B, LILRA5, RSAD2, and FCHO2.
  • the method of embodiment 116 wherein the first type I IFN or IFN ⁇ -inducible PD marker expression profile comprises up-regulated expression or activity of genes SERPING1, IFIT2, IFIT3, IFI6, LY6E, MX1, OAS1, ISG15, IFI27, OAS3, IFI44, LAMP3, DNAPTP6, ETV7, HERC5, OAS2, USP18, XAF1, RTP4, SIGLEC1, and EPSTI1.
  • the first type I IFN or IFN ⁇ -inducible PD marker expression profile comprises up-regulated expression or activity of genes RTP4, RSAD2, HERC5, SIGLEC1, USP18, LY6E, ETV7, SERPING1, IFIT3, OAS1, HSXIAPAF1, G1P3, MX1, OAS3, IFI27, DNAPTP6, LAMP3, EPSTI1, IFI44, OAS2, IFIT2, and ISG15.
  • the method of embodiment 116 wherein the first type I IFN or IFN ⁇ -inducible PD marker expression profile comprises up-regulated expression or activity of genes LAMP3, SIGLEC1, DNAPTP6, IFIT2, ETV7, RTP4, SERPING1, HERC5, XAF1, MX1, EPSTI1, OAS2, OAS1, OAS3, IFIT3, IFI6, USP18, RSAD2, IFI44, LY6E, ISG15, and IFI27.
  • the method of embodiment 116 wherein the first type I IFN or IFN ⁇ -inducible PD marker expression profile comprises up-regulated expression or activity of genes DNAPTP6, EPSTI1, HERC5, IFI27, IFI44, IFI44L, IFI6, IFIT1, IFIT3, ISG15, LAMP3, LY6E, MX1, OAS1, OAS2, OAS3, PLSCR1, RSAD2, RTP4, SIGLEC1, and USP18.
  • the first type I IFN or IFN ⁇ -inducible PD marker expression profile comprises up-regulated expression or activity of genes SAMD9L, IFI6, IFI44, IFIT2, ZC3HAV1, ETV6, DAPP1, IL1RN, CEACAM1, OAS1, IFI27, OAS3, IFI44L, HERC5, IFIT1, EPSTI1, ISG15, SERPING1, OASL, GBP1, and MX1.
  • the method of embodiment 116 wherein the first type I IFN or IFN ⁇ -inducible PD marker expression profile comprises up-regulated expression or activity of genes SAMD9L, IFI6, IFI44, IFIT2, OAS1, IFI27, OAS3, IFI44L, HERC5, IFIT1, EPSTI1, ISG15, SERPING1, OASL, GBP1, and MX1.
  • the method of embodiment 116 wherein the first type I IFN or IFN ⁇ -inducible PD marker expression profile comprises up-regulated expression or activity of genes IFI6, RSAD2, IFI44, IFI44L, IFI27, MX1, IFIT1, ISG15, LAMP3, OAS3, OAS1, EPSTI1, IFIT3, OAS2, SIGLEC1, and USP18.
  • the method of embodiment 116 wherein the first type I IFN or IFN ⁇ -inducible PD marker expression profile comprises up-regulated expression or activity of genes IFI6, RSAD2, IFI44, IFI44L, and IFI27.
  • invention 116 further comprising obtaining a third IFN ⁇ -inducible PD marker expression profile in a third sample from the patient.
  • the method of 137 further comprising obtaining a fourth IFN ⁇ -inducible PD marker expression profile in a fourth sample from the patient.
  • the method of 138 further comprising obtaining a fifth IFN ⁇ -inducible PD marker expression profile in a fifth sample from the patient.
  • the method of 139 further comprising obtaining a sixth IFN ⁇ -inducible PD marker expression profile in a sixth sample from the patient.
  • the method of 116 wherein the second sample is obtained at least one week, at least 2 weeks, at least three weeks, at least one month or at least two months following administration of the therapeutic agent.
  • the method of 137 wherein the third sample is obtained at least 2 days, at least 5 days, at least one week, at least 2 weeks, at least three weeks, at least one month or at least two months following obtaining the second sample.
  • the method of 138 wherein the fourth sample is obtained at least 2 days, at least 5 days, at least one week, at least 2 weeks, at least three weeks, at least one month or at least two months following obtaining the third sample.
  • the method of 139 wherein the fifth sample is obtained at least 2 days, at least 5 days, at least one week, at least 2 weeks, at least three weeks, at least one month or at least two months following obtaining the fourth sample.
  • the method of embodiment 145 wherein the decrease is at least 10%, at least 20%, at least 25%, at least 30%, at least 40%, at least 45%, at least 50%, at least 60%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or 100%.
  • a method of identifying a patient as a candidate for a therapeutic agent that binds to and modulates IFN ⁇ activity comprising:
  • the method of embodiment 147 wherein the IFN ⁇ -inducible PD marker expression profile comprises up-regulated expression or activity of genes MX1, LY6E, IFI27, OAS1, IFIT1, IFI6, IFI44L, ISG15, LAMP3, OASL, RSAD2, and IFI44.
  • type I IFN or IFN ⁇ -inducible PD marker expression profile comprises up-regulated expression or activity of genes IFI27, SIGLEC1, RSAD2, IFI6, IFI44L, IFI44, USP18, IFIT2, SAMD9L, BIRC4BP, DNAPTP6, OAS3, LY6E, IFIT1, LIPA, LOC129607, ISG15, PARP14, MX1, OAS2, OASL, CCL2, HERC5, OAS1.
  • the type I IFN or IFN ⁇ -inducible PD marker expression profile comprises up-regulated expression or activity of genes IFIT1, IFIT3, IRF7, IFI6, IL6ST, IRF2, LY6E, MARCKS, MX1, MX2, OAS1, EIF2AK2, ISG15, STAT2, OAS3, IFI44, IFI44L, HERC5, RAB8B, LILRA5, RSAD2, and FCHO2.
  • the type I IFN or IFN ⁇ -inducible PD marker expression profile comprises up-regulated expression or activity of genes SERPING1, IFIT2, IFIT3, IFI6, LY6E, MX1, OAS1, ISG15, IFI27, OAS3, IFI44, LAMP3, DNAPTP6, ETV7, HERC5, OAS2, USP18, XAF1, RTP4, SIGLEC1, and EPSTI1.
  • the type I IFN or IFN ⁇ -inducible PD marker expression profile comprises up-regulated expression or activity of genes RTP4, RSAD2, HERC5, SIGLEC1, USP18, LY6E, ETV7, SERPING1, IFIT3, OAS1, HSXIAPAF1, G1P3, MX1, OAS3, IFI27, DNAPTP6, LAMP3, EPSTI1, IFI44, OAS2, IFIT2, and ISG15.
  • the method of embodiment 147 wherein the type I IFN or IFN ⁇ -inducible PD marker expression profile comprises up-regulated expression or activity of genes LAMP3, SIGLEC1, DNAPTP6, IFIT2, ETV7, RTP4, SERPING1, HERC5, XAF1, MX1, EPSTI1, OAS2, OAS1, OAS3, IFIT3, IFI6, USP18, RSAD2, IFI44, LY6E, ISG15, and IFI27.
  • the method of embodiment 147 wherein the type I IFN or IFN ⁇ -inducible PD marker expression profile comprises up-regulated expression or activity of genes DNAPTP6, EPSTI1, HERC5, IFI27, IFI44, IFI44L, IFI6, IFIT1, IFIT3, ISG15, LAMP3, LY6E, MX1, OAS1, OAS2, OAS3, PLSCR1, RSAD2, RTP4, SIGLEC1, and USP18.
  • the type I IFN or IFN ⁇ -inducible PD marker expression profile comprises up-regulated expression or activity of genes SAMD9L, IFI6, IFI44, IFIT2, ZC3HAV1, ETV6, DAPP1, IL1RN, CEACAM1, OAS1, IFI27, OAS3, IFI44L, HERC5, IFIT1, EPSTI1, ISG15, SERPING1, OASL, GBP1, and MX1.
  • the method of embodiment 147 wherein the type I IFN or IFN ⁇ -inducible PD marker expression profile comprises up-regulated expression or activity of genes SAMD9L, IFI6, IFI44, IFIT2, OAS1, IFI27, OAS3, IFI44L, HERC5, IFIT1, EPSTI1, ISG15, SERPING1, OASL, GBP1, and MX1.
  • the method of embodiment 147 wherein the type I IFN or IFN ⁇ -inducible PD marker expression profile comprises up-regulated expression or activity of genes IFI6, RSAD2, IFI44, IFI44L, IFI27, MX1, IFIT1, ISG15, LAMP3, OAS3, OAS1, EPSTI1, IFIT3, OAS2, SIGLEC1, and USP18.
  • the method of embodiment 147 wherein the type I IFN or IFN ⁇ -inducible PD marker expression profile comprises up-regulated expression or activity of genes IFI6, RSAD2, IFI44, IFI44L, and IFI27.
  • invention 147 wherein the patient has been diagnosed as having a disorder selected from the group consisting of lupus, idiopathic inflammatory myositis, Sjogren's syndrome, vasculitis, sarcoidosis, and psoriasis.
  • the method of any one of embodiments 148-158 wherein the up-regulated expression or activity comprises an increase in mRNA levels of one or more of the genes.
  • any one of embodiments 148-158 wherein the up-regulated expression or activity comprises an increase in enzymatic activity of a protein expressed from one or more of the genes.
  • the method of embodiment 147 wherein the type I IFN or IFN ⁇ -inducible PD marker expression profile comprises down-regulated expression or activity of genes NOG, SLC4A1, PRSS33, and FEZ1.
  • the method of embodiment 147 wherein the type I IFN or IFN ⁇ -inducible PD marker expression profile comprises increased serum levels of polypeptides cancer antigen 125, ferritin, tissue factor, and MMP-3.
  • the method of embodiment 147 wherein the type I IFN or IFN ⁇ -inducible PD marker expression profile comprises decreased serum levels of polypeptides EGF, thrombopoietin, and CD40 ligand.
  • a method of diagnosing a patient as a having a disorder associated with increased IFN ⁇ levels comprising:
  • the IFN ⁇ -inducible PD marker expression profile comprises up-regulated expression or activity of genes MX1, LY6E, IFI27, OAS1, IFIT1, IFI6, IFI44L, ISG15, LAMP3, OASL, RSAD2, and IFI44.
  • the IFN ⁇ -inducible PD marker expression profile comprises up-regulated expression or activity of genes IFI27, SIGLEC1, RSAD2, IFI6, IFI44L, IFI44, USP18, IFIT2, SAMD9L, BIRC4BP, DNAPTP6, OAS3, LY6E, IFIT1, LIPA, LOC129607, ISG15, PARP14, MX1, OAS2, OASL, CCL2, HERC5, OAS1.
  • the IFN ⁇ -inducible PD marker expression profile comprises up-regulated expression or activity of genes IFIT1, IFIT3, IRF7, IFI6, IL6ST, IRF2, LY6E, MARCKS, MX1, MX2, OAS1, EIF2AK2, ISG15, STAT2, OAS3, IFI44, IFI44L, HERC5, RAB8B, LILRA5, RSAD2, and FCHO2.
  • the IFN ⁇ -inducible PD marker expression profile comprises up-regulated expression or activity of genes SERPING1, IFIT2, IFIT3, IFI6, LY6E, MX1, OAS1, ISG15, IFI27, OAS3, IFI44, LAMP3, DNAPTP6, ETV7, HERC5, OAS2, USP18, XAF1, RTP4, SIGLEC1, and EPSTI1.
  • the IFN ⁇ -inducible PD marker expression profile comprises up-regulated expression or activity of genes RTP4, RSAD2, HERC5, SIGLEC1, USP18, LY6E, ETV7, SERPING1, IFIT3, OAS1, HSXIAPAF1, G1P3, MX1, OAS3, IFI27, DNAPTP6, LAMP3, EPSTI1, IFI44, OAS2, IFIT2, and ISG15.
  • the IFN ⁇ -inducible PD marker expression profile comprises up-regulated expression or activity of genes LAMP3, SIGLEC1, DNAPTP6, IFIT2, ETV7, RTP4, SERPING1, HERC5, XAF1, MX1, EPSTI1, OAS2, OAS1, OAS3, IFIT3, IFI6, USP18, RSAD2, IFI44, LY6E, ISG15, and IFI27.
  • the IFN ⁇ -inducible PD marker expression profile comprises up-regulated expression or activity of genes DNAPTP6, EPSTI1, HERC5, IFI27, IFI44, IFI44L, IFI6, IFIT1, IFIT3, ISG15, LAMP3, LY6E, MX1, OAS1, OAS2, OAS3, PLSCR1, RSAD2, RTP4, SIGLEC1, and USP18.
  • the IFN ⁇ -inducible PD marker expression profile comprises up-regulated expression or activity of genes SAMD9L, IFI6, IFI44, IFIT2, ZC3HAV1, ETV6, DAPP1, IL1RN, CEACAM1, OAS1, IFI27, OAS3, IFI44L, HERC5, IFIT1, EPSTI1, ISG15, SERPING1, OASL, GBP1, and MX1.
  • the IFN ⁇ -inducible PD marker expression profile comprises up-regulated expression or activity of genes SAMD9L, IFI6, IFI44, IFIT2, OAS1, IFI27, OAS3, IFI44L, HERC5, IFIT1, EPSTI1, ISG15, SERPING1, OASL, GBP1, and MX1.
  • the IFN ⁇ -inducible PD marker expression profile comprises up-regulated expression or activity of genes IFI6, RSAD2, IFI44, IFI44L, IFI27, MX1, IFIT1, ISG15, LAMP3, OAS3, OAS1, EPSTI1, IFIT3, OAS2, SIGLEC1, and USP18.
  • IFN ⁇ -inducible PD marker expression profile comprises up-regulated expression or activity of genes IFI6, RSAD2, IFI44, IFI44L, and IFI27.
  • the up-regulated expression or activity comprises at least a 2-fold increase in expression or activity of one or more of the genes.
  • the method of embodiment 187 wherein the up-regulated expression or activity comprises at least a 3-fold increase in expression or activity of one or more of the genes.
  • the method of any one of embodiments 174-184 wherein the up-regulated expression or activity comprises an increase in mRNA levels of one or more of the genes.
  • the method of any one of embodiments 174-184 wherein the up-regulated expression or activity comprises an increase in protein levels of one or more of the genes.
  • the up-regulated expression or activity comprises an increase in enzymatic activity of a protein expressed from one or more of the genes.
  • the method of any one of embodiments 174-184 wherein the type I IFN or IFN ⁇ -inducible PD marker expression profile further comprises down-regulated expression or activity of genes NOGSLC4A1, PRSS33, and FEZ1.
  • the method any one of embodiments 174-184 wherein the type I IFN or IFN ⁇ -inducible PD marker expression profile further comprises increased serum levels of polypeptides cancer antigen 125, ferritin, tissue factor, and MMP-3.
  • the method of any one of embodiments 174-184 wherein the type I IFN or IFN ⁇ -inducible PD marker expression profile further comprises decreased serum levels of polypeptides EGF, thrombopoietin, and CD40 ligand.
  • a method of identifying a candidate therapeutic for treating IFN ⁇ -mediated disorders comprising:
  • IFN ⁇ -inducible PD marker expression profile comprises up-regulated expression or activity of genes MX1, LY6E, IFI27, OAS1, IFIT1, IFI6, IFI44L, ISG15, LAMP3, OASL, RSAD2, and IFI44.
  • the IFN ⁇ -inducible PD marker expression profile comprises up-regulated expression or activity of genes IFI27, SIGLEC1, RSAD2, IFI6, IFI44L, IFI44, USP18, IFIT2, SAMD9L, BIRC4BP, DNAPTP6, OAS3, LY6E, IFIT1, LIPA, LOC129607, ISG15, PARP14, MX1, OAS2, OASL, CCL2, HERC5, and OAS 1.
  • the IFN ⁇ -inducible PD marker expression profile comprises up-regulated expression or activity of genes IFIT1, IFIT3, IRF7, IFI6, IL6ST, IRF2, LY6E, MARCKS, MX1, MX2, OAS1, EIF2AK2, ISG15, STAT2, OAS3, IFI44, IFI44L, HERC5, RAB8B, LILRA5, RSAD2, and FCHO2.
  • the IFN ⁇ -inducible PD marker expression profile comprises up-regulated expression or activity of genes SERPING1, IFIT2, IFIT3, IFI6, LY6E, MX1, OAS1, ISG15, IFI27, OAS3, IFI44, LAMP3, DNAPTP6, ETV7, HERC5, OAS2, USP18, XAF1, RTP4, SIGLEC1, and EPSTI1.
  • the IFN ⁇ -inducible PD marker expression profile comprises up-regulated expression or activity of genes RTP4, RSAD2, HERC5, SIGLEC1, USP18, LY6E, ETV7, SERPING1, IFIT3, OAS1, HSXIAPAF1, G1P3, MX1, OAS3, IFI27, DNAPTP6, LAMP3, EPSTI1, IFI44, OAS2, IFIT2, and ISG15.
  • the IFN ⁇ -inducible PD marker expression profile comprises up-regulated expression or activity of genes LAMP3, SIGLEC1, DNAPTP6, IFIT2, ETV7, RTP4, SERPING1, HERC5, XAF1, MX1, EPSTI1, OAS2, OAS1, OAS3, IFIT3, IFI6, USP18, RSAD2, IFI44, LY6E, ISG15, and IFI27.
  • the IFN ⁇ -inducible PD marker expression profile comprises up-regulated expression or activity of genes DNAPTP6, EPSTI1, HERC5, IFI27, IFI44, IFI44L, IFI6, IFIT1, IFIT3, ISG15, LAMP3, LY6E, MX1, OAS1, OAS2, OAS3, PLSCR1, RSAD2, RTP4, SIGLEC1, and USP18.
  • the IFN ⁇ -inducible PD marker expression profile comprises up-regulated expression or activity of genes SAMD9L, IFI6, IFI44, IFIT2, ZC3HAV1, ETV6, DAPP1, IL1RN, CEACAM1, OAS1, IFI27, OAS3, IFI44L, HERC5, IFIT1, EPSTI1, ISG15, SERPING1, OASL, GBP1, and MX1.
  • IFN ⁇ -inducible PD marker expression profile comprises up-regulated expression or activity of genes SAMD9L, IFI6, IFI44, IFIT2, OAS1, IFI27, OAS3, IFI44L, HERC5, IFIT1, EPSTI1, ISG15, SERPING1, OASL, GBP1, and MX1.
  • IFN ⁇ -inducible PD marker expression profile comprises up-regulated expression or activity of genes IFI6, RSAD2, IFI44, IFI44L, IFI27, MX1, IFIT1, ISG15, LAMP3, OAS3, OAS1, EPSTI1, IFIT3, OAS2, SIGLEC1, and USP18.
  • the method of embodiment 195 wherein the IFN ⁇ -inducible PD marker expression profile comprises up-regulated expression or activity of genes IFI6, RSAD2, IFI44, IFI44L, and IFI27.
  • the method of embodiment 195 wherein the up-regulation of the genes of the IFN ⁇ -inducible PD marker expression profile comprises an increase in mRNA levels of one or more of the genes of the IFN ⁇ -inducible PD marker expression profile.
  • the method of embodiment 195 wherein the up-regulation of the genes of the IFN ⁇ -inducible PD marker expression profile comprises an increase in protein levels of one or more of the genes of the IFN ⁇ -inducible PD marker expression profile.
  • the method of embodiment 195 wherein the up-regulation of the genes of the IFN ⁇ -inducible PD marker expression profile comprises an increase in enzymatic activity of a protein expressed from one or more of the genes of the IFN ⁇ -inducible PD marker expression profile.
  • the type I IFN or IFN ⁇ -inducible PD marker expression profile further comprises down-regulated expression or activity of genes NOGSLC4A1, PRSS33, and FEZ1; and wherein the presence of a change comprising an increase in expression or activity of the down-regulated genes indicates the agent is a candidate therapeutic agent.
  • the type I IFN or IFN ⁇ -inducible PD marker expression profile further comprises decreased serum levels of polypeptides EGF, thrombopoietin, and CD40 ligand wherein the presence of a change comprising an increase in serum levels of the polypeptide indicates the agent is a candidate therapeutic agent.
  • a set of probes comprising:
  • a kit comprising any of the set of probes recited in embodiment 217.
  • a method of detecting IFN activity in a sample comprising:
  • reporter gene is luciferase, chloramphenicol acetyl transferase, ⁇ -galactosidase, green fluorescent protein, ⁇ -glucuronidase, or secreted placental alkaline phosphatase.
  • the method of embodiment 219 further comprising quantitating level of expression of the reporter gene.
  • invention 224 further comprising correlating the level of expression of the reporter gene to level of IFN activity in the sample.
  • Gene expression in whole blood of 5 (2 cutaneous and 3 severe) lupus patients and 5 healthy volunteers was profiled using Affymetrix whole genome array technology and qPCR validation. Gene expression fold-change values were determined by calculating the log 2 signal intensity difference between individual lupus patient samples and the mean log 2 signal intensity for the 5 healthy donor samples. 118 genes were identified as up-regulated by at least 2-fold in whole blood of all 5 lupus patients relative to the healthy volunteers.
  • Table 1 provides a summary for 71 of the 118 annotated genes identified as up-regulated by at least 2-fold in all 5 lupus patients.
  • Table 2 provides the fold-up-regulation in gene expression for a subset of the 118 genes for each of the five lupus patients relative to the healthy volunteers.
  • Table 2 also provides a comparison between fold-change values determined on two unique platforms (Affy GENECHIP microarray and TAQMAN (i.e. qPCR)).
  • the Affymetrix Human Genome U133 Plus 2.0 GENECHIP® array platform was used to profile WB from 46 SLE patients and WB from 24 age- and sex-matched healthy donors. It was observed that 245 and 77 probe sets were upregulated and downregulated, respectively, in WB of SLE patients compared with that from healthy control donors.
  • Table 30 lists the 50 most upregulated probe sets in WB of these SLE patients; 76% of them are type I IFN inducible. Table 30 also lists the prevalence of the overexpression of these genes in WB of SLE patients. The majority of these genes are overexpressed by at least 2-fold in 65% to 80% of the patients profiled. The robust and prevalent overexpression of a large number of type I IFN-inducible genes in SLE patients suggests that they might be suitable PD markers for clinical trials that investigate an anti-IFN- ⁇ mAb therapy for SLE.
  • FIG. 80 shows a heat map of the expression of the 114 upregulated type I IFN-inducible probe sets in SLE patients and healthy controls. A total of 32/46 of the SLE patients profiled showed significant overexpression of the type I IFN gene signature. To confirm the observation that type I IFN-inducible genes are overexpressed in WB of SLE patients, WB was procured from 54 SLE patients in a prospective study.
  • FIG. 81A shows the PCA plot of the 46 SLE patients in the first study using the 114 overexpressed type I IFN-inducible probes. A clear difference was observed between SLE patients that had distinct overexpression of type I IFN gene signature from healthy donors and SLE patients that had weak or nondetectable type I IFN gene signature in WB.
  • FIG. 81B shows the PCA plot from the 54 SLE patients in the prospective study using the same 114 type I IFN-inducible probe sets identified. A similar separation of SLE patients was observed based on type I IFN gene signature as in FIG. 81A . The distribution of the type I IFN gene signature scores in the prospective study was also similar to that of the first study (data not shown). The ability to use the overexpressed type I IFN-inducible genes identified to segregate SLE patients into 2 distinct groups—patients with or without type I IFN gene signature—validated the accurate identification of overexpression in the type I IFN gene signature in WB of SLE patients.
  • the granulocyte gene signature included (but was not limited to) the following genes: AZU, DEFA1, DEFA4, ELA2, MMP8, MMP9, RNAS2, MPO, CAMP, FCAR, and CYBB ( FIG. 80 , second panel).
  • the granulocyte gene signature was present in about 50% of the SLE patients profiled.
  • the 50 most downregulated probe sets observed in WB of SLE patients are shown in Table 31.
  • the downregulation of T, NK, and B cell gene signatures was observed in WB of SLE patients ( FIG. 80 , panels three, four, and five, respectively); this is in agreement with the observation of lymphopenia in SLE patients previously reported in the literature (Bennett L, Palucka A K, Arce E et al.: Interferon and granulopoiesis signatures in systemic lupus erythematosus blood. J Exp Med. 197(6), 711-723 (2003), Rivero S J, Diaz-Jouanen E and Alarcon-Segovia D: Lymphopenia in systemic lupus erythematosus. Clinical, diagnostic, and prognostic significance. Arthritis Rheum. 21(3), 295-305 (1978).
  • BIOMARKTM 48.48 dynamic array was used to perform high throughput (HTP) TAQMAN QRT-PCR on 40 of the type I IFN-inducible genes (selected based on their magnitude and prevalence of overexpression in whole blood of SLE patients).
  • TAQMAN QRT-PCR assays confirmed the overexpression of all 40 genes in whole blood of 35 of the originally profiled 46 SLE patients.
  • the overexpression of 15 of the 40 type I IFN-inducible genes using TAQMAN QRT-PCR assays is shown in FIG. 83A . These genes were upregulated by an average of 8- to 92-fold, and all were significantly overexpressed (P ⁇ 0.05).
  • Example 3 Using the whole genome profiling data described in Example 1a, a group of candidate PD markers were selected. These candidate markers are provided in Table 3.
  • qPCR was conducted for a selected group of candidate PD markers to determine whether they exhibited variation at baseline in the whole blood of healthy volunteers. qPCR indicated that baseline variation was minimal. See Table 4, which provides the baseline qPCR data (healthy volunteers shown in shaded columns).
  • Whole blood of healthy volunteers was collected in heparinized tubes, transferred to the appropriate wells of 6-well culture plates, and incubated with leukocyte IFN doses of 3, 30, 100, and 300 I.U. and then incubated for 4 hours at 37° C., 5% CO 2 .
  • Fold-induction of expression of candidate PD markers for genes IFI44, IRF2, RSAD2, G1P3, and HERC5 was determined using RNA isolated from PBMCs (Peripheral Blood Mononuclear Cells) with Qiagen's RNAeasy kit.
  • leukocyte IFN causes up-regulation in expression of each of these candidate PD markers. See also FIG. 1 (IFI44), FIG. 2 (IRF2), FIG. 3 (RSAD2), FIG. 4 (G1P3), and FIG. 5 (HERC5) for a graphical analysis of these candidate PD marker expression results.
  • FIG. 17 A summary hierarchical clustering of all samples using 1384 genes differentially regulated by IFN type 1, IFN type 2, or TNF ⁇ obtained from a separate experiment is shown in FIG. 17 .
  • a heat map with a summary hierarchical clustering is also provided for 689 type I IFN inducible probe sets used on whole blood samples from healthy donors ex vivo stimulated with IFN type 1, IFN type 2, or TNF ⁇ . See FIG. 64 .
  • IFN ⁇ treatment of healthy volunteers' whole blood induced expression of candidate PD markers it was determined whether IFN ⁇ Ab, MEDI-545, could neutralize the induction of expression of these markers.
  • Blood was drawn from each of three donors into heparin tubes. Aliquots of 2.5 ml of drawn blood were added to each of 4 wells of 6- or 24-well treatment plates. The 4 wells were designated for treatment as follows: (a) blood+vehicle, (b) blood+100 IU IFN ⁇ 2a, (c) blood+100 IU IFN ⁇ 2a+MEDI-545 (IFN ⁇ Ab), and (d) blood+100 IU IFN ⁇ 2a+R347 (control Ab).
  • Wells containing blood to be treated with Ab were first incubated with either MEDI-545 (IFN ⁇ Ab; well (c)) or R347 (control Ab; well (d)) for 30 minutes. Following Ab treatment, vehicle (well (a)) or IFN ⁇ 2a (wells (b), (c), and (d)) was added to the appropriate wells and was then incubated for an additional 4 hours at 37° C., 5% CO 2 . The samples were then transferred to PAXgene tubes and incubated at room temperature for 2 hr. Following the 2 hr incubation the tubes were transferred to ⁇ 80° C. for storage.
  • RNA of the cells was prepared according to the PAXgene protocol.
  • First and second strand cDNA was prepared via Affy GRP methods and TAQMAN was conducted on the cDNA samples.
  • Expression of at least 11 candidate PD markers could be neutralized by MEDI-545 in the IFN ⁇ 2a-stimulated whole blood. See Table 8 (RAB8B), Table 9 (IRF7), Table 10 (MARCKS), Table 11 (IL6ST), Table 12 (LY6E), Table 13 (IFIT3), Table 14 (IFIT1), Table 15 (HERC5), Table 16 (OAS1), Table 17 (OAS3), and Table 18 (RSAD2), which provide quantitative gene expression analysis for each of these 11 genes in the whole blood of each of the 3 healthy volunteers.
  • IFN ⁇ 2a-Induced IFIT3 Gene Expression is Neutralized by MEDI-545 Sample Gene Average StDev 107 VEH IFIT3 1.00 107 IFN IFIT3 38.43 0.78 107 IFN + 545 IFIT3 6.78 0.14 107 IFN + R347 IFIT3 42.59 0.75 163 VEH IFIT3 0.62 0.01 163 IFN IFIT3 25.94 0.57 163 IFN + 545 IFIT3 4.58 0.08 163 IFN + R3437 IFIT3 44.83 0.44 175 VEH IFIT3 1.32 0.02 175 IFN IFIT3 35.02 0.48 175 IFN + 545 IFIT3 5.28 0.05 175 IFN + R347 IFIT3 29.71 0.79
  • IFN ⁇ 2a-Induced IFIT1 Gene Expression is Neutralized by MEDI-545 Sample Gene Average StDev 107 VEH IFIT1 1.00 107 IFN IFIT1 80.21 3.44 107 IFN + 545 IFIT1 13.14 0.02 107 IFN + R347 IFIT1 86.44 0.57 163 VEH IFIT1 0.92 0.03 163 IFN IFIT1 51.65 1.21 163 IFN + 545 IFIT1 7.60 0.05 163 IFN + R3437 IFIT1 86.63 2.67 175 VEH IFIT1 1.47 0.17 175 IFN IFIT1 82.98 2.94 175 IFN + 545 IFIT1 8.40 0.24 175 IFN + R347 IFIT1 58.50 1.47
  • FIG. 6 See also FIG. 6 (RAB8B), FIG. 7 (IRF7), FIG. 8 (MARCKS), FIG. 9 (IL6ST), FIG. 10 (LY6E), FIG. 11 (IFIT3), FIG. 12 (IFIT1), FIG. 13 , (HERC5), FIG. 14 (OAS1), FIG. 15 (OAS3), and FIG. 16 (RSAD2) for graphical representations of the gene expression data for each of the 11 genes.
  • Source of Interferon SLE Patient Serum
  • Serum from SLE patients was preincubated for one hour with MEDI-545 (0.1, 1, 10 ⁇ g/mL), anti-IFN- ⁇ antibody (1 ⁇ g/mL) or control antibody (10 ⁇ g/mL).
  • SLE serum was added to the PBMC at a final concentration 25% (62.5 ⁇ L per well). Additional volume of RPMI+10% FBS was added to the wells to obtain a final volume of 250 L per well. Plates were incubated at 37° C. for either 4 or 18 hours. Following the incubation, RNA was harvested by adding 750 ⁇ L of Trizol LS to each well. Samples were frozen at ⁇ 70° C. until the time of RNA isolation. Table 21 provides the MEDI-545 blockade of 74 type I IFN genes in healthy volunteers' whole blood stimulated ex vivo with SLE patient serum.
  • MEDI-545 blocks overexpression of type I IFN genes in whole blood of healthy volunteers stimulated ex vivo with lupus patient serum Probe ID D1_002_545.10 D1_004_545.10 D1_17021_545.10 UniGene. ID Gene.
  • Heatmap analysis was also performed to examine induction of a type I IFN signature in PBMCs of a healthy donor by serum of an SLE patient and neutralization of the type I IFN signature by MEDI-545. See FIG. 67 .
  • the anti-IFN- ⁇ mAb treatment (lanes 4-6) demonstrated strong neutralization of a large number of genes stimulated with the serum of an SLE patient.
  • neutralization by the anti-IFN- ⁇ mAb was dose-dependent, which suggests that these genes could be good candidates for PD.
  • the reference mAb itself inhibited the overexpression of some of the genes upregulated when challenged with SLE patient sera; some of these were identified as type I IFN-inducible genes.
  • FIG. 70 a shows the range of levels of type I IFN activity in each of the four SLE patient serum samples.
  • PBMCs isolated from a healthy volunteer.
  • the PBMCs from the healthy volunteer previously determined to be IFN-signature negative
  • Isolated PBMCs were incubated with 25% SLE patient serum or with 25% autologous patient serum (as a negative control).
  • cells were harvested with Trizol LS and stored at ⁇ 70° C. for RNA isolation. Total RNA was extracted and RNA purity and concentration were determined spectrophotometrically (260/280>1.9).
  • FIG. 70 b shows the number of probes detected as 3-fold or more upregulated in the healthy volunteer PBMCs by each of the four SLE patient serum samples.
  • the number of probes detected as 3-fold or more upregulated by an SLE patient serum sample correspondingly increased with the level of type I IFN activity detected in the SLE serum sample.
  • PBMCs isolated from a healthy volunteer were incubated with 25% SLE patient serum in the presence or absence of neutralizing antibodies against IFN- ⁇ , or irrelevant mAb, for 4 or 18 hours.
  • PBMC were incubated with 25% of autologous patient serum.
  • cells were harvested with Trizol LS and stored at ⁇ 70° C. for RNA isolation. Total RNA was extracted and RNA purity and concentration were determined spectrophotometrically (260/280>1.9).
  • cRNA biotin-labeled amplified complementary RNA
  • FIG. 71 a provides heat maps showing the percent neutralization of probes that were identified as upregulated following anti-IFN ⁇ treatment for type I IFN genes (689 probes) and non-type I IFN genes (probes induced by SLE serum outside of type I IFN gene list) 4 and 18 h post incubation.
  • FIG. 71 b shows, for each of the four SLE patient serum samples, the percentage of type I IFN gene signature or non-type I IFN gene signature probes that were neutralized by the anti-IFN ⁇ treatment following both the 4 and 18 hour incubations.
  • FIG. 72 provides the (a) type I IFN genes and (b) non-type I IFN genes that were identified as unique genes. Shaded areas indicate greater than 50% neutralization by anti-IFN ⁇ in that patient sample.
  • FIG. 73 provides a table showing the pathway analysis of altered genes and proteins at the 18 hr time point. Pathways highlighted in yellow were also significantly altered in SLE serum samples.
  • the cell pathways and processes neutralized by anti-IFN ⁇ treatment at the 18 hr time point were analyzed with the MetaCore integrated software suite from GeneGo, Inc. using the identified unique genes. Only pathways with p-values S 0.05 were considered significant. The pathways shown were altered in at least 2 out of 4 SLE serum samples.
  • MEDI-545 Whole blood of lupus patients receiving placebo, 0.3 mg/kg, 1.0 mg/kg, and 3.0 mg/kg MEDI-545 were analyzed for expression of IFN ⁇ -inducible PD markers over the course of 28 days.
  • Whole blood ( ⁇ 2.5 mL) was drawn into PAXgene RNA tubes and processed as outlined above. With increasing doses of MEDI-545, up-regulated expression of the top 25 PD markers was neutralized. See FIG. 18 , FIG. 23 , and FIG. 24 which provide graphical representations of neutralization of these top 25 PD markers following administration of varying concentrations of the MEDI-545 IFN ⁇ Ab over various lengths of time.
  • the top 25 PD markers measured in this study are provided in Table 19.
  • FIGS. 19-21 are heatmaps showing the neutralization of the top 25 PD markers (see Table 19) for two individual lupus patients ( FIG. 19 , patient 1541; and FIG. 20 , patient 1449). Each of these lupus patients received 3 mg/kg MEDI-545. Each exhibited neutralization of the top 25 inducible PD markers at 7 and 14 days post-MEDI-545 treatment.
  • FIG. 25( a ) is a PCA of target modulation based on the top 25 type I IFN inducible genes.
  • the PCA diagram shows the progression of the treated SLE patient from a position directly opposite that of normal healthy donors prior to administration of MEDI-545 to a position where it clusters with the healthy donors after administration of MEDI-545.
  • MEDI-545 neutralized most of the 165 candidate PD markers in this lupus patient.
  • the 165 candidate PD markers are shown as the first 165 entries of Table 20.
  • Table 22 provides a list of the 63 type I IFN inducible probes upregulated in whole blood of lupus patients and neutralized by MEDI-545 or placebo by at least 30% at day 7, day 14, or day 28 post administration.
  • Each set of columns provides neutralization data for each of the indicated genes at 7, 14, and 28 days post-administration.
  • the first set of columns provides percentage neutralization of each of the indicated genes for lupus patients having a type I IFN signature and that were treated with MEDI-545. It can be noted that for each of the indicated genes, neutralization ranged from 30% to 68% at day 7 post-administration. Meanwhile, at day 7 in the placebo treated group, neutralization of the same genes ranged from 0% to 27%.
  • PCA Principal Component Analysis
  • Table 23 The overexpression of type I IFN genes in SLE patient whole blood for a larger number of patients, determined using an Affymetrix whole genome array, is provided in Table 23.
  • Table 23 and FIG. 65 provide further evidence that a high percentage of SLE patients share at least 2-fold overexpression of each individual type I IFN genes.
  • MEDI-545 Considerably Neutralizes the Type I IFN Gene Signature of SLE
  • FIG. 29( a ) shows that in a group of SLE patients having a type-I IFN gene signature, virtually all of the top 39 genes neutralized 14 days post-MEDI-545 treatment are type I IFN signature genes (see yellow highlighted genes; percentage inhibition of the type I IFN signature genes ranged from 30.5-64.7). By contrast, none of the top 39 neutralized genes in SLE patients who received placebo were type I IFN signature genes. See FIG. 29( c ). The SLE patients who lacked a type I IFN signature and were treated with MEDI-545 displayed an intermediate neutralization pattern, with some type I IFN signature genes neutralized. (See FIG. 29( b ); yellow highlighting indicates type I IFN signature genes, which were neutralized from 19%-44.9%).
  • FIG. 84 shows the distribution of the type I IFN gene signature scores of the 46 SLE patients profiled. The SLE patients were profiled into 3 groups based on their type I IFN gene signature score: high type I IFN gene signature (score >10); moderate type I IFN gene signature (score 4-10); and weak type I IFN gene signature (score ⁇ 4).
  • the gene panel was narrowed to 21 genes.
  • 807 IFN- ⁇ / ⁇ -inducible probes identified by ex vivo stimulation of healthy donor WB with 10 IFN- ⁇ subtypes (2a, 4b, 5, 6, 7, 8, 10, 14, 16, and 17) and IFN- ⁇ were used as a candidate marker starting point.
  • the WB samples from a total of 46 SLE patients procured from commercial vendors and 24 healthy normal controls were used to determine the type I IFN-inducible probes that are upregulated in WB of SLE patients.
  • 114 overexpressed probes (q ⁇ 0.05; fold change ⁇ 2) were identified in WB of SLE patients were type I IFN-inducible using SAM and FDR.
  • one healthy donor PBMC was stimulated ex vivo with sera from six individual SLE patients.
  • the healthy donor was prescreened to exclude those donors that might have viral infection.
  • 161 type I IFN-inducible probes were upregulated by ⁇ 2-fold in the PBMC of the healthy donor following stimulation with ⁇ 1 SLE patient serum in which the overexpression of these genes was suppressed by ⁇ 50% and ⁇ 70% by an anti-IFN- ⁇ mAb and an anti-IFN- ⁇ R mAb, respectively.
  • the intersection between this list of 161 probes and previously determined list of 114 probes was 80 probes. Each of these 80 probes was ranked by both the average fold change magnitude across all SLE patients and the percentage of patients displaying a change ⁇ 2-fold. Generally, the 21 most prevalently overexpressed type I IFN-inducible genes (that represent unique genes using the NetAffx annotation file for the Affymetrix U133 2.0 plus array; ESTs were excluded) from this ranking were retained for a static list of probes used to measure PD. The type I IFN signature score was then defined by the median of these 21 genes.
  • This method was implemented to compensate for 3 primary differences between the 2 platforms: (1) the number of probes used for the type I IFN signature (25 genes dynamically determined for each patient on the Affymetrix platform versus a 21 static gene list on the TAQMAN-based assay), (2) the differences in sensitivity between the 2 platforms, and (3) the scales of the dynamic ranges within each platform.
  • the fold change values were calculated (on a log 2 scale) for the 155 type I-inducible probes between the 35 randomly selected SLE patients and the average of a set of normal healthy controls.
  • the genes with the top 25-fold change values were determined for each patient on the Affymetrix platform (this gene set is allowed to vary from patient to patient depending on which type I IFN-inducible genes are most highly expressed).
  • the median fold change was calculated from the top 25 genes for each SLE patient. The same calculation was conducted across the same patients using the static 21 gene set on the TAQMAN-based assay. This gene set was identical for each patient and the median fold change was calculated based on 21 genes, rather than 25 dynamic genes, as was conducted for the Affymetrix platform.
  • a simple regression model was then computed using these 2 vectors of equal length (35 median fold change values), and the coefficients from the model were used to calculate the conversion factor (from the Affymetrix platform to the TAQMAN-based assay) for the response threshold values to partition the SLE patients into a type I IFN gene signature category of strong (>10 on Affymetrix; >5.53 on TAQMAN), moderate (between 4 and 10 on Affymetrix; between 1.91 and 5.53 on TAQMAN), or weak ( ⁇ 4 on Affymetrix; ⁇ 1.91 on TAQMAN).
  • the signature ie, median fold change
  • the signature ie, median fold change
  • FIGS. 86 and 89 Heatmap ( FIG. 87 a ) and PCA calculations ( FIG. 87 b ) using these 21 genes showed neutralization of the upregulated IFN ⁇ / ⁇ gene signature in an SLE patient treated with 30 mg/kg MEDI-545, but not in placebo-treated SLE patients ( FIG. 88 ). Thus, it is evident that these genes could be used as a PD marker set.
  • FIG. 85 shows the stratification of 35 SLE patients into groups of high (20 patients), moderate (8 patients), and weak (7 patients) type I IFN gene signatures based on the distribution of fold change values (log 2 scale) of all 21 type I IFN-inducible genes and partitioned into each group by the median fold change of this distribution of 21 genes for each patient (vertical dashed lines), as measured by the dynamic array from Fluidigm. From FIG. 85 , it is apparent that each patient distribution exhibits slight differences in skewness and basic shape/form, as this indicates the diversity in the various severity levels of SLE, based on the 21 type IFN-inducible gene selected.
  • type-I IFN subtypes responsible for the induction of the type-I IFN signature of SLE patients To identify the type-I IFN subtypes responsible for the induction of the type-I IFN signature of SLE patients, mRNA levels of type-I IFN genes in SLE patient whole blood were measured.
  • TAQMAN Low Density Array TLDA
  • type-I IFN ⁇ subtypes 1, 2, 5, 6, 7, 8, 14, 17, and 21 was monitored and compared in whole blood of SLE patients relative to healthy volunteers.
  • Double-stranded cDNA for each patient sample was pre-amplified using the TAQMAN PreAmp Master Mix kit (Applied Biosystems).
  • cDNA was pre-amplified by conducting 10 cycles of PCR on each patient sample using a pooled solution of primers, a pair for each gene analyzed on the array.
  • the pre-amplified cDNA were diluted 1:5 with TE.
  • a 50 ⁇ L volume of the diluted pre-amplified cDNA was added to a 50 ⁇ L volume of 2 ⁇ TAQMAN Universal PCR Master Mix (Applied Biosystems) and mixed.
  • the array was loaded with the mixture using standard procedures and the loaded array was run on a 7900HT Fast Real-Time PCR System (Applied Biosystems). Data analysis of the resulting Ct values was conducted with the SDSv2.2.2 software tool (Applied Biosystems).
  • FIG. 27 shows the relative overexpression of mRNA of nine IFN ⁇ subtypes in the whole blood of lupus patients relative to healthy volunteers. Many of these IFN ⁇ subtypes were upregulated at the mRNA level in the whole blood of SLE patients.
  • FIG. 66 shows that IFN ⁇ , IFN ⁇ and IFNAR1 and IFNAR2 genes are also overexpressed in whole blood of lupus patients relative to healthy volunteers.
  • FIG. 82 shows that TNF- ⁇ , IFN- ⁇ , IFN- ⁇ R1, and IFN- ⁇ R2 transcripts were also upregulated in WB of SLE patients ( FIG. 82 ). However, the relative magnitude of overexpression of these transcripts was less than that of the type I IFN family members, especially the IFN- ⁇ subtypes.
  • FIG. 30 provides the hierarchical clustering of 1384 probe sets differentially regulated by either IFN ⁇ / ⁇ , or IFN ⁇ , or TNF ⁇ in ex vivo stimulated whole blood. From this hierarchical clustering the similar response of whole blood to challenge with IFN ⁇ subtypes and IFN ⁇ can easily be observed, as can the similar but distinctly different effect of IFN ⁇ from IFN ⁇ / ⁇ , and the drastically different effect of TNF ⁇ from IFN ⁇ / ⁇ .
  • FIG. 31 a provides the hierarchical clustering of the relative expression of only the top 25 type-I IFN inducible probe sets identified in the ex vivo stimulated whole blood.
  • Keratinocytes Normal human keratinocytes (EpiDerm system, MatTek, Inc.) were grown under serum-free conditions according to the manufacturers instructions. Briefly, keratinocytes were maintained on tissue culture inserts at the air-liquid interface to maintain a multilayered, fully differentiated epithelial phenotype. Keratinocytes were stimulated with human leukocyte IFN (15, 50, 150, IU/mL, PBL Biomedical Labs), human IFN ⁇ 2a (15-350 IU/ml, PBL Biomedical Labs), recombinant human TNF ⁇ (0.1 ng/ml, R+D Systems) or recombinant human IFN ⁇ (3 ng/ml, R+D Systems). Epidermal cultures were harvested at 2, 4, or 18 hours post treatment for transcript analysis. Over 100 probe sets were identified as overexpressed in keratinocytes cultures stimulated with human IFN ⁇ 2a and leukocyte IFN.
  • FIG. 31 b provides the hierarchical clustering of the relative expression of 25 type-I IFN inducible genes in ex vivo stimulated keratinocytes.
  • the 25 type-I IFN inducible probe sets used to prepare the hierarchical clustering are the top 25 type-I IFN inducible probes identified in the ex vivo stimulated whole blood (those shown in FIG. 31 a ). Many of the top 25 type-I IFN inducible probe sets in ex vivo stimulated whole blood are also induced in ex vivo stimulated keratinocytes. See, e.g., MX1, IFI27, OAS1, IFI6, IFI44L, etc.
  • a comparison of gene expression profiles of skin samples from healthy donors and paired non-lesional/lesional skin samples from psoriasis patients was performed to identify a type-I interferon induced gene expression signature associated with psoriatic skin lesions. Briefly, skin samples of 21 normal healthy control donors (5 samples obtained from Biochain, 14 from ILSbio, and 2 from Dr. James Krueger's lab) and 26 paired non-lesional/lesional skin samples of 24 psoriatic patients (21 pairs obtained from Asterand, and 5 from Dr. James Krueger's lab) were obtained. Three additional lesional skin samples from 3 psoriatic patients were obtained.
  • RNA from the samples was extracted using the Qiagen RNAeasy-Mini kit (Hilden, Germany). The purity and concentration of the extracted RNA were determined spectrophotometrically (260/280>1.9). RNA quality was assessed on an Agilent 2100 Bioanalyzer using the RNA 6000 NANO LABCHIP®. Generation of biotin-labeled amplified cRNA, from 2 ⁇ g of total RNA, was accomplished using the Affymetrix GENECHIP® One-Cycle cDNA Synthesis kit and the Affymetrix GENECHIP® IVT Labeling kit. Concentration and purity of the cRNA product were determined spectrophotometrically.
  • ArrayAssist® Lite software was used to calculate probe-level summaries (GC-RMA normalization algorithm) from the array CEL files.
  • R packages R development core team
  • samr & qvalue were used to generate differentially regulated genes.
  • PCA and hierarchical clustering analyses were performed in both SpotFire and R (R Development Core Team).
  • SAM & FDR were used to select differentially regulated genes (pairwise comparison between lesional and non-lesional skin, lesional and normal skin, and non-lesional and normal skin).
  • Probe sets with a fold-change of at least 2 and q value less than or equal to 0.05 were considered to be differentially regulated.
  • PCA and hierarchical clustering were performed in both SpotFire and bioconductor R.
  • 1408 probe sets were up-regulated and 1465 probe sets were down-regulated in lesional skin compared to non-lesional skin.
  • the downregulated genes outnumbered the upregulated genes in the lesional skin, the magnitude of differential regulation of the upregulated genes was much greater as a whole.
  • 318 probe sets were upregulated by at least four fold in the lesional skin, while only 84 probe sets were downregulated by at least four fold in the lesional skin.
  • 96 probe sets were upregulated by at least eight fold in the lesional skin, while only six probe sets were downregulated by at least eight fold.
  • FIG. 45 provides a Venn diagram of the probe sets both upregulated (downregulated) in lesional skin and non-lesional skin relative to normal healthy skin. Only 70 of the 1408 upregulated probe sets in the lesional skin were also upregulated in non-lesional skin. Meanwhile, only 43 of the 1465 probe sets downregulated in the lesional skin were also downregulated in the non-lesional skin. These data suggested that the molecular events and biological changes from the non-lesional skin to lesional skin were quite different from those from the normal skin to the non-lesional skin.
  • IFN ⁇ / ⁇ signaling pathway members such as IFN ⁇ , IFN ⁇ , IFNAR1, IFNAR2, STAT1, IRF1, MPL, ISG15, IFI6 were all significantly overexpressed in lesional skin compared to uninvolved skin.
  • Components of the pathway like IFN ⁇ subtypes, IFN ⁇ , IFNAR1, IFNAR2, STAT1, IRF1, MPL, ISG15, IFI6 were all significantly overexpressed in lesional skin compared to non-lesional skin of psoriatic patients.
  • probe sets identified to be type-I IFN inducible in the whole blood and keratinocyte ex vivo stimulation studies 164 of the 1408 (approximately 11.7%) probe sets upregulated in lesional relative to non-lesional skin were identified as type-I IFN inducible. Fisher's exact test calculated a p value (one-tailed t test) less than 0.0001, suggesting that the observed overexpression of type-I IFN genes in lesional skin of psoriatic patients was statistically significant.
  • the type-I IFN induced genes were also many of the most highly upregulated genes in the lesional relative to non-lesional psoriatic skin.
  • type-I IFN genes Nineteen percent of the top 100 and 200 most upregulated probe sets in lesional skin relative to non-lesional skin were type-I IFN genes. See FIGS. 47 a and b for the top 100 upregulated probe sets in lesional skin. These genes included STAT1, a key component in forming the ISGF3 complex; IRF7, a master regulator of the IFN ⁇ / ⁇ mediated immune response; MYD88, which governs the induction of CD8 + T-cell responses with IRF7; IRF1, a transcriptional activator for the type-I IFN genes; OAS family members OAS1, OAS2, OAS3, mediators of resistance to virus infection; ISG15, a ubiquitin-like protein that becomes conjugated to many cellular proteins upon activation by IFN ⁇ / ⁇ ; and members of the ISG15 signaling pathways such as USP18, UBE2L6, and HERC5. This enrichment of type I IFN genes indicated them as the most overexpressed genes in lesional skin of psoriatic patients.
  • Table 26 lists, in descending order, the top 50 IFN induced probes in lesional skin compared to non-lesional skin of psoriasis patients. Table 26 not only compares the log 2-based fold change (log 2 fc) and q value for each of the 50 most upregulated type I IFN inducible genes in lesional relative to non-lesional skin of psoriasis patients, it also compares the log 2-based fold change and q value for these 50 genes in non-lesional skin of psoriasis patients relative to healthy control patients.
  • Table 28 provides the average and median fold change of the top 25 most upregulated type-I IFN probe sets for each paired lesional/non-lesional skin sample. The top 25 most upregulated type-I IFN probe sets were consistently observed to detect elevated gene expression in the lesional relative to non-lesional skin of each individual psoriasis patient.
  • FIG. 32 provides a graphic of the distribution of the average and median fold changes among the different pairs of lesional and non-lesional skin.
  • the prevalent and uniform upregulation of the most overexpressed type-I IFN genes in lesional skin of psoriatic patients verified their usefulness as PD markers.
  • Type-I IFN Genes is not Significantly Altered in Normal Skin Relative to Non-Lesional Skin of Psoriatic Patients
  • Example 11 Although the array data obtained in Example 11 identified overexpression of numerous type-I IFN-inducible genes in lesional relative to non-lesional skin, it identified only 5 probe sets overexpressed in non-lesional skin relative to normal control skin. The p value of Fisher's exact test (two-tailed t-test) was 0.581, which suggested that the overexpression of the type-I IFN genes is not statistically significant in the non-lesional skin of the psoriasis patients over normal skin.
  • 33 provides a graphical representation of the relative expression of 3 type-I IFN inducible genes (HPSE, OASL, and HERC6; included as top 50 type-I IFN-induced probe sets in lesional relative to non-lesional skin), and 1 non type-I IFN inducible gene (SERPINB4) in both (a) lesional skin compared to non-lesional skin and (b) non-lesional skin compared to normal skin.
  • HPSE, OASL, and HERC6 in lesional skin compared to non-lesional skin is both statistically significant (as evidenced by the very small p value) and large in scale (between 12-250 fold overexpression on average).
  • SERPINB4 is overexpressed in non-lesional skin by about 3-4 fold compared to normal skin, but upregulated by well over 200 fold in lesional skin compared to non-lesional skin.
  • FIG. 34 a provides heatmap of unsupervised hierarchical clustering of all lesional, non-lesional, and normal skin samples profiled using the 164 type-I IFN-inducible probe sets in lesional skin compared to non-lesional skin of psoriasis patients.
  • FIG. 34 b provides a PCA plot of the skin samples using the same 164 upregulated type-I IFN inducible probe sets. Again, the normal skin samples and the non-lesional skin samples mostly clustered together, indicating similar levels of expression of the 164 genes. Also, the majority of the lesional skin samples were separated from the normal and non-lesional skin samples, indicating that the lesional samples exhibited a distinct overexpression of the type-I IFN inducible genes that was separable from the gene expression levels of the normal and non-lesional skin samples.
  • BIOMARKTM 48.48 dynamic array (TAQMAN-based assay) from Fluidigm was used to validate the results of the Affymetrix GENECHIP® human genome U133 plus v2.0 arrays, results indicating that type-I IFN genes are up-regulated in lesional psoriatic relative to non-lesional psoriatic or normal skin samples.
  • 35 provides TAQMAN data showing overexpression of each of ten (OAS2, OASL, EPSTI1, MX1, IFI44L, IFI44, HERC6, HPSE, ISG15, and STAT1) type-I IFN-inducible genes in lesional skin in the 18 paired lesional/non-lesional samples.
  • the TAQMAN-based assay and Affymetrix array results correlated well, validating the selected genes as overexpressed type-I IFN-induced genes in lesional psoriatic skin.
  • the distribution of correlation coefficients between the TAQMAN-based assay and the Affymetrix array for the 40 overexpressed genes is provided in FIG. 36 a .
  • Nineteen of the overexpressed genes had correlation coefficients greater than 0.85, indicating excellent correlation between the microarray and TAQMAN-based assay.
  • Another 17 genes had high correlation coefficients between the microarray and TAQMAN-based assay of 0.5-0.85.
  • 36 b provides the distribution of correlation coefficients between the TAQMAN-based assay and the Affymetrix array for the 29 type-I IFN-induced genes of the 18 psoriasis patients. Again, many of the genes had high correlation coefficients, greater than 0.90. These genes include, inter alia, IFI27, CXCL10, ISG15, and MX1.
  • FIGS. 37 a - 37 d and 38 provide detailed gene expression data obtained from the microarray and TAQMAN-based assays for several type-I IFN-inducible genes in the paired lesional/non-lesional samples. These data evidence that similar levels of overexpression of type-I IFN-induced genes in lesional psoriatic skin is detected between the TAQMAN and array assays, and thus the high correlation coefficients discussed above.
  • FIGS. 37 a and 37 b show similar overexpression of ISG15 in each of the 18 paired lesional/non-lesional skin samples as determined by TAQMAN ( 37 a ) and microarray ( 37 b ) analysis.
  • FIG. 38 shows measurement of similar overexpression of type-I IFN-inducible genes IFI27 and CXCL10 by TAQMAN and microarray analysis in each if the 18 paired lesional/non-lesional skin samples.
  • the correlation coefficient between the TAQMAN and microarray results for IFI27 and CXCL10 was 0.9456 and 0.9455, respectively.
  • IFN ⁇ Ab Neutralizes Type-I IFN ⁇ -Induced Gene Expression in Ex Vivo Stimulated Keratinocytes of Healthy Volunteers
  • Keratinocytes of healthy volunteers were isolated and stimulated ex vivo with escalating doses of IFN ⁇ 2a and leukocyte IFN to induce an escalating type I IFN ⁇ -induced gene expression pattern.
  • Anti-IFN ⁇ antibody was able to neutralize the type I IFN ⁇ -induced gene expression pattern in a dose-dependent manner.
  • keratinocytes Normal human keratinocytes (EpiDerm system, MatTek, Inc.) were grown under serum-free conditions according to manufacturer's instructions. Briefly, keratinocytes were maintained on tissue culture inserts at the air-liquid interface to maintain a multilayered, fully differentiated epithelial phenotype. Keratinocytes were stimulated with human leukocyte IFN (15-150 IU/ml, PBL Biomedical Labs) and human IFN ⁇ 2a (15-350 IU/ml, PBL Biomedical Labs).
  • a humanized anti-human IFN ⁇ monoclonal antibody (0.01-100 ⁇ g/ml; MEDI-545, MedImmune, Inc) or isotype matched control antibody of irrelevant specificity (R347, MedImmune, Inc) was added simultaneously with cytokine stimulus.
  • Epidermal cultures were harvested at 2, 4, or 18 hours post treatment for transcript analysis.
  • Expression of type-I IFN-induced genes was measured using a BIOMARKTM 48.48 dynamic array.
  • Type-I IFN-induced genes Expression of a majority of type-I IFN-induced genes was upregulated in the IFN ⁇ 2a and leukocyte interferon stimulated keratinocytes in a dose-dependent manner. This upregulation of type-I IFN-induced genes, by either IFN ⁇ 2a or leukocyte interferon, was likewise inhibited in a dose-dependent manner by IFN ⁇ monoclonal antibody (MEDI-545). Control antibody, R347, did not have a significant effect on neutralization of the type-I IFN-induced genes.
  • FIGS. 39 ( a ), ( c ), and ( e ) show that MEDI-545 neutralizes overexpression of type-I IFN induced genes ISG15, USP18, and IFIT2, respectively, in keratinocytes stimulated with 350 IU/mL IFN ⁇ 2a. Each of these genes was neutralized 100% by MEDI-545.
  • FIGS. 39 ( a ), ( c ), and ( e ) show that MEDI-545 neutralizes overexpression of type-I IFN induced genes ISG15, USP18, and IFIT2, respectively, in keratinocytes stimulated with 350 IU/mL IFN ⁇ 2a. Each of these genes was neutralized 100% by MEDI-545.
  • MEDI-545 neutralizes overexpression of type-I IFN induced genes ISG15, USP18, and IFIT2, respectively, in keratinocytes stimulated with 150 I.U./mL leukocyte IFN. Neutralization of these genes by MEDI-545 was between 70 and 100%, which is not surprising because leukocyte IFN contains both IFN ⁇ and IFN ⁇ . MEDI-545 neutralizes a majority of IFN ⁇ subtypes efficiently, but not IFN ⁇ .
  • type-I IFN-inducible genes identified in ex vivo stimulated whole blood and keratinocytes are type-I IFN-inducible genes. It also provides further support that upregulated expression of these genes in lesional psoriatic skin relative to non-lesional skin due to type-I IFN induction.
  • type-I IFN subtypes responsible for the induction of the type-I IFN signature in lesional skin of psoriasis patients mRNA levels of type-I IFN genes in psoriatic lesions were measured.
  • TAQMAN Low Density Array (TLDA) from Applied Biosystems. Expression of 23 genes, including type-I IFN ⁇ subtypes 1, 2, 5, 6, 7, 8, 14, 17, and 21; type-I IFNs IFN ⁇ , ⁇ , and ⁇ ; IFN ⁇ ; IFN ⁇ receptors IFNAR1 and IFNAR2; IFN ⁇ receptors IFNGR1 and IFNGR2; type-I IFN ⁇ inducible genes RSAD2, OAS3, IFI44, MX1, and CXCL10; and TNF ⁇ was monitored and compared in paired lesional and non-lesional skin of 18 psoriasis patients.
  • TLDA TAQMAN Low Density Array
  • Double-stranded cDNA for each patient sample was pre-amplified using the TAQMAN PreAmp Master Mix kit (Applied Biosystems).
  • cDNA was pre-amplified by conducting 10 cycles of PCR on each patient sample using a pooled solution of primers, a pair for each gene analyzed on the array.
  • the pre-amplified cDNA were diluted 1:5 with TE.
  • a 50 ⁇ L volume of the diluted pre-amplified cDNA was added to a 50 ⁇ L volume of 2 ⁇ TAQMAN Universal PCR Master Mix (Applied Biosystems) and mixed.
  • the array was loaded with the mixture using standard procedures and the loaded array was run on a 7900HT Fast Real-Time PCR System (Applied Biosystems). Data analysis of the resulting Ct values was conducted with the SDSv2.2.2 software tool (Applied Biosystems).
  • FIG. 40 a shows the relative overexpression of mRNA of nine IFN ⁇ subtypes in the lesional skin compared to either non-lesional skin or normal skin.
  • IFN ⁇ 5 upregulated by about 4.6 fold; median fold change, p ⁇ 0.001
  • none of the IFN ⁇ subtypes were significantly altered at the mRNA level in the non-lesional skin compared to that in the normal skin (p ⁇ 0.05).
  • all of these IFN ⁇ subtypes were upregulated at the mRNA level in the lesional skin compared to that in the normal skin (or non-lesional skin), with the overexpression of IFN ⁇ 1, IFN ⁇ 5, IFN ⁇ 8, IFN ⁇ 14, IFN ⁇ 17, IFN ⁇ 21 being statistically significant (p ⁇ 0.05).
  • FIG. 40 a shows the relative overexpression of mRNA of nine IFN ⁇ subtypes in the lesional skin compared to either non-lesional skin or normal skin.
  • IFN ⁇ , - ⁇ , and - ⁇ mRNA show that the overexpression of other members of type I IFN family members, IFN ⁇ , - ⁇ , and - ⁇ mRNA in the lesional skin compared to either non-lesional skin or normal skin.
  • the alterations of IFN ⁇ and IFN ⁇ mRNAs in the non-lesional skin were not significant. However, the upregulation of these mRNAs were significant in the lesional skin compared to normal skin (p values of 0.022 and 0.049 respectively).
  • Table 29 lists the correlation coefficients of the overexpression of type-I IFN family member (type-I IFN ⁇ subtypes 1, 2, 5, 6, 7, 8, 14, 17, and 21; and IFN ⁇ , IFN ⁇ , and IFN ⁇ ) mRNAs in lesional skin compared to non-lesional skin of psoriatic patients.
  • type-I IFN family member type-I IFN ⁇ subtypes 1, 2, 5, 6, 7, 8, 14, 17, and 21; and IFN ⁇ , IFN ⁇ , and IFN ⁇
  • Table 29 lists the correlation coefficients of the overexpression of type-I IFN family member (type-I IFN ⁇ subtypes 1, 2, 5, 6, 7, 8, 14, 17, and 21; and IFN ⁇ , IFN ⁇ , and IFN ⁇ ) mRNAs in lesional skin compared to non-lesional skin of psoriatic patients.
  • overexpression of IFN ⁇ 1, 2, 8, and 14 in lesional skin correlated most consistently with overexpression of other members in the type-I IFN family, with the exception of IFN ⁇ 5 which showed the weakest correlation with other type-
  • Type-I IFN Co-Overexpression of Type-I IFN, Type-II IFN, and TNF ⁇ and their Gene Signatures in Lesional Skin or Psoriasis Patients
  • IFN ⁇ and TNF ⁇ mRNA signaling pathways were also evaluated in the paired lesional/non-lesional psoriasis and normal skin samples. As discussed in Example 15, above, TLDA from Applied Biosciences was used to measure IFN ⁇ , IFNGR1 and IFNGR2, and TNF ⁇ mRNA in lesional and non-lesional skin of psoriasis patients and in normal healthy skin.
  • IFN ⁇ , IFNGR1, IFNGR2, and TNF ⁇ mRNAs were significantly overexpressed in non-lesional skin compared to healthy normal skin ( FIG. 41 ; p values of 0.02, ⁇ 0.001, ⁇ 0.001 and ⁇ 0.001 respectively).
  • TNF ⁇ mRNA was upregulated by about 5.7 fold, while IFN ⁇ , IFNGR1 and IFNGR2 mRNAs were upregulated by about 1.5, 2.2, and 2.8 fold compared to that in the normal skin (median fold change; FIG. 41 ).
  • TNF ⁇ , IFN ⁇ , IFNGR1 and IFNGR2 mRNAs were upregulated by about 33.5, 116.7, 11.6, and 8.4 fold in the lesional skin compared to that in the normal skin.
  • IFN ⁇ subtypes As described in Example 10, whole blood of healthy donors was stimulated ex vivo with a panel of IFN ⁇ subtypes, as well as IFN ⁇ , IFN ⁇ , and TNF ⁇ . Stimulating whole blood ex vivo with IFN ⁇ or TNF ⁇ identified probe sets associated with potential IFN ⁇ - or TNF ⁇ -inducible genes. Three hundred four probe sets were identified as at least 2-fold upregulated by IFN ⁇ four hours post-stimulation. Two hundred thirty four probe sets were identified as at least 2-fold upregulated by TNF ⁇ both 2 and 4 hours post-stimulation.
  • the probe sets identified as associated with ex vivo IFN ⁇ or TNF ⁇ induction were compared with the total 1408 probe sets (Example 11) found to be upregulated in lesional skin relative to non-lesional skin of psoriasis patients.
  • 106 and 35 of the probe sets included in the total 1408 upregulated in lesional skin were identified as IFN ⁇ or TNF ⁇ inducible, respectively ( FIG. 42 ).
  • the 106 probe sets identified as IFN ⁇ inducible are provided in FIG. 49 .
  • the 35 probe sets identified as TNF ⁇ inducible are provided in FIG. 50 .
  • the 164 probes sets shown in FIG. 42 as identified as type-I IFN inducible are provided in FIG. 51 .
  • the Fisher's exact test indicated that the p values (one-tailed t-test) of the overexpression of IFN ⁇ or TNF ⁇ inducible genes in lesional skin were both less than 0.0001. The overexpression of IFN ⁇ and TNF ⁇ inducible genes was significant.
  • type I IFN, IFN ⁇ and TNF ⁇ inducible genes upregulated at least 2-fold in each of the lesional relative to non-lesional skin sample were identified.
  • FIG. 43 shows the number of type I IFN, IFN ⁇ and TNF ⁇ inducible genes upregulated in each of the 26 paired lesional and non-lesional skin. The larger the number of type I IFN inducible genes upregulated in a particular lesional skin biopsy usually gave rise to the overexpression of larger numbers of IFN ⁇ and TNF ⁇ inducible genes in the same lesional skin biopsy.
  • IFN ⁇ and TNF ⁇ mRNAs were found to be upregulated in the non-lesional skin of psoriatic patients when compared to healthy normal skin, IFN ⁇ and TNF ⁇ inducible genes did not appear to be significantly overexpressed in the non-lesional skin ( FIG. 42 ).
  • Snap-frozen lesional psoriatic, non-lesional psoriatic, and normal skin biopsies were divided in half. One-half of each sample was embedded in O.C.T., sectioned at 5 ⁇ M, placed on a “plus” slide, and fixed in cold acetone. The sectioned samples were incubated with primary antibodies (specific for BDCA2, CD83, CD4, STAT1, and ISG15) for 4 hours and washed with TBS.
  • primary antibodies specific for BDCA2, CD83, CD4, STAT1, and ISG15
  • lesional skin contained increased numbers of pDCs, and/or mDCs, increased numbers of CD4+ cells, as well as the significant upregulation of STAT-1 and ISG15 protein in the epidermis and dermis compared to non-lesional biopsies.
  • skin biopsies from normal donors did not contain appreciable numbers of pDCs, mDCs or staining for STAT-1 and ISG15. See FIG. 44 for example immunohistochemistry slides.
  • transcripts of the top 25 type I IFN inducible genes in skin lesions of an SLE patient were neutralized by MEDI-545.
  • biopsies from patients treated with 10 mg/kg MEDI-545 were examined.
  • a heatmap of neutralization of the top 25 type I IFN inducible genes in skin lesions at 0 and 14 days post-treatment is provided in FIG. 58( a ). All of the top 25 genes are neutralized 14 days following administration of MEDI-545.
  • a PCA diagram of target modulation based on these top 25 type I IFN-inducible genes is provided in FIG. 58( b ).
  • the PCA diagram shows the progression of the treated SLE patient from a position directly opposite that of normal healthy donors prior to administration of MEDI-545 to a position nearing that of the healthy donors 14 days after administration of MEDI-545.
  • Snap-frozen skin lesion samples of MEDI-545 treated SLE patients and placebo treated SLE patients were divided in half. One-half of each sample was embedded in O.C.T., sectioned at 5 ⁇ M, placed on a “plus” slide, and fixed in cold acetone. The sectioned samples were incubated with primary antibodies (specific for BDCA2, CD83, CD4, IP10, and ISG15) for 4 hours and washed with TBS. The slides were then incubated with peroxidase-labeled polymer conjugated to goat anti-mouse immunoglobulin antibody (Envision+; Dakocytomation, Carpenteria, Calif.) for 30 minutes and washed with Tris-buffered saline, pH 7.2.
  • primary antibodies specific for BDCA2, CD83, CD4, IP10, and ISG15
  • TBS washed with TBS.
  • the slides were then incubated with peroxidase-labeled polymer conjugated to goat anti-mouse immunoglob
  • Detection was performed with 3,3′-diaminobenzidiine tetrahydrochloride (DAB+; DakoCytomation) as the chromogen. Slides were washed with dH 2 O), counterstained with hematoxylin, dehydrated and coverslipped.
  • DAB+ 3,3′-diaminobenzidiine tetrahydrochloride
  • FIG. 52 shows an increase in (worsening of) mDC (CD83 staining) and T cell (CD4 staining) infiltration in skin lesions.
  • FIG. 52 also shows no change in pDC (BDCA2 staining) infiltration in the placebo-treated SLE patient skin lesions over the 14 days.
  • FIG. 53 shows an increase in staining for proteins expressed from overexpressed type I IFN inducible genes HERC and IP10. No change in staining for ISG15 was observed.
  • FIGS. 54 and 55 which provide immunohistochemical data from a first SLE patient treated with MEDI-545
  • FIGS. 56 and 57 which provide immunohistochemical data from a second SLE patient treated with MEDI-545.
  • ISRE interferon-stimulated response element
  • HEK293H cells were stably transfected with the construct and these cells were used for the IFN detection assays.
  • 25,000 of the stably transfected HEK293H cells were seeded per assay well in 50 uL of cell culture medium overnight in a CO 2 incubator.
  • patient serum samples or normal pooled human serum spiked with the various sub-types of IFN alpha or IFN-beta, IFN-omega, IFN-gamma
  • IFN-induced luciferase activity was detected the following day, by observing chemiluminescence in the culture supernatants.
  • Chemiluminescence was observed by transferring 50 uL of supernatant from the wells to a B&W Isoplate, adding 50 uL of chemiluminescent substrate, and detecting luminescence at 6 minutes. Samples generating a signal greater than 1.5-times the Negative Control wells on each assay plate are classified as Positive for IFN activity. See FIG. 59 a - d , which provide detected levels of type I and type II IFN activity in the IFN bioassay for different plates of cells treated with patient serum and spiked control serum. Each of panels a-d show that increased dose of IFN in the assay results in increased detection of IFN activity.
  • Anti-IFN-type specific antibodies are preincubated with either the positive serum sample(s) (in the case of MEDI 545, anti-IFN beta, anti-IFN gamma and anti-IFN omega that bind to the IFN ligand itself) or with the cells (in the case of MEDI 546 that binds to the Type I interferon receptor on the HEK293H cells) followed by addition of the samples to the cells and chemiluminescence determination as above. Spiked samples that demonstrate lower chemiluminescence following specific antibody treatment are considered to be positive for the presence of the particular IFN(s) that is neutralized by the IFN-specific antibodies.
  • FIG. 60( a ) shows that increasing dose of MEDI-545 in the treated wells increasingly neutralizes of IFN activity as does increasing dose of MEDI-546 ( FIG. 60( b )).
  • FIGS. 61-63 show that IFN ⁇ , IFN ⁇ , and IFN ⁇ , respectively, are neutralized by antibodies specific for IFN ⁇ , IFN ⁇ , and IFN ⁇ , as expected.
  • Fifty-nine percent were receiving at least 1 potential disease-modifying medication other than corticosteroids.
  • Luminex xMAP technology was used to detect changes in 89 analytes and was performed by Rules Based Medicine (see the world wide web at domain name rulesbasedmedicine.com).
  • FIG. 74 shows analytes whose levels were significantly (a) increased or (b) decreased from the mean of the normal serum (p value ⁇ 0.05). Significant alterations in levels of cytokines chemokines, metabolic proteins, and other soluble mediators were detected in serum of lupus patients.
  • QuantiGenePlex assay was first performed to assess the ability of QuantiGenePlex to detect 22 IFN-inducible transcripts in whole blood stimulated with IFN ⁇ 2b.
  • the 22 IFN-inducible transcripts detected by this initial QuantiGenePlex assay were selected based on their consistent up-regulation in SLE patients and are shown on the x-axis of the graphs shown in FIGS. 75 and 76 .
  • Stimulation of the whole blood was performed by incubating freshly drawn Na-EDTA whole blood from 5 healthy donors with 20 IU/mL IFN ⁇ 2b for 4 hours. Following this incubation, 2.5 mL of the stimulated whole blood was added to PAXgene tubes, mixed, and held overnight at room temperature. After overnight incubation, the samples were frozen at ⁇ 80° C. These sample-handling procedures were selected to mimic those to be used during clinical trials.
  • PAXgene blood was analyzed for expression levels of the IFN-inducible transcripts.
  • PAXgene blood 500 L was pelleted and then lysed in 139 L of buffer according to the QuantiGenePlex PAXgene Blood Lysis Protocol. Processed blood from each donor was split into duplicate wells and hybridized overnight with a multiplex probe set for the 22 IFN-inducible genes. Gene expression was assessed the following day using a Luminex 100 instrument with BioRad BioPlex software. Fold changes were assessed for each individual based on the increase in signal observed between IFN-stimulated and PBS-stimulated control wells.
  • FIG. 75 shows the fold-change in expression of each of the 22 IFN-inducible genes following IFN stimulation of each of the 5 healthy volunteer whole blood samples. The dashed line indicates a 2-fold change over PBS-stimulated control samples.
  • QuantiGenePlex assay was used to detect levels of IFN-inducible transcripts in whole blood of SLE patients. Twenty of the 22 probes from the original QuantiGenePlex kit, probes identified in FIGS. 75 and 76 , were retained in the QuantiGenePlex assay used for this data analysis. Two probes, HSXIAPAF1 and GIP3, were substituted with different probes, XAF1 and IFI6. Using this panel of 22 probes, a baseline gene signature was established based on whole blood samples of ten healthy donors (blue bars in each panel).
  • the baseline gene signature based on the whole blood samples of the healthy donors, was compared to (1) the gene signature of an SLE patient that had detectable IFN serum activity and (2) the gene signature of an SLE patient that did not have detectable IFN serum activity.
  • IFN serum activity was detected in the SLE patient serum samples using the assay described in Example 20.
  • FIG. 77 a shows a comparison of the gene signature of an SLE patient (red bars) having no detectable serum IFN ⁇ activity (i.e. serum IFN activity ⁇ 2.5 IU/mL) relative to the baseline gene signature (blue bars). With the exception of LAMP3, all transcript levels were detected as elevated in blood from the SLE patient with no IFN serum activity.
  • 77 b shows a comparison of the gene signature of an SLE patient with high levels of serum IFN ⁇ activity (red bars) relative to the baseline gene signature (blue bars). All transcripts were elevated at least 2-fold in the blood of the patient with high IFN serum activity, with maximal inductions of nearly 80-fold for IFI27.
  • QuantiGenePlex was next evaluated for its comparability to data obtained from a Fluidigm Real-Time PCR assay.
  • QuantiGenePlex and Fluidigm methods were each used to analyze and compare transcript levels in PAXgene-preserved whole blood samples from 16 SLE patients participating in a Phase I clinical trial (of a monoclonal antibody against IFN ⁇ ) relative to a composite median gene score from 10 healthy donors.
  • Fluidigm analyses were carried out using a mixture of TAQMAN Gene Expression assays, including 4 reference control genes prepared using the TAQMAN PreAmp Master Mix Kit (Applied Biosystems).
  • Dynamic arrays were loaded using a NanoFlex 4-IFC Controller (Fluidigm Corp) and real-time reactions were performed using a BIOMARK Real-Time PCR System. Results were analyzed using BIOMARK Real-Time PCR Analysis software. Delta-delta Cts (DDCt) were calculated using the mean of 4 reference genes (GAPDH, TFRC, b2M, and 18S) and a calibrator sample. The results obtained using whole blood samples from SLE patients demonstrated a high degree of correlation between QuantiGenePlex and Real-Time PCR approaches to detect disease-related gene expression profiles.
  • FIG. 79 a shows the changes in gene signature for placebo- or antibody-treated SLE patients using Fluidigm technology.
  • 79 b shows the changes in gene signature of the placebo- or antibody-treated SLE patients using QuantiGenePlex technology.
  • a decrease in IFN gene signature is observed within 24 hours following drug administration and is consistent between Fluidigm and QuantiGenePlex.
  • Subsequent changes in transcript levels post-administration were also highly similar between QuantiGenePlex and Fluidigm technologies.
  • IFN- ⁇ / ⁇ -inducible genes in whole blood (WB) of SLE patients was observed as discussed in the Examples above.
  • Affymetrix whole genome array (WGA) transcript profiling was used to quantify the abundance of over-expressed IFN- ⁇ / ⁇ -inducible genes in patients diagnosed with autoimmune disorders dermatomyositis (DM), polymyositis (PM), inclusion body myositis (IBM), and rheumatoid arthritis (RA) to see if there was a similar IFN- ⁇ / ⁇ -inducible gene over-expression pattern.
  • DM dermatomyositis
  • PM polymyositis
  • IBM inclusion body myositis
  • RA rheumatoid arthritis
  • IFN- ⁇ / ⁇ -inducible genes The prevalence of the overexpression of IFN- ⁇ / ⁇ -inducible genes in the WB of SLE, DM, PM, IBM, and RA patients provides evidence for type I IFN-inducible genes as pharmacodynamic markers across multiple autoimmune diseases.

Abstract

The present invention encompasses type-I IFN and IFNα-induced PD marker expression profiles, kits, and methods for identifying such IFNα-induced PD marker expression profiles. The type-I IFN and IFNα-induced PD marker expression profiles may also be used in, for example, methods of treating patients having a type-I IFN or IFNα-mediated disorder, methods of monitoring disease progression of patients receiving treatment with a therapeutic agent that binds to and modulates IFNα activity, identifying patients as candidates to receive a therapeutic that binds to and neutralizes IFNα activity, and in diagnosing or providing a prognosis to patients having IFNα-induced disorders.

Description

  • This application is a continuation of U.S. patent application Ser. No. 12/598,526, filed May 5, 2008, entitled Interferon Alpha-Induced Pharmacodynamic Markers and Uses Thereof, which is a U.S. National Phase Application filed under 35 U.S.C. 371 of International Patent Application No. PCT/US2008/062646, filed May 5, 2008, entitled Interferon Alpha-Induced Pharmacodynamic Markers, which claims priority to and benefit of U.S. Provisional Application No. 60/924,219, filed May 3, 2007, entitled Interferon Alpha-Induced Pharmacodynamic Markers, U.S. Provisional Application No. 60/924,220 filed May 3, 2007, entitled Auto-Antibody Markers of Autoimmune Disease, U.S. Provisional Application No. 60/924,584, filed May 21, 2007, entitled Interferon Alpha-Induced Pharmacodynamic Markers, U.S. Provisional Application No. 60/960,187, filed Sep. 19, 2007, entitled Interferon Alpha-Induced Pharmacodynamic Markers, U.S. Provisional Application No. 60/996,174, filed Nov. 5, 2007, entitled Methods of Treating Systemic Lupus Erythematosus, U.S. Provisional Application No. 60/996,176, filed Nov. 5, 2007, entitled Interferon Alpha-Induced Pharmacodynamic Markers, U.S. Provisional Application No. 60/996,219, filed Nov. 6, 2007, entitled Auto-Antibody Markers of Autoimmune Disease, U.S. Provisional Application No. 60/996,820, filed Dec. 6, 2007, entitled Auto-Antibody Markers of Autoimmune Disease, International Patent Application Number PCT/US2007/024947, filed Dec. 6, 2007, entitled Interferon Alpha-Induced Pharmacodynamic Markers and International Application Number PCT/US2007/024941, filed Dec. 6, 2007, entitled Methods of Treating Systemic Lupus Erythematosus and U.S. Provisional Application No. 61/006,963, filed Feb. 8, 2008, entitled Interferon Alpha-Induced Pharmacodynamic Markers. The entirety of each of the foregoing patent applications is incorporated herein by reference for all purposes.
    • SEQUENCE LISTING
  • The instant application contains a Sequence Listing which has been submitted electronically in ASCII format and is hereby incorporated by reference in its entirety. Said ASCII copy, created on Oct. 23, 2014, is named MDI-0400-CT_SL.txt and is 1,378 bytes in size.
    • FIELD OF THE INVENTION
  • The present invention relates to pharmacodynamic (PD) markers inducible by interferon (IFN) alpha, probes and kits that detect the PD markers, and methods employing the same.
    • BACKGROUND OF THE INVENTION
  • The present invention encompasses PD markers that are induced by IFNα. The PD markers can be used in methods of treating patients with a therapeutic agent that binds to and modulates IFNα activity, methods that identify patients as candidates for a therapeutic agent that binds to and modulates IFNα activity, methods of diagnosing a patient as having a disorder associated with increased IFNα levels, methods of monitoring disease progression of a patient receiving treatment with a therapeutic agent that binds to and modulates IFNα activity, and methods of identifying a candidate therapeutic for treating IFNα-mediated disorders.
    • SUMMARY OF THE INVENTION
  • One embodiment of the invention encompasses a method of identifying a patient as a candidate for a therapeutic agent that binds to and modulates IFNα activity. Presence or absence of an IFNα-inducible PD marker expression profile is detected in a sample from the patient.
  • Another embodiment of the invention encompasses a method of treating a patient having a type I IFN or IFNα-mediated disease or disorder. An agent that binds to and modulates type I IFN or IFNα activity is administered to the patient. The agent neutralizes a type I IFN or IFNα-inducible PD marker expression profile of the patient.
  • Yet another embodiment of the invention encompasses a method of treating an autoimmune disease patient comprising a moderate or strong type I IFN or an IFNα PD marker profile. An agent that binds to and modulates type I IFN or IFNα activity is administered to the patient. The agent neutralizes the type I IFN or IFNα-inducible PD marker expression profile of the patient.
  • A further embodiment of the invention encompasses a method of neutralizing a type I IFN or IFNα-inducible PD marker expression profile in a patient in need thereof. An agent that binds to and modulates type I IFN or IFNα activity is administered to the patient. The agent neutralizes the type I IFN or IFNα-inducible PD marker expression profile of the patient.
  • Another embodiment of the invention encompasses a method of diagnosing a patient as having a disorder associated with increased IFNα levels. Presence or absence of an IFNα-inducible PD marker expression profile is detected in a sample from the patient.
  • A further embodiment of the invention encompasses a method of monitoring disease progression of a patient receiving treatment with a therapeutic agent that binds to and modulates IFNα activity. A first IFNα-inducible PD marker expression profile is obtained in a first sample from the patient. A therapeutic agent that binds to and modulates IFNα activity is administered to the patient. A second IFNα-inducible PD marker expression profile is obtained from a second sample from the patient. The first and the second IFNα-inducible PD marker expression profiles are compared.
  • Yet another embodiment of the invention encompasses a method of identifying a candidate therapeutic for treating IFNα-mediated disorders. Cells comprising an IFNα-inducible PD marker expression profile are contacted with an agent. Presence or absence of a change in the IFNα-induced PD marker expression profile of the cells is detected.
  • A further embodiment of the invention encompasses a set of probes.
  • Yet a further embodiment of the invention encompasses kits that comprise the probes.
  • Another embodiment of the invention encompasses a method of detecting IFN activity in a sample. Cells comprising a polynucleotide sequence comprising a reporter gene under the control of an IFN-stimulated response element are incubated with a sample. Expression of the reporter gene is detected.
    • BRIEF DESCRIPTION OF THE FIGURES
  • FIG. 1: TAQMAN qPCR IFI44 gene expression analysis of IFNα-stimulated whole blood of healthy donors.
  • FIG. 2: TAQMAN qPCR IRF2 gene expression analysis of IFNα-stimulated whole blood of healthy donors.
  • FIG. 3: TAQMAN qPCR RSAD2 gene expression analysis of IFNα-stimulated whole blood of healthy donors.
  • FIG. 4: TAQMAN qPCR G1P3 gene expression analysis of IFNα-stimulated whole blood of healthy donors.
  • FIG. 5: TAQMAN qPCR HERC5 gene expression analysis of IFNα-stimulated whole blood of healthy donors.
  • FIG. 6: MEDI-545 neutralization of RAB8B gene expression induced by IFN-α in whole blood of healthy donors.
  • FIG. 7: MEDI-545 neutralization of IRF7 gene expression induced by IFN-α in whole blood of healthy donors.
  • FIG. 8: MEDI-545 neutralization of MARCKS gene expression induced by IFN-α in whole blood of healthy donors.
  • FIG. 9: MEDI-545 neutralization of IL6ST gene expression induced by IFN-α in whole blood of healthy donors.
  • FIG. 10: MEDI-545 neutralization of Ly6E gene expression induced by IFN-α in whole blood of healthy donors.
  • FIG. 11: MEDI-545 neutralization of IFIT3 gene expression induced by IFN-α in whole blood of healthy donors.
  • FIG. 12: MEDI-545 neutralization of IFIT1 gene expression induced by IFN-α in whole blood of healthy donors.
  • FIG. 13: MEDI-545 neutralization of HERC5 gene expression induced by IFN-α in whole blood of healthy donors.
  • FIG. 14: MEDI-545 neutralization of OAS1 gene expression induced by IFN-α in whole blood of healthy donors.
  • FIG. 15: MEDI-545 neutralization of OAS3 gene expression induced by IFN-α in whole blood of healthy donors.
  • FIG. 16: MEDI-545 neutralization of RSAD2 gene expression induced by IFN-α in whole blood of healthy donors.
  • FIG. 17: Ex vivo stimulation in whole blood identifies genes inducible by type I IFN.
  • FIG. 18: MEDI-545 neutralization of top 25 type I IFN inducible genes in individual lupus patients' whole blood.
  • FIG. 19: Heatmap of target modulation and PCA plot using top 25 up-regulated type I IFN inducible probe sets in whole blood of patient 1541 before and after MEDI-545 treatment.
  • FIG. 20: Heatmap of target modulation and PCA plot based on 25 most up-regulated type I IFN inducible genes in whole blood of patient 1449 before and after MEDI-545 treatment.
  • FIG. 21: Heatmap of target modulation calculated based on 165 type I IFN inducible genes up-regulated in whole blood of one patient treated with 0.3 mg/kg MEDI-545.
  • FIG. 22: PCA using 169 probe sets that are type I IFN inducible-24/35 SLE patients have statistically significant type I IFN signature in whole blood.
  • FIG. 23: MEDI-545 neutralizes the top 25 most upregulated type I IFN inducible probe sets of lupus patients. Target neutralization of the top 25 most upregulated type I IFN inducible genes was measured at days 1, 4, 7, 14, 28, and 84 for each patient. Dose range was from 1 (placebo) to 3 mg/kg MedI 545.
  • FIG. 24: MEDI-545 neutralizes the top 25 most upregulated type I IFN inducible probe sets of lupus patients. Target neutralization of the top 25 most upregulated type I IFN inducible genes was measured at days 1, 4, 7, 14, and 28 for each patient. Dose range was from 0 (placebo) to 30 mg/kg MEDI-545.
  • FIGS. 25 a and 25 b: Heatmap (a) and PCA (b) showing neutralization of the top 25 type I IFN inducible probe sets in whole blood of a SLE patient treated with 30 mg/kg MEDI-545 at 0, 1, 4, 7, and 14 days post-dosing.
  • FIGS. 26 a and 26 b: PCA plots of lupus patient before (a) and after (b) dosing with placebo control show no trend in the change of type I IFN inducible gene signature. The 25 most upregulated type I IFN inducible probe sets were used to perform the PCA analysis.
  • FIG. 27: Type-I IFNα subtypes are upregulated in the whole blood of individual lupus patients.
  • FIG. 28: Distribution of average fold-change of top 25 type I IFN inducible probe sets in whole blood of individual lupus patients.
  • FIG. 29 a-29 c: Pair-wise fold change ranking test proves MEDI-545 neutralizes type I IFN genes in a clinical trial. Top genes neutralized are shown for (a) SLE patients having a type I IFN gene signature at 14 days following MEDI-545 treatment; (FIG. 29 a discloses “DEAD (Asp-Glu-Ala-Asp)” as SEQ ID NO: 1) (b) SLE patients not having a type I IFN gene signature at 14 days following MEDI-545 treatment; and (c) SLE patients 14 days following treatment with placebo. Genes highlighted in yellow are genes identified as having a type-I IFN signature.
  • FIG. 30: Hierarchical clustering of 1384 probe sets differentially regulated by IFNα subtypes, IFNβ, IFNγ, and TNFα in ex vivo stimulated whole blood. Each row corresponds to a single probe set, while each column corresponds to a single sample. The branch lengths indicate the correlation with which probe sets/samples are joined, with a longer branch indicating a weaker correlation. Color represents relative expression level of individual probe sets as compared to the average expression of the no treatment controls. Red indicates up-regulation versus control; green indicates down-regulation versus control; black indicates no change.
  • FIG. 31 a-31 b: a. Hierarchical clustering of the relative expression of the top 25 most overexpressed type-I IFN inducible probe sets in whole blood ex vivo challenged with a variety of IFNα subtypes, IFNβ, IFNγ, and TNFα. b. Heatmap of the relative expression of the same 25 probe sets compared to no-treatment control in keratinocyte ex vivo challenged with IFNα2a, IFNβ, IFNγ, and TNFα. Red indicates upregulated gene expression relative to no treatment control, green indicates downregulated gene expression relative to no treatment control, black indicates no significant change in gene expression of challenged samples relative to control.
  • FIG. 32 a-32 c: The distribution of the average (a) and median (b) fold change of the top 25 most overexpressed type-I IFN inducible probe sets in 26 pairs of lesional skin compared to non-lesional skin. (c) the average of the average and median fold change of the top 25 most overexpressed type-I IFN inducible probe sets in 26 pairs of lesional and non-lesional skin.
  • FIG. 33 a-33 d: Relative expression of selected type-I IFN inducible genes ((a) HPSE, (b) OASL, and (c) HERC6) and non type-IFN inducible genes ((d) SERPINB4) in lesional skin (LS) compared to non-lesional skin (NS), and non-lesional skin compared to normal skin (NN) in psoriatic patients based on microarray data. The fold change of these genes in LS is compared to its paired NS, while NS is compared to the average of 21 normal skin controls. The p value for HPSE, OASL, HERC6, and SERPINB4 is a comparison between NS and NN, between LS and NS are (listed in pairs): 0.468, <0.00001; 0.376, <0.00001; 0.03, <0.00001; 0.0002, <0.00001.
  • FIG. 34 a-34 b: (a) Hierarchical clustering of all psoriasis samples profiled (21 normal (blue bars)) 26 paired non lesional (black bars) and lesional skin (red bars) from 24 psoriatic patients, and 3 lesional skin (red bars) from 3 psoriatic patients whose paired non lesional skin either did not yield sufficient cRNA for hybridization or scanned arrays had scaling factors that were more than 3 times the average) using the 164 upregulated type-I IFN inducible probe sets in lesional skin compared to those in mostly paired non-lesional skin. Each row corresponds to a single probe set, while each column corresponds to a single sample. The branch lengths indicate the degree of correlation with which samples are joined, with a longer branch indicating a weaker correlation. Color represents relative expression level of individual probe set as compared to the average expression of the 21 normals. Red represents upregulation vs. control and green represents downregulation vs. control. (b) PCA of all psoriasis samples profiled using the 164 upregulated type-I IFN inducible probe sets in lesional skin compared to those in mostly paired non-lesional skin. (PCA is calculated and data is visualized in Spotfire). Each circle represents one sample (blue circles=normal skin; black circles=non-lesional skin; red circles=lesional skin).
  • FIG. 35: Overexpression of selected type-I IFN inducible genes in 18 pairs of lesional and non-lesional skin from 18 psoriatic patients based on TAQMAN QRT-PCR assays using Fluidigm's BIOMARK™ 48.48 dynamic array.
  • FIG. 36 a-36 b: Correlation coefficient distribution of overexpressed genes in lesional skin of psoriatic patients between TAQMAN and array results. The genes are grouped based on correlation coefficient between TAQMAN QRT-PCR and microarray measurement. (a) correlation coefficient distribution of all 40 upregulated genes in lesional skin that are validated by TAQMAN QRT-PCR; (b) correlation coefficient distribution of 29 type-IFN inducible genes.
  • FIG. 37 a-37 d: Comparison of TAQMAN QRT-PCR based assay using BIOMARK™48.48 dynamic array and Affymetrix® GENECHIP microarray results for selected type-I IFN inducible genes ISG 15 and MX1.
  • FIG. 38: TAQMAN QRT-PCR validation of Affymetrix® GENECHIP microarray results of overexpression of type-I IFN inducible genes IFI27 and CXCL10.
  • FIG. 39 a-39 f: Ex vivo stimulation of normal keratinocytes with leukocyte IFN and IFNα2a and dose-dependent neutralization of type-I IFN induced genes by IFNα antibody. (a) neutralization of ISG15 overexpression in response to 350 I.U./mL IFNα2a, (b) neutralization of ISG 15 overexpression in response to 150 I.U./mL leukocyte IFN, (c) neutralization of USP18 overexpression in response to 350 I.U./mL IFNα2a, (d) neutralization of USP18 overexpression in response to 150 I.U./mL leukocyte IFN, (e) neutralization of IFIT2 overexpression in response to 350 I.U./mL IFNα2a, and (f) neutralization of IFIT2 overexpression in response to 150 I.U./mL leukocyte IFN. Each dose titration curve is generated on three technical replicates. The overexpression of individual genes with no IFNα antibody is normalized to 1.
  • FIG. 40 a-40 c: Relative expression of mRNA and median fold changes of type-I IFNα subtypes (FIG. 40 a), other members of the type-I IFNs (FIG. 40 b), and IFNα receptors (FIG. 40 c) in the lesional skin (LS) or the non-lesional skin (NS) compared to skin from healthy normal controls (NN). The averages of the relative mRNA levels of these cytokines and their receptors in the normal skin of two healthy donors were scaled to be 1 based on TAQMAN QRT-PCR assays using TLDA from Applied Biosciences. Black: the relative fold change of mRNA in the non-lesional skin compared to normal skin (NS/NN); Red: the relative fold change of mRNA in the lesional skin compared to normal skin (LS/NS). The p values for the overexpression of these individual genes in the non-lesional skin or lesional skin compared to healthy normal skin (listed in pairs) are as follows: IFNα1, 0.303, <0.001; IFNα2, 0.389, 0.072; IFNα5, <0.001, 0.002; IFNα6, 0.664, 0.093; IFNα7, 0.586, 0.077; IFNα8, 0.430, 0.049; IFNα14, 0.224, 0.049; IFNα17, 0.552, 0.0203; IFNα21, 0.113, 0.003; IFNβ3, 0.255, 0.022; IFNκ, 0.03, <0.001; IFNω, 0.516, 0.049; IFNAR1, 0.192, <0.001; IFNAR2, <0.001, <0.001, respectively.
  • FIG. 41: Relative expression of mRNA and median fold changes of IFNγ, TNFα, and IFNγ receptors in the lesional skin (LS), or the non-lesional skin (NS) compared to skin from healthy normal controls (NN). The averages of the relative mRNA levels of these cytokines and their receptors in the normal skin of two healthy donors were scaled to be 1 based on TAQMAN QRT-PCR assays using TLDA from Applied Biosciences. Black: the relative fold change of mRNA in the non-lesional skin compared to normal skin; Red: the relative fold change of mRNA in the lesional skin compared to normal skin. The p values for the overexpression of these individual genes in the non-lesional skin or lesional skin compared to healthy normal skin (listed in pairs) are as follows: IFNγ, 0.02, <0.001; IFNGR1, <0.001, <0.001; IFNGR2, <0.001, <0.001; TNFα, <0.001, <0.001, respectively.
  • FIG. 42: A Venn diagram illustrating both the number of probe sets that are altered by type I IFN, IFNγ, and TNFα during ex vivo stimulation, and probe sets that are altered in the lesional skin compared to non-lesional skin. Red numbers: probe sets that show increased expression with cytokine treatment or compared to non-lesional skin baseline; Green numbers: probe sets that show decreased expression with cytokine treatment or compared to non-lesional skin baseline. The intersecting regions represent the probe sets that are common to both comparisons.
  • FIGS. 43 a and 43 b: Co-overexpression type-I IFN, type-II IFN, and TNF-inducible genes in lesional/non-lesional skin of psoriatic patients based on Affymetrix GENECHIP® microarray results. The type-I IFN, type-II IFN, and TNFα inducible genes were selected based on ex vivo stimulation experiments (Examples 10 and 16). A probe set with an at least 2-fold change from non-lesional to lesion skin was considered overexpressed. (a) the number of up-regulated type I IFN, IFNγ, and TNFα inducible genes in the lesional skin shows strong correlation. (b) the number of type I IFN, IFNγ, and TNFα inducible genes in the lesional skin were significantly different amongst pairwise comparisons.
  • FIG. 44: Immunohistochemical analysis of biopsies from psoriatic skin, non-lesional skin and skin from normal donors. BDCA2 is a specific marker for pDCs which are present at greater numbers in lesional skin compared to non-lesional skin, and not at all in normal skin. CD83 is a marker for mDCs, CD4 is present on T cells and dendritic cells. STAT1 protein staining was observed in the epidermis of lesional skin (both nuclear and cytoplasmic) and dermal mononuclear inflammatory cells, but not in non-lesional or normal skin. ISG15 protein increase was observed in psoriatic skin and to a lesser extent in non-lesional skin, but was not detected in normal skin.
  • FIG. 45: A Venn diagram illustrating the number of probe sets that show altered expression at mRNA level in the lesional skin compared to non-lesional skin, or in the non-lesional skin compared to normal skin of psoriatic patients. Values shaded in red indicate the number of probe sets significantly upregulated while those values shaded in green indicate the number of probe sets significantly downregulated. The intersecting region represents probe sets that are common to both comparisons.
  • FIG. 46: Graphic representation of type-IFN signaling pathway that is activated in the lesional skin of psoriatic patients. Pathway image was generated with GeneGo's MetaCore integrated software suite. Individual symbols within the image represent well characterized proteins or protein complexes. Arrows linking the proteins represent the stimulatory, inhibitory, or interactive effect of the protein on the target protein. Thermometers adjacent to the individual symbols represent relative expression levels (red indicates overexpression, while green indicates underexpression) of transcripts that comprise the protein (or protein complex) within the particular pathway.
  • FIGS. 47 a and 47 b: Table providing fold change (fc; log 2 transformed) and q value (calculated by FDR) of the top 100 probe sets upregulated in the lesional skin compared to non-lesional skin in psoriasis. Also listed are the log 2 transformed fold change and q values of these genes when comparing non-lesional skin with healthy normal skin controls. Type I IFN inducible genes are listed in bold font.
  • FIG. 48: Distinctive separation of the lesional skin from non-lesional skin and normal skin—hierarchical clustering of all samples using transcript profiles of all genes on a whole genome (Affymetrix whole genome U133 plus v2.0 array) array.
  • FIG. 49 a-49 d: Probe sets identified as IFNγ inducible by overlap in FIG. 42. FIG. 49 b discloses “DEAD (Asp-Glu-Ala-Asp)” as SEQ ID NO: 1.
  • FIG. 50 a-50 b: Probe sets identified as TNFα inducible by overlap in FIG. 42.
  • FIG. 51 a-51 g: Probe sets identified as type I IFN inducible by overlap in FIG. 42. FIG. 51 c discloses “DEAD (Asp-Glu-Ala-Asp)” as SEQ ID NO: 1.
  • FIG. 52: Immunohistochemical analysis of biopsies from skin lesions of a placebo-treated SLE patient to detect pDC, mDC, and T cell infiltrates.
  • FIG. 53: Immunohistochemical analysis of biopsies from skin lesions of a placebo-treated SLE patient to detect HERC5, ISG15, and IP10 proteins, proteins expressed from type I IFN-induced genes.
  • FIG. 54: Immunohistochemical analysis of biopsies from skin lesions of an SLE patient treated with 10 mg/kg MEDI-545 to detect pDC, mDC, and T cell infiltrates.
  • FIG. 55: Immunohistochemical analysis of biopsies from skin lesions of an SLE patient treated with 10 mg/kg MEDI-545 to detect HERC5, ISG15, and IP10 proteins, proteins expressed from type I IFN-induced genes.
  • FIG. 56: Immunohistochemical analysis of biopsies from skin lesions of an SLE patient treated with 10 mg/kg MEDI-545 to detect pDC, mDC, and T cell infiltrates.
  • FIG. 57: Immunohistochemical analysis of biopsies from skin lesions of an SLE patient treated with 10 mg/kg MEDI-545 to detect HERC5, ISG15, and IP10 proteins, proteins expressed from type I IFN-induced genes.
  • FIGS. 58 a and 58 b: Heatmap (a) and PCA (b) showing neutralization of the top 25 type I IFN inducible genes in a skin biopsy of an SLE patient treated with 10 mg/kg MEDI-545 at 0 and 7 days post-dosing.
  • FIG. 59 a-d: Detection of type I and type II IFN activity in an IFN bioassay.
  • FIGS. 60 a and 60 b: Detection of MEDI-545 (a) and MEDI-546 (b)-mediated neutralization of IFNα activity in the IFN bioassay.
  • FIG. 61: Detection of anti-IFNγ-mediated neutralization of IFNγ activity in the IFN bioassay.
  • FIG. 62: Detection of anti-IFNω-mediated neutralization of IFNω activity in the IFN bioassay.
  • FIG. 63: Detection of anti-IFNβ-mediated neutralization of IFNβ activity in the IFN bioassay.
  • FIG. 64: Heat map showing modulation of gene expression in whole blood from healthy donors ex vivo stimulated with IFNγ, TNFα, or IFNα/β. Negative control (NT).
  • FIG. 65: Type I IFN-inducible genes were among the most upregulated genes in whole blood of SLE patients.
  • FIG. 66: IFNγ, IFNω, IFNAR1 and IFNAR2 mRNAs are upregulated in whole blood of lupus patients.
  • FIG. 67: Heat map showing modulation of gene expression in healthy donor PBMCs ex vivo stimulated with lupus patient serum.
  • FIGS. 68 a and 68 b: (A) PCA plot showing lupus patients having a strong/moderate type I IFN inducible signature (approximately 66% in this sampling) cluster together. (b) Table providing the 25 genes used for PCA analysis.
  • FIG. 69: Confirmation of overexpression of selected type-I IFN inducible genes in lupus patients based on TAQMAN QRT-PCR assays using Fluidigm's BIOMARK™48.48 dynamic array.
  • FIGS. 70 a and 70 b: (a) Ability of four different SLE patient serum samples to induce type I IFN activity in a reporter gene assay. (b) Number of transcripts induced at least 3-fold in healthy human PBMCs by each of the four different SLE patient serum samples following 4 hour co-incubation.
  • FIGS. 71 a and 71 b: The majority of genes neutralized by an anti-IFNα Ab 4 hours post co-incubation of SLE patient serum and healthy human PBMCs are type I IFN genes, while the majority of genes neutralized by the anti-IFNα Ab 18 hours post co-incubation of SLE patient serum and healthy human PBMCs are non-type I IFN genes as shown by (a) heatmap analysis and represented (b) in bar graphs.
  • FIGS. 72 a and 72 b: Provides the (a) type I IFN genes and (b) non-type I IFN genes that were upregulated and neutralized by an anti-IFNα Ab 18 hours post co-incubation of SLE patient serum and healthy human PBMCs, but that were not upregulated 4 hours post co-incubation of SLE patient serum and healthy human PBMCs.
  • FIG. 73: Provides pathways and cell processes neutralized by an anti-IFNα Ab 18 hours following co-incubation of SLE patient serum and healthy human PBMCs.
  • FIGS. 74 a and 74 b: Detection of (a) increased and (b) decreased levels of specific proteins in serum of lupus patients.
  • FIG. 75: QuantiGenePlex 1.0 analysis of IFN-inducible gene signatures from whole blood of 5 healthy donors stimulated with 20 IU/mL IFNα2b.
  • FIG. 76: Dose-dependent changes in gene expression in blood from a single healthy donor treated with multiple concentrations of IFNα2b.
  • FIG. 77: Detection of IFN-inducible transcripts in PAXgene-preserved whole blood samples from SLE subjects with and without detectable serum IFNα activity.
  • FIGS. 78 a and 78 b: Correlation between QuantiGenePlex and Fluidigm technologies in SLE PAXgene-preserved whole blood samples.
  • FIGS. 79 a and 79 b: Longitudinal testing of SLE samples following administration of an anti-IFNα monoclonal antibody: comparison of QuantiGenePlex 2.0 and Fluidigm technologies.
  • FIG. 80: Representative heat map visualizing the (in descending order) overexpression of type I IFN gene signature; overexpression of granulocyte signature; underexpression of T-cell signature, underexpression of NK-cell signature, and underexpression of B-cell signature, in whole blood from 46 SLE patients (indicated by red bar under the heat map) compared with whole blood from 24 healthy donors (indicated by blue bar under the heat map) IFN=interferon; SLE=systemic lupus erythematosus.
  • FIG. 81 a-81 c: Type I IFN-inducible genes in whole blood of SLE patients can be used to separate SLE patients with a type I IFN gene signature from healthy normal controls. (a) Three-dimensional PCA plot of whole blood from 46 SLE samples using a 114 type I IFN-inducible probe sets upregulated in whole blood of SLE patients compared with those from 24 healthy donors. (b) PCA plot of whole blood from 54 SLE patients in the prospective study using the 114 upregulated type I IFN-inducible probe set confirmed the overexpression of type I IFN gene signatures in SLE patients. (c) PCA plot of whole blood from 100 SLE samples in both discovery and prospective study using 21 upregulated type I IFN-inducible gene panel in SLE patients compared with 24 healthy donors. Each point represents one sample (blue dots, healthy normals; red dots, SLE patients). IFN=interferon; PCA=principal components analysis; SLE=systemic lupus erythematosus.
  • FIG. 82: Relative expression of mRNAs and median fold changes (horizontal bars) of TNF-α, IFN-γ, and IFN-γ receptors in whole blood of SLE patients compared with healthy controls (P<0.05 for all). Averages of relative mRNA levels of these cytokines and their receptors in whole blood from 24 healthy donors were scaled to 1 based on TAQMAN QRT-PCR assays. IFN=interferon; QRT-PCR=quantitative real-time reverse transcriptase polymerase chain reaction; SLE=systemic lupus erythematosus; TNF=tumor necrosis factor.
  • FIG. 83 a-83 c: TAQMAN QRT-PCR confirmed the overexpression of type I IFN-inducible genes in whole blood of SLE patients. (a) Relative fold changes of 15 type I IFN-inducible genes (generically labeled 1-15) in SLE patients were compared with healthy donors (p<0.05 for all). Averages of relative mRNA levels of genes in the pooled RNA from 24 healthy donors were scaled to 1 based on TAQMAN QRT-PCR assays. Horizontal bars represent average fold change. (b and c) TAQMAN QRT-PCR validation of overexpression of the 21-gene panel of type I IFN-inducible genes in whole blood of SLE patients as determined by whole genome array. The relative overexpression of 21 type I IFN-inducible genes in 2 SLE patients is shown via microarray (left) and TAQMAN QRT-PCR (right) assays. Correlation coefficients between TAQMAN QRT-PCR and microarray were 0.9861 and 0.9888 for patient X and Y, respectively. IFN=interferon; QRT-PCR=quantitative real-time reverse transcriptase polymerase chain reaction; SLE=systemic lupus erythematosus.
  • FIG. 84: Magnitude of overexpression of type I IFN gene signature in whole blood of SLE patients as measured by the median fold change of the 25 most overexpressed type I IFN-inducible genes or type I IFN gene signature score in individual SLE patients. The horizontal bars represent the median values. Patients whose type I IFN gene signature score was ≧10 were considered to have strong type I IFN gene signatures; those with scores between 4 and 10 were considered to have moderate type I IFN gene signatures, whereas those with scores ≦4 were considered to have weak type I IFN gene signatures. IFN=interferon; SLE=systemic lupus erythematosus.
  • FIG. 85 a-85 c: Stratification of 35 SLE patients into groups of low (a; green), moderate (b; gray), and high (c; red) type I IFN gene signature based on median fold change across the 21-gene panel of type I IFN-inducible genes. Densities for each SLE patient are calculated and graphed using the fold change for each of the 21 genes from each SLE patient on the log2 scale to provide a representation of the distribution of 21 genes fold change values. The vertical dashed lines partition the 3 classes of signature scores: 7 patients with a weak type I IFN gene signature=median fold change <1.91 (0.93 on log2 scale), 8 patients with a moderate type I IFN gene signature=median fold change between 1.91 and 5.53, and 20 patients with a strong type I IFN gene signature=median fold change >5.53 (2.47 on log2 scale). IFN=interferon; SLE=systemic lupus erythematosus.
  • FIG. 86: Dose-dependent neutralization of 21 upregulated IFN-α/β-inducible genes in SLE patients by MEDI-545.
  • FIGS. 87 a and 87 b: Heatmap (a) and PCA (b) showing neutralization of 21 upregulated IFN-α/β-inducible genes in whole blood of an SLE patient treated with 30 mg/kg MEDI-545 (0, 1, 4, 7, and 14 days post-dose).
  • FIGS. 88 a and 88 b: PCA plots prepared using the 21 upregulated IFN-α/β-inducible probe sets do not show IFN signature neutralization in placebo-treated patients.
  • FIG. 89: Neutralization of the 21 upregulated IFN-α/β-inducible probe sets in patients treated with 0.3, 1.0, 3.0, 10.0, and 30.0 mg/kg MEDI-545.
  • FIG. 90: Methodology for calculating target neutralization for FIG. 89.
    •  DETAILED DESCRIPTION
  • The invention encompasses methods of identifying, diagnosing, treating, and monitoring disease progression in patients. Patients include any animal having a type I IFN or an IFNα-inducible disease, disorder, or condition. The patient may have the disease, disorder, or condition as a result of experimental research, e.g., it may be an experimental model developed for the disease, disorder, or condition. Alternatively, the patient may have the disease, disorder, or condition in the absence of experimental manipulation. Patients include humans, mice, rats, horses, pigs, cats, dogs, and any animal used for research.
  • The patient may comprise a type I IFN or IFNα-inducible PD marker expression profile. The type I IFN or IFNα-inducible PD marker expression profile may be a strong profile, a moderate profile, or a weak profile. The type I IFN or IFNα-inducible PD marker expression profile can readily be designated as strong, moderate, or weak by determining the fold dysregulation of the type I IFN or IFNα-inducible PD marker expression profile of the patient, (e.g., the fold increase in expression of upregulated type I IFN or IFNα-inducible PD markers in the patient), relative to a control sample(s) or control patient(s) and comparing the patient's fold dysregulation to that of other patients having a type I IFN or IFNα-inducible PD marker expression profile. Fold dysregulation can be calculated by well known methods in the art as can the comparing. See, e.g., Example 8.
  • The type I IFN or IFNα-inducible PD marker expression profile may comprise upregulation of any group of genes or group of genes detected by the probes identified in Tables 19, 20, 21, 22, 23, 24, 26, 28, or 30. The group of genes or group of genes detected by the probes identified in Tables 19, 20, 21, 22, 23, 24, 26, 28 or 30 may include any at least 2, any at least 3, any at least 4, any at least 5, any at least 6, any at least 7, any at least 8, any at least 9, any at least 10, any at least 11, any at least 12, any at least 13, any at least 14, any at least 15, any at least 16, any at least 17, any at least 18, any at least 19, any at least 20, any at least 21, any at least 22, any at least 23, any at least 24, any at least 25, any at least 26, any at least 27, any at least 28, any at least 29, any at least 30, any at least 40, or any at least 50 of the genes or genes detected by the probes identified in the Tables.
  • The group of genes that may be included in the type I IFN or IFNα-inducible PD marker expression profile of the patient may be MX1, LY6E, IFI27, OAS1, IFIT1, IFI6, IFI44L, ISG15, LAMP3, OASL, RASD2, and IFI44. The genes or genes detected by the probes may include IFI44, IFI27, IFI44L, DNAPTP6, LAMP3, LY6E, RSAD2, HERC5, IFI6, ISG15, OAS3, SIGLEC1, OAS2, USP18, RTP4, IFIT1, MX1, OAS1, EPSTI1, PLSCR1, and IFRG28.
  • The genes may include any at least 2, any at least 3, any at least 4, any at least 5, any at least 6, any at least 7, any at least 8, any at least 9, any at least 10, or any at least 11, or any at least 12, or any at least 13, or any at least 14, or any at least 15, or any at least 16, or any at least 17, or any at least 18, or any at least 19, or at least 20, or any at least 21, or any at least 22, or any at least 23, or any at least 24, or any least 25, or any at least 26, or any at least 27, or any at least 28, or any at least 29, or any at least 30 of LAMP3, DNAPTP6, FLJ31033, HERC6, SERPING1, EPST11, RTP4, OASL, FBXO6, IFIT2, IFI44, OAS3, BATF2, ISG15, IRF7, RSAD2, IFI35, OAS1, LAP3, IFIT1, IFIT5, PLSCR1, IFI44L, MS4A4A, GALM, UBE2L6, TOR1B, SAMD9L, HERC5, TDRD7, TREX1, PARP12, and AXUD1.
  • The type I IFN or IFNα-inducible PD marker expression profile may contain upregulation of the entire group of genes or group of genes detected by the probes identified in one of Table 19, or Table 20, or Table 21, or Table 22, or Table 23, or Table 24, or Table 26, or Table 28, or Table 30 or may be any one or more of the genes identified in FIG. 72. The type I IFN or IFNα-inducible PD marker expression profile may include upregulation of all the genes identified in Table 24. The type I IFN or IFNα-inducible PD marker expression profile may include upregulation of the genes identified in FIG. 72 A or FIG. 72 b, or FIG. 72 a and FIG. 72 b.
  • The patient comprising the type I IFN or IFNα-inducible PD marker expression profile may further comprise downregulated type I IFN or IFNα PD marker(s). The downregulated PD markers may include any one, any two, any three, any four, any five, any six, any seven, any eight, any nine, any ten, any 15, any 20, any 25, any 30, any 35, any 40, any 45, or any 50 of the genes in Table 31 or any of CYP1B1, TGST1, RRAGD, IRS2, MGST1, TGFBR3, and RGS2.
  • The patient comprising the type I IFN or IFNα-inducible PD marker expression profile may further comprise upregulation of expression of any number of IFNα or type-I IFN subtypes. The IFNα or type-I IFN subtypes may include any more than one, more than two, more than three, more than four, more than five, more than six, more than seven, more than eight, more than nine, or more than ten IFNα or type-I IFN subtypes. These subtypes may include IFNα1, IFNα2, IFNα4, IFNα5, IFNα6, IFNα7, IFNα8, IFNα10, IFNα14, IFNα17, IFNα21, IFNβ, or IFNω. The patient may comprise upregulation of expression of IFN subtypes IFNα1, IFNα2, IFNα8, and IFNα14.
  • Alternatively, a patient treated in the methods encompassed by the invention may simply be one identified as comprising a gene expression profile with upregulation of expression of any number of IFNα or type-I IFN subtypes. The IFNα or type-I IFN subtypes may include any more than one, more than two, more than three, more than four, more than five, more than six, more than seven, more than eight, more than nine, or more than ten IFNα or type-I IFN subtypes. These subtypes may include IFNα1, IFNα2, IFNα4, IFNα5, IFNα6, IFNα7, IFNα8, IFNα10, IFNα14, IFNα17, IFNα21, IFNβ, or IFNω. These subtypes may include IFNα1, IFNα2, IFNα8, and IFNα14.
  • The patient comprising the type I IFN or IFNα-inducible PD marker expression profile may further comprise upregulation of expression of IFNα receptors, either IFNAR1 or IFNAR2, or both, or TNFα, or IFNγ, or IFNγ receptors (either IFNGR1, IFNGR2, or both IFNGR1 and IFNGR2). The patient may simply be identified as one who comprises upregulation of expression of IFNα receptors, either IFNAR1 or IFNAR2, or both, or TNFα, or IFNγ, or IFNγ receptors (either IFNGR1, IFNGR2, or both IFNGR1 and IFNGR2).
  • The upregulation or downregulation of the type I IFN or IFNα-inducible PD markers in the patient's expression profile may be by any degree relative to that of a sample from a control (which may be from a sample that is not disease tissue of the patient (e.g., non-lesional skin of a psoriasis patient) or from a healthy person not afflicted with the disease or disorder). The degree upregulation or downregulation may be at least 10%, at least 15%, at least 20%, at least 25%, at least 30%, at least 40%, at least 50%, at least 60%, at least 70%, at least 75%, at least 80%, at least 90%, at least 100%, at least 125%, at least 150%, or at least 200%, or at least 300%, or at least 400%, or at least 500% that of the control or control sample.
  • Furthermore, the patient may overexpress or have a tissue that overexpresses a type I IFN subtype at least 10%, at least 15%, at least 20%, at least 25%, at least 30%, at least 40%, at least 50%, at least 60%, at least 70%, at least 75%, at least 80%, at least 90%, at least 100%, at least 125%, at least 150%, or at least 200%, or at least 300%, or at least 400%, or at least 500% that of the control. The type I IFN subtype may be any one of IFNα1, IFNα2, IFNα4, IFNα5, IFNα6, IFNα7, IFNα8, IFNα10, IFNα14, IFNα17, IFNα21, IFNβ, or IFNω. The type I IFN subtypes may include all of IFNα1, IFNα2, IFNα8, and IFNα14.
  • The patient may further comprise or alternatively comprise alterations in levels of proteins in serum. The patient may have increased serum levels of proteins such as adiponectin, alpha-fetoprotein, apolipoprotein CIII, beta-2 microglobulin, cancer antigen 125, cancer antigen 19-9, eotaxin, FABP, factor VII, ferritin, IL-10, IL-12p70, IL-16, IL-18, IL-1ra, IL-3, MCP-1, MMP-3, myoglobin, SGOT, tissue factor, TIMP-1, TNF RII, TNF-alpha, VCAM-1, or vWF. The patient may have increased serum levels of any 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13 14, 15, 16, 17, 18, 19, 20, 21, o 22, 23, 24, 25, or 26 of these proteins in serum. The increased level may be at least 10%, at least 15%, at least 20%, at least 25%, at least 30%, at least 40%, at least 50%, at least 60%, at least 70%, at least 75%, at least 80%, at least 90%, at least 100%, at least 125%, at least 150%, or at least 200%, or at least 300%, or at least 400%, or at least 500% that of a control, e.g., a healthy subject. The alteration may be a decrease in serum levels of proteins such as BDNK, complement 3, CD40 ligand, EGF, ENA-78, EN-RAGE, IGF-1, MDC, myeloperoxidase, RANTES, or thrombopoietin, The patient may have decreased serum levels of any 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or 11 or these proteins. The decreased level may be at least 10%, at least 15%, at least 20%, at least 25%, at least 30%, at least 40%, at least 50%, at least 60%, at least 70%, at least 75%, at least 80%, at least 90%, or at least 100% that of a control, e.g., a healthy subject. The PD marker profile may comprise one or more of these increased or decreased serum levels of proteins.
  • The patient may further comprise auto-antibodies that bind to any one of the following auto-antigens: (a) Myxovirus (influenza virus) resistance 1, interferon-inducible protein p78; (b) surfeit 5, transcript variant c; (c) proteasome (posome, macropain) activator subunit 3 (PA28 gamma; Ki) transc; (d) retinoic acid receptor, alpha; (e) Heat shock 10 kDa protein 1 (chaperonin 10); (f) tropomyosin 3; (g) pleckstrin homology-like domain, family A, member 1; (h) cytoskeleton-associated protein 1; (i) Sjogren syndrome antigen A2 (60 kDa, ribonucleoprotein auto-antigen SS-A/Ro); (j) NADH dehydrogenase (ubiquinone) 1, alpha/beta subcomplex 1, 8 kDa; (k) NudE nuclear distribution gene E homolog 1 (A. nidulans); (l) MutL homolog 1, colon cancer, nonpolyposis type 2 (E. coli); (m) leucine rich repeat (in FLII) interacting protein 2; (n) tropomyosin 1 (alpha); (o) spastic paraplegia 20, spartin (Troyer syndrome); (p) preimplantation protein, transcript variant 1; (r) mitochondrial ribosomal protein L45; (s) Lin-28 homolog (C. elegans); (t) heat shock 90 kDa protein 1, alpha; (u) dom-3 homolog Z (C. elegans); (v) dynein, cytoplasmic, light intermediate polypeptide 2; (w) Ras-related C3 botulinum toxin substrate 1 (rho family, small GTP binding protein); (x) synovial sarcoma, X breakpoint 2, transcript variant 2; (y) moesin; (z) homer homolog (Drosophila), transcript variant 1; (aa) GCN5 general control of amino-acid synthesis 5-like 2 (yeast); (bb) eukaryotic translation elongation factor 1 gamma; (cc) eukaryotic translation elongation factor 1, delta; (dd) DNA-damage-inducible transcript 3; (ee) CCAAT/enhancer binding protein (C/EBP) gamma; and any other auto-antigen described in provisional application entitled “Auto-antibody markers of autoimmune disease” filed May 3, 2007 or in provisional application entitled “Auto-antibody markers of autoimmune disease” to be filed Nov. 6, 2007 (for example, but not limited to, those described on Tables 2, 4, 5, and 9). The patient may comprise auto-antibodies that bind to any number of these auto-antigens, e.g., any at least 2, at least 3, at least 4, at least 5, at least 6, at least 7, at least 8, at least 9 at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 20, at least 25.
  • A type I IFN or an IFNα-inducible disease, disorder, or condition is any that exhibits a type I IFN or an IFNα PD marker expression profile or gene signature. A PD marker expression profile and a gene signature will be understood to be equivalent. These diseases, disorders, or conditions include those with an autoimmune component such as systemic lupus erythematosus, insulin dependent diabetes mellitus, inflammatory bowel disease (including Crohn's disease, ulcerative colitis, and Celiac's disease), multiple sclerosis, psoriasis, autoimmune thyroiditis, rheumatoid arthritis, glomerulonephritis, idiopathic inflammatory myositis, Sjogren's syndrome, vasculitis, dermatomyositis, polymyositis, and sarcoidosis. Other diseases, disorders, or conditions include graft versus host disease and transplant rejection.
  • The patients may also exhibit any of a number of symptoms as discussed in, e.g., provisional patent application Methods of Treating Systemic Lupus Erythematosis filed Apr. 16, 2007, or may have a clinical SLEDAI score or BILAG score as discussed in the same. These symptoms may include fatigue, organ damage, malar rash, and alopecia. The patient may be scored using a known clinical scoring system, e.g., SLEDAI which is an index of SLE disease activity as measured and evaluated within the last 10 days (Bombardier C, Gladman D D, Urowitz M B, Caron D, Chang C H and the Committee on Prognosis Studies in SLE: Derivation of the SLEDAI for Lupus Patients. Arthritis Rheum 35:630-640, 1992.). Disease activity under the SLEDAI scoring system can range from 0 to 105. The following categories of SLEDAI activity have been defined: no activity (SLEDAI=0); mild activity (SLEDAI=1-5); moderate activity (SLEDAI=6-10); high activity (SLEDAI=11-19); very high activity (SLEDAI=20 or higher). (Griffiths, et al., Assessment of Patients with Systemic Lupus Erythematosus and the use of Lupus Disease Activity Indices). Another disease scoring index is the BILAG index which is an activity index of SLE that is based on specific clinical manifestations in eight organ systems: general, mucocutaneous, neurological, musculoskeletal, cardiovascular, respiratory, renal, and hematology results. Scoring is based on a letter system, but weighted numerical scores can also be assigned to each letter, making it possible to calculate a BILAG score in the range of 0-72. (Griffiths, et al., Assessment of Patients with Systemic Lupus Erythematosus and the use of Lupus Disease Activity Indices). Other scoring indices include the PGA score, the composite responder index (CRI), and the ANAM4™ test. The methods described herein, e.g., of treating an autoimmune disorder, may be used for any subject identified as having any activity level of disease activity as measured by any classification methodology known in the art, e.g., mild, moderate, high, or very high. The methods described herein, e.g., of treating an autoimmune disorder, may result in a decrease in a patient's symptoms or may result in an improvement in a score of disease for the patient's type I IFN or an IFNα-inducible disease, disorder, or condition.
  • A therapeutic agent may be administered to a patient or a patient may be identified as a candidate for administration of an agent or a therapeutic agent. A therapeutic agent is any molecule that binds to and modulates type I IFN or IFNα activity. The therapeutic agent may be a small molecule or a biological agent. If the therapeutic agent is a small molecule it may be synthesized or identified and isolated from a natural source.
  • If the therapeutic agent is a biological agent, it may be an antibody specific for any subtype(s) of type I IFN or IFNα. For instance, the antibody may be specific for any one of IFNα1, IFNα2, IFNα4, IFNα5, IFNα6, IFNα7, IFNα8, IFNα10, IFNα14, IFNα17, IFNα21, IFNβ, or IFNω. Alternatively, the antibody may be specific for any two, any three, any four, any five, any six, any seven, any eight, any nine, any ten, any eleven, any twelve type I IFN of IFNα subtypes. If the antibody is specific for more than one type I IFN subtype, the antibody may be specific for IFNα1, IFNα2, IFNα4, IFNα5, IFNα8, IFNα10, and IFNα21; or it may be specific for IFNα1, IFNα2, IFNα4, IFNα5, IFNα8, and IFNα10; or it may be specific for IFNα1, IFNα2, IFNα4, IFNα5, IFNα8, and IFNα21; or it may be specific for IFNα1, IFNα2, IFNα4, IFNα5, IFNα10, and IFNα21. Antibodies specific for type I IFN or IFNα include MEDI-545, any biologic or antibody other than MEDI-545, antibodies described in U.S. patent application Ser. No. 11/009,410 filed Dec. 10, 2004 which published as U.S. Patent Application Publication No. US20070014724 on Jan. 18, 2007 and issued as U.S. Pat. No. 7,741,449; and Ser. No. 11/157,494 filed Jun. 20, 2005 which published as U.S. Patent Application Publication No. US20060029601 on Feb. 9, 2006 and issued as U.S. Pat. No. 7,662,381, 9F3 and other antibodies described in U.S. Pat. No. 7,087,726 (Example 1 and Example 2, those disclosed in Table 3 and Table 4, and/or those disclosed in the table entitled “Deposit of Material” on lines 25-54, column 56), NK-2 and YOK5/19 (WO 84/03105), LO-22 (U.S. Pat. No. 4,902,618), 144 BS (U.S. Pat. No. 4,885,166), and EBI-1, EBI-2, and EBI-3 (EP 119476). A therapeutic agent that modulates IFNα activity may neutralize IFNα activity. One of skill in the art is well aware of preparation and formulation of such biological agents and methods of their administration.
  • The antibody may be a synthetic antibody, a monoclonal antibody, polyclonal antibodies, a recombinantly produced antibody, an intrabody, a multispecific antibody (including bi-specific antibodies), a human antibody, a humanized antibody, a chimeric antibody, a single-chain Fv (scFv) (including bi-specific scFv), a BiTE molecule, a single chain antibody, a Fab fragments, a F(ab′) fragment, a disulfide-linked Fv (sdFv), or an epitope-binding fragment of any of the above. The antibody may be any of an immunoglobulin molecule or immunologically active portion of an immunoglobulin molecule. Furthermore, the antibody may be of any isotype. For example, it may be any of isotypes IgG1, IgG2, IgG3 or IgG4. The antibody may be a full-length antibody comprising variable and constant regions, or an antigen-binding fragment thereof, such as a single chain antibody, or a Fab or Fab′2 fragment. The antibody may also be conjugated or linked to a therapeutic agent, such as a cytotoxin or a radioactive isotope.
  • In the methods of treatment a second agent other than the agent that binds to modulates IFNα activity may be administered to the patient. Second agents include, but are not limited to non-steroidal anti-inflammatory drugs such as ibuprofen, naproxen, sulindac, diclofenac, piroxicam, ketoprofen, diflunisal, nabumetone, etodolac, and oxaprozin, indomethacin; anti-malarial drugs such as hydroxychloroquine; corticosteroid hormones, such as prednisone, hydrocortisone, methylprednisolone, and dexamethasone; methotrexate; immunosuppressive agents, such as azathioprine and cyclophosphamide; and biologic agents that, e.g., target T cells such as Alefacept and Efalizumab, or target TNFα, such as, Enbrel, Remicade, and Humira.
  • Treatment with the agent may result in neutralization of the type I IFN or IFNα-inducible profile. Treatment with the agent may result in a decrease in one or more symptoms of the type I IFN or an IFNα-mediated disease or disorder. Treatment with the agent may result in fewer flare-ups related to the type I IFN or an IFNα-mediated disease or disorder. Treatment with the agent may result in improved prognosis for the patient having the type I IFN or an IFNα-mediated disease or disorder. Treatment with the agent may result in a higher quality of life for the patient. Treatment with the agent may alleviate the need to co-administer second agents or may lessen the dosage of administration of the second agent to the patient. Treatment with the agent may reduce the number of hospitalizations of the patient that are related to the type I IFN or an IFNα-mediated disease or disorder.
  • The agent that binds to and modulates type I IFN or IFNα activity may neutralize a type I IFN or IFNα-inducible profile. Neutralization of the type I IFN or IFNα-inducible profile may be a reduction in at least one, at least two, at least three, at least five, at least seven, at least eight, at least ten, at least twelve, at least fifteen, at least twenty, at least twenty five, at least thirty, at least thirty five, at least forty, at least forty five, or at least fifty genes up-regulated by type I IFN or IFNα. The genes upregulated by type I IFN or IFNα may be any group of genes in Tables 19, 20, 21, 22, 23, 24, 26, 28, or 30 as discussed above. Neutralization of the type I IFN or IFNα-inducible profile is a reduction of at least 2%, at least 3%, at least 4%, at least 5%, at least 7%, at least 8%, at least 10%, at least 15%, at least 25%, at least 30%, at least 35%, at least 40%, at least 45%, at least 50%, at least 60%, at least 70%, at least 75%, at least 80%, or at least 90% of any of the at least one, at least two, at least three, at least five, at least seven, at least eight, at least ten, at least twelve, at least fifteen, at least twenty, at least twenty five, at least thirty, at least thirty five, at least forty, at least forty five, or at least fifty genes up-regulated in any type I IFN or IFNα-inducible profile. Alternatively, neutralization of the type I IFN or IFNα-inducible profile refers to a reduction of expression of up-regulated type I IFN or IFNα-inducible genes that is within at most 50%, at most 45%, at most 40%, at most 35%, at most 30%, at most 25%, at most 20%, at most 15%, at most 10%, at most 5%, at most 4%, at most 3%, at most 2%, or at most 1% of expression levels of those type I IFN or IFNα-inducible genes in a control sample. If the agent that binds to and modulates type I IFN or IFNα activity is a biologic agent, such as an antibody, the agent may neutralize the type I IFN or IFNα profile at doses of 0.3 to 30 mg/kg, 0.3 to 10 mg/kg, 0.3 to 3 mg/kg, 0.3 to 1 mg/kg, 1 to 30 mg/kg, 3 to 30 mg/kg, 5 to 30 mg/kg, 10 to 30 mg/kg, 1 to 10 mg/kg, 3 to 10 mg/kg, or 1 to 5 mg/kg.
  • Neutralization of the type I IFN or IFNα-inducible profile may be increased expression of at least one, at least two, at least three, at least five, at least seven, at least eight, at least ten, at least twelve, at least fifteen, at least twenty, at least twenty five, at least thirty, at least thirty five, at least forty, at least forty five, or at least fifty genes whose expression is reduced by type I IFN or IFNα. The genes whose expression is reduced by type I IFN or IFNα may be any group of genes in Table 30. Neutralization of down-regulated genes in a type I IFN or IFNα-inducible profile is an increase of at least 2%, at least 3%, at least 4%, at least 5%, at least 7%, at least 8%, at least 10%, at least 15%, at least 25%, at least 30%, at least 35%, at least 40%, at least 45%, at least 50%, at least 60%, at least 70%, at least 75%, at least 80%, or at least 90%, or at least 100%, or at least 125%, or at least 130%, or at least 140%, or at least 150%, or at least 175%, or at least 200%, or at least 250%, or at least 300%, or at least 500% of any of the at least one, at least two, at least three, at least five, at least seven, at least eight, at least ten, at least twelve, at least fifteen, at least twenty, or at least twenty five genes whose expression is downregulated in any type I IFN or IFNα-inducible profile. Alternatively, neutralization of the type I IFN or IFNα-inducible profile refers to an increase in expression of type I IFN or IFNα-inducible genes to within at most 50%, at most 45%, at most 40%, at most 35%, at most 30%, at most 25%, at most 20%, at most 15%, at most 10%, at most 5%, at most 4%, at most 3%, at most 2%, or at most 1% of expression levels of those type I IFN or IFNα-inducible (downregulated) genes in a control sample. If the agent that binds to and modulates type I IFN or IFNα activity is a biologic agent, such as an antibody, the agent may neutralize the type I IFN or IFNα profile at doses of 0.3 to 30 mg/kg, 0.3 to 10 mg/kg, 0.3 to 3 mg/kg, 0.3 to 1 mg/kg, 1 to 30 mg/kg, 3 to 30 mg/kg, 5 to 30 mg/kg, 10 to 30 mg/kg, 1 to 10 mg/kg, 3 to 10 mg/kg, or 1 to 5 mg/kg.
  • The agent that binds to and modulates type I IFN or IFNα activity may further or alternatively neutralize expression of one or more type I IFN or IFNα subtypes. The IFNα or type-I IFN subtypes may include any more than one, more than two, more than three, more than four, more than five, more than six, more than seven, more than eight, more than nine, or more than ten IFNα or type-I IFN subtypes. These subtypes may include IFNα1, IFNα2, IFNα4, IFNα5, IFNα6, IFNα7, IFNα8, IFNα10, IFNα14, IFNα17, IFNα21, IFNβ, or IFNω. These subtypes may include all of IFNα1, IFNα2, IFNα8, and IFNα14. Alternatively, these subtypes may include IFNα1, IFNα2, IFNα4, IFNα5, IFNα8, IFNα10, IFNα21. Neutralization of the IFNα or type-I IFN subtypes may be a reduction of at least 2%, at least 3%, at least 4%, at least 5%, at least 7%, at least 8%, at least 10%, at least 15%, at least 25%, at least 30%, at least 35%, at least 40%, at least 45%, at least 50%, at least 60%, at least 70%, at least 75%, at least 80%, or at least 90% of any of the at least one, at least two, at least three, at least five, at least seven, at least eight, or at least ten of the subtypes. Neutralization of the IFNα or type-I IFN subtypes may be a reduction in expression of IFNα or type-I IFN subtype genes that is within at most 50%, at most 45%, at most 40%, at most 35%, at most 30%, at most 25%, at most 20%, at most 15%, at most 10%, at most 5%, at most 4%, at most 3%, at most 2%, or at most 1% of expression levels of those IFNα or type I IFN subtypes in a control sample. If the agent that binds to and modulates IFNα activity or type I IFN activity is a biologic agent, such as an antibody, the agent may neutralize the IFNα or type I IFN subtypes at doses of 0.3 to 30 mg/kg, 0.3 to 10 mg/kg, 0.3 to 3 mg/kg, 0.3 to 1 mg/kg, 1 to 30 mg/kg, 3 to 30 mg/kg, 5 to 30 mg/kg, 10 to 30 mg/kg, 1 to 10 mg/kg, 3 to 10 mg/kg, or 1 to 5 mg/kg.
  • The agent that binds to and modulates type I IFN or IFNα activity may further or alternatively neutralize expression of IFNα receptors, either IFNAR1 or IFNAR2, or both, or TNFα, or IFNγ, or IFNγ receptors (either IFNGR1, IFNGR2, or both IFNGR1 and IFNGR2). Neutralization of expression of IFNα receptors, either IFNAR1 or IFNAR2, or both, or TNFα, or IFNγ, or IFNγ receptors (either IFNGR1, IFNGR2, or both IFNGR1 and IFNGR2) may be a reduction of at least 2%, at least 3%, at least 4%, at least 5%, at least 7%, at least 8%, at least 10%, at least 15%, at least 25%, at least 30%, at least 35%, at least 40%, at least 45%, at least 50%, at least 60%, at least 70%, at least 75%, at least 80%, or at least 90% of any of the at least one, at least two, at least three, at least five, or at least six of these genes. Neutralization of expression of IFNα receptors, either IFNAR1 or IFNAR2, or TNFα, or IFNγ, or IFNγ receptors (either IFNGR1, IFNGR2, or both IFNGR1 and IFNGR2) is a reduction of expression of at most 50%, at most 45%, at most 40%, at most 35%, at most 30%, at most 25%, at most 20%, at most 15%, at most 10%, at most 5%, at most 4%, at most 3%, at most 2%, or at most 1% of expression levels of these genes in a control sample. If the agent that binds to and modulates type I IFN or IFNα activity is a biologic agent, such as an antibody, the agent may neutralize expression of IFNα receptors IFNAR1 or IFNAR2, or TNFα, or IFNγ, or IFNγ receptors IFNGR1 or IFNGR2 at doses of 0.3 to 30 mg/kg, 0.3 to 10 mg/kg, 0.3 to 3 mg/kg, 0.3 to 1 mg/kg, 1 to 30 mg/kg, 3 to 30 mg/kg, 5 to 30 mg/kg, 10 to 30 mg/kg, 1 to 10 mg/kg, 3 to 10 mg/kg, or 1 to 5 mg/kg.
  • The agent that binds to and modulates type I IFN or IFNα activity may further or alternatively neutralize alterations of levels of proteins in serum, e.g., increase levels of those proteins whose serum levels are downregulated or decrease levels of those proteins whose serum levels are upregulated to levels closer to those of control subjects. Neutralization of expression of proteins in serum, such as adiponectin, alpha-fetoprotein, apolipoprotein CIII, beta-2 microglobulin, cancer antigen 125, cancer antigen 19-9, eotaxin, FABP, factor VII, ferritin, IL-10, IL-12p70, IL-16, IL-18, IL-1ra, IL-3, MCP-1, MMP-3, myoglobin, SGOT, tissue factor, TIMP-1, TNF RII, TNF-alpha, VCAM-1, vWF, BDNK, complement 3, CD40 ligand, EGF, ENA-78, EN-RAGE, IGF-1, MDC, myeloperoxidase, RANTES, or thrombopoietin may be by bringing the level of at least one, at least two, at least three, at least five, at least six, at least seven, at least eight, at least nine, at least ten, at least twelve, at least fifteen, at least twenty, or at least 25 of these proteins to within at least 2%, at least 3%, at least 4%, at least 5%, at least 7%, at least 8%, at least 10%, at least 15%, at least 25%, at least 30%, at least 35%, at least 40%, at least 45%, at least 50%, at least 60%, at least 70%, at least 75%, at least 80%, or at least 90% levels of the protein in serum of a healthy subject. If the agent that binds to and modulates type I IFN or IFNα activity is a biologic agent, such as an antibody, the agent may neutralize levels of the serum proteins, e.g., adiponectin, alpha-fetoprotein, apolipoprotein CIII, beta-2 microglobulin, cancer antigen 125, cancer antigen 19-9, eotaxin, FABP, factor VII, ferritin, IL-10, IL-12p70, IL-16, IL-18, IL-1ra, IL-3, MCP-1, MMP-3, myoglobin, SGOT, tissue factor, TIMP-1, TNF RII, TNF-alpha, VCAM-1, vWF, BDNK, complement 3, CD40 ligand, EGF, ENA-78, EN-RAGE, IGF-1, MDC, myeloperoxidase, RANTES, or thrombopoietin, at doses of 0.3 to 30 mg/kg, 0.3 to 10 mg/kg, 0.3 to 3 mg/kg, 0.3 to 1 mg/kg, 1 to 30 mg/kg, 3 to 30 mg/kg, 5 to 30 mg/kg, 10 to 30 mg/kg, 1 to 10 mg/kg, 3 to 10 mg/kg, or 1 to 5 mg/kg.
  • The agent that binds to and modulates type I IFN or IFNα activity may further or alternatively reduce number or level of auto-antibodies that bind to any one, any at least 2, any at least 3, any at least 4, any at least 5, any at least 6, any at least 7, any at least 8, any at least 9, any at least 10, any at least 15, or any at least 20 of the following auto-antigens: (a) Myxovirus (influenza virus) resistance 1, interferon-inducible protein p78; (b) surfeit 5, transcript variant c; (c) proteasome (posome, macropain) activator subunit 3 (PA28 gamma; Ki) transc; (d) retinoic acid receptor, alpha; (e) Heat shock 10 kDa protein 1 (chaperonin 10); (f) tropomyosin 3; (g) pleckstrin homology-like domain, family A, member 1; (h) cytoskeleton-associated protein 1; (i) Sjogren syndrome antigen A2 (60 kDa, ribonucleoprotein auto-antigen SS-A/Ro); (j) NADH dehydrogenase (ubiquinone) 1, alpha/beta subcomplex 1, 8 kDa; (k) NudE nuclear distribution gene E homolog 1 (A. nidulans); (l) MutL homolog 1, colon cancer, nonpolyposis type 2 (E. coli); (m) leucine rich repeat (in FLII) interacting protein 2; (n) tropomyosin 1 (alpha); (o) spastic paraplegia 20, spartin (Troyer syndrome); (p) preimplantation protein, transcript variant 1; (r) mitochondrial ribosomal protein LA5; (s) Lin-28 homolog (C. elegans); (t) heat shock 90 kDa protein 1, alpha; (u) dom-3 homolog Z (C. elegans); (v) dynein, cytoplasmic, light intermediate polypeptide 2; (w) Ras-related C3 botulinum toxin substrate 1 (rho family, small GTP binding protein); (x) synovial sarcoma, X breakpoint 2, transcript variant 2; (y) moesin; (z) homer homolog (Drosophila), transcript variant 1; (aa) GCN5 general control of amino-acid synthesis 5-like 2 (yeast); (bb) eukaryotic translation elongation factor 1 gamma; (cc) eukaryotic translation elongation factor 1, delta; (dd) DNA-damage-inducible transcript 3; (ee) CCAAT/enhancer binding protein (C/EBP) gamma; and any other auto-antigen described in provisional application entitled “Auto-antibody markers of autoimmune disease” filed May 3, 2007; and any other auto-antigen described in provisional application entitled “Auto-antibody markers of autoimmune disease” filed Nov. 6, 2007 (for example, but not limited to, those described on Tables 2, 4, 5, and 9). Reduction in level of auto-antibody may be a reduction of at least 2%, at least 3%, at least 4%, at least 5%, at least 7%, at least 8%, at least 10%, at least 15%, at least 25%, at least 30%, at least 35%, at least 40%, at least 45%, at least 50%, at least 60%, at least 70%, at least 75%, at least 80%, or at least 90% in presence of any of the auto-antibodies. If the agent that binds to and modulates type I IFN or IFNα activity is a biologic agent, such as an antibody, the agent may reduce number or level or auto-antibodies at doses of 0.3 to 30 mg/kg, 0.3 to 10 mg/kg, 0.3 to 3 mg/kg, 0.3 to 1 mg/kg, 1 to 30 mg/kg, 3 to 30 mg/kg, 5 to 30 mg/kg, 10 to 30 mg/kg, 1 to 10 mg/kg, 3 to 10 mg/kg, or 1 to 5 mg/kg.
  • The agent that binds to and modulates type I IFN or IFNα activity may not neutralize expression of genes that are not included in an interferon-inducible signature or PD marker profile.
  • Samples may also be obtained from patients in the methods of the invention. Samples include any biological fluid or tissue, such as whole blood, saliva, urine, synovial fluid, bone marrow, cerebrospinal fluid, nasal secretions, sputum, amniotic fluid, bronchoalveolar lavage fluid, peripheral blood mononuclear cells, total white blood cells, lymph node cells, spleen cells, tonsil cells, or skin. The samples may be obtained by any means known in the art.
  • IFNα-inducible PD marker expression profiles may include up-regulated expression or activity of genes in cells exposed to elevated IFNα levels relative to baseline. Up-regulated expression or activity of genes includes an increase in expression of mRNA from a gene, an increase in expression of a protein encoded by a gene, or an increase in activity of a protein encoded by a gene. The expression or activity of the genes may be up-regulated as a direct or indirect response to IFNα.
  • The up-regulated expression or activity of any gene detected in a sample, by probes, or by probes in kits in an IFNα-inducible PD marker expression profile may be at least 1.2-fold, at least 1.25-fold, at least 1.3-fold, at least 1.4-fold, at least 1.5-fold, at least 2.0-fold, at least 2.25-fold, at least 2.5-fold, at least 2.75-fold, at least 3.0-fold, at least 3.5-fold, at least 4.0-fold, at least 4.5-fold, at least 5.0-fold, at least 6.0-fold, at least 7.0-fold, at least 8.0-fold, at least 9.0-fold, at least 10.0-fold, at least 15.0-fold, at least 20.0-fold, at least 25.0-fold, or at least 50.0-fold relative to baseline levels of control cells, e.g., cells of healthy volunteers or cells of control animals or cells not exposed to IFNα in culture. All of the genes in the IFNα-inducible PD marker expression profile may have up-regulated expression or activity at the same fold increase. Alternatively, the genes in the PD marker expression profile may have varying levels of up-regulated expression or activity.
  • The down-regulated expression or activity of any gene detected in a sample, by probes, or by probes in kits in an IFNα-inducible PD marker expression profile may be at least 5%, at least 10%, at least 15%, at least 20%, at least 25%, at least 30%, at least 35%, at least 40%, at least 45%, at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% relative to baseline levels of control cells, e.g., cells of healthy volunteers or cells of control animals or cells not exposed to IFNα in culture. All of the genes in the IFNα-inducible PD marker expression profile may have down-regulated expression or activity at the same fold decrease. Alternatively, the genes in the PD marker expression profile may have varying levels of down-regulated expression or activity.
  • The number of genes included in IFNα-inducible PD marker expression profile may be at least 2, at least 3, at least 4, at least 5, at least 10, at least 20, at least 25 at least 30, at least 50, at least 75, at least 100, at least 150, at least 200, at least 250, at least 300, at least 400, at least 500, at least 750, at least 1000, at least 1500, at least 2000, at least 2500, at least 5000, at least 10000, or at least 15000 genes. These genes may include those listed in Tables 19 and/or 20 and/or 21 and/or 22 and/or 23 and/or 24 and/or 26 and/or 28 and/or 30 and/or 31 and/or any of the genes identified in FIG. 72, 74, 75, or 77. The genes included in IFNα-inducible PD marker expression profile may be up-regulated genes, down-regulated genes, or a combination of up- and down-regulated genes.
  • The genes included in the IFNα-inducible PD marker expression profile may be the genes provided in Tables 19 and/or 20 and/or 21 and/or 22 and/or 23 and/or 24 and/or 26 and/or 28 and/or 30 and/or 31 and/or any of the genes identified in FIG. 72, 74, 75, or 77. The genes included in the IFNα-inducible PD marker expression profile may consist of or comprise at least 10%, at least 20%, at least 25%, at least 30%, at least 40%, at least 50%, at least 60%, at least 75%, at least 80%, at least 85% at least 90%, at least 95%, or at least 100% of the genes provided in Tables 19 and/or 20 and/or 21 and/or 22 and/or 23 and/or 24 and/or 26 and/or 28 and/or 30 and/or 31 and/or any of the genes identified in FIG. 72, 74, 75, or 77.
  • The IFNα-inducible PD markers in an expression profile may include any at least 5 genes such as, for example: MX1, LLY6E, IFI27, OAS1, IFIT1; or MX1, LLY6E, IFI27, OAS1, IFI6; or MX1, LLY6E, IFI27, OAS1, IFI44L; or MX1, LLY6E, IFI27, OAS1, ISG15; or MX1, LLY6E, IFI27, OAS1, LAMP3; or MX1, LLY6E, IFI27, OAS1, OASL; or MX1, LLY6E, IFI27, OAS1, RSAD2; or MX1, LLY6E, IFI27, OAS1, IFI44; or MX1, LLY6E, IFI27, OAS1, IFIT2; or MX1, LLY6E, IFI27, OAS1, OAS3; or MX1, LLY6E, IFI27, OAS1, USP18; or MX1, LLY6E, IFI27, OAS1, SIGLEC1; or MX1, LLY6E, IFI27, OAS1, HERC5; or MX1, LLY6E, IFI27, OAS1, DNAPTP6; or MX1, LLY6E, IFI27, OAS1, LOC129607; or MX1, LLY6E, IFI27, OAS1, EPSTI1; or MX1, LLY6E, IFI27, OAS1, BIRC4BP; or MX1, LLY6E, IFI27, OAS1, SIGLEC1; or MX1, LLY6E, IFI27, OAS1, gene detected by probe 229450_at; or MX1, LLY6E, IFI27, OAS1, gene detected by probe 235276_at; or LLY6E, IFI27, OAS1, IFIT1, IFI6; or LLY6E, IFI27, OAS1, IFIT1, IFI44L; or LLY6E, IFI27, OAS1, IFIT1, ISG15; or LLY6E, IFI27, OAS1, IFIT1, LAMP3; or LLY6E, IFI27, OAS1, IFIT1, OASL; or LLY6E, IFI27, OAS1, IFIT1, RSAD2; or LLY6E, IFI27, OAS1, IFIT1, IFI44; or LLY6E, IFI27, OAS1, IFIT1, IFIT2; or LLY6E, IFI27, OAS1, IFIT1, OAS3; or LLY6E, IFI27, OAS1, IFIT1, USP18; or LLY6E, IFI27, OAS1, IFIT1, SIGLEC1; or LLY6E, IFI27, OAS1, IFIT1, HERC5; or LLY6E, IFI27, OAS1, IFIT1, DNAPTP6; or LLY6E, IFI27, OAS1, IFIT1, LOC129607; or LLY6E, IFI27, OAS1, IFIT1, EPSTI1; or LLY6E, IFI27, OAS1, IFIT1, BIRC4BP; or LLY6E, IFI27, OAS1, IFIT1, SIGLEC1; or LLY6E, IFI27, OAS1, IFIT1, gene detected by probe 229450_at; or LLY6E, IFI27, OAS1, IFIT1, gene detected by probe 235276_at; or IFI27, OAS1, IFIT1, IFI6, IFI44L, ISG15; or IFI27, OAS1, IFIT1, IFI6, LAMP3; or IFI27, OAS1, IFIT1, IFI6, OASL; or IFI27, OAS1, IFIT1, IFI6, RSAD2; or IFI27, OAS1, IFIT1, IFI6, IFI44; or IFI27, OAS1, IFIT1, IFI6, IFIT2; or IFI27, OAS1, IFIT1, IFI6, OAS3; or IFI27, OAS1, IFIT1, IFI6, USP18; or IFI27, OAS1, IFIT1, IFI6, SIGLEC1; or IFI27, OAS1, IFIT1, IFI6, HERC5; or IFI27, OAS1, IFIT1, IFI6, DNAPTP6; or IFI27, OAS1, IFIT1, IFI6, LOC129607; or IFI27, OAS1, IFIT1, IFI6, EPSTI1; or IFI27, OAS1, IFIT1, IFI6, BIRC4BP; or IFI27, OAS1, IFIT1, IFI6, SIGLEC1; or IFI27, OAS1, IFIT1, IFI6, gene detected by probe 229450_at; or IFI27, OAS1, IFIT1, IFI6, gene detected by probe 235276_at; or OAS1, IFIT1, IFI6, IFI44L, ISG15; or OAS1, IFIT1, IFI6, IFI44L, LAMP3; or OAS1, IFIT1, IFI6, IFI44L, OASL; or OAS1, IFIT1, IFI6, IFI44L, RSAD2; or OAS1, IFIT1, IFI6, IFI44L, IFI44; or OAS1, IFIT1, IFI6, IFI44L, IFIT2; or OAS1, IFIT1, IFI6, IFI44L, OAS3; or OAS1, IFIT1, IFI6, IFI44L, USP18; or OAS1, IFIT1, IFI6, IFI44L, SIGLEC1; or OAS1, IFIT1, IFI6, IFI44L, HERC5; or OAS1, IFIT1, IFI6, IFI44L, DNAPTP6; or OAS1, IFIT1, IFI6, IFI44L, LOC129607; or OAS1, IFIT1, IFI6, IFI44L, EPSTI1; or OAS1, IFIT1, IFI6, IFI44L, BIRC4BP; or OAS1, IFIT1, IFI6, IFI44L, SIGLEC1; or OAS1, IFIT1, IFI6, IFI44L, gene detected by probe 229450_at; or OAS1, IFIT1, IFI6, IFI44L, gene detected by probe 235276_at; or IFIT1, IFI6, IFI44L, ISG15, LAMP3; or IFIT1, IFI6, IFI44L, ISG15, OASL; or IFIT1, IFI6, IFI44L, ISG15, RSAD2; or IFIT1, IFI6, IFI44L, ISG15, IFI44; or IFIT1, IFI6, IFI44L, ISG15, IFIT2 or IFIT1, IFI6, IFI44L, ISG15, OAS3; or IFIT1, IFI6, IFI44L, ISG15, USP18; or IFIT1, IFI6, IFI44L, ISG15, SIGLEC1; or IFIT1, IFI6, IFI44L, ISG15, HERC5; or IFIT1, IFI6, IFI44L, ISG15, DNAPTP6; or IFIT1, IFI6, IFI44L, ISG15, LOC129607; or IFIT1, IFI6, IFI44L, ISG15, EPSTI1; or IFIT1, IFI6, IFI44L, ISG15, BIRC4BP; or IFIT1, IFI6, IFI44L, ISG15, gene detected by probe 229450_at; or IFIT1, IFI6, IFI44L, ISG15, gene detected by probe 235276_at; or IFI6, IFI44L, ISG155, LAMP3, HERC5; or IFI6, IFI44L, ISG155, LAMP3, DNAPTP6; or IFI6, IFI44L, ISG155, LAMP3, LOC129607; or IFI6, IFI44L, ISG155, LAMP3, EPSTI1; or IFI6, IFI44L, ISG155, LAMP3, BIRC4BP; or IFI6, IFI44L, ISG155, LAMP3, gene detected by probe 229450_at; or IFI6, IFI44L, ISG15, LAMP3, gene detected by probe 23527_at; or IFI6, IFI44L, ISG155, LAMP3, SIGLEC11; or IFI6, IFI44L, ISG155, LAMP3, USP18; or IFI6, IFI44L, ISG15, LAMP3, OAS3; or IFI6, IFI44L, ISG15, LAMP3, IFIT2; or IFI6, IFI44L, ISG155, LAMP3, IFI44; or IFI6, IFI44L, ISG 15, LAMP3, RSAD2; or IFI6, IFI44L, ISG15, LAMP3, OASL; or IFI44L, ISG15, LAMP3, OASL, RSAD2; or IFI44L, ISG15, LAMP3, OASL, IFI44; or IFI44L, ISG15, LAMP3, OASL, IFIT2; or IFI44L, ISG15, LAMP3, OASL, OAS3; or IFI44L, ISG15, LAMP3, OASL, USP18; or IFI44L, ISG15, LAMP3, OASL, SIGLEC1; or IFI44L, ISG15, LAMP3, OASL, HERC5; or IFI44L, ISG15, LAMP3, OASL, DNAPTP6; or IFI44L, ISG15, LAMP3, OASL, LOC129607; or IFI44L, ISG15, LAMP3, OASL, EPSTI1;or IFI44L, ISG15, LAMP3, OASL, BIRC4BP; or IFI44L, ISG15, LAMP3, OASL, gene detected by probe 22945_at; or IFI44L, ISG15, LAMP3, OASL, gene detected by probe 23527_at; or ISG15, LAMP3, OASL, RSAD2, IFI44; or ISG15, LAMP3, OASL, RSAD2, IFIT2; or ISG15, LAMP3, OASL, RSAD2, OAS3; or ISG15, LAMP3, OASL, RSAD2, USP18; or ISG15, LAMP3, OASL, RSAD2, SIGLEC1; or ISG15, LAMP3, OASL, RSAD2, HERC5; or ISG15, LAMP3, OASL, RSAD2, DNAPTP6; or ISG15, LAMP3, OASL, RSAD2, LOC129607; or ISG15, LAMP3, OASL, RSAD2, EPSTI1; or ISG15, LAMP3, OASL, RSAD2, BIRC4BP; or ISG15, LAMP3, OASL, RSAD2, gene detected by probe 22945_at; or ISG15, LAMP3, OASL, RSAD2, gene detected by probe 23527_at; or LAMP3, OASL, RSAD2, IFI44, IFIT2; or LAMP3, OASL, RSAD2, IFI44, OAS3; or LAMP3, OASL, RSAD2, IFI44, USP18; or LAMP3, OASL, RSAD2, IFI44, SIGLEC1; or LAMP3, OASL, RSAD2, IFI44, HERC5; or LAMP3, OASL, RSAD2, IFI44, DNAPTP6; or LAMP3, OASL, RSAD2, IFI44, LOC129607; or LAMP3, OASL, RSAD2, IFI44, EPSTI1; or LAMP3, OASL, RSAD2, IFI44, BIRC4BP; or LAMP3, OASL, RSAD2, IFI44, gene detected by probe 22945_at; or LAMP3, OASL, RSAD2, IFI44, gene detected by probe 23527_at; or OASL, RSAD2, IFI44, IFIT2, OAS3; or OASL, RSAD2, IFI44, IFIT2, USP18; or OASL, RSAD2, IFI44, IFIT2, SIGLEC1; or OASL, RSAD2, IFI44, IFIT2, HERC5; or OASL, RSAD2, IFI44, IFIT2, DNAPTP6; or OASL, RSAD2, IFI44, IFIT2, LOC129607; or OASL, RSAD2, IFI44, IFIT2, EPSTI1; or OASL, RSAD2, IFI44, IFIT2, BIRC4BP; or OASL, RSAD2, IFI44, IFIT2, gene detected by probe 22945_at; or OASL, RSAD2, IFI44, IFIT2, gene detected by probe 23527_at; or RSAD2, IFI44, IFIT2, OAS3, USP18; or RSAD2, IFI44, IFIT2, OAS3, SIGLEC1; or RSAD2, IFI44, IFIT2, OAS3, HERC5; or RSAD2, IFI44, IFIT2, OAS3, DNAPTP6; or RSAD2, IFI44, IFIT2, OAS3, LOC129607; or RSAD2, IFI44, IFIT2, OAS3, EPSTI1; or RSAD2, IFI44, IFIT2, OAS3, BIRC4BP; or RSAD2, IFI44, IFIT2, OAS3, gene detected by probe 22945_at; or RSAD2, IFI44, IFIT2, OAS3, gene detected by probe 23527_at; or IFI44, IFIT2, OAS3, USP18, SIGLEC1; or IFI44, IFIT2, OAS3, USP18, HERC5; or IFI44, IFIT2, OAS3, USP18, DNAPTP6; or IFI44, IFIT2, OAS3, USP18, LOC129607; or IFI44, IFIT2, OAS3, USP18, EPSTI1; or IFI44, IFIT2, OAS3, USP18, BIRC4BP; or IFI44, IFIT2, OAS3, USP18, gene detected by probe 22945_at; or IFI44, IFIT2, OAS3, USP18, gene detected by probe 23527_at; or IFIT2, OAS3, USP18, SIGLEC1, HERC5; or IFIT2, OAS3, USP18, SIGLEC1, DNAPTP6; or IFIT2, OAS3, USP18, SIGLEC1, LOC129607; or IFIT2, OAS3, USP18, SIGLEC1, EPSTI1; or IFIT2, OAS3, USP18, SIGLEC1, BIRC4BP; or IFIT2, OAS3, USP18, SIGLEC1, gene detected by probe 22945_at; or IFIT2, OAS3, USP18, SIGLEC1, gene detected by probe 23527_at; or OAS3, USP18, SIGLEC1, HERC5, DNAPTP6; or OAS3, USP18, SIGLEC1, HERC5, LOC129607; or OAS3, USP18, SIGLEC1, HERC5, EPSTI1; or OAS3, USP18, SIGLEC1, HERC5, BIRC4BP; or OAS3, USP18, SIGLEC1, HERC5, gene detected by probe 22945_at; or OAS3, USP18, SIGLEC1, HERC5, gene detected by probe 23527_at; or USP18, SIGLEC1, HERC5, DNAPTP6, LOC129607; or USP18, SIGLEC1, HERC5, DNAPTP6, EPSTI1; or USP18, SIGLEC1, HERC5, DNAPTP6, BIRC4BP; or USP18, SIGLEC1, HERC5, DNAPTP6, gene detected by probe 22945_at; or USP18, SIGLEC1, HERC5, DNAPTP6, gene detected by probe 23527_at; or SIGLEC1, HERC5, DNAPTP6, LOC129607, EPSTI1; or SIGLEC1, HERC5, DNAPTP6, LOC129607, BIRC4BP; or SIGLEC1, HERC5, DNAPTP6, LOC129607, gene detected by probe 22945_at; or SIGLEC1, HERC5, DNAPTP6, LOC129607, gene detected by probe 23527_at; or HERC5, DNAPTP6, LOC129607, EPSTI1, BIRC4BP; or HERC5, DNAPTP6, LOC129607, EPSTI1, gene detected by probe 22945_at; or HERC5, DNAPTP6, LOC129607, EPSTI1, gene detected by probe 23527_at; or DNAPTP6, LOC129607, EPSTI1, BIRC4BP, gene detected by probe 22945_at; or DNAPTP6, LOC129607, EPSTI1, BIRC4BP, gene detected by probe 23527_at; or LOC129607, EPSTI1, BIRC4BP, gene detected by probe 22945_at, gene detected by probe 23527_at. The IFNα-inducible PD markers in such an expression profile may further include at least one or more gene listed in Tables 19 and/or 20 and/or 21 and/or 22 and/or 23 and/or 24 and/or 26 and/or 28 and/or 30.
  • The IFNα-inducible PD markers in an expression profile may include any at least 6 genes such as, for example: MX1, LLY6E, IFI27, OAS1, IFIT1, IFI6; or MX1, LLY6E, IFI27, OAS1, IFIT1, IFI44L; or MX1, LLY6E, IFI27, OAS1, IFIT1, ISG15; or MX1, LLY6E, IFI27, OAS1, IFIT1, LAMP3; or MX1, LLY6E, IFI27, OAS1, IFIT1, OASL; or MX1, LLY6E, IFI27, OAS1, IFIT1, RSAD2; or MX1, LLY6E, IFI27, OAS1, IFIT1, IFI44; or MX1, LLY6E, IFI27, OAS1, IFIT1, IFIT2; or MX1, LLY6E, IFI27, OAS1, IFIT1, OAS3; or MX1, LLY6E, IFI27, OAS1, IFIT1, USP18; or MX1, LLY6E, IFI27, OAS1, IFIT1, SIGLEC1; or MX1, LLY6E, IFI27, OAS1, IFIT1, HERC5; or MX1, LLY6E, IFI27, OAS1, IFIT1, DNAPTP6; or MX1, LLY6E, IFI27, OAS1, IFIT1, LOC129607; or MX1, LLY6E, IFI27, OAS1, IFIT1, EPSTI1; or MX1, LLY6E, IFI27, OAS1, IFIT1, BIRC4BP; or MX1, LLY6E, IFI27, OAS1, IFIT1, gene detected by probe 22945_at; or MX1, LLY6E, IFI27, OAS1, IFIT1, gene detected by probe 23527_at; or LLY6E, IFI27, OAS1, IFIT1, IFI6, IFI44L; or LLY6E, IFI27, OAS1, IFIT1, IFI6, ISG15; or LLY6E, IFI27, OAS1, IFIT1, IFI6, LAMP3; or LLY6E, IFI27, OAS1, IFIT1, IFI6, OASL; or LLY6E, IFI27, OAS1, IFIT1, IFI6, RSAD2; or LLY6E, IFI27, OAS1, IFIT1, IFI6, IFI44; or LLY6E, IFI27, OAS1, IFIT1, IFI6, IFIT2; or LLY6E, IFI27, OAS1, IFIT1, IFI6, OAS3; or LLY6E, IFI27, OAS1, IFIT1, IFI6, USP18; or LLY6E, IFI27, OAS1, IFIT1, IFI6, SIGLEC1; or LLY6E, IFI27, OAS1, IFIT1, IFI6, HERC5; or LLY6E, IFI27, OAS1, IFIT1, IFI6, DNAPTP6; or LLY6E, IFI27, OAS1, IFIT1, IFI6, LOC129607; or LLY6E, IFI27, OAS1, IFIT1, IFI6, EPSTI1; or LLY6E, IFI27, OAS1, IFIT1, IFI6, BIRC4BP; or LLY6E, IFI27, OAS1, IFIT1, IFI6, gene detected by probe 22945_at; or LLY6E, IFI27, OAS1, IFIT1, IFI6, gene detected by probe 23527_at; or IFI27, OAS1, IFIT1, IFI6, IFI44L, ISG15; or IFI27, OAS1, IFIT1, IFI6, IFI44L, LAMP3; or IFI27, OAS1, IFIT1, IFI6, IFI44L, OASL; or IFI27, OAS1, IFIT1, IFI6, IFI44L, RSAD2; or IFI27, OAS1, IFIT1, IFI6, IFI44L, IFI44; or IFI27, OAS1, IFIT1, IFI6, IFI44L, IFIT2; or IFI27, OAS1, IFIT1, IFI6, IFI44L, OAS3; or IFI27, OAS1, IFIT1, IFI6, IFI44L, USP18; or IFI27, OAS1, IFIT1, IFI6, IFI44L, SIGLEC1; or IFI27, OAS1, IFIT1, IFI6, IFI44L, HERC5; or IFI27, OAS1, IFIT1, IFI6, IFI44L, DNAPTP6; or IFI27, OAS1, IFIT1, IFI6, IFI44L, LOC129607; or IFI27, OAS1, IFIT1, IFI6, IFI44L, EPSTI1; or IFI27, OAS1, IFIT1, IFI6, IFI44L, BIRC4BP; or IFI27, OAS1, IFIT1, IFI6, IFI44L, gene detected by probe 22945_at; or IFI27, OAS1, IFIT1, IFI6, IFI44L, gene detected by probe 23527_at; or OAS1, IFIT1, IFI6, IFI44L, ISG15, LAMP3; or OAS1, IFIT1, IFI6, IFI44L, ISG15, OASL; or OAS1, IFIT1, IFI6, IFI44L, ISG15, RSAD2; or OAS1, IFIT1, IFI6, IFI44L, ISG15, IFI44; or OAS1, IFIT1, IFI6, IFI44L, ISG15, IFIT2; or OAS1, IFIT1, IFI6, IFI44L, ISG15, OAS3; or OAS1, IFIT1, IFI6, IFI44L, ISG15, USP18; or OAS1, IFIT1, IFI6, IFI44L, ISG15, SIGLEC1; or OAS1, IFIT1, IFI6, IFI44L, ISG15, HERC5; or OAS1, IFIT1, IFI6, IFI44L, ISG15, DNAPTP6; or OAS1, IFIT1, IFI6, IFI44L, ISG15, LOC129607; or OAS1, IFIT1, IFI6, IFI44L, ISG15, EPSTI1; or OAS1, IFIT1, IFI6, IFI44L, ISG15, BIRC4BP; or OAS1, IFIT1, IFI6, IFI44L, ISG15, gene detected by probe 22945_at; or OAS1, IFIT1, IFI6, IFI44L, ISG15, gene detected by probe 23527_at; or IFIT1, IFI6, IFI44L, ISG15, LAMP3, OASL; or IFIT1, IFI6, IFI44L, ISG15, LAMP3, RSAD2; or IFIT1, IFI6, IFI44L, ISG15, LAMP3, IFI44; or IFIT1, IFI6, IFI44L, ISG15, LAMP3, IFIT2; or IFIT1, IFI6, IFI44L, ISG15, LAMP3, OAS3; or IFIT1, IFI6, IFI44L, ISG15, LAMP3, USP18; or IFIT1, IFI6, IFI44L, ISG15, LAMP3, SIGLEC1; or IFIT1, IFI6, IFI44L, ISG15, LAMP3, HERC5; or IFIT1, IFI6, IFI44L, ISG15, LAMP3, DNAPTP6; or IFIT1, IFI6, IFI44L, ISG15, LAMP3, LOC129607; or IFIT1, IFI6, IFI44L, ISG15, LAMP3, EPSTI1; or IFIT1, IFI6, IFI44L, ISG15, LAMP3, BIRC4BP; or IFIT1, IFI6, IFI44L, ISG15, LAMP3, gene detected by probe 22945_at; or IFIT1, IFI6, IFI44L, ISG15, LAMP3, gene detected by probe 23527_at; or IFI6, IFI44L, ISG15, LAMP3, OASL, RSAD2; or IFI6, IFI44L, ISG15, LAMP3, OASL, IFI44; or IFI6, IFI44L, ISG15, LAMP3, OASL, IFIT2; or IFI6, IFI44L, ISG15, LAMP3, OASL, OAS3; or IFI6, IFI44L, ISG15, LAMP3, OASL, USP18; or IFI6, IFI44L, ISG15, LAMP3, OASL, SIGLEC1; or IFI6, IFI44L, ISG15, LAMP3, OASL, HERC5; or IFI6, IFI44L, ISG15, LAMP3, OASL, DNAPTP6; or IFI6, IFI44L, ISG15, LAMP3, OASL, LOC129607; or IFI6, IFI44L, ISG15, LAMP3, OASL, EPSTI1; or IFI6, IFI44L, ISG15, LAMP3, OASL, BIRC4BP; or IFI6, IFI44L, ISG15, LAMP3, OASL, gene detected by probe 22945_at; or IFI6, IFI44L, ISG15, LAMP3, OASL, gene detected by probe 23527_at; or IFI44L, ISG15, LAMP3, OASL, RSAD2, IFI44; or IFI44L, ISG15, LAMP3, OASL, RSAD2, IFIT2; or IFI44L, ISG15, LAMP3, OASL, RSAD2, OAS3; or IFI44L, ISG15, LAMP3, OASL, RSAD2, USP18; or IFI44L, ISG15, LAMP3, OASL, RSAD2, SIGLEC1; or IFI44L, ISG15, LAMP3, OASL, RSAD2, HERC5; or IFI44L, ISG15, LAMP3, OASL, RSAD2, DNAPTP6; or IFI44L, ISG15, LAMP3, OASL, RSAD2, LOC129607; or IFI44L, ISG15, LAMP3, OASL, RSAD2, EPSTI1; or IFI44L, ISG15, LAMP3, OASL, RSAD2, BIRC4BP; or IFI44L, ISG15, LAMP3, OASL, RSAD2, gene detected by probe 22945_at; or IFI44L, ISG15, LAMP3, OASL, RSAD2, gene detected by probe 23527_at; or ISG15, LAMP3, OASL, RSAD2, IFI44, IFIT2; or ISG15, LAMP3, OASL, RSAD2, IFI44, OAS3; or ISG15, LAMP3, OASL, RSAD2, IFI44, USP18; or ISG15, LAMP3, OASL, RSAD2, IFI44, SIGLEC1; or ISG15, LAMP3, OASL, RSAD2, IFI44, HERC5; or ISG15, LAMP3, OASL, RSAD2, IFI44, DNAPTP6; or ISG15, LAMP3, OASL, RSAD2, IFI44, LOC129607; or ISG15, LAMP3, OASL, RSAD2, IFI44, EPSTI1; or ISG15, LAMP3, OASL, RSAD2, IFI44, BIRC4BP; or ISG15, LAMP3, OASL, RSAD2, IFI44, gene detected by probe 22945_at; or ISG15, LAMP3, OASL, RSAD2, IFI44, gene detected by probe 23527_at; or LAMP3, OASL, RSAD2, IFI44, IFIT2, OAS3; or LAMP3, OASL, RSAD2, IFI44, IFIT2, USP18; or LAMP3, OASL, RSAD2, IFI44, IFIT2, SIGLEC1; or LAMP3, OASL, RSAD2, IFI44, IFIT2, HERC5; or LAMP3, OASL, RSAD2, IFI44, IFIT2, DNAPTP6; or LAMP3, OASL, RSAD2, IFI44, IFIT2, LOC129607; or LAMP3, OASL, RSAD2, IFI44, IFIT2, EPSTI1; or LAMP3, OASL, RSAD2, IFI44, IFIT2, BIRC4BP; or LAMP3, OASL, RSAD2, IFI44, IFIT2, gene detected by probe 22945_at; or LAMP3, OASL, RSAD2, IFI44, IFIT2, gene detected by probe 23527_at; or OASL, RSAD2, IFI44, IFIT2, OAS3, USP18; or OASL, RSAD2, IFI44, IFIT2, OAS3, SIGLEC1; or OASL, RSAD2, IFI44, IFIT2, OAS3, HERC5; or OASL, RSAD2, IFI44, IFIT2, OAS3, DNAPTP6; or OASL, RSAD2, IFI44, IFIT2, OAS3, LOC129607; or OASL, RSAD2, IFI44, IFIT2, OAS3, EPSTI1; or OASL, RSAD2, IFI44, IFIT2, OAS3, BIRC4BP; or OASL, RSAD2, IFI44, IFIT2, OAS3, gene detected by probe 22945_at; or OASL, RSAD2, IFI44, IFIT2, OAS3, gene detected by probe 23527_at; or RSAD2, IFI44, IFIT2, OAS3, USP18, SIGLEC1; or RSAD2, IFI44, IFIT2, OAS3, USP18, HERC5; or RSAD2, IFI44, IFIT2, OAS3, USP18, DNAPTP6; or RSAD2, IFI44, IFIT2, OAS3, USP18, LOC129607; or RSAD2, IFI44, IFIT2, OAS3, USP18, EPSTI1; or RSAD2, IFI44, IFIT2, OAS3, USP18, BIRC4BP; or RSAD2, IFI44, IFIT2, OAS3, USP18, gene detected by probe 22945_at; or RSAD2, IFI44, IFIT2, OAS3, USP18, gene detected by probe 23527_at; or IFI44, IFIT2, OAS3, USP18, SIGLEC1, HERC5; or IFI44, IFIT2, OAS3, USP18, SIGLEC1, DNAPTP6; or IFI44, IFIT2, OAS3, USP18, SIGLEC1, LOC129607; or IFI44, IFIT2, OAS3, USP18, SIGLEC1, EPSTI1; or IFI44, IFIT2, OAS3, USP18, SIGLEC1, BIRC4BP; or IFI44, IFIT2, OAS3, USP18, SIGLEC1, gene detected by probe 22945_at; or IFI44, IFIT2, OAS3, USP18, SIGLEC1, gene detected by probe 23527_at; or IFIT2, OAS3, USP18, SIGLEC1, HERC5, DNAPTP6; or IFIT2, OAS3, USP18, SIGLEC1, HERC5, LOC129607; or IFIT2, OAS3, USP18, SIGLEC1, HERC5, EPSTI1; or IFIT2, OAS3, USP18, SIGLEC1, HERC5, BIRC4BP; or IFIT2, OAS3, USP18, SIGLEC1, HERC5, gene detected by probe 22945_at; or IFIT2, OAS3, USP18, SIGLEC1, HERC5, gene detected by probe 23527_at; or OAS3, USP18, SIGLEC1, HERC5, DNAPTP6, LOC129607; or OAS3, USP18, SIGLEC1, HERC5, DNAPTP6, EPSTI1; or OAS3, USP18, SIGLEC1, HERC5, DNAPTP6, BIRC4BP; or OAS3, USP18, SIGLEC1, HERC5, DNAPTP6, gene detected by probe 22945_at; or OAS3, USP18, SIGLEC1, HERC5, DNAPTP6, gene detected by probe 23527_at; or USP18, SIGLEC1, HERC5, DNAPTP6, LOC129607, EPSTI1; or USP18, SIGLEC1, HERC5, DNAPTP6, LOC129607, BIRC4BP; or USP18, SIGLEC1, HERC5, DNAPTP6, LOC129607, gene detected by probe 22945_at; or USP18, SIGLEC1, HERC5, DNAPTP6, LOC129607, gene detected by probe 23527_at; or SIGLEC1, HERC5, DNAPTP6, LOC129607, EPSTI1, BIRC4BP; or SIGLEC1, HERC5, DNAPTP6, LOC129607, EPSTI1, gene detected by probe 22945_at; or SIGLEC1, HERC5, DNAPTP6, LOC129607, EPSTI1, gene detected by probe 23527_at; or HERC5, DNAPTP6, LOC129607, EPSTI1, BIRC4BP, gene detected by probe 22945_at; or HERC5, DNAPTP6, LOC129607, EPSTI1, BIRC4BP, gene detected by probe 23527_at; or DNAPTP6, LOC129607, EPSTI1, BIRC4BP, gene detected by probe 22945_at, gene detected by probe 23527_at. The IFNα-inducible PD markers in such an expression profile may further include at least one or more gene listed in Tables 19 and/or 20 and/or 21 and/or 22 and/or 23 and/or 24 and/or 26 and/or 28 and/or 30.
  • The IFNα-inducible PD markers in an expression profile may include any at least 7 genes such as, for example: MX1, LLY6E, IFI27, OAS1, IFIT1, IFI6, IFI44L; or MX1, LLY6E, IFI27, OAS1, IFIT1, IFI6, ISG15; or MX1, LLY6E, IFI27, OAS1, IFIT1, IFI6, LAMP3; or MX1, LLY6E, IFI27, OAS1, IFIT1, IFI6, OASL; or MX1, LLY6E, IFI27, OAS1, IFIT1, IFI6, RSAD2; or MX1, LLY6E, IFI27, OAS1, IFIT1, IFI6, IFI44; or MX1, LLY6E, IFI27, OAS1, IFIT1, IFI6, IFIT2; or MX1, LLY6E, IFI27, OAS1, IFIT1, IFI6, OAS3; or MX1, LLY6E, IFI27, OAS1, IFIT1, IFI6, USP18; or MX1, LLY6E, IFI27, OAS1, IFIT1, IFI6, SIGLEC1; or MX1, LLY6E, IFI27, OAS1, IFIT1, IFI6, HERC5; or MX1, LLY6E, IFI27, OAS1, IFIT1, IFI6, DNAPTP6; or MX1, LLY6E, IFI27, OAS1, IFIT1, IFI6, LOC129607; or MX1, LLY6E, IFI27, OAS1, IFIT1, IFI6, EPSTI1; or MX1, LLY6E, IFI27, OAS1, IFIT1, IFI6, BIRC4BP; or MX1, LLY6E, IFI27, OAS1, IFIT1, IFI6, gene detected by probe 22945_at; or MX1, LLY6E, IFI27, OAS1, IFIT1, IFI6, gene detected by probe 23527_at; or LLY6E, IFI27, OAS1, IFIT1, IFI6, IFI44L, ISG15; or LLY6E, IFI27, OAS1, IFIT1, IFI6, IFI44L, LAMP3; or LLY6E, IFI27, OAS1, IFIT1, IFI6, IFI44L, OASL; or LLY6E, IFI27, OAS1, IFIT1, IFI6, IFI44L, RSAD2; or LLY6E, IFI27, OAS1, IFIT1, IFI6, IFI44L, IFI44; or LLY6E, IFI27, OAS1, IFIT1, IFI6, IFI44L, IFIT2; or LLY6E, IFI27, OAS1, IFIT1, IFI6, IFI44L, OAS3; or LLY6E, IFI27, OAS1, IFIT1, IFI6, IFI44L, USP18; or LLY6E, IFI27, OAS1, IFIT1, IFI6, IFI44L, SIGLEC1; or LLY6E, IFI27, OAS1, IFIT1, IFI6, IFI44L, HERC5; or LLY6E, IFI27, OAS1, IFIT1, IFI6, IFI44L, DNAPTP6; or LLY6E, IFI27, OAS1, IFIT1, IFI6, IFI44L, LOC129607; or LLY6E, IFI27, OAS1, IFIT1, IFI6, IFI44L, EPSTI1; or LLY6E, IFI27, OAS1, IFIT1, IFI6, IFI44L, BIRC4BP; or LLY6E, IFI27, OAS1, IFIT1, IFI6, IFI44L, gene detected by probe 22945_at; or LLY6E, IFI27, OAS1, IFIT1, IFI6, IFI44L, gene detected by probe 23527_at; or IFI27, OAS1, IFIT1, IFI6, IFI44L, ISG15, LAMP3; or IFI27, OAS1, IFIT1, IFI6, IFI44L, ISG15, OASL; or IFI27, OAS1, IFIT1, IFI6, IFI44L, ISG15, RSAD2; or IFI27, OAS1, IFIT1, IFI6, IFI44L, ISG15, IFI44; or IFI27, OAS1, IFIT1, IFI6, IFI44L, ISG15, IFIT2; or IFI27, OAS1, IFIT1, IFI6, IFI44L, ISG15, OAS3; or IFI27, OAS1, IFIT1, IFI6, IFI44L, ISG15, USP18; or IFI27, OAS1, IFIT1, IFI6, IFI44L, ISG15, SIGLEC1; or IFI27, OAS1, IFIT1, IFI6, IFI44L, ISG15, HERC5; or IFI27, OAS1, IFIT1, IFI6, IFI44L, ISG15, DNAPTP6; or IFI27, OAS1, IFIT1, IFI6, IFI44L, ISG15, LOC129607; or IFI27, OAS1, IFIT1, IFI6, IFI44L, ISG15, EPSTI1; or IFI27, OAS1, IFIT1, IFI6, IFI44L, ISG15, BIRC4BP; or IFI27, OAS1, IFIT1, IFI6, IFI44L, ISG 15, gene detected by probe 22945_at; or IFI27, OAS1, IFIT1, IFI6, IFI44L, ISG15, gene detected by probe 23527_at; or OAS1, IFIT1, IFI6, IFI44L, ISG15, LAMP3, OASL; or OAS1, IFIT1, IFI6, IFI44L, ISG15, LAMP3, RSAD2; or OAS1, IFIT1, IFI6, IFI44L, ISG15, LAMP3, IFI44; or OAS1, IFIT1, IFI6, IFI44L, ISG15, LAMP3, IFIT2; or OAS1, IFIT1, IFI6, IFI44L, ISG15, LAMP3, OAS3; or OAS1, IFIT1, IFI6, IFI44L, ISG15, LAMP3, USP18; or OAS1, IFIT1, IFI6, IFI44L, ISG15, LAMP3, SIGLEC1; or OAS1, IFIT1, IFI6, IFI44L, ISG15, LAMP3, HERC5; or OAS1, IFIT1, IFI6, IFI44L, ISG15, LAMP3, DNAPTP6; or OAS1, IFIT1, IFI6, IFI44L, ISG15, LAMP3, LOC129607; or OAS1, IFIT1, IFI6, IFI44L, ISG15, LAMP3, EPSTI1; or OAS1, IFIT1, IFI6, IFI44L, ISG15, LAMP3, BIRC4BP; or OAS1, IFIT1, IFI6, IFI44L, ISG15, LAMP3, gene detected by probe 22945_at; or OAS1, IFIT1, IFI6, IFI44L, ISG15, LAMP3, gene detected by probe 23527_at; or IFIT1, IFI6, IFI44L, ISG15, LAMP3, OASL, RSAD2; or IFIT1, IFI6, IFI44L, ISG15, LAMP3, OASL, IFI44; or IFIT1, IFI6, IFI44L, ISG15, LAMP3, OASL, IFIT2; or IFIT1, IFI6, IFI44L, ISG15, LAMP3, OASL, OAS3; or IFIT1, IFI6, IFI44L, ISG15, LAMP3, OASL, USP18; or IFIT1, IFI6, IFI44L, ISG15, LAMP3, OASL, SIGLEC1; or IFIT1, IFI6, IFI44L, ISG15, LAMP3, OASL, HERC5; or IFIT1, IFI6, IFI44L, ISG15, LAMP3, OASL, DNAPTP6; or IFIT1, IFI6, IFI44L, ISG15, LAMP3, OASL, LOC129607; or IFIT1, IFI6, IFI44L, ISG15, LAMP3, OASL, EPSTI1; or IFIT1, IFI6, IFI44L, ISG15, LAMP3, OASL, BIRC4BP; or IFIT1, IFI6, IFI44L, ISG15, LAMP3, OASL, gene detected by probe 22945_at; or IFIT1, IFI6, IFI44L, ISG15, LAMP3, OASL, gene detected by probe 23527_at; or IFI6, IFI44L, ISG15, LAMP3, OASL, RSAD2, IFI44; or IFI6, IFI44L, ISG15, LAMP3, OASL, RSAD2, IFIT2; or IFI6, IFI44L, ISG15, LAMP3, OASL, RSAD2, OAS3; or IFI6, IFI44L, ISG15, LAMP3, OASL, RSAD2, USP18; or IFI6, IFI44L, ISG15, LAMP3, OASL, RSAD2, SIGLEC1; or IFI6, IFI44L, ISG15, LAMP3, OASL, RSAD2, HERC5; or IFI6, IFI44L, ISG15, LAMP3, OASL, RSAD2, DNAPTP6; or IFI6, IFI44L, ISG15, LAMP3, OASL, RSAD2, LOC129607; or IFI6, IFI44L, ISG15, LAMP3, OASL, RSAD2, EPSTI1; or IFI6, IFI44L, ISG15, LAMP3, OASL, RSAD2, BIRC4BP; or IFI6, IFI44L, ISG15, LAMP3, OASL, RSAD2, gene detected by probe 22945_at; or IFI6, IFI44L, ISG15, LAMP3, OASL, RSAD2, gene detected by probe 23527_at; or IFI44L, ISG15, LAMP3, OASL, RSAD2, IFI44, IFIT2; or IFI44L, ISG15, LAMP3, OASL, RSAD2, IFI44, OAS3; or IFI44L, ISG15, LAMP3, OASL, RSAD2, IFI44, USP18; or IFI44L, ISG15, LAMP3, OASL, RSAD2, IFI44, SIGLEC1; or IFI44L, ISG15, LAMP3, OASL, RSAD2, IFI44, HERC5; or IFI44L, ISG15, LAMP3, OASL, RSAD2, IFI44, DNAPTP6; or IFI44L, ISG15, LAMP3, OASL, RSAD2, IFI44, LOC129607; or IFI44L, ISG15, LAMP3, OASL, RSAD2, IFI44, EPSTI1; or IFI44L, ISG15, LAMP3, OASL, RSAD2, IFI44, BIRC4BP; or IFI44L, ISG15, LAMP3, OASL, RSAD2, IFI44, gene detected by probe 22945_at; or IFI44L, ISG15, LAMP3, OASL, RSAD2, IFI44, gene detected by probe 23527_at; or ISG15, LAMP3, OASL, RSAD2, IFI44, IFIT2, OAS3; or ISG15, LAMP3, OASL, RSAD2, IFI44, IFIT2, USP18; or ISG15, LAMP3, OASL, RSAD2, IFI44, IFIT2, SIGLEC1; or ISG15, LAMP3, OASL, RSAD2, IFI44, IFIT2, HERC5; or ISG15, LAMP3, OASL, RSAD2, IFI44, IFIT2, DNAPTP6; or ISG15, LAMP3, OASL, RSAD2, IFI44, IFIT2, LOC129607; or ISG15, LAMP3, OASL, RSAD2, IFI44, IFIT2, EPSTI1; or ISG15, LAMP3, OASL, RSAD2, IFI44, IFIT2, BIRC4BP; or ISG15, LAMP3, OASL, RSAD2, IFI44, IFIT2, gene detected by probe 22945_at; or ISG15, LAMP3, OASL, RSAD2, IFI44, IFIT2, gene detected by probe 23527_at; or LAMP3, OASL, RSAD2, IFI44, IFIT2, OAS3, USP18; or LAMP3, OASL, RSAD2, IFI44, IFIT2, OAS3, SIGLEC1; or LAMP3, OASL, RSAD2, IFI44, IFIT2, OAS3, HERC5; or LAMP3, OASL, RSAD2, IFI44, IFIT2, OAS3, DNAPTP6; or LAMP3, OASL, RSAD2, IFI44, IFIT2, OAS3, LOC129607; or LAMP3, OASL, RSAD2, IFI44, IFIT2, OAS3, EPSTI1; or LAMP3, OASL, RSAD2, IFI44, IFIT2, OAS3, BIRC4BP; or LAMP3, OASL, RSAD2, IFI44, IFIT2, OAS3, gene detected by probe 22945_at; or LAMP3, OASL, RSAD2, IFI44, IFIT2, OAS3, gene detected by probe 23527_at; or OASL, RSAD2, IFI44, IFIT2, OAS3, USP18, SIGLEC1; or OASL, RSAD2, IFI44, IFIT2, OAS3, USP18, HERC5; or OASL, RSAD2, IFI44, IFIT2, OAS3, USP18, DNAPTP6; or OASL, RSAD2, IFI44, IFIT2, OAS3, USP18, LOC129607; or OASL, RSAD2, IFI44, IFIT2, OAS3, USP18, EPSTI1; or OASL, RSAD2, IFI44, IFIT2, OAS3, USP18, BIRC4BP; or OASL, RSAD2, IFI44, IFIT2, OAS3, USP18, gene detected by probe 22945_at; or OASL, RSAD2, IFI44, IFIT2, OAS3, USP18, gene detected by probe 23527_at; or RSAD2, IFI44, IFIT2, OAS3, USP18, SIGLEC1, HERC5; or RSAD2, IFI44, IFIT2, OAS3, USP18, SIGLEC1, DNAPTP6; or RSAD2, IFI44, IFIT2, OAS3, USP18, SIGLEC1, LOC129607; or RSAD2, IFI44, IFIT2, OAS3, USP18, SIGLEC1, EPSTI1; or RSAD2, IFI44, IFIT2, OAS3, USP18, SIGLEC1, BIRC4BP; or RSAD2, IFI44, IFIT2, OAS3, USP18, SIGLEC1, gene detected by probe 22945_at; or RSAD2, IFI44, IFIT2, OAS3, USP18, SIGLEC1, gene detected by probe 23527_at; or IFI44, IFIT2, OAS3, USP18, SIGLEC1, HERC5, DNAPTP6; or IFI44, IFIT2, OAS3, USP18, SIGLEC1, HERC5, LOC129607; or IFI44, IFIT2, OAS3, USP18, SIGLEC1, HERC5, EPSTI1; or IFI44, IFIT2, OAS3, USP18, SIGLEC1, HERC5, BIRC4BP; or IFI44, IFIT2, OAS3, USP18, SIGLEC1, HERC5, gene detected by probe 22945_at; or IFI44, IFIT2, OAS3, USP18, SIGLEC1, HERC5, gene detected by probe 23527_at; or IFIT2, OAS3, USP18, SIGLEC1, HERC5, DNAPTP6, LOC129607; or IFIT2, OAS3, USP18, SIGLEC1, HERC5, DNAPTP6, EPSTI1; or IFIT2, OAS3, USP18, SIGLEC1, HERC5, DNAPTP6, BIRC4BP; or IFIT2, OAS3, USP18, SIGLEC1, HERC5, DNAPTP6, gene detected by probe 22945_at; or IFIT2, OAS3, USP18, SIGLEC1, HERC5, DNAPTP6, gene detected by probe 23527_at; or OAS3, USP18, SIGLEC1, HERC5, DNAPTP6, LOC129607, EPSTI1; or OAS3, USP18, SIGLEC1, HERC5, DNAPTP6, LOC129607, BIRC4BP; or OAS3, USP18, SIGLEC1, HERC5, DNAPTP6, LOC129607, gene detected by probe 22945_at; or OAS3, USP18, SIGLEC1, HERC5, DNAPTP6, LOC129607, gene detected by probe 23527_at; or USP18, SIGLEC1, HERC5, DNAPTP6, LOC129607, EPSTI1, BIRC4BP; or USP18, SIGLEC1, HERC5, DNAPTP6, LOC129607, EPSTI1, gene detected by probe 22945_at; or USP18, SIGLEC1, HERC5, DNAPTP6, LOC129607, EPSTI1, gene detected by probe 23527_at; or SIGLEC1, HERC5, DNAPTP6, LOC129607, EPSTI1, BIRC4BP, gene detected by probe 22945_at; or SIGLEC1, HERC5, DNAPTP6, LOC129607, EPSTI1, BIRC4BP, gene detected by probe 23527_at; or HERC5, DNAPTP6, LOC129607, EPSTI1, BIRC4BP, gene detected by probe 22945_at, gene detected by probe 23527_at. The IFNα-inducible PD markers in such an expression profile may further include at least one or more gene listed in Tables 19 and/or 20 and/or 21 and/or 22 and/or 23 and/or 24 and/or 26 and/or 28 and/or 30.
  • The IFNα-inducible PD markers in an expression profile may include any at least 8 genes such as, for example: MX1, LLY6E, IFI27, OAS1, IFIT1, IFI6, IFI44L, ISG15; or MX1, LLY6E, IFI27, OAS1, IFIT1, IFI6, IFI44L, LAMP3; or MX1, LLY6E, IFI27, OAS1, IFIT1, IFI6, IFI44L, OASL; or MX1, LLY6E, IFI27, OAS1, IFIT1, IFI6, IFI44L, RSAD2; or MX1, LLY6E, IFI27, OAS1, IFIT1, IFI6, IFI44L, IFI44; or MX1, LLY6E, IFI27, OAS1, IFIT1, IFI6, IFI44L, IFIT2; or MX1, LLY6E, IFI27, OAS1, IFIT1, IFI6, IFI44L, OAS3; or MX1, LLY6E, IFI27, OAS1, IFIT1, IFI6, IFI44L, USP18; or MX1, LLY6E, IFI27, OAS1, IFIT1, IFI6, IFI44L, SIGLEC1; or MX1, LLY6E, IFI27, OAS1, IFIT1, IFI6, IFI44L, HERC5; or MX1, LLY6E, IFI27, OAS1, IFIT1, IFI6, IFI44L, DNAPTP6; or MX1, LLY6E, IFI27, OAS1, IFIT1, IFI6, IFI44L, LOC129607; or MX1, LLY6E, IFI27, OAS1, IFIT1, IFI6, IFI44L, EPSTI1; or MX1, LLY6E, IFI27, OAS1, IFIT1, IFI6, IFI44L, BIRC4BP; or MX1, LLY6E, IFI27, OAS1, IFIT1, IFI6, IFI44L, gene detected by probe 22945_at; or MX1, LLY6E, IFI27, OAS1, IFIT1, IFI6, IFI44L, gene detected by probe 23527_at; or LLY6E, IFI27, OAS1, IFIT1, IFI6, IFI44L, ISG15, LAMP3; or LLY6E, IFI27, OAS1, IFIT1, IFI6, IFI44L, ISG15, OASL; or LLY6E, IFI27, OAS1, IFIT1, IFI6, IFI44L, ISG15, RSAD2; or LLY6E, IFI27, OAS1, IFIT1, IFI6, IFI44L, ISG15, IFI44; or LLY6E, IFI27, OAS1, IFIT1, IFI6, IFI44L, ISG15, IFIT2; or LLY6E, IFI27, OAS1, IFIT1, IFI6, IFI44L, ISG15, OAS3; or LLY6E, IFI27, OAS1, IFIT1, IFI6, IFI44L, ISG15, USP18; or LLY6E, IFI27, OAS1, IFIT1, IFI6, IFI44L, ISG15, SIGLEC1; or LLY6E, IFI27, OAS1, IFIT1, IFI6, IFI44L, ISG15, HERC5; or LLY6E, IFI27, OAS1, IFIT1, IFI6, IFI44L, ISG 15, DNAPTP6; or LLY6E, IFI27, OAS1, IFIT1, IFI6, IFI44L, ISG15, LOC129607; or LLY6E, IFI27, OAS1, IFIT1, IFI6, IFI44L, ISG15, EPSTI1; or LLY6E, IFI27, OAS1, IFIT1, IFI6, IFI44L, ISG15, BIRC4BP; or LLY6E, IFI27, OAS1, IFIT1, IFI6, IFI44L, ISG15, gene detected by probe 22945_at; or LLY6E, IFI27, OAS1, IFIT1, IFI6, IFI44L, ISG15, gene detected by probe 23527_at; or IFI27, OAS1, IFIT1, IFI6, IFI44L, ISG15, LAMP3, OASL; or IFI27, OAS1, IFIT1, IFI6, IFI44L, ISG15, LAMP3, RSAD2; or IFI27, OAS1, IFIT1, IFI6, IFI44L, ISG15, LAMP3, IFI44; or IFI27, OAS1, IFIT1, IFI6, IFI44L, ISG15, LAMP3, IFIT2; or IFI27, OAS1, IFIT1, IFI6, IFI44L, ISG15, LAMP3, OAS3; or IFI27, OAS1, IFIT1, IFI6, IFI44L, ISG15, LAMP3, USP18; or IFI27, OAS1, IFIT1, IFI6, IFI44L, ISG15, LAMP3, SIGLEC1; or IFI27, OAS1, IFIT1, IFI6, IFI44L, ISG15, LAMP3, HERC5; or IFI27, OAS1, IFIT1, IFI6, IFI44L, ISG15, LAMP3, DNAPTP6; or IFI27, OAS1, IFIT1, IFI6, IFI44L, ISG 15, LAMP3, LOC129607; or IFI27, OAS1, IFIT1, IFI6, IFI44L, ISG 15, LAMP3, EPSTI1; or IFI27, OAS1, IFIT1, IFI6, IFI44L, ISG15, LAMP3, gene detected by probe 22945_at; or IFI27, OAS1, IFIT1, IFI6, IFI44L, ISG15, LAMP3, BIRC4BP; or IFI27, OAS1, IFIT1, IFI6, IFI44L, ISG15, LAMP3, gene detected by probe 23527_at; or OAS1, IFIT1, IFI6, IFI44L, ISG15, LAMP3, OASL, RSAD2; or OAS1, IFIT1, IFI6, IFI44L, ISG15, LAMP3, OASL, IFI44; or OAS1, IFIT1, IFI6, IFI44L, ISG15, LAMP3, OASL, IFIT2; or OAS1, IFIT1, IFI6, IFI44L, ISG15, LAMP3, OASL, OAS3; or OAS1, IFIT1, IFI6, IFI44L, ISG15, LAMP3, OASL, USP18; or OAS1, IFIT1, IFI6, IFI44L, ISG15, LAMP3, OASL, SIGLEC1; or OAS1, IFIT1, IFI6, IFI44L, ISG15, LAMP3, OASL, HERC5; or OAS1, IFIT1, IFI6, IFI44L, ISG15, LAMP3, OASL, DNAPTP6; or OAS1, IFIT1, IFI6, IFI44L, ISG15, LAMP3, OASL, LOC129607; or OAS1, IFIT1, IFI6, IFI44L, ISG15, LAMP3, OASL, EPSTI1; or OAS1, IFIT1, IFI6, IFI44L, ISG15, LAMP3, OASL, BIRC4BP; or OAS1, IFIT1, IFI6, IFI44L, ISG15, LAMP3, OASL, gene detected by probe 22945_at; or OAS1, IFIT1, IFI6, IFI44L, ISG15, LAMP3, OASL, gene detected by probe 23527_at; or IFIT1, IFI6, IFI44L, ISG15, LAMP3, OASL, RSAD2, IFI44; or IFIT1, IFI6, IFI44L, ISG15, LAMP3, OASL, RSAD2, IFIT2; or IFIT1, IFI6, IFI44L, ISG15, LAMP3, OASL, RSAD2, OAS3; or IFIT1, IFI6, IFI44L, ISG15, LAMP3, OASL, RSAD2, USP18; or IFIT1, IFI6, IFI44L, ISG15, LAMP3, OASL, RSAD2, SIGLEC1; or IFIT1, IFI6, IFI44L, ISG15, LAMP3, OASL, RSAD2, HERC5; or IFIT1, IFI6, IFI44L, ISG15, LAMP3, OASL, RSAD2, DNAPTP6; or IFIT1, IFI6, IFI44L, ISG15, LAMP3, OASL, RSAD2, LOC129607; or IFIT1, IFI6, IFI44L, ISG15, LAMP3, OASL, RSAD2, EPSTI1; or IFIT1, IFI6, IFI44L, ISG15, LAMP3, OASL, RSAD2, BIRC4BP; or IFIT1, IFI6, IFI44L, ISG15, LAMP3, OASL, RSAD2, gene detected by probe 22945_at; or IFIT1, IFI6, IFI44L, ISG15, LAMP3, OASL, RSAD2, gene detected by probe 23527_at; or IFI6, IFI44L, ISG15, LAMP3, OASL, RSAD2, IFI44, IFIT2; or IFI6, IFI44L, ISG15, LAMP3, OASL, RSAD2, IFI44, OAS3; or IFI6, IFI44L, ISG15, LAMP3, OASL, RSAD2, IFI44, USP18; or IFI6, IFI44L, ISG15, LAMP3, OASL, RSAD2, IFI44, SIGLEC1; or IFI6, IFI44L, ISG15, LAMP3, OASL, RSAD2, IFI44, HERC5; or IFI6, IFI44L, ISG15, LAMP3, OASL, RSAD2, IFI44, DNAPTP6; or IFI6, IFI44L, ISG15, LAMP3, OASL, RSAD2, IFI44, LOC129607; or IFI6, IFI44L, ISG15, LAMP3, OASL, RSAD2, IFI44, EPSTI1; or IFI6, IFI44L, ISG15, LAMP3, OASL, RSAD2, IFI44, BIRC4BP; or IFI6, IFI44L, ISG15, LAMP3, OASL, RSAD2, IFI44, gene detected by probe 22945_at; or IFI6, IFI44L, ISG15, LAMP3, OASL, RSAD2, IFI44, gene detected by probe 23527_at; or IFI44L, ISG15, LAMP3, OASL, RSAD2, IFI44, IFIT2, OAS3; or IFI44L, ISG15, LAMP3, OASL, RSAD2, IFI44, IFIT2, USP18; or IFI44L, ISG15, LAMP3, OASL, RSAD2, IFI44, IFIT2, SIGLEC1; or IFI44L, ISG15, LAMP3, OASL, RSAD2, IFI44, IFIT2, HERC5; or IFI44L, ISG15, LAMP3, OASL, RSAD2, IFI44, IFIT2, DNAPTP6; or IFI44L, ISG15, LAMP3, OASL, RSAD2, IFI44, IFIT2, LOC129607; or IFI44L, ISG 15, LAMP3, OASL, RSAD2, IFI44, IFIT2, EPSTI1; or IFI44L, ISG15, LAMP3, OASL, RSAD2, IFI44, IFIT2, BIRC4BP; or IFI44L, ISG15, LAMP3, OASL, RSAD2, IFI44, IFIT2, gene detected by probe 22945_at; or IFI44L, ISG15, LAMP3, OASL, RSAD2, IFI44, IFIT2, gene detected by probe 23527_at; or ISG15, LAMP3, OASL, RSAD2, IFI44, IFIT2, OAS3, USP18; or ISG15, LAMP3, OASL, RSAD2, IFI44, IFIT2, OAS3, SIGLEC1; or ISG15, LAMP3, OASL, RSAD2, IFI44, IFIT2, OAS3, HERC5; or ISG15, LAMP3, OASL, RSAD2, IFI44, IFIT2, OAS3, DNAPTP6; or ISG15, LAMP3, OASL, RSAD2, IFI44, IFIT2, OAS3, LOC129607; or ISG15, LAMP3, OASL, RSAD2, IFI44, IFIT2, OAS3, EPSTI1; or ISG15, LAMP3, OASL, RSAD2, IFI44, IFIT2, OAS3, BIRC4BP; or ISG15, LAMP3, OASL, RSAD2, IFI44, IFIT2, OAS3, gene detected by probe 22945_at; or ISG15, LAMP3, OASL, RSAD2, IFI44, IFIT2, OAS3, gene detected by probe 23527_at; or LAMP3, OASL, RSAD2, IFI44, IFIT2, OAS3, USP18, SIGLEC1; or LAMP3, OASL, RSAD2, IFI44, IFIT2, OAS3, USP18, HERC5; or LAMP3, OASL, RSAD2, IFI44, IFIT2, OAS3, USP18, DNAPTP6; or LAMP3, OASL, RSAD2, IFI44, IFIT2, OAS3, USP18, LOC129607; or LAMP3, OASL, RSAD2, IFI44, IFIT2, OAS3, USP18, EPSTI1; or LAMP3, OASL, RSAD2, IFI44, IFIT2, OAS3, USP18, BIRC4BP; or LAMP3, OASL, RSAD2, IFI44, IFIT2, OAS3, USP18, gene detected by probe 22945_at; or LAMP3, OASL, RSAD2, IFI44, IFIT2, OAS3, USP18, gene detected by probe 23527_at; or OASL, RSAD2, IFI44, IFIT2, OAS3, USP18, SIGLEC1, HERC5; or OASL, RSAD2, IFI44, IFIT2, OAS3, USP18, SIGLEC1, DNAPTP6; or OASL, RSAD2, IFI44, IFIT2, OAS3, USP18, SIGLEC1, LOC129607; or OASL, RSAD2, IFI44, IFIT2, OAS3, USP18, SIGLEC1, EPSTI1; or OASL, RSAD2, IFI44, IFIT2, OAS3, USP18, SIGLEC1, BIRC4BP; or OASL, RSAD2, IFI44, IFIT2, OAS3, USP18, SIGLEC1, gene detected by probe 22945_at; or OASL, RSAD2, IFI44, IFIT2, OAS3, USP18, SIGLEC1, gene detected by probe 23527_at; or RSAD2, IFI44, IFIT2, OAS3, USP18, SIGLEC1, HERC5, DNAPTP6; or RSAD2, IFI44, IFIT2, OAS3, USP18, SIGLEC1, HERC5, LOC129607; or RSAD2, IFI44, IFIT2, OAS3, USP18, SIGLEC1, HERC5, EPSTI1; or RSAD2, IFI44, IFIT2, OAS3, USP18, SIGLEC1, HERC5, gene detected by probe 22945_at; or RSAD2, IFI44, IFIT2, OAS3, USP18, SIGLEC1, HERC5, BIRC4BP; or RSAD2, IFI44, IFIT2, OAS3, USP18, SIGLEC1, HERC5, gene detected by probe 23527_at; or IFI44, IFIT2, OAS3, USP18, SIGLEC1, HERC5, DNAPTP6, LOC129607; or IFI44, IFIT2, OAS3, USP18, SIGLEC1, HERC5, DNAPTP6, EPSTI1; or IFI44, IFIT2, OAS3, USP18, SIGLEC1, HERC5, DNAPTP6, BIRC4BP; or IFI44, IFIT2, OAS3, USP18, SIGLEC1, HERC5, DNAPTP6, gene detected by probe 22945_at; or IFI44, IFIT2, OAS3, USP18, SIGLEC1, HERC5, DNAPTP6, gene detected by probe 23527_at; or IFIT2, OAS3, USP18, SIGLEC1, HERC5, DNAPTP6, LOC129607, EPSTI1; or IFIT2, OAS3, USP18, SIGLEC1, HERC5, DNAPTP6, LOC129607, BIRC4BP; or IFIT2, OAS3, USP18, SIGLEC1, HERC5, DNAPTP6, LOC129607, gene detected by probe 22945_at; or IFIT2, OAS3, USP18, SIGLEC1, HERC5, DNAPTP6, LOC129607, gene detected by probe 23527_at; or OAS3, USP18, SIGLEC1, HERC5, DNAPTP6, LOC129607, EPSTI1, BIRC4BP; or OAS3, USP18, SIGLEC1, HERC5, DNAPTP6, LOC129607, EPSTI1, gene detected by probe 22945_at; or OAS3, USP18, SIGLEC1, HERC5, DNAPTP6, LOC129607, EPSTI1, gene detected by probe 23527_at; or USP18, SIGLEC1, HERC5, DNAPTP6, LOC129607, EPSTI1, BIRC4BP, gene detected by probe 22945_at; or USP18, SIGLEC1, HERC5, DNAPTP6, LOC129607, EPSTI1, BIRC4BP, gene detected by probe 23527_at; or SIGLEC1, HERC5, DNAPTP6, LOC129607, EPSTI1, BIRC4BP, gene detected by probe 22945_at, gene detected by probe 23527_at. The IFNα-inducible PD markers in such an expression profile may further include at least one or more gene listed in Tables 19 and/or 20 and/or 21 and/or 22 and/or 23 and/or 24 and/or 26 and/or 28 and/or 30.
  • The IFNα-inducible PD markers in an expression profile may include any at least 12 genes such as, for example: MX1, LLY6E, IFI27, OAS1, IFIT1, IFI6, IFI44L, ISG15, LAMP3, OASL, RSAD2, IFI44; or MX1, LLY6E, IFI27, OAS1, IFIT1, IFI6, IFI44L, ISG15, LAMP3, OASL, RSAD2, IFIT2; or MX1, LLY6E, IFI27, OAS1, IFIT1, IFI6, IFI44L, ISG15, LAMP3, OASL, RSAD2, OAS3; or MX1, LLY6E, IFI27, OAS1, IFIT1, IFI6, IFI44L, ISG15, LAMP3, OASL, RSAD2, USP18; or MX1, LLY6E, IFI27, OAS1, IFIT1, IFI6, IFI44L, ISG15, LAMP3, OASL, RSAD2, SIGLEC1; or MX1, LLY6E, IFI27, OAS1, IFIT1, IFI6, IFI44L, ISG15, LAMP3, OASL, RSAD2, HERC5; or MX1, LLY6E, IFI27, OAS1, IFIT1, IFI6, IFI44L, ISG15, LAMP3, OASL, RSAD2, DNAPTP6; or MX1, LLY6E, IFI27, OAS1, IFIT1, IFI6, IFI44L, ISG15, LAMP3, OASL, RSAD2, LOC129607; or MX1, LLY6E, IFI27, OAS1, IFIT1, IFI6, IFI44L, ISG15, LAMP3, OASL, RSAD2, EPSTI1; or MX1, LLY6E, IFI27, OAS1, IFIT1, IFI6, IFI44L, ISG15, LAMP3, OASL, RSAD2, BIRC4BP; or MX1, LLY6E, IFI27, OAS1, IFIT1, IFI6, IFI44L, ISG15, LAMP3, OASL, RSAD2, gene detected by probe 22945_at; or MX1, LLY6E, IFI27, OAS1, IFIT1, IFI6, IFI44L, ISG15, LAMP3, OASL, RSAD2, gene detected by probe 23527_at; or LLY6E, IFI27, OAS1, IFIT1, IFI6, IFI44L, ISG15, LAMP3, OASL, RSAD2, IFI44, IFIT2; or LLY6E, IFI27, OAS1, IFIT1, IFI6, IFI44L, ISG15, LAMP3, OASL, RSAD2, IFI44, OAS3; or LLY6E, IFI27, OAS1, IFIT1, IFI6, IFI44L, ISG15, LAMP3, OASL, RSAD2, IFI44, USP18; or LLY6E, IFI27, OAS1, IFIT1, IFI6, IFI44L, ISG15, LAMP3, OASL, RSAD2, IFI44, SIGLEC1; or LLY6E, IFI27, OAS1, IFIT1, IFI6, IFI44L, ISG15, LAMP3, OASL, RSAD2, IFI44, HERC5; or LLY6E, IFI27, OAS1, IFIT1, IFI6, IFI44L, ISG15, LAMP3, OASL, RSAD2, IFI44, DNAPTP6; or LLY6E, IFI27, OAS1, IFIT1, IFI6, IFI44L, ISG15, LAMP3, OASL, RSAD2, IFI44, LOC129607; or LLY6E, IFI27, OAS1, IFIT1, IFI6, IFI44L, ISG15, LAMP3, OASL, RSAD2, IFI44, EPSTI1; or LLY6E, IFI27, OAS1, IFIT1, IFI6, IFI44L, ISG15, LAMP3, OASL, RSAD2, IFI44, BIRC4BP; or LLY6E, IFI27, OAS1, IFIT1, IFI6, IFI44L, ISG15, LAMP3, OASL, RSAD2, IFI44, gene detected by probe 22945_at; or LLY6E, IFI27, OAS1, IFIT1, IFI6, IFI44L, ISG15, LAMP3, OASL, RSAD2, IFI44, gene detected by probe 23527_at; or IFI27, OAS1, IFIT1, IFI6, IFI44L, ISG15, LAMP3, OASL, RSAD2, IFI44, IFIT2, OAS; or IFI27, OAS1, IFIT1, IFI6, IFI44L, ISG15, LAMP3, OASL, RSAD2, IFI44, IFIT2, USP18; or IFI27, OAS1, IFIT1, IFI6, IFI44L, ISG15, LAMP3, OASL, RSAD2, IFI44, IFIT2, SIGLEC1; or IFI27, OAS1, IFIT1, IFI6, IFI44L, ISG15, LAMP3, OASL, RSAD2, IFI44, IFIT2, HERC5; or IFI27, OAS1, IFIT1, IFI6, IFI44L, ISG15, LAMP3, OASL, RSAD2, IFI44, IFIT2, DNAPTP6; or IFI27, OAS1, IFIT1, IFI6, IFI44L, ISG15, LAMP3, OASL, RSAD2, IFI44, IFIT2, LOC129607; or IFI27, OAS1, IFIT1, IFI6, IFI44L, ISG15, LAMP3, OASL, RSAD2, IFI44, IFIT2, EPSTI1; or IFI27, OAS1, IFIT1, IFI6, IFI44L, ISG15, LAMP3, OASL, RSAD2, IFI44, IFIT2, BIRC4BP; or IFI27, OAS1, IFIT1, IFI6, IFI44L, ISG15, LAMP3, OASL, RSAD2, IFI44, IFIT2, gene detected by probe 22945_at; or IFI27, OAS1, IFIT1, IFI6, IFI44L, ISG 15, LAMP3, OASL, RSAD2, IFI44, IFIT2, gene detected by probe 23527_at; or OAS1, IFIT1, IFI6, IFI44L, ISG15, LAMP3, OASL, RSAD2, IFI44, IFIT2, OAS3, USP18; or OAS1, IFIT1, IFI6, IFI44L, ISG15, LAMP3, OASL, RSAD2, IFI44, IFIT2, OAS3, SIGLEC1; or OAS1, IFIT1, IFI6, IFI44L, ISG15, LAMP3, OASL, RSAD2, IFI44, IFIT2, OAS3, HERC5; or OAS1, IFIT1, IFI6, IFI44L, ISG15, LAMP3, OASL, RSAD2, IFI44, IFIT2, OAS3, DNAPTP6; or OAS1, IFIT1, IFI6, IFI44L, ISG15, LAMP3, OASL, RSAD2, IFI44, IFIT2, OAS3, LOC129607; or OAS1, IFIT1, IFI6, IFI44L, ISG15, LAMP3, OASL, RSAD2, IFI44, IFIT2, OAS3, EPSTI1; or OAS1, IFIT1, IFI6, IFI44L, ISG15, LAMP3, OASL, RSAD2, IFI44, IFIT2, OAS3, BIRC4BP; or OAS1, IFIT1, IFI6, IFI44L, ISG15, LAMP3, OASL, RSAD2, IFI44, IFIT2, OAS3, gene detected by probe 22945_at; or OAS1, IFIT1, IFI6, IFI44L, ISG15, LAMP3, OASL, RSAD2, IFI44, IFIT2, OAS3, gene detected by probe 23527_at; or IFIT1, IFI6, IFI44L, ISG15, LAMP3, OASL, RSAD2, IFI44, IFIT2, OAS3, USP18, SIGLEC1; or IFIT1, IFI6, IFI44L, ISG15, LAMP3, OASL, RSAD2, IFI44, IFIT2, OAS3, USP18, HERC5; or IFIT1, IFI6, IFI44L, ISG15, LAMP3, OASL, RSAD2, IFI44, IFIT2, OAS3, USP18, DNAPTP6; or IFIT1, IFI6, IFI44L, ISG15, LAMP3, OASL, RSAD2, IFI44, IFIT2, OAS3, USP18, LOC129607; or IFIT1, IFI6, IFI44L, ISG15, LAMP3, OASL, RSAD2, IFI44, IFIT2, OAS3, USP18, EPSTI1; or IFIT1, IFI6, IFI44L, ISG15, LAMP3, OASL, RSAD2, IFI44, IFIT2, OAS3, USP18, BIRC4BP; or IFIT1, IFI6, IFI44L, ISG15, LAMP3, OASL, RSAD2, IFI44, IFIT2, OAS3, USP18, gene detected by probe 22945_at; or IFIT1, IFI6, IFI44L, ISG15, LAMP3, OASL, RSAD2, IFI44, IFIT2, OAS3, USP18, gene detected by probe 23527_at; or IFI6, IFI44L, ISG15, LAMP3, OASL, RSAD2, IFI44, IFIT2, OAS3, USP18, SIGLEC1, HERC5; or IFI6, IFI44L, ISG15, LAMP3, OASL, RSAD2, IFI44, IFIT2, OAS3, USP18, SIGLEC1, DNAPTP6; or IFI6, IFI44L, ISG15, LAMP3, OASL, RSAD2, IFI44, IFIT2, OAS3, USP18, SIGLEC1, LOC129607; or IFI6, IFI44L, ISG15, LAMP3, OASL, RSAD2, IFI44, IFIT2, OAS3, USP18, SIGLEC1, EPSTI1; or IFI6, IFI44L, ISG15, LAMP3, OASL, RSAD2, IFI44, IFIT2, OAS3, USP18, SIGLEC1, BIRC4BP; or IFI6, IFI44L, ISG15, LAMP3, OASL, RSAD2, IFI44, IFIT2, OAS3, USP18, SIGLEC1, gene detected by probe 22945_at; or IFI6, IFI44L, ISG15, LAMP3, OASL, RSAD2, IFI44, IFIT2, OAS3, USP18, SIGLEC1, gene detected by probe 23527_at; or IFI44L, ISG15, LAMP3, OASL, RSAD2, IFI44, IFIT2, OAS3, USP18, SIGLEC1, HERC5, DNAPTP6; or IFI44L, ISG15, LAMP3, OASL, RSAD2, IFI44, IFIT2, OAS3, USP18, SIGLEC1, HERC5, LOC129607; or IFI44L, ISG15, LAMP3, OASL, RSAD2, IFI44, IFIT2, OAS3, USP18, SIGLEC1, HERC5, EPSTI1; or IFI44L, ISG15, LAMP3, OASL, RSAD2, IFI44, IFIT2, OAS3, USP18, SIGLEC1, HERC5, BIRC4BP; or IFI44L, ISG15, LAMP3, OASL, RSAD2, IFI44, IFIT2, OAS3, USP18, SIGLEC1, HERC5, gene detected by probe 22945_at; or IFI44L, ISG15, LAMP3, OASL, RSAD2, IFI44, IFIT2, OAS3, USP18, SIGLEC1, HERC5, gene detected by probe 23527_at; or ISG15, LAMP3, OASL, RSAD2, IFI44, IFIT2, OAS3, USP18, SIGLEC1, HERC5, DNAPTP6, LOC129607; or ISG15, LAMP3, OASL, RSAD2, IFI44, IFIT2, OAS3, USP18, SIGLEC1, HERC5, DNAPTP6, EPSTI1; or ISG15, LAMP3, OASL, RSAD2, IFI44, IFIT2, OAS3, USP18, SIGLEC1, HERC5, DNAPTP6, BIRC4BP; or ISG15, LAMP3, OASL, RSAD2, IFI44, IFIT2, OAS3, USP18, SIGLEC1, HERC5, DNAPTP6, gene detected by probe 22945_at; or ISG15, LAMP3, OASL, RSAD2, IFI44, IFIT2, OAS3, USP18, SIGLEC1, HERC5, DNAPTP6, gene detected by probe 23527_at; or LAMP3, OASL, RSAD2, IFI44, IFIT2, OAS3, USP18, SIGLEC1, HERC5, DNAPTP6, LOC129607, EPSTI1; or LAMP3, OASL, RSAD2, IFI44, IFIT2, OAS3, USP18, SIGLEC1, HERC5, DNAPTP6, LOC129607, BIRC4BP; or LAMP3, OASL, RSAD2, IFI44, IFIT2, OAS3, USP18, SIGLEC1, HERC5, DNAPTP6, LOC129607, gene detected by probe 22945_at; or LAMP3, OASL, RSAD2, IFI44, IFIT2, OAS3, USP18, SIGLEC1, HERC5, DNAPTP6, LOC129607, gene detected by probe 23527_at; or OASL, RSAD2, IFI44, IFIT2, OAS3, USP18, SIGLEC1, HERC5, DNAPTP6, LOC129607, EPSTI1, BIRC4BP; or OASL, RSAD2, IFI44, IFIT2, OAS3, USP18, SIGLEC1, HERC5, DNAPTP6, LOC129607, EPSTI1, gene detected by probe 22945_at; or OASL, RSAD2, IFI44, IFIT2, OAS3, USP18, SIGLEC1, HERC5, DNAPTP6, LOC129607, EPSTI1, gene detected by probe 23527_at; or RSAD2, IFI44, IFIT2, OAS3, USP18, SIGLEC1, HERC5, DNAPTP6, LOC129607, EPSTI1, BIRC4BP, gene detected by probe 22945_at; or RSAD2, IFI44, IFIT2, OAS3, USP18, SIGLEC1, HERC5, DNAPTP6, LOC129607, EPSTI1, BIRC4BP, gene detected by probe 22945_at; or IFI44, IFIT2, OAS3, USP18, SIGLEC1, HERC5, DNAPTP6, LOC129607, EPSTI1, BIRC4BP, gene detected by probe 22945_at gene detected by probe 23527_at. The IFNα-inducible PD markers in such an expression profile may further include at least one or more gene listed in Table 19 and/or 20 and/or 21, and/or 22, and/or 23, and/or 24, and/or 26, and/or 28 and/or 30.
  • The IFNα-inducible PD markers in an expression profile may include any at least 8 genes such as, for example: IFI44, IFI6, SAMD9L, GBP1, OAS1, BIRC4BP, SRGAP2, and RSAD2. The IFNα-inducible PD markers in such an expression profile may further include at least one or more gene listed in Tables 19 and/or 20 and/or 21 and/or 22 and/or 23 and/or 24 and/or 26 and/or 28 and/or 30.
  • The IFNα-inducible PD markers in an expression profile may include any at least 7 genes such as, for example: IFI44, SAMD9L, GBP1, OAS1, BIRC4BP, SRGAP2, and RSAD2; or IFI44, IFI6, GBP1, OAS1, BIRC4BP, SRGAP2, and RSAD2; or IFI44, IFI6, SAMD9L, OAS1, BIRC4BP, SRGAP2, and RSAD2; or IFI44, IFI6, SAMD9L, GBP1, BIRC4BP, SRGAP2, and RSAD2; or IFI44, IFI6, SAMD9L, GBP1, OAS1, SRGAP2, and RSAD2; or IFI44, IFI6, SAMD9L, GBP1, OAS1, BIRC4BP, and RSAD2. The IFNα-inducible PD markers in such an expression profile may further include at least one or more gene listed in Tables 19 and/or 20 and/or 21 and/or 22 and/or 23 and/or 24 and/or 26 and/or 28 and/or 30.
  • The IFNα-inducible PD markers in an expression profile may include any at least 6 genes such as, for example: IFI44, IFI6, SAMD9L, GBP1, OAS1, and BIRC4BP; or IFI6, SAMD9L, GBP1, OAS1, BIRC4BP, and SRGAP2; or SAMD9L, GBP1, OAS1, BIRC4BP, SRGAP2, and RSAD2; or IFI44, GBP1, OAS1, BIRC4BP, SRGAP2, and RSAD2; or IFI44, IFI6, OAS1, BIRC4BP, SRGAP2, and RSAD2; or IFI44, IFI6, SAMD9L, BIRC4BP, SRGAP2, and RSAD2; or IFI44, IFI6, SAMD9L, GBP1, SRGAP2, and RSAD2; or IFI44, IFI6, SAMD9L, GBP1, OAS1, and RSAD2; or IFI44, IFI6, SAMD9L, GBP1, OAS1, and BIRC4BP; or IFI6, GBP1, OAS1, BIRC4BP, SRGAP2, and RSAD2; or IFI6, SAMD9L, OAS1, BIRC4BP, SRGAP2, and RSAD2; or IFI6, SAMD9L, GBP1, BIRC4BP, SRGAP2, and RSAD2; or IFI6, SAMD9L, GBP1, OAS1, SRGAP2, and RSAD2; or IFI6, SAMD9L, GBP1, OAS1, BIRC4BP, and RSAD2; or IFI44, SAMD9L, OAS1, BIRC4BP, SRGAP2, and RSAD2; or IFI44, SAMD9L, GBP1, BIRC4BP, SRGAP2, and RSAD2; or IFI44, SAMD9L, GBP1, OAS1, SRGAP2, and RSAD2; or IFI44, SAMD9L, GBP1, OAS1, BIRC4BP, and RSAD2; or IFI44, SAMD9L, GBP1, OAS1, BIRC4BP, and SRGAP2; or IFI44, IFI6, GBP1, BIRC4BP, SRGAP2, and RSAD2; or IFI44, IFI6, GBP1, OAS1, SRGAP2, and RSAD2; or IFI44, IFI6, GBP1, OAS1, BIRC4BP, and RSAD2; or IFI44, IFI6, GBP1, OAS1, BIRC4BP, and SRGAP2; or IFI44, IFI6, SAMD9L, OAS1, SRGAP2, and RSAD2; or IFI44, IFI6, SAMD9L, OAS1, BIRC4BP, and RSAD2; or IFI44, IFI6, SAMD9L, OAS1, BIRC4BP, and SRGAP2; or IFI44, IFI6, SAMD9L, GBP1, BIRC4BP, and RSAD2; or IFI44, IFI6, SAMD9L, GBP1, BIRC4BP, and SRGAP2; or IFI44, IFI6, SAMD9L, GBP1, OAS1, and SRGAP2. The IFNα-inducible PD markers in such an expression profile may further include at least one or more gene listed in Tables 19 and/or 20 and/or 21 and/or 22 and/or 23 and/or 24 and/or 26 and/or 28 and/or 30.
  • The IFNα-inducible PD markers in an expression profile may include any at least 5 genes such as, for example: GBP1, OAS1, BIRC4BP, SRGAP2, and RSAD2; or IFI44, OAS1, BIRC4BP, SRGAP2, and RSAD2; or IFI44, IFI6, BIRC4BP, SRGAP2, and RSAD2; or IFI44, IFI6, SAMD9L, SRGAP2, and RSAD2; or IFI44, IFI6, SAMD9L, GBP1, and RSAD2; or IFI44, IFI6, SAMD9L, GBP1, and OAS1; or SAMD9L, OAS1, BIRC4BP, SRGAP2, and RSAD2; or SAMD9L, GBP1, BIRC4BP, SRGAP2, and RSAD2; or SAMD9L, GBP1, OAS1, SRGAP2, and RSAD2; or SAMD9L, GBP1, OAS1, BIRC4BP, and RSAD2; or SAMD9L, GBP1, OAS1, BIRC4BP, and SRGAP2; or IFI6, OAS1, BIRC4BP, SRGAP2, and RSAD2; or IFI6, GBP1, BIRC4BP, SRGAP2, and RSAD2; or IFI6, GBP1, OAS1, SRGAP2, and RSAD2; or IFI6, GBP1, OAS1, BIRC4BP, and RSAD2; or IFI6, GBP1, OAS1, BIRC4BP, and SRGAP2; or IFI6, SAMD9L, BIRC4BP, SRGAP2, and RSAD2; or IFI6, SAMD9L, OAS1, SRGAP2, and RSAD2; or IFI6, SAMD9L, OAS1, BIRC4BP, and RSAD2; or IFI6, SAMD9L, OAS1, BIRC4BP, and SRGAP2; or IFI6, SAMD9L, GBP1, SRGAP2, and RSAD2; or IFI6, SAMD9L, GBP1, BIRC4BP, and RSAD2; or IFI6, SAMD9L, GBP1, BIRC4BP, and SRGAP2; or IFI6, SAMD9L, GBP1, OAS1, and RSAD2; or IFI6, SAMD9L, GBP1, OAS1, and SRGAP2; or IFI6, SAMD9L, GBP1, OAS1, and BIRC4BP; or IFI44, GBP1, BIRC4BP, SRGAP2, and RSAD2; or IFI44, GBP1, OAS1, SRGAP2, and RSAD2; or IFI44, GBP1, OAS1, BIRC4BP, and RSAD2; or IFI44, GBP1, OAS1, BIRC4BP, and SRGAP2; or IFI44, SAMD9L, BIRC4BP, SRGAP2, and RSAD2; or IFI44, SAMD9L, OAS1, SRGAP2, and RSAD2; or IFI44, SAMD9L, OAS1, BIRC4BP, and RSAD2; or IFI44, SAMD9L, OAS1, BIRC4BP, and SRGAP2; or IFI44, SAMD9L, GBP1, SRGAP2, and RSAD2; or IFI44, SAMD9L, GBP1, BIRC4BP, and RSAD2; or IFI44, SAMD9L, GBP1, BIRC4BP, and SRGAP2; or IFI44, SAMD9L, GBP1, OAS1, and RSAD2; or IFI44, SAMD9L, GBP1, OAS1, and SRGAP2; or IFI44, SAMD9L, GBP1, OAS1, and BIRC4BP; or IFI44, IFI6, OAS1, SRGAP2, and RSAD2; or IFI44, IFI6, OAS1, BIRC4BP, and RSAD2; or IFI44, IFI6, OAS1, BIRC4BP, and SRGAP2; or IFI44, IFI6, GBP1, SRGAP2, and RSAD2; or IFI44, IFI6, GBP1, BIRC4BP, and RSAD2; or IFI44, IFI6, GBP1, BIRC4BP, and SRGAP2; or IFI44, IFI6, GBP1, OAS1, and RSAD2; or IFI44, IFI6, GBP1, OAS1, and SRGAP2; or IFI44, IFI6, GBP1, OAS1, and BIRC4BP; or IFI44, IFI6, SAMD9L, BIRC4BP, and RSAD2; or IFI44, IFI6, SAMD9L, BIRC4BP, and SRGAP2; or IFI44, IFI6, SAMD9L, OAS1, and RSAD2; or IFI44, IFI6, SAMD9L, OAS1, and SRGAP2; or IFI44, IFI6, SAMD9L, OAS1, and BIRC4BP; or IFI44, IFI6, SAMD9L, GBP1, and SRGAP2. The IFNα-inducible PD markers in such an expression profile may further include at least one or more gene listed in Tables 19 and/or 20 and/or 21 and/or 22 and/or 23 and/or 24 and/or 26 and/or 28 and/or 30.
  • The IFNα-inducible PD markers in an expression profile may include any at least 4 genes selected from the group consisting of: IFI44, IFI6, SAMD9L, GBP1, OAS1, BIRC4BP, SRGAP2, and RSAD2. The IFNα-inducible PD markers in such an expression profile may further include at least one or more gene listed in Tables 19 and/or 20 and/or 21 and/or 22 and/or 23 and/or 24 and/or 26 and/or 28 and/or 30.
  • The IFNα-inducible PD markers in an expression profile may include any at least 3 genes selected from the group consisting of: IFI44, IFI6, SAMD9L, GBP1, OAS1, BIRC4BP, SRGAP2, and RSAD2. The IFNα-inducible PD markers in such an expression profile may further include at least one or more gene listed in Tables 19 and/or 20 and/or 21 and/or 22 and/or 23 and/or 24 and/or 26 and/or 28 and/or 30.
  • The IFNα-inducible PD markers in an expression profile may include any at least 2 genes selected from the group consisting of: IFI44, IFI6, SAMD9L, GBP1, OAS1, BIRC4BP, SRGAP2, and RSAD2. The IFNα-inducible PD markers in such an expression profile may further include at least one or more gene listed in Tables 19 and/or 20 and/or 21 and/or 22 and/or 23 and/or 24 and/or 26 and/or 28 and/or 30.
  • The IFNα-inducible PD markers in an expression profile may include at least genes IFI27, SIGLEC1, RSAD2, IFI6, IFI44L, IFI44, USP18, IFIT2, SAMD9L, BIRC4BP, DNAPTP6, OAS3, LY6E, IFIT1, LIPA, LOC129607, ISG15, PARP14, MX1, OAS2, OASL, CCL2, HERC5, OAS1. The IFNα-inducible PD markers in such an expression profile may further include at least one or more gene listed in Table 19 and/or 20 and/or 21, and/or 22, and/or 23, and/or 24, and/or 26, and/or 28, and/or 30.
  • The IFNα-inducible PD markers in an expression profile may include at least genes IFIT1, IFIT3, IRF7, IFI6, IL6ST, IRF2, LY6E, MARCKS, MX1, MX2, OAS1, EIF2AK2, ISG15, STAT2, OAS3, IFI44, IFI44L, HERC5, RAB8B, LILRA5, RSAD2, and FCHO2. The IFNα-inducible PD markers in such an expression profile may further include at least one or more gene listed in Table 19 and/or 20 and/or 21, and/or 22, and/or 23, and/or 24, and/or 26, and/or 28 and/or 30.
  • The IFNα-inducible PD markers in an expression profile may include at least genes SERPING1, IFIT2, IFIT3, IFI6, LY6E, MX1, OAS1, ISG15, IFI27, OAS3, IFI44, LAMP3, DNAPTP6, ETV7, HERC5, OAS2, USP18, XAF1, RTP4, SIGLEC1, and EPSTI1. The IFNα-inducible PD markers in such an expression profile may further include at least one or more gene listed in Table 19 and/or 20 and/or 21, and/or 22, and/or 23, and/or 24, and/or 26, and/or 28 and/or 30.
  • The IFNα-inducible PD markers in an expression profile may include at least genes SERPING1, IFIT2, IFIT3, IFI6, LY6E, MX1, OAS1, ISG15, IFI27, OAS3, IFI44, LAMP3, DNAPTP6, ETV7, HERC5, OAS2, USP18, XAF1, RTP4, SIGLEC1, EPSTI1, and RSAD2. The IFNα-inducible PD markers in such an expression profile may further include at least one or more gene listed in Table 19 and/or 20 and/or 21, and/or 22, and/or 23, and/or 24, and/or 26, and/or 28 and/or 30.
  • The IFNα-inducible PD markers in an expression profile may include at least genes BCL2, BAK1, BAD, BAX, and BCL2L1. The IFNα-inducible PD markers in such an expression profile may further include at least one or more gene listed in Table 19 and/or 20 and/or 21, and/or 22, and/or 23, and/or 24, and/or 26, and/or 28 and/or 30.
  • The IFNα-inducible PD markers in an expression profile may include at least genes RTP4, RSAD2, HERC5, SIGLEC1, USP18, LY6E, ETV7, SERPING1, IFIT3, OAS1, HSXIAPAF1, G1P3, MX1, OAS3, IFI27, DNAPTP6, LAMP3, EPSTI1, IFI44, OAS2, IFIT2, and ISG15. The IFNα-inducible PD markers in such an expression profile may further include at least one or more gene listed in Table 19 and/or 20 and/or 21, and/or 22, and/or 23, and/or 24, and/or 26, and/or 28 and/or 30.
  • The IFNα-inducible PD markers in an expression profile may include at least genes LAMP3, SIGLEC1, DNAPTP6, IFIT2, ETV7, RTP4, SERPING1, HERC5, XAF1, MX1, EPSTI1, OAS2, OAS1, OAS3, IFIT3, IFI6, USP18, RSAD2, IFI44, LY6E, ISG15, and IFI27. The IFNα-inducible PD markers in such an expression profile may further include at least one or more gene listed in Table 19 and/or 20 and/or 21, and/or 22, and/or 23, and/or 24, and/or 26, and/or 28 and/or 30.
  • The IFNα-inducible PD markers in an expression profile may include at least genes DNAPTP6, EPSTI1, HERC5, IFI27, IFI44, IFI44L, IFI6, IFIT1, IFIT3, ISG15, LAMP3, LY6E, MX1, OAS1, OAS2, OAS3, PLSCR1, RSAD2, RTP4, SIGLEC1, and USP18. The IFNα-inducible PD markers in such an expression profile may further include at least one or more gene listed in Table 19 and/or 20 and/or 21, and/or 22, and/or 23, and/or 24, and/or 26, and/or 28 and/or 30.
  • The IFNα-inducible PD markers in an expression profile may include at least genes SAMD9L, IFI6, IFI44, IFIT2, ZC3HAV1, ETV6, DAPP1, IL1RN, CEACAM1, OAS1, IFI27, OAS3, IFI44L, HERC5, IFIT1, EPSTI1, ISG15, SERPING1, OASL, GBP1, and MX1. The IFNα-inducible PD markers in such an expression profile may further include at least one or more gene listed in Table 19 and/or 20 and/or 21, and/or 22, and/or 23, and/or 24, and/or 26, and/or 28 and/or 30.
  • The IFNα-inducible PD markers in an expression profile may include at least genes IFI6, RSAD2, IFI44, IFI44L, IFI27, MX1, IFIT1, ISG15, LAMP3, OAS3, OAS1, EPSTI1, IFIT3, OAS2, SIGLEC1, and USP18. The IFNα-inducible PD markers in such an expression profile may further include at least one or more gene listed in Table 19 and/or 20 and/or 21, and/or 22, and/or 23, and/or 24, and/or 26, and/or 28 and/or 30.
  • The IFNα-inducible PD markers in an expression profile may include at least genes IFI6, RSAD2, IFI44, IFI44L, IFI27, MX1, IFIT1, HERC5, ISG15, LAMP3, OAS3, OAS1, EPSTI1, IFIT3, OAS2, LY6E, SIGLEC1, and USP18. The IFNα-inducible PD markers in such an expression profile may further include at least one or more gene listed in Table 19 and/or 20 and/or 21, and/or 22, and/or 23, and/or 24, and/or 26, and/or 28 and/or 30.
  • The IFNα-inducible PD markers in an expression profile may include at least genes IFI6, RSAD2, IFI44, IFI44L, IFI27, MX1, and IFIT1. The IFNα-inducible PD markers in such an expression profile may further include at least one or more gene listed in Table 19 and/or 20 and/or 21, and/or 22, and/or 23, and/or 24, and/or 26, and/or 28 and/or 30.
  • The IFNα-inducible PD markers in an expression profile may include at least genes IFI6, RSAD2, IFI44, IFI44L, and IFI27. The IFNα-inducible PD markers in such an expression profile may further include at least one or more gene listed in Table 19 and/or 20 and/or 21, and/or 22, and/or 23, and/or 24, and/or 26, and/or 28 and/or 30.
  • The IFNα-inducible PD markers in an expression profile may include at least genes SAMD9L, IFI6, IFI44, IFIT2, OAS1, IFI27, OAS3, IFI44L, HERC5, IFIT1, EPSTI1, ISG15, SERPING1, OASL, GBP1, and MX1. The IFNα-inducible PD markers in such an expression profile may further include at least one or more gene listed in Table 19 and/or 20 and/or 21, and/or 22, and/or 23, and/or 24, and/or 26, and/or 28 and/or 30.
  • The IFNα-inducible PD markers in an expression profile may include at least genes IFI27, IL-121R beta2, IL-15R alpha, IL-15, suppressor of cytokine signaling 1 (SOCS1), janus kinase 2, CXCL11 (T-TAC), TNFSF13B (BAFF), TRAF-type domain 1 (TRAFD1), SERPING1, CD274 (PD1-L), indoleamine 2,3 dioxygenase (INDO), lymphocyte-activation gene 3 (LAG3), and caspase 5. The IFNα-inducible PD markers in such an expression profile may further include at least one or more gene listed in Table 19 and/or 20 and/or 21, and/or 22, and/or 23, and/or 24, and/or 26, and/or 28 and/or 30.
  • The IFNα-inducible PD markers in an expression profile may include at least genes complement factor B, insulin-like growth factor (IGF2BP3), cyclin A1, neuropilin 2, complement 1qB, complement 1qC, CD80, CD47, MMP14, toll-like receptor 3 (TLR3), TLR adaptor molecule 2 (TICAM2), macrophage scavenger receptor-1 (MSR1), desmoplakin, PDGR receptor, CCL13 (MCP-4), CXCL13 (BCA-1), CCL19 (CCR7), IL-1 family 5, purinergic receptor P2X7, IRS 1, caspase 3, and cyclin-dependent kinase-like 1 (CDKL1). The IFNα-inducible PD markers in such an expression profile may further include at least one or more gene listed in Table 19 and/or 20 and/or 21, and/or 22, and/or 23, and/or 24, and/or 26, and/or 28 and/or 30.
  • The IFNα-inducible PD markers in an expression profile may include alterations in any one or more of serum protein levels of adiponectin, alpha-fetoprotein, apolipoprotein CIII, beta-2 microglobulin, cancer antigen 125, cancer antigen 19-9, eotaxin, FABP, factor VII, ferritin, IL-10, IL-12p70, IL-16, IL-18, IL-1ra, IL-3, MCP-1, MMP-3, myoglobin, SGOT, tissue factor, TIMP-1, TNF RII, TNF-alpha, VCAM-1, vWF, BDNK, complement 3, CD40 ligand, EGF, ENA-78, EN-RAGE, IGF-1, MDC, myeloperoxidase, RANTES, or thrombopoietin.
  • The IFNα-inducible PD markers in an expression profile may include alterations in any one or more of serum protein levels of adiponectin, alpha-fetoprotein, apolipoprotein CIII, beta-2 microglobulin, cancer antigen 125, cancer antigen 19-9, eotaxin, FABP, factor VII, ferritin, IL-10, IL-12p70, IL-16, IL-18, IL-1ra, IL-3, MCP-1, MMP-3, myoglobin, SGOT, tissue factor, TIMP-1, TNF RII, TNF-alpha, VCAM-1, or vWF. The IFNα-inducible PD markers in such an expression profile may further include at least one or more gene listed in Table 19 and/or 20 and/or 21, and/or 22, and/or 23, and/or 24, and/or 26, and/or 28 and/or 30.
  • The IFNα-inducible PD markers in an expression profile may include alterations in any one or more of serum protein levels of BDNK, complement 3, CD40 ligand, EGF, ENA-78, EN-RAGE, IGF-1, MDC, myeloperoxidase, RANTES, or thrombopoietin. The IFNα-inducible PD markers in such an expression profile may further include at least one or more gene listed in Table 19 and/or 20 and/or 21, and/or 22, and/or 23, and/or 24, and/or 26, and/or 28 and/or 30.
  • An IFNα-inducible PD marker expression profile may further include genes whose expression or activity is down-regulated in cells exposed to non-baseline IFNα levels. The genes whose expression or activity is down-regulated may be any of the genes that are identified in Table 31. The genes may include any one or more of SLC4A1, PRSS33, FCER1A, BACH2, KLRB1, D4S234E, T cell receptor alpha locus/l cell receptor delta locus, FEZ1, AFF3, CD160, ABCB1, PTCH1, OR2W3, IGHD, NOG, NR3C2, TNS1, PDZK1IP1, SH2D1B, STRBP, ZMYND11, TMOD1, FCRLA, DKFZp761P0423, EPB42, NR6A1, LOC341333, MS4A1, IGHM, SIGLECP3, KIR2DS2, PKIA, BLR1, C5orf4, MYLK, LOC283663, MAD1L1, CXCL5, D4S234E, FCRLA, KRT1, c16orf74, ABCB4, or GPRASP1. Any number of these genes may serve as PD markers in an IFNα-inducible PD marker expression profile. For example, at least 2, at least 3, at least 4, at least 5, at least 6, at least 7, at least 8, at least 9, at least 10, at least 11, at least 12 at least 15, at least 20, at least 25, at least 30, at least 35, at least 40, at least 45, or at least 50 down-regulated genes may be included in the IFNα-inducible PD marker expression profile. The IFNα-inducible PD marker expression profile may further include genes listed in Tables 19 and/or 20 and/or 21 and/or 22 and/or 23 and/or 24 and/or 26 and/or 28.
  • The IFNα-inducible PD marker expression profile may include gene FEZ1, or may include genes FEZ1 and NOG, or may include gene NOG, or may include genes FEZ1, NOG, and SLC4A1, or may include gene SLC4A1, or may include genes NOG and SLC4A1, or may include genes FEZ1, NOG, SLC4A1, and D4S234E, or may include genes FEZ1, NOG, SLC4A1, D4S234E, and PRSS33. The IFNα-inducible PD marker expression profile may further include genes listed in Tables 19 and/or 20 and/or 21 and/or 22 and/or 23 and/or 24 and/or 26 and/or 28 and/or 30, and/or 31.
  • Down-regulated genes may have down-regulated expression or activity of at least 5%, at least 10%, at least 15%, at least 20%, at least 25%, at least 30%, at least 35%, at least 40%, at least 45%, at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% that of control cells, e.g., cells of healthy volunteers or cells of control animals or cells not exposed to IFNα in culture.
  • Up- or down-regulation of gene expression or activity of IFNα-inducible PD markers may be determined by any means known in the art. For example, up- or down-regulation of gene expression may be detected by determining mRNA levels. mRNA expression may be determined by northern blotting, slot blotting, quantitative reverse transcriptase polymerase chain reaction, or gene chip hybridization techniques. See U.S. Pat. Nos. 5,744,305 and 5,143,854 for examples of making nucleic acid arrays for gene chip hybridization techniques.
  • Up- or down-regulation of gene expression or activity of IFNα-inducible PD markers may be determined by detecting protein levels. The up- or down-regulated gene whose protein levels are detected may be any one, any two, any three, any four, any five, any six, any seven, any eight, any nine, any ten, any twelve, any fifteen, any twenty, any twenty five, any thirty, any thirty five, or more of adiponectin, alpha-fetoprotein, apolipoprotein CIII, beta-2 microglobulin, cancer antigen 125, cancer antigen 19-9, eotaxin, FABP, factor VII, ferritin, IL-10, IL-12p70, IL-16, IL-18, IL-1ra, IL-3, MCP-1, MMP-3, myoglobin, SGOT, tissue factor, TIMP-1, TNF RII, TNF-alpha, VCAM-1, vWF, BDNK, complement 3, CD40 ligand, EGF, ENA-78, EN-RAGE, IGF-1, MDC, myeloperoxidase, RANTES, or thrombopoietin. Methods for detecting protein expression levels include immuno-based assays such as enzyme-linked immunosorbant assays, western blotting, protein arrays, and silver staining.
  • An IFNα-inducible PD marker expression profile may comprise a profile of protein activity. Up- or down-regulation of gene expression or activity of IFNα-inducible PD markers may be determined by detecting activity of proteins including, but not limited to, detectable phosphorylation activity, de-phosphorylation activity, or cleavage activity. Furthermore, up- or down-regulation of gene expression or activity of IFNα-inducible PD markers may be determined by detecting any combination of these gene expression levels or activities.
  • A candidate therapeutic for treating IFNα-mediated disorders may be identified by the methods encompassed by the invention. Candidate therapeutics may be any type of molecule including a small molecule or a biological agent. A candidate therapeutic identified by the methods encompassed by the invention may immediately be identified as useful as a therapeutic for a disease, disorder, or condition. Alternatively, a candidate therapeutic identified by the methods encompassed by the invention may need to be further tested and/or modified before selection for treating patients. Alternatively, a candidate therapeutic identified by the methods encompassed by the invention may, after further testing, be de-selected as a molecule for treating patients.
  • In methods that identify candidate therapeutics, cells comprising an IFNα-inducible PD marker expression profile are contacted with an agent. The cells may be any type of cells, such as commercially available immortalized cell lines that comprise an IFNα-inducible PD marker expression profile, commercially available immortalized cell lines that have been treated with IFNα to induce an IFNα-inducible PD marker expression profile, cells isolated from a patient having an IFNα-inducible PD marker expression profile, or cells isolated from a healthy patient and treated with IFNα to induce an IFNα-inducible PD marker expression profile.
  • Presence or absence of a change in the IFNα-inducible PD marker expression profile of the cells is detected following contacting the cells with the agent. Presence of change may be any change in IFNα-inducible PD marker expression profile including at least a 10% decrease in up-regulated expression or activity of at least 1 gene in the IFNα-inducible PD marker expression profile, at least a 20% decrease of the at least 1 up-regulated gene, at least a 30% decrease of the at least up-regulated 1 gene, at least a 40% decrease of the at least 1 up-regulated gene, at least a 50% decrease of the at least 1 up-regulated gene, at least a 60% decrease of the at least 1 up-regulated gene, at least a 70% decrease of the at least 1 up-regulated gene, at least a 75% decrease of the at least 1 up-regulated gene, at least an 80% decrease of the at least 1 up-regulated gene, at least an 85% decrease of the at least 1 up-regulated gene, at least a 90% decrease of the at least 1 up-regulated gene, at least a 95% decrease of the at least 1 up-regulated gene, at least a 96% decrease of the at least 1 up-regulated gene, at least a 97% decrease of the at least 1 up-regulated gene, at least a 98% decrease of the at least 1 up-regulated gene, at least a 99% decrease of the at least 1 up-regulated gene, or a 100% decrease of the at least 1 up-regulated gene. Alternatively, or in addition, presence of change may be any change in IFNα-inducible PD marker expression profile including at least a 10% increase in expression or activity of at least 1 down-regulated gene in the IFNα-inducible PD marker expression profile, at least a 20% increase of the at least 1 down-regulated gene, at least a 30% increase of the at least 1 down-regulated gene, at least a 40% increase of the at least 1 down-regulated gene, at least a 50% increase of the at least 1 down-regulated gene, at least a 60% increase of the at least 1 down-regulated gene, at least a 70% increase of the at least 1 down-regulated gene, at least a 75% increase of the at least 1 down-regulated gene, at least an 80% increase of the at least 1 down-regulated gene, at least an 85% increase of the at least 1 down-regulated gene, at least a 90% increase of the at least 1 down-regulated gene, at least a 95% increase of the at least 1 down-regulated gene, at least a 96% increase of the at least 1 down-regulated gene, at least a 97% increase of the at least 1 down-regulated gene, at least a 98% increase of the at least 1 down-regulated gene, at least a 99% increase of the at least 1 down-regulated gene, or a 100% increase of the at least 1 down-regulated gene.
  • In methods of monitoring disease progression of a patient samples from the patient may be obtained before and after administration of an agent, e.g., an agent that binds to and modulates type I IFN or IFNα activity, or an agent that binds to and does not modulate type I IFN or IFNα activity, or a combination of agents that may or may not include an agent that binds to and modulates type I IFN or IFNα activity. Type I IFN or IFNα inducible PD marker expression profiles are obtained in the (before and after agent administration) samples. The type I IFN or IFNα inducible PD marker expression profiles in the samples are compared. Comparison may be of the number of type I IFN or IFNα inducible PD markers present in the samples or may be of the quantity of type I IFN or IFNα inducible PD markers present in the samples, or any combination thereof. Variance indicating efficacy of the therapeutic agent may be indicated if the number or level (or any combination thereof) of up-regulated type I IFN or IFNα inducible PD markers decreases in the sample obtained after administration of the therapeutic agent relative to the sample obtained before administration of the therapeutic agent. The number of up-regulated type I IFN or IFNα inducible PD markers may decrease by at least 1, at least 2, at least 3, at least 4, at least 5, at least 6, at least 7, at least 8, at least 9, or at least 10. The level of any given up-regulated type I IFN or IFNα inducible PD marker may decrease by at least 10%, at least 20%, at least 25%, at least 30%, at least 35%, at least 40%, at least 50%, at least 60%, at least 70%, at least 80%, at least 90%, or at least 95%. The number of up-regulated type I IFN or IFNα inducible PD markers with decreased levels may be at least 1, at least 2, at least 3, at least 4, at least 5, at least 6, at least 7, at least 8, at least 9, at least 10, at least 15, at least 20, at least 25, at least 30, or at least 35. Any combination of decreased number and decreased level of up-regulated type I IFN or IFNα inducible PD markers may indicate efficacy. Variance indicating efficacy of the therapeutic agent may be indicated if the number or level (or any combination thereof) of down-regulated type I IFN or IFNα inducible PD markers decreases in the sample obtained after administration of the therapeutic agent relative to the sample obtained before administration of the therapeutic agent. The number of down-regulated type I IFN or IFNα inducible PD markers may decrease by at least 1, at least 2, at least 3, at least 4, at least 5, at least 6, at least 7, at least 8, at least 9, or at least 10. The level of any given down-regulated type I IFN or IFNα inducible PD marker may increase by at least 10%, at least 20%, at least 25%, at least 30%, at least 35%, at least 40%, at least 50%, at least 60%, at least 70%, at least 80%, at least 90%, or at least 95%. The number of down-regulated type I IFN or IFNα inducible PD markers with increased levels may be at least 1, at least 2, at least 3, at least 4, at least 5, at least 6, at least 7, at least 8, at least 9, at least 10, at least 15, at least 20, at least 25, at least 30, or at least 35. Any combination of decreased number and increased level of down-regulated type I IFN or IFNα inducible PD markers may indicate efficacy.
  • The sample obtained from the patient may be obtained prior to a first administration of the agent, i.e., the patient is naïve to the agent. Alternatively, the sample obtained from the patient may occur after administration of the agent in the course of treatment. For example, the agent may have been administered prior to the initiation of the monitoring protocol. Following administration of the agent an additional samples may be obtained from the patient and type I IFN or IFNα inducible PD markers in the samples are compared. The samples may be of the same or different type, e.g., each sample obtained may be a blood sample, or each sample obtained may be a serum sample. The type I IFN or IFNα inducible PD markers detected in each sample may be the same, may overlap substantially, or may be similar.
  • The samples may be obtained at any time before and after the administration of the therapeutic agent. The sample obtained after administration of the therapeutic agent may be obtained at least 2, at least 3, at least 4, at least 5, at least 6, at least 7, at least 8, at least 9, at least 10, at least 12, or at least 14 days after administration of the therapeutic agent. The sample obtained after administration of the therapeutic agent may be obtained at least 2, at least 3, at least 4, at least 5, at least 6, at least 7, or at least 8 weeks after administration of the therapeutic agent. The sample obtained after administration of the therapeutic agent may be obtained at least 2, at least 3, at least 4, at least 5, or at least 6 months following administration of the therapeutic agent.
  • Additional samples may be obtained from the patient following administration of the therapeutic agent. At least 2, at least 3, at least 4, at least 5, at least 6, at least 7, at least 8, at least 9, at least 10, at least 12, at least 15, at least 20, at least 25 samples may be obtained from the patient to monitor progression or regression of the disease or disorder over time. Disease progression may be monitored over a time period of at least 1 week, at least 2 weeks, at least 3 weeks, at least 4 weeks, at least 5 weeks, at least 6 weeks, at least 7 weeks, at least 2 months, at least 3 months, at least 4 months, at least 5 months, at least 6 months, at least 1 year, at least 2 years, at least 3 years, at least 4 years, at least 5 years, at least 10 years, or over the lifetime of the patient. Additional samples may be obtained from the patient at regular intervals such as at monthly, bi-monthly, once a quarter year, twice a year, or yearly intervals. The samples may be obtained from the patient following administration of the agent at regular intervals. For instance, the samples may be obtained from the patient at one week following each administration of the agent, or at two weeks following each administration of the agent, or at three weeks following each administration of the agent, or at one month following each administration of the agent, or at two months following each administration of the agent. Alternatively, multiple samples may be obtained from the patient following an or each administration of the agent.
  • Disease progression in a patient may similarly be monitored in the absence of administration of an agent. Samples may periodically be obtained from the patient having the disease or disorder. Disease progression may be identified if the number of type I IFN or IFNα inducible PD markers increases in a later-obtained sample relative to an earlier obtained sample. The number of type I IFN or IFNα inducible PD markers may increase by at least 1, at least 2, at least 3, at least 4, at least 5, at least 6, at least 7, at least 8, at least 9, or at least 10. Disease progression may be identified if level of any given up-regulated type I IFN or IFNα inducible PD marker increases by at least 10%, at least 20%, at least 25%, at least 30%, at least 35%, at least 40%, at least 50%, at least 60%, at least 70%, at least 80%, at least 90%, or at least 95%. Disease progression may be identified if level of any given down-regulated type I IFN or IFNα inducible PD marker decreases by at least 10%, at least 20%, at least 25%, at least 30%, at least 35%, at least 40%, at least 50%, at least 60%, at least 70%, at least 80%, at least 90%, or at least 95%. The number of up-regulated type I IFN or IFNα inducible PD markers with increased levels may be at least 1, at least 2, at least 3, at least 4, at least 5, at least 6, at least 7, at least 8, at least 9, at least 10, at least 15, at least 20, at least 25, at least 30, or at least 35. The number of down-regulated type I IFN or IFNα inducible PD markers with decreased levels may be at least 1, at least 2, at least 3, at least 4, at least 5, at least 6, at least 7, at least 8, at least 9, at least 10, at least 15, at least 20, at least 25, at least 30, or at least 35. Any combination of increased number and increased level of up-regulated type I IFN or IFNα inducible PD marker may indicate disease progression. Alternatively, or in combination, any combination of decreased number and decreased level of down-regulated type I IFN or IFNα inducible PD marker may indicate disease progression. Disease regression may also be identified in a patient having a disease or disorder, not treated by an agent. In this instance, regression may be identified if the number of type I IFN or IFNα inducible PD markers decreases in a later-obtained sample relative to an earlier obtained sample. The number of type I IFN or IFNα inducible PD markers may decrease by at least 1, at least 2, at least 3, at least 4, at least 5, at least 6, at least 7, at least 8, at least 9, or at least 10. Disease regression may be identified if level of any given up-regulated type I IFN or IFNα inducible PD marker decreases by at least 10%, at least 20%, at least 25%, at least 30%, at least 35%, at least 40%, at least 50%, at least 60%, at least 70%, at least 80%, at least 90%, or at least 95%. Disease regression may be identified if level of any given down-regulated type I IFN or IFNα inducible PD marker increases by at least 10%, at least 20%, at least 25%, at least 30%, at least 35%, at least 40%, at least 50%, at least 60%, at least 70%, at least 80%, at least 90%, or at least 95%. The number of up-regulated type I IFN or IFNα inducible PD markers with decreased levels may be at least 1, at least 2, at least 3, at least 4, at least 5, at least 6, at least 7, at least 8, at least 9, at least 10, at least 15, at least 20, at least 25, at least 30, or at least 35. The number of down-regulated type I IFN or IFNα inducible PD markers with increased levels may be at least 1, at least 2, at least 3, at least 4, at least 5, at least 6, at least 7, at least 8, at least 9, at least 10, at least 15, at least 20, at least 25, at least 30, or at least 35. Disease progression or disease regression may be monitored by obtaining samples over any period of time and at any interval. Disease progression or disease regression may be monitored by obtaining samples over the course of at least 1 week, at least 2 weeks, at least 3 weeks, at least 4 weeks, at least 5 weeks, at least 6 weeks, at least 7 weeks, at least 2 months, at least 3 months, at least 4 months, at least 5 months, at least 6 months, at least 1 year, at least 2 years, at least 3 years, at least 4 years, at least 5 years, at least 10 years, or over the lifetime of the patient. Disease progression or disease regression may be monitored by obtaining samples at least monthly, bi-monthly, once a quarter year, twice a year, or yearly. The samples need not be obtained at strict intervals.
  • The invention also encompasses kits and probes. The probes may be any molecule that detects any expression or activity of any gene that may be included in an IFNα-inducible PD marker expression profile.
  • The invention also encompasses methods of detecting IFN activity. These methods may employ cells comprising a polynucleotide sequence comprising a reporter gene under the control of an interferon-stimulated response element. The cells comprising the polynucleotide sequence may be any cells amenable to transfection or transformation with a polynucleotide sequence and that can be maintained in culture. These cells include animal cells, bacterial cells, yeast cells, insect cells, or plant cells. These cells may be adherent or may grow in suspension. If the cells are animal cells, they may be from a known cell line such as HeLa, COS, NIH3T3, AGS, 293, CHO, Huh-7, HUVEC, MCF-7, C6, BHK-21, BNL CL 2, C2C12, HepG2, and ATDC5. Countless other cell lines are known and can be obtained by those of skill in the art. The cells may alternatively be primary cells that have or have not been immortalized.
  • The cells may comprise a polynucleotide sequence comprising a reporter gene under the control of an interferon-stimulated response element. The polynucleotide sequence may be stably integrated in the DNA of the cell or may be an extrachomosomal element that is stably or transiently in the cell. The polynucleotide may have been introduced to the cell as a naked polynucleotide molecule, a polynucleotide molecule complexed with lipids or other molecules, or a polynucleotide in a virus particle.
  • If the polynucleotide was introduced as a naked polynucleotide molecule, the polynucleotide may have been a linear or a circular molecule. Non-limiting examples of circular polynucleotide molecules include plasmids, and artificial chromosomes. These vectors may be cleaved with enzymes, for example, to generate linear polynucleotide molecules.
  • Furthermore, if the polynucleotide was introduced as a naked polynucleotide it may have been introduced into the cells by any of many well known techniques in the art. These techniques include, but are not limited to, electroporation, microinjection, and biolistic particle delivery. See, also, e.g., Loeffler and Behr, 1993, Meth. Enzymol. 217:599-618; Cohen et al., 1993, Meth. Enzymol. 217:618-644; Clin. Pharma. Ther. 29:69-92 (1985), Sambrook, et al. Molecular Cloning: A Laboratory Manual. 2nd, ed., Cold Spring Harbor Laboratory, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y., 1989 and Ausubel et al., ed. Current Protocols in Molecular Biology, John Wiley & Sons, Inc., N.Y., N.Y. (1987-2001).
  • If the polynucleotide was introduced as a complex with lipids or liposomes, it too may have been introduced by one of many known techniques to the skilled artisan. Lipids or liposomes comprise a mixture of fat particles or lipids which bind to DNA or RNA to provide a hydrophobic coated delivery vehicle. Suitable liposomes may comprise any of the conventional synthetic or natural phospholipid liposome materials including phospholipids from natural sources such as egg, plant or animal sources such as phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol, sphingomyelin, phosphatidylserine or phosphatidylinositol. Synthetic phospholipids also may be used, e.g., dimyristoylphosphatidylcholine, dioleoylphosphatidylcholine, dioleoylphosphatidycholine and corresponding synthetic phosphatidylethanolamines and phosphatidylglycerols. Lipids or liposomes that may be conjugated with the vector are also commercially available to the skilled artisan. Examples of commercially available lipid or liposome transfection reagents known to those of skill in the art include LIPOFECTAMINE™ (Invitrogen), GENEJUICE® (Novagen), GENEJAMMER® (Stratagene), FUGENE® HD (Roche), MEGAFECTIN™ (Qbiogene), SUPERFECT® (Qiagen), and EFFECTENE® (Qiagen).
  • If the polynucleotide was introduced as a complex with other molecules it may have been compacted or in a nanosphere. Compacted polynucleotide complexes are described in U.S. Pat. Nos. 5,972,901, 6,008,336, and 6,077,835. Nanospheres are described in U.S. Pat. Nos. 5,718,905 and 6,207,195. These compacted polynucleotide complexes and nanospheres that complex nucleic acids utilize polymeric cations. Typical polymeric cations include gelatin, poly-L-lysine, and chitosan. Alternatively, the polynucleotide may have been complexed with DEAE-dextran, or transfected using techniques such as calcium phosphate coprecipitation, or calcium chloride coprecipitation.
  • If the polynucleotide was introduced associated with a virus, the virus may have been any well known suitable virus for polynucleotide delivery. Example viruses that may be used as vectors include adenovirus, adeno-associated virus, lentivirus, retrovirus, herpes virus (e.g. herpes simplex virus), vaccina virus, papovirus, Sendai virus, SV40 virus, respiratory syncytial virus, etc.
  • The polynucleotide sequence may include a reporter gene and an interferon-stimulated response element. The reporter gene may be any one of luciferase, chloramphenicol acetyl transferase, β-galactosidase, green fluorescent protein, β-glucuronidase, or secreted placental alkaline phosphatase. Variations of many of these reporter genes, e.g., green fluorescent protein and luceriferase, are known and can be readily identified and/or produced by those of skill in the art. Other reporter genes in addition to those listed will also be known to those of skill in the art and are readily available. Interferon-stimulated response elements are also known to those of skill in the art. They may be obtained from commercial vendors such as Stratagene, Clonetech, and Biomyx. They have also been reported in, for instance, Alcantara et al. (Nuc. Acid. Res. 30 (2002):2068-2075 and Kirchhoff et al. (Oncogene 18 (1999):3725-3736).
  • The cells employed in the assay may be incubated with a sample. The sample may be obtained from a patient, from a vendor with patient samples, or a control sample used for calibration or as a control. If the sample is obtained from a patient it may be any biological fluid or tissue, such as whole blood, saliva, urine, synovial fluid, bone marrow, cerebrospinal fluid, nasal secretions, sputum, amniotic fluid, bronchoalveolar lavage fluid, peripheral blood mononuclear cells, total white blood cells, lymph node cells, spleen cells, tonsil cells, or skin.
  • Expression of the reporter gene is detected by any well known means in the art. The expression, even if “0” indicates IFN activity in the sample. One of skill in the art may further quantitate any level of expression of the reporter gene which may then correlate to level of IFN activity in the sample.
  • Applicants provide a set of non-limiting embodiments to describe some of the aspects of the invention.
    • EMBODIMENTS Embodiment 1
  • A method of treating a patient having a type I IFN or an IFNα-mediated disease or disorder comprising:
      • administering an agent that binds to and modulates type I IFN or IFNα activity;
      • wherein the patient comprises a type I IFN or IFNα-inducible PD marker expression profile;
      • and wherein the agent neutralizes the type I IFN or IFNα-inducible PD marker expression profile of the patient.
    Embodiment 2
  • The method of 1 further comprising detecting neutralization of the type I IFN or IFNα-inducible PD marker expression profile of the patient.
    • Embodiment 3
  • The method of embodiment 1 wherein the type I IFN or IFNα-inducible PD marker expression profile comprises up-regulated expression or activity of genes MX1, LY6E, IFI27, OAS1 IFIT1, IFI6, IFI44L, ISG15, LAMP3, OASL, RSAD2, and IFI44.
    • Embodiment 4
  • The method of embodiment 1 wherein the agent is a biologic agent.
    • Embodiment 5
  • The method of embodiment 4 wherein the agent is an antibody.
    • Embodiment 6
  • The method of embodiment 5 wherein the antibody is MEDI-545.
    • Embodiment 7
  • The method of embodiment 5 wherein the antibody is specific for one or more type I IFN or IFNα subtype but is not MEDI-545.
    • Embodiment 8
  • The method of embodiment 1 wherein the administering the agent alleviates one or more symptoms of the disease or disorder.
    • Embodiment 9
  • The method of embodiment 5 wherein the antibody is administered at a dose between approximately 0.03 and 30 mg/kg.
    • Embodiment 10
  • The method of embodiment 9 wherein the antibody is administered at a dose between 0.3 and 3 mg/kg.
    • Embodiment 11
  • The method of embodiment 10 wherein the antibody is administered at a dose between 0.03 and 1 mg/kg.
    • Embodiment 12
  • The method of any one of embodiments 9-11 wherein the agent neutralizes the type I IFN or IFNα-inducible PD marker expression profile of the patient by at least 10%.
    • Embodiment 13
  • The method of embodiment 12 wherein the agent neutralizes the type I IFN or IFNα-inducible PD marker expression profile of the patient by at least 20%.
    • Embodiment 14
  • The method of embodiment 13 wherein the agent neutralizes the type I IFN or IFNα-inducible PD marker expression profile of the patient by at least 30%.
    • Embodiment 15
  • The method of embodiment 14 wherein the agent neutralizes the type I IFN or IFNα-inducible PD marker expression profile of the patient by at least 40%.
    • Embodiment 16
  • The method of embodiment 15 wherein the agent neutralizes the type I IFN or IFNα-inducible PD marker expression profile of the patient by at least 50%.
    • Embodiment 17
  • The method of embodiment 1 wherein the type I IFN or an IFNα-mediated disease or disorder is one of lupus, psoriasis, vasculitis, sarcoidosis, Sjogren's syndrome, or idiopathic inflammatory myositis.
    • Embodiment 18
  • The method of embodiment 17 wherein the type I IFN or an IFNα-mediated disease or disorder is lupus.
    • Embodiment 19
  • The method of embodiment 17 wherein the type I IFN or an IFNα-mediated disease or disorder is psoriasis.
    • Embodiment 20
  • The method of embodiment 1 wherein the type I IFN or IFNα-inducible PD marker expression profile comprises up-regulated expression or activity of at least IFNα subtypes 1, 2, 8, and 14.
    • Embodiment 21
  • The method of embodiment 1 wherein the type I IFN or IFNα-inducible PD marker expression profile comprises transcripts of PD marker genes.
    • Embodiment 22
  • The method of embodiment 1 wherein the type I IFN or IFNα-inducible PD marker expression profile comprises polypeptides expressed from PD marker genes.
    • Embodiment 23
  • The method of embodiment 1 wherein the type I IFN or IFNα-inducible PD marker expression profile comprises up-regulated expression or activity of genes IFI27, SIGLEC1, RSAD2, IFI6, IFI44L, IFI44, USP18, IFIT2, SAMD9L, BIRC4BP, DNAPTP6, OAS3, LY6E, IFIT1, LIPA, LOC129607, ISG15, PARP14, MX1, OAS2, OASL, CCL2, HERC5, OAS1
    • Embodiment 24
  • The method of embodiment 1 wherein the type I IFN or IFNα-inducible PD marker expression profile comprises up-regulated expression or activity of genes IFIT1, IFIT3, IRF7, IFI6, IL6ST, IRF2, LY6E, MARCKS, MX1, MX2, OAS1, EIF2AK2, ISG15, STAT2, OAS3, IFI44, IFI44L, HERC5, RAB8B, LILRA5, RSAD2, and FCHO2
    • Embodiment 25
  • The method of embodiment 1 wherein the type I IFN or IFNα-inducible PD marker expression profile comprises up-regulated expression or activity of genes SERPING1, IFIT2, IFIT3, IFI6, LY6E, MX1, OAS1, ISG15, IFI27, OAS3, IFI44, LAMP3, DNAPTP6, ETV7, HERC5, OAS2, USP18, XAF1, RTP4, SIGLEC1, and EPSTI1.
    • Embodiment 26
  • The method of embodiment 1 wherein the type I IFN or IFNα-inducible PD marker expression profile comprises up-regulated expression or activity of genes RTP4, RSAD2, HERC5, SIGLEC1, USP18, LY6E, ETV7, SERPING1, IFIT3, OAS1, HSXIAPAF1, G1P3, MX1, OAS3, IFI27, DNAPTP6, LAMP3, EPSTI1, IFI44, OAS2, IFIT2, and ISG15.
    • Embodiment 27
  • The method of embodiment 1 wherein the type I IFN or IFNα-inducible PD marker expression profile comprises up-regulated expression or activity of genes LAMP3, SIGLEC1, DNAPTP6, IFIT2, ETV7, RTP4, SERPING1, HERC5, XAF1, MX1, EPSTI1, OAS2, OAS1, OAS3, IFIT3, IFI6, USP18, RSAD2, IFI44, LY6E, ISG15, and IFI27.
    • Embodiment 28
  • The method of embodiment 1 wherein the type I IFN or IFNα-inducible PD marker expression profile comprises up-regulated expression or activity of genes DNAPTP6, EPSTI1, HERC5, IFI27, IFI44, IFI44L, IFI6, IFIT1, IFIT3, ISG15, LAMP3, LY6E, MX1, OAS1, OAS2, OAS3, PLSCR1, RSAD2, RTP4, SIGLEC1, and USP18.
    • Embodiment 29
  • The method of embodiment 1 wherein the type I IFN or IFNα-inducible PD marker expression profile comprises up-regulated expression or activity of genes SAMD9L, IFI6, IFI44, IFIT2, ZC3HAV1, ETV6, DAPP1, IL1RN, CEACAM1, OAS1, IFI27, OAS3, IFI44L, HERC5, IFIT1, EPSTI1, ISG15, SERPING1, OASL, GBP1, and MX1.
    • Embodiment 30
  • The method of embodiment 1 wherein the type I IFN or IFNα-inducible PD marker expression profile comprises up-regulated expression or activity of genes SAMD9L, IFI6, IFI44, IFIT2, OAS1, IFI27, OAS3, IFI44L, HERC5, IFIT1, EPSTI1, ISG15, SERPING1, OASL, GBP1, and MX1.
    • Embodiment 31
  • The method of embodiment 1 wherein the type I IFN or IFNα-inducible PD marker expression profile comprises up-regulated expression or activity of genes IFI6, RSAD2, IFI44, IFI44L, IFI27, MX1, IFIT1, ISG15, LAMP3, OAS3, OAS1, EPSTI1, IFIT3, OAS2, SIGLEC1, and USP18.
    • Embodiment 32
  • The method of embodiment 1 wherein the type I IFN or IFNα-inducible PD marker expression profile comprises up-regulated expression or activity of genes IFI6, RSAD2, IFI44, IFI44L, and IFI27.
    • Embodiment 33
  • The method of embodiment 32 wherein the type I IFN or IFNα-inducible PD marker expression profile further comprises up-regulated expression or activity of genes MX1 and IFIT1.
    • Embodiment 34
  • The method of embodiment 33 wherein the type I IFN or IFNα-inducible PD marker expression profile further comprises up-regulated expression or activity of genes OAS2 and OAS1.
    • Embodiment 35
  • The method of any one of embodiments 3 or 23-33 wherein the type I IFN or IFNα-inducible PD marker expression profile further comprises down-regulated expression or activity of genes NOG, SLC4A1, PRSS33, and FEZ1.
    • Embodiment 36
  • The method of embodiment 1 wherein the type I IFN or IFNα-inducible PD marker expression profile comprises down-regulated expression or activity of genes NOG, SLC4A1, PRSS33, and FEZ1.
    • Embodiment 37
  • The method of embodiment 22 wherein the polypeptides are detected at increased levels in serum.
    • Embodiment 38
  • The method of embodiment 37 wherein polypeptides include cancer antigen 125, ferritin, tissue factor, and MMP-3.
    • Embodiment 39
  • The method of embodiment 22 wherein the polypeptides are detected at decreased levels in serum.
    • Embodiment 40
  • The method of embodiment 39 wherein the polypeptides include EGF, thrombopoietin, and CD40 ligand.
    • Embodiment 41
  • A method of treating an autoimmune disease patient comprising a moderate or strong type I IFN or an IFNα PD marker profile comprising: administering an agent that binds to and modulates type I IFN or IFNα activity; wherein the agent neutralizes the type I IFN or IFNα-inducible PD marker expression profile of the patient.
    • Embodiment 42
  • The method of 41 further comprising detecting neutralization of the type I IFN or IFNα-inducible PD marker expression profile of the patient.
    • Embodiment 43
  • The method of embodiment 41 wherein the type I IFN or IFNα-inducible PD marker expression profile comprises up-regulated expression or activity of genes MX1, LY6E, IFI27, OAS1 IFIT1, IFI6, IFI44L, ISG15, LAMP3, OASL, RSAD2, and IFI44.
    • Embodiment 44
  • The method of embodiment 41 wherein the type I IFN or IFNα-inducible PD marker expression profile comprises up-regulated expression or activity of genes IFI27, SIGLEC1, RSAD2, IFI6, IFI44L, IFI44, USP18, IFIT2, SAMD9L, BIRC4BP, DNAPTP6, OAS3, LY6E, IFIT1, LIPA, LOC129607, ISG15, PARP14, MX1, OAS2, OASL, CCL2, HERC5, OAS1
    • Embodiment 45
  • The method of embodiment 41 wherein the type I IFN or IFNα-inducible PD marker expression profile comprises up-regulated expression or activity of genes IFIT1, IFIT3, IRF7, IFI6, IL6ST, IRF2, LY6E, MARCKS, MX1, MX2, OAS1, EIF2AK2, ISG15, STAT2, OAS3, IFI44, IFI44L, HERC5, RAB8B, LILRA5, RSAD2, and FCHO2
    • Embodiment 46
  • The method of embodiment 41 wherein the type I IFN or IFNα-inducible PD marker expression profile comprises up-regulated expression or activity of genes SERPING1, IFIT2, IFIT3, IFI6, LY6E, MX1, OAS1, ISG15, IFI27, OAS3, IFI44, LAMP3, DNAPTP6, ETV7, HERC5, OAS2, USP18, XAF1, RTP4, SIGLEC1, and EPSTI1.
    • Embodiment 47
  • The method of embodiment 41 wherein the type I IFN or IFNα-inducible PD marker expression profile comprises up-regulated expression or activity of genes RTP4, RSAD2, HERC5, SIGLEC1, USP18, LY6E, ETV7, SERPING1, IFIT3, OAS1, HSXIAPAF1, G1P3, MX1, OAS3, IFI27, DNAPTP6, LAMP3, EPSTI1, IFI44, OAS2, IFIT2, and ISG15.
    • Embodiment 48
  • The method of embodiment 41 wherein the type I IFN or IFNα-inducible PD marker expression profile comprises up-regulated expression or activity of genes LAMP3, SIGLEC1, DNAPTP6, IFIT2, ETV7, RTP4, SERPING1, HERC5, XAF1, MX1, EPSTI1, OAS2, OAS1, OAS3, IFIT3, IFI6, USP18, RSAD2, IFI44, LY6E, ISG15, and IFI27.
    • Embodiment 49
  • The method of embodiment 41 wherein the type I IFN or IFNα-inducible PD marker expression profile comprises up-regulated expression or activity of genes DNAPTP6, EPSTI1, HERC5, IFI27, IFI44, IFI44L, IFI6, IFIT1, IFIT3, ISG15, LAMP3, LY6E, MX1, OAS1, OAS2, OAS3, PLSCR1, RSAD2, RTP4, SIGLEC1, and USP18.
    • Embodiment 50
  • The method of embodiment 41 wherein the type I IFN or IFNα-inducible PD marker expression profile comprises up-regulated expression or activity of genes SAMD9L, IFI6, IFI44, IFIT2, ZC3HAV1, ETV6, DAPP1, IL1RN, CEACAM1, OAS1, IFI27, OAS3, IFI44L, HERC5, IFIT1, EPSTI1, ISG15, SERPING1, OASL, GBP1, and MX1.
    • Embodiment 51
  • The method of embodiment 41 wherein the type I IFN or IFNα-inducible PD marker expression profile comprises up-regulated expression or activity of genes SAMD9L, IFI6, IFI44, IFIT2, OAS1, IFI27, OAS3, IFI44L, HERC5, IFIT1, EPSTI1, ISG15, SERPING1, OASL, GBP1, and MX1.
    • Embodiment 52
  • The method of embodiment 41 wherein the type I IFN or IFNα-inducible PD marker expression profile comprises up-regulated expression or activity of genes IFI6, RSAD2, IFI44, IFI44L, IFI27, MX1, IFIT1, ISG15, LAMP3, OAS3, OAS1, EPSTI1, IFIT3, OAS2, SIGLEC1, and USP18.
    • Embodiment 53
  • The method of embodiment 41 wherein the type I IFN or IFNα-inducible PD marker expression profile comprises up-regulated expression or activity of genes IFI6, RSAD2, IFI44, and IFI27.
    • Embodiment 54
  • The method of embodiment 53 wherein the type I IFN or IFNα-inducible PD marker expression profile further comprises up-regulated expression or activity of genes MX1 and IFIT1.
    • Embodiment 55
  • The method of embodiment 41 wherein the type I IFN or IFNα-inducible PD marker expression profile comprises up-regulated expression or activity of at least IFNα subtypes 1, 2, 8, and 14.
    • Embodiment 56
  • The method of embodiment 41 wherein the agent is a biologic agent.
    • Embodiment 57
  • The method of embodiment 41 wherein the agent is an antibody.
    • Embodiment 58
  • The method of embodiment 57 wherein the antibody is MEDI-545.
    • Embodiment 59
  • The method of embodiment 57 wherein the antibody is specific for one or more type I IFN or IFNα subtype but is not MEDI-545.
    • Embodiment 60
  • The method of embodiment 41 wherein the administering the agent alleviates one or more symptoms of the disease or disorder.
    • Embodiment 61
  • The method of embodiment 57 wherein the antibody is administered at a dose between approximately 0.03 and 30 mg/kg.
    • Embodiment 62
  • The method of embodiment 57 wherein the antibody is administered at a dose between 0.3 and 3 mg/kg.
    • Embodiment 63
  • The method of embodiment 57 wherein the antibody is administered at a dose between 0.03 and 1 mg/kg.
    • Embodiment 64
  • The method of embodiment 41 wherein the wherein the agent neutralizes the type I IFN or IFNα-inducible PD marker expression profile by at least 10%.
    • Embodiment 65
  • The method of embodiment 64 wherein the wherein the agent neutralizes the type I IFN or IFNα-inducible PD marker expression profile by at least 20%.
    • Embodiment 66
  • The method of embodiment 65 wherein the agent neutralizes the type I IFN or IFNα-inducible PD marker expression profile by at least 30%.
    • Embodiment 67
  • The method of embodiment 66 wherein the wherein the agent neutralizes the type I IFN or IFNα-inducible PD marker expression profile by at least 40%.
    • Embodiment 68
  • The method of embodiment 67 wherein the wherein the agent neutralizes the type I IFN or IFNα-inducible PD marker expression profile by at least 50%.
    • Embodiment 69
  • The method of embodiment 41 wherein the autoimmune disease patient is a lupus, psoriasis, vasculitis, sarcoidosis, Sjogren's syndrome, or idiopathic inflammatory myositis patient.
    • Embodiment 70
  • The method of embodiment 69 wherein the patient is a lupus patient.
    • Embodiment 71
  • The method of embodiment 69 wherein the patient is a psoriasis patient.
    • Embodiment 72
  • A method of neutralizing a type I IFN or IFNα-inducible PD marker expression profile in a patient in need thereof, comprising:
      • administering an agent that binds to and modulates type I IFN or IFNα activity to the patient;
      • wherein the agent neutralizes the type I IFN or IFNα-inducible PD marker expression profile of the patient.
    Embodiment 73
  • The method of 72 further comprising detecting neutralization of the type I IFN or IFNα-inducible PD marker expression profile of the patient.
    • Embodiment 74
  • The method of embodiment 72 wherein the type I IFN or IFNα-inducible PD marker expression profile comprises up-regulated expression or activity of genes MX1, LY6E, IFI27, OAS1 IFIT1, IFI6, IFI44L, ISG15, LAMP3, OASL, RSAD2, and IFI44.
    • Embodiment 75
  • The method of embodiment 72 wherein the agent is a biologic agent.
    • Embodiment 76
  • The method of embodiment 75 wherein the agent is an antibody.
    • Embodiment 77
  • The method of embodiment 76 wherein the antibody is MEDI-545.
    • Embodiment 78
  • The method of embodiment 76 wherein the antibody is specific for one or more type I IFN or IFNα subtype but is not MEDI-545.
    • Embodiment 79
  • The method of embodiment 72 wherein the administering the agent alleviates one or more symptoms of the disease or disorder.
    • Embodiment 80
  • The method of embodiment 76 wherein the antibody is administered at a dose between approximately 0.03 and 30 mg/kg.
    • Embodiment 81
  • The method of embodiment 80 wherein the antibody is administered at a dose between 0.3 and 3 mg/kg.
    • Embodiment 82
  • The method of embodiment 81 wherein the antibody is administered at a dose between 0.03 and 1 mg/kg.
    • Embodiment 83
  • The method of any one of embodiments 80-82 wherein the agent neutralizes the type I IFN or IFNα-inducible PD marker expression profile of the patient by at least 10%.
    • Embodiment 84
  • The method of embodiment 83 wherein the agent neutralizes the type I IFN or IFNα-inducible PD marker expression profile of the patient by at least 20%.
    • Embodiment 85
  • The method of embodiment 84 wherein the agent neutralizes the type I IFN or IFNα-inducible PD marker expression profile of the patient at least 30%.
    • Embodiment 86
  • The method of embodiment 85 wherein the agent neutralizes the type I IFN or IFNα-inducible PD marker expression profile of the patient at least 40%.
    • Embodiment 87
  • The method of embodiment 86 wherein the agent neutralizes the type I IFN or IFNα-inducible PD marker expression profile of the patient at least 50%.
    • Embodiment 88
  • The method of embodiment 72 wherein the patient is a lupus, psoriasis, vasculitis, sarcoidosis, Sjogren's syndrome, or idiopathic inflammatory myositis patient.
    • Embodiment 89
  • The method of embodiment 88 wherein the patient is a lupus patient.
    • Embodiment 90
  • The method of embodiment 88 wherein the patient is a psoriasis patient.
    • Embodiment 91
  • The method of embodiment 72 wherein the type I IFN or IFNα-inducible PD marker expression profile comprises up-regulated expression or activity of at least IFNα subtypes 1, 2, 8, and 14.
    • Embodiment 92
  • The method of embodiment 72 wherein the type I IFN or IFNα-inducible PD marker expression profile comprises transcripts of PD marker genes.
    • Embodiment 93
  • The method of embodiment 72 wherein the type I IFN or IFNα-inducible PD marker expression profile comprises polypeptides expressed from PD marker genes.
    • Embodiment 94
  • The method of embodiment 72 wherein the type I IFN or IFNα-inducible PD marker expression profile comprises up-regulated expression or activity of genes IFI27, SIGLEC1, RSAD2, IFI6, IFI44L, IFI44, USP18, IFIT2, SAMD9L, BIRC4BP, DNAPTP6, OAS3, LY6E, IFIT1, LIPA, LOC129607, ISG15, PARP14, MX1, OAS2, OASL, CCL2, HERC5, OAS1.
    • Embodiment 95
  • The method of embodiment 72 wherein the type I IFN or IFNα-inducible PD marker expression profile comprises up-regulated expression or activity of genes IFIT1, IFIT3, IRF7, IFI6, IL6ST, IRF2, LY6E, MARCKS, MX1, MX2, OAS1, EIF2AK2, ISG15, STAT2, OAS3, IFI44, IFI44L, HERC5, RAB8B, LILRA5, RSAD2, and FCHO2.
    • Embodiment 96
  • The method of embodiment 72 wherein the type I IFN or IFNα-inducible PD marker expression profile comprises up-regulated expression or activity of genes SERPING1, IFIT2, IFIT3, IFI6, LY6E, MX1, OAS1, ISG15, IFI27, OAS3, IFI44, LAMP3, DNAPTP6, ETV7, HERC5, OAS2, USP18, XAF1, RTP4, SIGLEC1, and EPSTI1.
    • Embodiment 97
  • The method of embodiment 72 wherein the type I IFN or IFNα-inducible PD marker expression profile comprises up-regulated expression or activity of genes RTP4, RSAD2, HERC5, SIGLEC1, USP18, LY6E, ETV7, SERPING1, IFIT3, OAS1, HSXIAPAF1, G1P3, MX1, OAS3, IFI27, DNAPTP6, LAMP3, EPSTI1, IFI44, OAS2, IFIT2, and ISG15.
    • Embodiment 98
  • The method of embodiment 72 wherein the type I IFN or IFNα-inducible PD marker expression profile comprises up-regulated expression or activity of genes LAMP3, SIGLEC1, DNAPTP6, IFIT2, ETV7, RTP4, SERPING1, HERC5, XAF1, MX1, EPSTI1, OAS2, OAS1, OAS3, IFIT3, IFI6, USP18, RSAD2, IFI44, LY6E, ISG15, and IFI27.
    • Embodiment 99
  • The method of embodiment 72 wherein the type I IFN or IFNα-inducible PD marker expression profile comprises up-regulated expression or activity of genes DNAPTP6, EPSTI1, HERC5, IFI27, IFI44, IFI44L, IFI6, IFIT1, IFIT3, ISG15, LAMP3, LY6E, MX1, OAS1, OAS2, OAS3, PLSCR1, RSAD2, RTP4, SIGLEC1, and USP18.
    • Embodiment 100
  • The method of embodiment 72 wherein the type I IFN or IFNα-inducible PD marker expression profile comprises up-regulated expression or activity of genes SAMD9L, IFI6, IFI44, IFIT2, ZC3HAV1, ETV6, DAPP1, IL1RN, CEACAM1, OAS1, IFI27, OAS3, IFI44L, HERC5, IFIT1, EPSTI1, ISG15, SERPING1, OASL, GBP1, and MX1.
    • Embodiment 101
  • The method of embodiment 72 wherein the type I IFN or IFNα-inducible PD marker expression profile comprises up-regulated expression or activity of genes SAMD9L, IFI6, IFI44, IFIT2, OAS1, IFI27, OAS3, IFI44L, HERC5, IFIT1, EPSTI1, ISG15, SERPING1, OASL, GBP1, and MX1.
    • Embodiment 102
  • The method of embodiment 72 wherein the type I IFN or IFNα-inducible PD marker expression profile comprises up-regulated expression or activity of genes IFI6, RSAD2, IFI44, IFI44L, IFI27, MX1, IFIT1, ISG15, LAMP3, OAS3, OAS1, EPSTI1, IFIT3, OAS2, SIGLEC1, and USP18.
    • Embodiment 103
  • The method of embodiment 72 wherein the type I IFN or IFNα-inducible PD marker expression profile comprises up-regulated expression or activity of genes IFI6, RSAD2, IFI44, IFI44L, and IFI27.
    • Embodiment 104
  • The method of embodiment 103 wherein the type I IFN or IFNα-inducible PD marker expression profile further comprises up-regulated expression or activity of genes MX1 and IFIT1.
    • Embodiment 105
  • The method of any one of embodiments 74 or 94-104 wherein the type I IFN or IFNα-inducible PD marker expression profile further comprises down-regulated expression or activity of genes NOG, SLC4A1, PRSS33, and FEZ1.
    • Embodiment 106
  • The method of embodiment 72 wherein the type I IFN or IFNα-inducible PD marker expression profile comprises down-regulated expression or activity of genes NOG, SLC4A1, PRSS33, and FEZ1.
    • Embodiment 107
  • The method of embodiment 93 wherein the polypeptides are detected at increased levels in serum.
    • Embodiment 108
  • The method of embodiment 107 wherein polypeptides include cancer antigen 125, ferritin, tissue factor, and MMP-3.
    • Embodiment 109
  • The method of embodiment 93 wherein the polypeptides are detected at decreased levels in serum.
    • Embodiment 110
  • The method of embodiment 109 wherein the polypeptides include EGF, thrombopoietin, and CD40 ligand.
    • Embodiment 111
  • A method of monitoring or prognosing autoimmune disease progression of a patient comprising:
      • obtaining a first IFNα-inducible PD marker expression profile in a first sample from a patient.
    Embodiment 112
  • The method of embodiment 111 wherein the first IFNα-inducible PD marker expression profile is a strong profile and the patient prognosis is disease progression.
    • Embodiment 113
  • The method of embodiment 112 wherein the autoimmune disease is SLE and the progression is an SLE flare.
    • Embodiment 114
  • The method of embodiment 111 wherein the first IFNα-inducible PD marker expression profile is a weak profile and the patient prognosis is disease regression.
    • Embodiment 115
  • The method of embodiment 111 further comprising:
      • obtaining a second IFNα-inducible PD marker expression profile in a second sample from a patient;
      • wherein an increase in number or level of type I IFN or IFNα inducible PD markers in the second relative to the first expression profile prognoses disease progression; or
      • wherein a decrease in number or level of type I IFN or IFNα inducible PD markers in the second relative to the first expression profile prognoses disease regression.
    Embodiment 116
  • A method of monitoring disease progression of a patient receiving treatment with a therapeutic agent that binds to and modulates IFNα activity comprising:
      • obtaining a first IFNα-inducible PD marker expression profile in a first sample from the patient;
      • administering a therapeutic agent that binds to and modulates IFNα activity;
      • obtaining a second IFNα-inducible PD marker expression profile in a second sample from the patient; and
      • comparing the first and the second IFNα-inducible PD marker expression profiles,
        • wherein a variance in the first and the second IFNα-inducible PD marker expression profiles indicates a level of efficacy of the therapeutic agent that binds to and modulates IFNα activity.
    Embodiment 117
  • The method of embodiment 116 wherein the first IFNα-inducible PD marker expression profile comprises up-regulated expression or activity of genes MX1, LY6E, IFI27, OAS1, IFIT1, IFI6, IFI44L, ISG15, LAMP3, OASL, RSAD2, and IFI44
    • Embodiment 118
  • The method of embodiment 116 wherein the first type I IFN or IFNα-inducible PD marker expression profile comprises up-regulated expression or activity of genes IFI27, SIGLEC1, RSAD2, IFI6, IFI44L, IFI44, USP18, IFIT2, SAMD9L, BIRC4BP, DNAPTP6, OAS3, LY6E, IFIT1, LIPA, LOC129607, ISG15, PARP14, MX1, OAS2, OASL, CCL2, HERC5, OAS1.
    • Embodiment 119
  • The method of embodiment 116 wherein the first type I IFN or IFNα-inducible PD marker expression profile comprises up-regulated expression or activity of genes IFIT1, IFIT3, IRF7, IFI6, IL6ST, IRF2, LY6E, MARCKS, MX1, MX2, OAS1, EIF2AK2, ISG15, STAT2, OAS3, IFI44, IFI44L, HERC5, RAB8B, LILRA5, RSAD2, and FCHO2.
    • Embodiment 120
  • The method of embodiment 116 wherein the first type I IFN or IFNα-inducible PD marker expression profile comprises up-regulated expression or activity of genes SERPING1, IFIT2, IFIT3, IFI6, LY6E, MX1, OAS1, ISG15, IFI27, OAS3, IFI44, LAMP3, DNAPTP6, ETV7, HERC5, OAS2, USP18, XAF1, RTP4, SIGLEC1, and EPSTI1.
    • Embodiment 121
  • The method of embodiment 116 wherein the first type I IFN or IFNα-inducible PD marker expression profile comprises up-regulated expression or activity of genes RTP4, RSAD2, HERC5, SIGLEC1, USP18, LY6E, ETV7, SERPING1, IFIT3, OAS1, HSXIAPAF1, G1P3, MX1, OAS3, IFI27, DNAPTP6, LAMP3, EPSTI1, IFI44, OAS2, IFIT2, and ISG15.
    • Embodiment 122
  • The method of embodiment 116 wherein the first type I IFN or IFNα-inducible PD marker expression profile comprises up-regulated expression or activity of genes LAMP3, SIGLEC1, DNAPTP6, IFIT2, ETV7, RTP4, SERPING1, HERC5, XAF1, MX1, EPSTI1, OAS2, OAS1, OAS3, IFIT3, IFI6, USP18, RSAD2, IFI44, LY6E, ISG15, and IFI27.
    • Embodiment 123
  • The method of embodiment 116 wherein the first type I IFN or IFNα-inducible PD marker expression profile comprises up-regulated expression or activity of genes DNAPTP6, EPSTI1, HERC5, IFI27, IFI44, IFI44L, IFI6, IFIT1, IFIT3, ISG15, LAMP3, LY6E, MX1, OAS1, OAS2, OAS3, PLSCR1, RSAD2, RTP4, SIGLEC1, and USP18.
    • Embodiment 124
  • The method of embodiment 116 wherein the first type I IFN or IFNα-inducible PD marker expression profile comprises up-regulated expression or activity of genes SAMD9L, IFI6, IFI44, IFIT2, ZC3HAV1, ETV6, DAPP1, IL1RN, CEACAM1, OAS1, IFI27, OAS3, IFI44L, HERC5, IFIT1, EPSTI1, ISG15, SERPING1, OASL, GBP1, and MX1.
    • Embodiment 125
  • The method of embodiment 116 wherein the first type I IFN or IFNα-inducible PD marker expression profile comprises up-regulated expression or activity of genes SAMD9L, IFI6, IFI44, IFIT2, OAS1, IFI27, OAS3, IFI44L, HERC5, IFIT1, EPSTI1, ISG15, SERPING1, OASL, GBP1, and MX1.
    • Embodiment 126
  • The method of embodiment 116 wherein the first type I IFN or IFNα-inducible PD marker expression profile comprises up-regulated expression or activity of genes IFI6, RSAD2, IFI44, IFI44L, IFI27, MX1, IFIT1, ISG15, LAMP3, OAS3, OAS1, EPSTI1, IFIT3, OAS2, SIGLEC1, and USP18.
    • Embodiment 127
  • The method of embodiment 116 wherein the first type I IFN or IFNα-inducible PD marker expression profile comprises up-regulated expression or activity of genes IFI6, RSAD2, IFI44, IFI44L, and IFI27.
    • Embodiment 128
  • The method of embodiment 116 wherein the variance is a decrease in up-regulated expression of activity levels of the genes.
    • Embodiment 129
  • The method of embodiment 116 wherein the disease is lupus, idiopathic inflammatory myositis, Sjogren's syndrome, vasculitis, sarcoidosis, and psoriasis.
    • Embodiment 130
  • The method of embodiment 131 wherein the disease is lupus.
    • Embodiment 131
  • The method of embodiment 116 wherein the therapeutic agent is a small molecule or a biologic agent.
    • Embodiment 132
  • The method of embodiment 131 wherein the biologic agent is an antibody.
    • Embodiment 133
  • The method of embodiment 132 wherein the antibody is MEDI-545.
    • Embodiment 134
  • The method of embodiment 116 wherein the first IFNα-inducible PD marker expression profile is obtained prior to administration of the therapeutic agent.
    • Embodiment 135
  • The method of embodiment 116 wherein the first IFNα-inducible PD marker expression profile is obtained at the time of administration of the therapeutic agent.
    • Embodiment 136
  • The method of embodiment 116 wherein the first and the second sample are whole blood or serum.
    • Embodiment 137
  • The method of embodiment 116 further comprising obtaining a third IFNα-inducible PD marker expression profile in a third sample from the patient.
    • Embodiment 138
  • The method of 137 further comprising obtaining a fourth IFNα-inducible PD marker expression profile in a fourth sample from the patient.
    • Embodiment 139
  • The method of 138 further comprising obtaining a fifth IFNα-inducible PD marker expression profile in a fifth sample from the patient.
    • Embodiment 140
  • The method of 139 further comprising obtaining a sixth IFNα-inducible PD marker expression profile in a sixth sample from the patient.
    • Embodiment 141
  • The method of 116 wherein the second sample is obtained at least one week, at least 2 weeks, at least three weeks, at least one month or at least two months following administration of the therapeutic agent.
    • Embodiment 142
  • The method of 137 wherein the third sample is obtained at least 2 days, at least 5 days, at least one week, at least 2 weeks, at least three weeks, at least one month or at least two months following obtaining the second sample.
    • Embodiment 143
  • The method of 138 wherein the fourth sample is obtained at least 2 days, at least 5 days, at least one week, at least 2 weeks, at least three weeks, at least one month or at least two months following obtaining the third sample.
    • Embodiment 144
  • The method of 139 wherein the fifth sample is obtained at least 2 days, at least 5 days, at least one week, at least 2 weeks, at least three weeks, at least one month or at least two months following obtaining the fourth sample.
    • Embodiment 145
  • The method of embodiment 116 wherein variance is a decrease in up-regulated expression or activity of the gene.
    • Embodiment 146
  • The method of embodiment 145 wherein the decrease is at least 10%, at least 20%, at least 25%, at least 30%, at least 40%, at least 45%, at least 50%, at least 60%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or 100%.
    • Embodiment 147
  • A method of identifying a patient as a candidate for a therapeutic agent that binds to and modulates IFNα activity comprising:
      • detecting presence or absence of an IFNα-inducible PD marker expression profile in a sample from the patient,
        • wherein detecting presence of the IFNα-induced PD marker expression profile identifies the patient as a candidate for the therapeutic agent that binds to and modulates IFNα activity.
    Embodiment 148
  • The method of embodiment 147 wherein the IFNα-inducible PD marker expression profile comprises up-regulated expression or activity of genes MX1, LY6E, IFI27, OAS1, IFIT1, IFI6, IFI44L, ISG15, LAMP3, OASL, RSAD2, and IFI44.
    • Embodiment 149
  • The method of embodiment 147 wherein type I IFN or IFNα-inducible PD marker expression profile comprises up-regulated expression or activity of genes IFI27, SIGLEC1, RSAD2, IFI6, IFI44L, IFI44, USP18, IFIT2, SAMD9L, BIRC4BP, DNAPTP6, OAS3, LY6E, IFIT1, LIPA, LOC129607, ISG15, PARP14, MX1, OAS2, OASL, CCL2, HERC5, OAS1.
    • Embodiment 150
  • The method of embodiment 147 wherein the type I IFN or IFNα-inducible PD marker expression profile comprises up-regulated expression or activity of genes IFIT1, IFIT3, IRF7, IFI6, IL6ST, IRF2, LY6E, MARCKS, MX1, MX2, OAS1, EIF2AK2, ISG15, STAT2, OAS3, IFI44, IFI44L, HERC5, RAB8B, LILRA5, RSAD2, and FCHO2.
    • Embodiment 151
  • The method of embodiment 147 wherein the type I IFN or IFNα-inducible PD marker expression profile comprises up-regulated expression or activity of genes SERPING1, IFIT2, IFIT3, IFI6, LY6E, MX1, OAS1, ISG15, IFI27, OAS3, IFI44, LAMP3, DNAPTP6, ETV7, HERC5, OAS2, USP18, XAF1, RTP4, SIGLEC1, and EPSTI1.
    • Embodiment 152
  • The method of embodiment 147 wherein the type I IFN or IFNα-inducible PD marker expression profile comprises up-regulated expression or activity of genes RTP4, RSAD2, HERC5, SIGLEC1, USP18, LY6E, ETV7, SERPING1, IFIT3, OAS1, HSXIAPAF1, G1P3, MX1, OAS3, IFI27, DNAPTP6, LAMP3, EPSTI1, IFI44, OAS2, IFIT2, and ISG15.
    • Embodiment 153
  • The method of embodiment 147 wherein the type I IFN or IFNα-inducible PD marker expression profile comprises up-regulated expression or activity of genes LAMP3, SIGLEC1, DNAPTP6, IFIT2, ETV7, RTP4, SERPING1, HERC5, XAF1, MX1, EPSTI1, OAS2, OAS1, OAS3, IFIT3, IFI6, USP18, RSAD2, IFI44, LY6E, ISG15, and IFI27.
    • Embodiment 154
  • The method of embodiment 147 wherein the type I IFN or IFNα-inducible PD marker expression profile comprises up-regulated expression or activity of genes DNAPTP6, EPSTI1, HERC5, IFI27, IFI44, IFI44L, IFI6, IFIT1, IFIT3, ISG15, LAMP3, LY6E, MX1, OAS1, OAS2, OAS3, PLSCR1, RSAD2, RTP4, SIGLEC1, and USP18.
    • Embodiment 155
  • The method of embodiment 147 wherein the type I IFN or IFNα-inducible PD marker expression profile comprises up-regulated expression or activity of genes SAMD9L, IFI6, IFI44, IFIT2, ZC3HAV1, ETV6, DAPP1, IL1RN, CEACAM1, OAS1, IFI27, OAS3, IFI44L, HERC5, IFIT1, EPSTI1, ISG15, SERPING1, OASL, GBP1, and MX1.
    • Embodiment 156
  • The method of embodiment 147 wherein the type I IFN or IFNα-inducible PD marker expression profile comprises up-regulated expression or activity of genes SAMD9L, IFI6, IFI44, IFIT2, OAS1, IFI27, OAS3, IFI44L, HERC5, IFIT1, EPSTI1, ISG15, SERPING1, OASL, GBP1, and MX1.
    • Embodiment 157
  • The method of embodiment 147 wherein the type I IFN or IFNα-inducible PD marker expression profile comprises up-regulated expression or activity of genes IFI6, RSAD2, IFI44, IFI44L, IFI27, MX1, IFIT1, ISG15, LAMP3, OAS3, OAS1, EPSTI1, IFIT3, OAS2, SIGLEC1, and USP18.
    • Embodiment 158
  • The method of embodiment 147 wherein the type I IFN or IFNα-inducible PD marker expression profile comprises up-regulated expression or activity of genes IFI6, RSAD2, IFI44, IFI44L, and IFI27.
    • Embodiment 159
  • The method of embodiment 147 wherein the patient has been diagnosed as having a disorder selected from the group consisting of lupus, idiopathic inflammatory myositis, Sjogren's syndrome, vasculitis, sarcoidosis, and psoriasis.
    • Embodiment 160
  • The method of embodiment 159 wherein the disorder is lupus.
    • Embodiment 161
  • The method of embodiment 147 wherein the therapeutic agent is a small molecule or a biologic agent.
    • Embodiment 162
  • The method of embodiment 161 wherein the biologic agent is an antibody.
    • Embodiment 163
  • The method of embodiment 162 wherein the antibody is MEDI-545.
    • Embodiment 164
  • The method of any one of embodiments 148-158 wherein the up-regulated expression or activity comprises at least a 2-fold increase in expression of one or more of the genes.
    • Embodiment 165
  • The method of any one of embodiments 148-158 wherein the up-regulated expression or activity comprises at least a 3-fold increase in expression of one or more of the genes.
    • Embodiment 166
  • The method of any one of embodiments 148-158 wherein the up-regulated expression or activity comprises an increase in mRNA levels of one or more of the genes.
    • Embodiment 167
  • The method of any one of embodiments 148-158 wherein the up-regulated expression or activity comprises an increase in protein levels of one or more of the genes.
    • Embodiment 168
  • The method of any one of embodiments 148-158 wherein the up-regulated expression or activity comprises an increase in enzymatic activity of a protein expressed from one or more of the genes.
    • Embodiment 169
  • The method of embodiment 147 wherein the sample is whole blood.
    • Embodiment 170
  • The method of embodiment 147 wherein the type I IFN or IFNα-inducible PD marker expression profile comprises down-regulated expression or activity of genes NOG, SLC4A1, PRSS33, and FEZ1.
    • Embodiment 171
  • The method of embodiment 147 wherein the type I IFN or IFNα-inducible PD marker expression profile comprises increased serum levels of polypeptides cancer antigen 125, ferritin, tissue factor, and MMP-3.
    • Embodiment 172
  • The method of embodiment 147 wherein the type I IFN or IFNα-inducible PD marker expression profile comprises decreased serum levels of polypeptides EGF, thrombopoietin, and CD40 ligand.
    • Embodiment 173
  • A method of diagnosing a patient as a having a disorder associated with increased IFNα levels comprising:
      • detecting presence or absence of an IFNα-inducible PD marker expression profile in a sample from the patient,
        • wherein detecting presence of the IFNα-induced PD marker expression profile identifies the patient as having a disorder associated with increased IFNα levels.
    Embodiment 174
  • The method of embodiment 173 wherein the IFNα-inducible PD marker expression profile comprises up-regulated expression or activity of genes MX1, LY6E, IFI27, OAS1, IFIT1, IFI6, IFI44L, ISG15, LAMP3, OASL, RSAD2, and IFI44.
    • Embodiment 175
  • The method of embodiment 173 wherein the IFNα-inducible PD marker expression profile comprises up-regulated expression or activity of genes IFI27, SIGLEC1, RSAD2, IFI6, IFI44L, IFI44, USP18, IFIT2, SAMD9L, BIRC4BP, DNAPTP6, OAS3, LY6E, IFIT1, LIPA, LOC129607, ISG15, PARP14, MX1, OAS2, OASL, CCL2, HERC5, OAS1.
    • Embodiment 176
  • The method of embodiment 173 wherein the IFNα-inducible PD marker expression profile comprises up-regulated expression or activity of genes IFIT1, IFIT3, IRF7, IFI6, IL6ST, IRF2, LY6E, MARCKS, MX1, MX2, OAS1, EIF2AK2, ISG15, STAT2, OAS3, IFI44, IFI44L, HERC5, RAB8B, LILRA5, RSAD2, and FCHO2.
    • Embodiment 177
  • 177 The method of embodiment 173 wherein the IFNα-inducible PD marker expression profile comprises up-regulated expression or activity of genes SERPING1, IFIT2, IFIT3, IFI6, LY6E, MX1, OAS1, ISG15, IFI27, OAS3, IFI44, LAMP3, DNAPTP6, ETV7, HERC5, OAS2, USP18, XAF1, RTP4, SIGLEC1, and EPSTI1.
    • Embodiment 178
  • The method of embodiment 173 wherein the IFNα-inducible PD marker expression profile comprises up-regulated expression or activity of genes RTP4, RSAD2, HERC5, SIGLEC1, USP18, LY6E, ETV7, SERPING1, IFIT3, OAS1, HSXIAPAF1, G1P3, MX1, OAS3, IFI27, DNAPTP6, LAMP3, EPSTI1, IFI44, OAS2, IFIT2, and ISG15.
    • Embodiment 179
  • The method of embodiment 173 wherein the IFNα-inducible PD marker expression profile comprises up-regulated expression or activity of genes LAMP3, SIGLEC1, DNAPTP6, IFIT2, ETV7, RTP4, SERPING1, HERC5, XAF1, MX1, EPSTI1, OAS2, OAS1, OAS3, IFIT3, IFI6, USP18, RSAD2, IFI44, LY6E, ISG15, and IFI27.
    • Embodiment 180
  • The method of embodiment 173 wherein the IFNα-inducible PD marker expression profile comprises up-regulated expression or activity of genes DNAPTP6, EPSTI1, HERC5, IFI27, IFI44, IFI44L, IFI6, IFIT1, IFIT3, ISG15, LAMP3, LY6E, MX1, OAS1, OAS2, OAS3, PLSCR1, RSAD2, RTP4, SIGLEC1, and USP18.
    • Embodiment 181
  • The method of embodiment 173 wherein the IFNα-inducible PD marker expression profile comprises up-regulated expression or activity of genes SAMD9L, IFI6, IFI44, IFIT2, ZC3HAV1, ETV6, DAPP1, IL1RN, CEACAM1, OAS1, IFI27, OAS3, IFI44L, HERC5, IFIT1, EPSTI1, ISG15, SERPING1, OASL, GBP1, and MX1.
    • Embodiment 182
  • The method of embodiment 173 wherein the IFNα-inducible PD marker expression profile comprises up-regulated expression or activity of genes SAMD9L, IFI6, IFI44, IFIT2, OAS1, IFI27, OAS3, IFI44L, HERC5, IFIT1, EPSTI1, ISG15, SERPING1, OASL, GBP1, and MX1.
    • Embodiment 183
  • The method of embodiment 173 wherein the IFNα-inducible PD marker expression profile comprises up-regulated expression or activity of genes IFI6, RSAD2, IFI44, IFI44L, IFI27, MX1, IFIT1, ISG15, LAMP3, OAS3, OAS1, EPSTI1, IFIT3, OAS2, SIGLEC1, and USP18.
    • Embodiment 184
  • The method of embodiment 173 wherein the IFNα-inducible PD marker expression profile comprises up-regulated expression or activity of genes IFI6, RSAD2, IFI44, IFI44L, and IFI27.
    • Embodiment 185
  • The method of embodiment 173 wherein the disorder is lupus, idiopathic inflammatory myositis, Sjogren's syndrome, vasculitis, sarcoidosis, or psoriasis.
    • Embodiment 186
  • The method of embodiment 185 wherein the disorder is lupus.
    • Embodiment 187
  • The method of any one of embodiments 174-184 wherein the up-regulated expression or activity comprises at least a 2-fold increase in expression or activity of one or more of the genes.
    • Embodiment 188
  • The method of embodiment 187 wherein the up-regulated expression or activity comprises at least a 3-fold increase in expression or activity of one or more of the genes.
    • Embodiment 189
  • The method of any one of embodiments 174-184 wherein the up-regulated expression or activity comprises an increase in mRNA levels of one or more of the genes.
    • Embodiment 190
  • The method of any one of embodiments 174-184 wherein the up-regulated expression or activity comprises an increase in protein levels of one or more of the genes.
    • Embodiment 191
  • The method of any one of embodiments 174-184 wherein the up-regulated expression or activity comprises an increase in enzymatic activity of a protein expressed from one or more of the genes.
    • Embodiment 192
  • The method of any one of embodiments 174-184 wherein the type I IFN or IFNα-inducible PD marker expression profile further comprises down-regulated expression or activity of genes NOGSLC4A1, PRSS33, and FEZ1.
    • Embodiment 193
  • The method any one of embodiments 174-184 wherein the type I IFN or IFNα-inducible PD marker expression profile further comprises increased serum levels of polypeptides cancer antigen 125, ferritin, tissue factor, and MMP-3.
    • Embodiment 194
  • The method of any one of embodiments 174-184 wherein the type I IFN or IFNα-inducible PD marker expression profile further comprises decreased serum levels of polypeptides EGF, thrombopoietin, and CD40 ligand.
    • Embodiment 195
  • A method of identifying a candidate therapeutic for treating IFNα-mediated disorders comprising:
      • contacting cells comprising an IFNα-inducible PD marker expression profile with an agent; and
      • detecting presence or absence of a change in the IFNα-induced PD marker expression profile of the cells,
        • wherein the presence of a change comprising a reduction in the up-regulation of the genes of the IFNα-inducible PD marker expression profile indicates the agent is a candidate therapeutic agent.
    Embodiment 196
  • The method of embodiment 195 wherein the IFNα-inducible PD marker expression profile comprises up-regulated expression or activity of genes MX1, LY6E, IFI27, OAS1, IFIT1, IFI6, IFI44L, ISG15, LAMP3, OASL, RSAD2, and IFI44.
    • Embodiment 197
  • The method of embodiment 195 wherein the IFNα-inducible PD marker expression profile comprises up-regulated expression or activity of genes IFI27, SIGLEC1, RSAD2, IFI6, IFI44L, IFI44, USP18, IFIT2, SAMD9L, BIRC4BP, DNAPTP6, OAS3, LY6E, IFIT1, LIPA, LOC129607, ISG15, PARP14, MX1, OAS2, OASL, CCL2, HERC5, and OAS 1.
    • Embodiment 198
  • The method of embodiment 195 wherein the IFNα-inducible PD marker expression profile comprises up-regulated expression or activity of genes IFIT1, IFIT3, IRF7, IFI6, IL6ST, IRF2, LY6E, MARCKS, MX1, MX2, OAS1, EIF2AK2, ISG15, STAT2, OAS3, IFI44, IFI44L, HERC5, RAB8B, LILRA5, RSAD2, and FCHO2.
    • Embodiment 199
  • 199 The method of embodiment 195 wherein the IFNα-inducible PD marker expression profile comprises up-regulated expression or activity of genes SERPING1, IFIT2, IFIT3, IFI6, LY6E, MX1, OAS1, ISG15, IFI27, OAS3, IFI44, LAMP3, DNAPTP6, ETV7, HERC5, OAS2, USP18, XAF1, RTP4, SIGLEC1, and EPSTI1.
    • Embodiment 200
  • The method of embodiment 195 wherein the IFNα-inducible PD marker expression profile comprises up-regulated expression or activity of genes RTP4, RSAD2, HERC5, SIGLEC1, USP18, LY6E, ETV7, SERPING1, IFIT3, OAS1, HSXIAPAF1, G1P3, MX1, OAS3, IFI27, DNAPTP6, LAMP3, EPSTI1, IFI44, OAS2, IFIT2, and ISG15.
    • Embodiment 201
  • The method of embodiment 195 wherein the IFNα-inducible PD marker expression profile comprises up-regulated expression or activity of genes LAMP3, SIGLEC1, DNAPTP6, IFIT2, ETV7, RTP4, SERPING1, HERC5, XAF1, MX1, EPSTI1, OAS2, OAS1, OAS3, IFIT3, IFI6, USP18, RSAD2, IFI44, LY6E, ISG15, and IFI27.
    • Embodiment 202
  • The method of embodiment 195 wherein the IFNα-inducible PD marker expression profile comprises up-regulated expression or activity of genes DNAPTP6, EPSTI1, HERC5, IFI27, IFI44, IFI44L, IFI6, IFIT1, IFIT3, ISG15, LAMP3, LY6E, MX1, OAS1, OAS2, OAS3, PLSCR1, RSAD2, RTP4, SIGLEC1, and USP18.
    • Embodiment 203
  • The method of embodiment 195 wherein the IFNα-inducible PD marker expression profile comprises up-regulated expression or activity of genes SAMD9L, IFI6, IFI44, IFIT2, ZC3HAV1, ETV6, DAPP1, IL1RN, CEACAM1, OAS1, IFI27, OAS3, IFI44L, HERC5, IFIT1, EPSTI1, ISG15, SERPING1, OASL, GBP1, and MX1.
    • Embodiment 204
  • The method of embodiment 195 wherein the IFNα-inducible PD marker expression profile comprises up-regulated expression or activity of genes SAMD9L, IFI6, IFI44, IFIT2, OAS1, IFI27, OAS3, IFI44L, HERC5, IFIT1, EPSTI1, ISG15, SERPING1, OASL, GBP1, and MX1.
    • Embodiment 205
  • The method of embodiment 195 wherein the IFNα-inducible PD marker expression profile comprises up-regulated expression or activity of genes IFI6, RSAD2, IFI44, IFI44L, IFI27, MX1, IFIT1, ISG15, LAMP3, OAS3, OAS1, EPSTI1, IFIT3, OAS2, SIGLEC1, and USP18.
    • Embodiment 206
  • The method of embodiment 195 wherein the IFNα-inducible PD marker expression profile comprises up-regulated expression or activity of genes IFI6, RSAD2, IFI44, IFI44L, and IFI27.
    • Embodiment 207
  • The method of embodiment 195 wherein the cells obtained from a patient comprising a disorder associated with increased IFNα levels.
    • Embodiment 208
  • The method of embodiment 195 wherein the cells are cells treated with IFNα to induce the IFNα-inducible PD marker expression profile.
    • Embodiment 209
  • The method of embodiment 195 wherein the up-regulation of the genes of the IFNα-inducible PD marker expression profile is at least a 2-fold increase in expression of one or more of the genes of the profile.
    • Embodiment 210
  • The method of embodiment 195 wherein the up-regulation of the genes of the IFNα-inducible PD marker expression profile is at least a 3-fold increase in expression of one or more of the genes of the IFNα-inducible PD marker expression profile.
    • Embodiment 211
  • The method of embodiment 195 wherein the up-regulation of the genes of the IFNα-inducible PD marker expression profile comprises an increase in mRNA levels of one or more of the genes of the IFNα-inducible PD marker expression profile.
    • Embodiment 212
  • The method of embodiment 195 wherein the up-regulation of the genes of the IFNα-inducible PD marker expression profile comprises an increase in protein levels of one or more of the genes of the IFNα-inducible PD marker expression profile.
    • Embodiment 213
  • The method of embodiment 195 wherein the up-regulation of the genes of the IFNα-inducible PD marker expression profile comprises an increase in enzymatic activity of a protein expressed from one or more of the genes of the IFNα-inducible PD marker expression profile.
    • Embodiment 214
  • The method of any one of embodiments 196-206 wherein the type I IFN or IFNα-inducible PD marker expression profile further comprises down-regulated expression or activity of genes NOGSLC4A1, PRSS33, and FEZ1; and wherein the presence of a change comprising an increase in expression or activity of the down-regulated genes indicates the agent is a candidate therapeutic agent.
    • Embodiment 215
  • The method of any one of embodiments 196-206 wherein the type I IFN or IFNα-inducible PD marker expression profile further comprises increased serum levels of polypeptides cancer antigen 125, ferritin, tissue factor, and MMP-3; and wherein the presence of a change comprising a decrease in serum levels of the polypeptide indicates the agent is a candidate therapeutic agent.
    • Embodiment 216
  • The method of any one of embodiments 196-206 wherein the type I IFN or IFNα-inducible PD marker expression profile further comprises decreased serum levels of polypeptides EGF, thrombopoietin, and CD40 ligand wherein the presence of a change comprising an increase in serum levels of the polypeptide indicates the agent is a candidate therapeutic agent.
    • Embodiment 217
  • A set of probes comprising:
      • polynucleotides that specifically detect expression of any one of the sets of genes:
        • (a) MX1, LY6E, IFI27, OAS1, IFIT1, IFI6, IFI44L, ISG15, LAMP3, OASL, RSAD2, and IFI44; or
        • (b) IFI27, SIGLEC1, RSAD2, IFI6, IFI44L, IFI44, USP18, IFIT2, SAMD9L, BIRC4BP, DNAPTP6, OAS3, LY6E, IFIT1, LIPA, LOC129607, ISG15, PARP14, MX1, OAS2, OASL, CCL2, HERC5, OAS1; or
        • (c) IFIT1, IFIT3, IRF7, IFI6, IL6ST, IRF2, LY6E, MARCKS, MX1, MX2, OAS1, EIF2AK2, ISG15, STAT2, OAS3, IFI44, IFI44L, HERC5, RAB8B, LILRA5, RSAD2, and FCHO2; or
        • (d) SERPING1, IFIT2, IFIT3, IFI6, LY6E, MX1, OAS1, ISG15, IFI27, OAS3, IFI44, LAMP3, DNAPTP6, ETV7, HERC5, OAS2, USP18, XAF1, RTP4, SIGLEC1, and EPSTI1; or
        • (e) RTP4, RSAD2, HERC5, SIGLEC1, USP18, LY6E, ETV7, SERPING1, IFIT3, OAS1, HSXIAPAF1, G1P3, MX1, OAS3, IFI27, DNAPTP6, LAMP3, EPSTI1, IFI44, OAS2, IFIT2, and ISG15; or
        • (f) LAMP3, SIGLEC1, DNAPTP6, IFIT2, ETV7, RTP4, SERPING1, HERC5, XAF1, MX1, EPSTI1, OAS2, OAS1, OAS3, IFIT3, IFI6, USP18, RSAD2, IFI44, LY6E, ISG15, and IFI27; or
        • (g) DNAPTP6, EPSTI1, HERC5, IFI27, IFI44, IFI44L, IFI6, IFIT1, IFIT3, ISG15, LAMP3, LY6E, MX1, OAS1, OAS2, OAS3, PLSCR1, RSAD2, RTP4, SIGLEC1, and USP18; or
        • (h) SAMD9L, IFI6, IFI44, IFIT2, ZC3HAV1, ETV6, DAPP1, IL1RN, CEACAM1, OAS1, IFI27, OAS3, IFI44L, HERC5, IFIT1, EPSTI1, ISG15, SERPING1, OASL, GBP1, and MX1; or
        • (i) SAMD9L, IFI6, IFI44, IFIT2, OAS1, IFI27, OAS3, IFI44L, HERC5, IFIT1, EPSTI1, ISG15, SERPING1, OASL, GBP1, and MX1; or
        • (j) IFI6, RSAD2, IFI44, IFI44L, IFI27, MX1, IFIT1, ISG15, LAMP3, OAS3, OAS1, EPSTI1, IFIT3, OAS2, SIGLEC1, and USP18; or
        • (k) IFI6, RSAD2, IFI44, IFI44L, and IFI27; or
        • (l) NOGSLC4A1, PRSS33, and FEZ1.
    Embodiment 218
  • A kit comprising any of the set of probes recited in embodiment 217.
    • Embodiment 218
  • A method of detecting IFN activity in a sample comprising:
      • incubating cells comprising a polynucleotide sequence comprising a reporter gene under the control of an interferon-stimulated response element with a sample; and
      • detecting expression of the reporter gene,
        • wherein expression of the reporter gene indicates IFN activity in the sample.
    Embodiment 220
  • The method of embodiment 219 wherein cells are HEK293H cells.
    • Embodiment 221
  • The method of embodiment 219 wherein the reporter gene is luciferase, chloramphenicol acetyl transferase, β-galactosidase, green fluorescent protein, β-glucuronidase, or secreted placental alkaline phosphatase.
    • Embodiment 222
  • The method of embodiment 221 wherein the reporter gene is luciferase.
    • Embodiment 223
  • The method of embodiment 222 wherein the luciferase is Gaussia princeps luciferase.
    • Embodiment 224
  • The method of embodiment 219 further comprising quantitating level of expression of the reporter gene.
    • Embodiment 225
  • The method of embodiment 224 further comprising correlating the level of expression of the reporter gene to level of IFN activity in the sample.
  • All publications, patents and patent applications mentioned in this specification are herein incorporated by reference into the specification to the same extent as if each individual publication, patent or patent application was specifically and individually indicated to be incorporated herein by reference.
  • This application claims the benefit of priority of U.S. Provisional Application Ser. No. 60/924,219 filed May 3, 2007, U.S. Provisional Application Ser. No. 60/924,584 filed May 21, 2007, U.S. Provisional Application Ser. No. 60/960,187 filed Sep. 19, 2007, U.S. Provisional Application Ser. No. 60/996,176 filed Nov. 5, 2007, and PCT application PCT/US2007/024947 filed Dec. 6, 2007 herein incorporated by reference for all purposes. This application also claims the benefit of priority of U.S. Provisional Application Ser. No. 60/924,220 filed May 3, 2007, U.S. Provisional Application Ser. No. 60/996,219 filed Nov. 6, 2007, and U.S. Provisional Application Ser. No. 60/996,820 filed Dec. 6, 2007, herein incorporated by reference for all purposes. This application further claims the benefit of priority of U.S. Provisional Application Ser. No. 60/996,174 filed Nov. 5, 2007, and PCT application PCT/US2007/024941 filed Dec. 6, 2007, herein incorporated by reference for all purposes. This application further claims the benefit of priority of U.S. Provisional Application Ser. No. 61/006,963 filed Feb. 8, 2008, herein incorporated by reference for all purposes.
  • The set of examples that follow are provided for the purpose of illustration only and the invention should in no way be construed as being limited to these examples.
    • EXAMPLES Example 1a Initial Identification of Up-Regulated Genes in Lupus Patients
  • Gene expression in whole blood of 5 (2 cutaneous and 3 severe) lupus patients and 5 healthy volunteers was profiled using Affymetrix whole genome array technology and qPCR validation. Gene expression fold-change values were determined by calculating the log2 signal intensity difference between individual lupus patient samples and the mean log2 signal intensity for the 5 healthy donor samples. 118 genes were identified as up-regulated by at least 2-fold in whole blood of all 5 lupus patients relative to the healthy volunteers.
  • Table 1 provides a summary for 71 of the 118 annotated genes identified as up-regulated by at least 2-fold in all 5 lupus patients. Table 2 provides the fold-up-regulation in gene expression for a subset of the 118 genes for each of the five lupus patients relative to the healthy volunteers. Table 2 also provides a comparison between fold-change values determined on two unique platforms (Affy GENECHIP microarray and TAQMAN (i.e. qPCR)).
  • TABLE 1
    Genes Identified as Up-Regulated at Least 2-Fold in Whole Blood of Lupus
    Patients (Table 1 discloses “DEAD (Asp-Glu-Ala-Asp)” as SEQ ID NO: 1)
    Probe_ID UniGene I
    Figure US20150132313A1-20150514-P00899
    		 Gene Title Gene Sym
    Figure US20150132313A1-20150514-P00899
    		 Gene Ontology Bi
    Figure US20150132313A1-20150514-P00899
    		 Gene Ont
    Figure US20150132313A1-20150514-P00899
    		 Gene Ont
    Figure US20150132313A1-20150514-P00899
    		 Pathway
    223674_s_
    Figure US20150132313A1-20150514-P00899
    		 Hs.22065 CDC42 small effector 1 CDC42SE
    Figure US20150132313A1-20150514-P00899
    		 7165 // signal tran
    Figure US20150132313A1-20150514-P00899
    		 5886 // pla
    Figure US20150132313A1-20150514-P00899
    		 5095 // GT
    Figure US20150132313A1-20150514-P00899
    		 —
    204415_at Hs.523847 interferon, alpha-inducible
    Figure US20150132313A1-20150514-P00899
    		 G1P3 6955 // immune re
    Figure US20150132313A1-20150514-P00899
    		 16021 // in
    Figure US20150132313A1-20150514-P00899
    		 — —
    228220_at Hs.165762 FCH domain only 2 FCHO2 — — — —
    226312_at Hs.407926 TORC2-specific protein A
    Figure US20150132313A1-20150514-P00899
    		 AVO3 — — 5488 // bin
    Figure US20150132313A1-20150514-P00899
    		 —
    215245_x_
    Figure US20150132313A1-20150514-P00899
    		 Hs.103183 fragile X mental retardatio
    Figure US20150132313A1-20150514-P00899
    		 FMR1 6397 // mRNA pro
    Figure US20150132313A1-20150514-P00899
    		 5629 // sol
    Figure US20150132313A1-20150514-P00899
    		 3723 // RN
    Figure US20150132313A1-20150514-P00899
    		 —
    202194_at Hs.482873 transmembrane emp24 p
    Figure US20150132313A1-20150514-P00899
    		 TMED5 6886 // intraoellul#,899; 5783 // e
    Figure US20150132313A1-20150514-P00899
    		 8320 // pro
    Figure US20150132313A1-20150514-P00899
    		 —
    226641_at Hs.432706 Ankyrin repeat domain 44
    Figure US20150132313A1-20150514-P00899
    		 LOC91526
    Figure US20150132313A1-20150514-P00899
    		 — — — —
    212585_at Hs.430849 oxysterol binding protein-
    Figure US20150132313A1-20150514-P00899
    		 OCBPL8 6869 // lipid trans
    Figure US20150132313A1-20150514-P00899
    		 — — —
    201237_at Hs.446123 capping protein (actin fila
    Figure US20150132313A1-20150514-P00899
    		 CAPZA2 6461 // protein co
    Figure US20150132313A1-20150514-P00899
    		 8290 // F-a
    Figure US20150132313A1-20150514-P00899
    		 3779 // act
    Figure US20150132313A1-20150514-P00899
    		 —
    226934_at Hs.369606 Cleavage and polyadenyl
    Figure US20150132313A1-20150514-P00899
    		 CPSF6 6397 // mRNA pro
    Figure US20150132313A1-20150514-P00899
    		 5634 // nu
    Figure US20150132313A1-20150514-P00899
    		 166 // nuc
    Figure US20150132313A1-20150514-P00899
    		 —
    203983_at Hs.96247 translin-associated factor
    Figure US20150132313A1-20150514-P00899
    		 TSNAX — 5634 // nu
    Figure US20150132313A1-20150514-P00899
    		 3677 // DN
    Figure US20150132313A1-20150514-P00899
    		 —
    221428_s_
    Figure US20150132313A1-20150514-P00899
    		 Hs.438970 transducin (beta)-like 1X-
    Figure US20150132313A1-20150514-P00899
    		 TBL1XR1 6350 // transcipti
    Figure US20150132313A1-20150514-P00899
    		 5634 // nu
    Figure US20150132313A1-20150514-P00899
    		 — —
    215838_at Hs.512233 leukocyte immunoglobuli
    Figure US20150132313A1-20150514-P00899
    		 LILRA5 — — — —
    209884_s_
    Figure US20150132313A1-20150514-P00899
    		 Hs.250072 solute carrier family 4, so
    Figure US20150132313A1-20150514-P00899
    		 SLC4A7 6820 // anion tran
    Figure US20150132313A1-20150514-P00899
    		 16020 // m
    Figure US20150132313A1-20150514-P00899
    		 5452 // ino
    Figure US20150132313A1-20150514-P00899
    		 —
    222605_at Hs.356399 REST corepressor 3 RCOR3 45449 // regulatio
    Figure US20150132313A1-20150514-P00899
    		 5634 // nu
    Figure US20150132313A1-20150514-P00899
    		 3677 // DN
    Figure US20150132313A1-20150514-P00899
    		 —
    202304_at Hs.508010 fibronectin type III domain FNDC3A — — — —
    212579_at Hs.8118 structural maintenance of
    Figure US20150132313A1-20150514-P00899
    		 SMCHD1 51276 // chromos
    Figure US20150132313A1-20150514-P00899
    		 5694 // ch
    Figure US20150132313A1-20150514-P00899
    		 5515 // pro
    Figure US20150132313A1-20150514-P00899
    		 —
    206783_s_
    Figure US20150132313A1-20150514-P00899
    		 Hs.510402 membrane cofactor prote
    Figure US20150132313A1-20150514-P00899
    		 MCP 6955 // immune re
    Figure US20150132313A1-20150514-P00899
    		 5885 // pla
    Figure US20150132313A1-20150514-P00899
    		 4872 // re
    Figure US20150132313A1-20150514-P00899
    		 —
    1555643_s Hs.512233 leukocyte immunoglobuli
    Figure US20150132313A1-20150514-P00899
    		 LILRA5 — — — —
    226617_at Hs.470233 ADP-ribosylation factor-li
    Figure US20150132313A1-20150514-P00899
    		 ARL5 6886 // intracellula
    Figure US20150132313A1-20150514-P00899
    		 — 166 // nuc
    Figure US20150132313A1-20150514-P00899
    		 —
    229584_at Hs.187636 leucine-rich repeat kinase
    Figure US20150132313A1-20150514-P00899
    		 LRRK2 6468 // protein am
    Figure US20150132313A1-20150514-P00899
    		 — 4672 // pro
    Figure US20150132313A1-20150514-P00899
    		 —
    211967_at Hs.503709 pro-oncosis receptor indu
    Figure US20150132313A1-20150514-P00899
    		 PORIMIN — 16021 // in
    Figure US20150132313A1-20150514-P00899
    		 4872 // rec
    Figure US20150132313A1-20150514-P00899
    		 —
    212192_at Hs.109438 potassium channel tetran
    Figure US20150132313A1-20150514-P00899
    		 KCTD12 6813 // potassium
    Figure US20150132313A1-20150514-P00899
    		 8076 // vol
    Figure US20150132313A1-20150514-P00899
    		 5249 // vol
    Figure US20150132313A1-20150514-P00899
    		 —
    208719_s_
    Figure US20150132313A1-20150514-P00899
    		 Hs.528305 DEAD (Asp-Glu-Ala-Asp)
    Figure US20150132313A1-20150514-P00899
    		 DDX17 6396 // RNA proce
    Figure US20150132313A1-20150514-P00899
    		 5634 // nu
    Figure US20150132313A1-20150514-P00899
    		 166 // nuc
    Figure US20150132313A1-20150514-P00899
    		 —
    201669_s_
    Figure US20150132313A1-20150514-P00899
    		 Hs.519909 myristoylated alanine-rich
    Figure US20150132313A1-20150514-P00899
    		 MARCKS 6928 // cell motilit
    Figure US20150132313A1-20150514-P00899
    		 5886 // pla
    Figure US20150132313A1-20150514-P00899
    		 5516 // ca
    Figure US20150132313A1-20150514-P00899
    		 —
    222572_at Hs.22265 protein phosphatase 2C,
    Figure US20150132313A1-20150514-P00899
    		 PPM2C 6470 // protein am
    Figure US20150132313A1-20150514-P00899
    		 5739 // mi
    Figure US20150132313A1-20150514-P00899
    		 287 // mag
    Figure US20150132313A1-20150514-P00899
    		 Krebs-TCA
    Figure US20150132313A1-20150514-P00899
    212195_at Hs.532082 Interleukin 6 signal trans
    Figure US20150132313A1-20150514-P00899
    		 IL6ST 6955 // immune re
    Figure US20150132313A1-20150514-P00899
    		 5886 // pla
    Figure US20150132313A1-20150514-P00899
    		 4872 // rec
    Figure US20150132313A1-20150514-P00899
    		 Ribosomal
    Figure US20150132313A1-20150514-P00899
    226711_at Hs.468478 human T-cell leukemia vi
    Figure US20150132313A1-20150514-P00899
    		 HTLF 6350 // transcipti
    Figure US20150132313A1-20150514-P00899
    		 5634 // nu
    Figure US20150132313A1-20150514-P00899
    		 3700 // tra
    Figure US20150132313A1-20150514-P00899
    		 —
    222846_at Hs.389733 RAB8B, member RAS o
    Figure US20150132313A1-20150514-P00899
    		 RAB8B 6886 // intracellula
    Figure US20150132313A1-20150514-P00899
    		 — 166 // nuc
    Figure US20150132313A1-20150514-P00899
    		 —
    203566_s_
    Figure US20150132313A1-20150514-P00899
    		 Hs.904 amylo-1, 6-glucosidase,
    Figure US20150132313A1-20150514-P00899
    		 AGL 5975 // carbohydr
    Figure US20150132313A1-20150514-P00899
    		 43033 // is
    Figure US20150132313A1-20150514-P00899
    		 4134 // 4-a
    Figure US20150132313A1-20150514-P00899
    		 Glycogen_
    Figure US20150132313A1-20150514-P00899
    207564_x_
    Figure US20150132313A1-20150514-P00899
    		 Hs.405410 O-linked N-acetylglucosa
    Figure US20150132313A1-20150514-P00899
    		 OGT 6493 // protein am
    Figure US20150132313A1-20150514-P00899
    		 5634 // nu
    Figure US20150132313A1-20150514-P00899
    		 5515 // pro
    Figure US20150132313A1-20150514-P00899
    		 —
    219237_s_
    Figure US20150132313A1-20150514-P00899
    		 Hs.512743 DnaJ (Hsp40) homolog, s
    Figure US20150132313A1-20150514-P00899
    		 DNAJB14 6457 // protein fol
    Figure US20150132313A1-20150514-P00899
    		 — 31072 // h
    Figure US20150132313A1-20150514-P00899
    		 —
    214093_s_
    Figure US20150132313A1-20150514-P00899
    		 Hs.567255 far upstream element (FU
    Figure US20150132313A1-20150514-P00899
    		 FUBP1 6350 // transcripti
    Figure US20150132313A1-20150514-P00899
    		 5634 // nu
    Figure US20150132313A1-20150514-P00899
    		 3697 // sin
    Figure US20150132313A1-20150514-P00899
    		 —
    218589_at Hs.123464 purinergic receptor P2Y,
    Figure US20150132313A1-20150514-P00899
    		 P2RY5 7165 // signal tran
    Figure US20150132313A1-20150514-P00899
    		 16021 // in
    Figure US20150132313A1-20150514-P00899
    		 1584 // rho
    Figure US20150132313A1-20150514-P00899
    		 GPCRDB_
    Figure US20150132313A1-20150514-P00899
    217941_s_
    Figure US20150132313A1-20150514-P00899
    		 Hs.519346 erbb2 interacting protein ERBB2IP 7049 // cell cycle
    Figure US20150132313A1-20150514-P00899
    		 5634 // nu
    Figure US20150132313A1-20150514-P00899
    		 5176 // Er
    Figure US20150132313A1-20150514-P00899
    		 —
    203603_s_
    Figure US20150132313A1-20150514-P00899
    		 Hs.34871 zinc finger homeobox 1b ZFHX1B 6355 // regulation
    Figure US20150132313A1-20150514-P00899
    		 5634 // nu
    Figure US20150132313A1-20150514-P00899
    		 3700 // tra
    Figure US20150132313A1-20150514-P00899
    		 TGF_Beta
    Figure US20150132313A1-20150514-P00899
    213111_at Hs.173939 phosphatidylinositol-3-ph
    Figure US20150132313A1-20150514-P00899
    		 PIP5K3 7242 // intracellula
    Figure US20150132313A1-20150514-P00899
    		 45121 // li
    Figure US20150132313A1-20150514-P00899
    		 5515 // pro
    Figure US20150132313A1-20150514-P00899
    		 —
    213070_at Hs.175343 Phosphoinositide-3-kinas
    Figure US20150132313A1-20150514-P00899
    		 PIK3C2A 6661 // phosphati
    Figure US20150132313A1-20150514-P00899
    		 5634 // nu
    Figure US20150132313A1-20150514-P00899
    		 4428 // ino
    Figure US20150132313A1-20150514-P00899
    		 Inositol ph
    Figure US20150132313A1-20150514-P00899
    218041_x_
    Figure US20150132313A1-20150514-P00899
    		 Hs.221847 solute carrier family 38,
    Figure US20150132313A1-20150514-P00899
    		 SLC38A2 6865 // amino aci
    Figure US20150132313A1-20150514-P00899
    		 16020 // m
    Figure US20150132313A1-20150514-P00899
    		 5279 // am
    Figure US20150132313A1-20150514-P00899
    		 —
    202033_s_
    Figure US20150132313A1-20150514-P00899
    		 Hs.196102 RB1-inducible coiled-coil
    Figure US20150132313A1-20150514-P00899
    		 RB1CC1 6350 // transcipti
    Figure US20150132313A1-20150514-P00899
    		 5634 // nu
    Figure US20150132313A1-20150514-P00899
    		 16301 // ki
    Figure US20150132313A1-20150514-P00899
    		 —
    200603_at Hs.280342 protein kinase, cAMP-de
    Figure US20150132313A1-20150514-P00899
    		 PRKAR1A
    Figure US20150132313A1-20150514-P00899
    		 6357 // regulation
    Figure US20150132313A1-20150514-P00899
    		 5952 // cA
    Figure US20150132313A1-20150514-P00899
    		 166 // nuc
    Figure US20150132313A1-20150514-P00899
    		 G_Protein_
    Figure US20150132313A1-20150514-P00899
    228996_at Hs.495097 ring finger and CCCH-typ
    Figure US20150132313A1-20150514-P00899
    		 RC3H1 16567 // protein u
    Figure US20150132313A1-20150514-P00899
    		 151 // ubiq
    Figure US20150132313A1-20150514-P00899
    		 3723 // RN
    Figure US20150132313A1-20150514-P00899
    		 —
    1554479_at Hs.446146 caspase recruitment dom
    Figure US20150132313A1-20150514-P00899
    		 CARD8 42981 // regulation
    Figure US20150132313A1-20150514-P00899
    		 5634 // nuc
    Figure US20150132313A1-20150514-P00899
    		 5515 // pro
    Figure US20150132313A1-20150514-P00899
    		 —
    203011_at Hs.492120 inositol(myo)-1(or 4)-mon
    Figure US20150132313A1-20150514-P00899
    		 IMPA1 5975 // carbohydra
    Figure US20150132313A1-20150514-P00899
    		 — 287 // mag
    Figure US20150132313A1-20150514-P00899
    		 Streptomy
    Figure US20150132313A1-20150514-P00899
    223940_x_
    Figure US20150132313A1-20150514-P00899
    		 Hs.187199 metastasis associated lu
    Figure US20150132313A1-20150514-P00899
    		 MALAT1 — — — —
    222317_at Hs.445711 Phosphodiesterase 3B, c
    Figure US20150132313A1-20150514-P00899
    		 PDE3B 7165 // signal tran
    Figure US20150132313A1-20150514-P00899
    		 16020 // m
    Figure US20150132313A1-20150514-P00899
    		 4119 // cG
    Figure US20150132313A1-20150514-P00899
    		 —
    228157_at Hs.500775 zinc finger protein 207 ZNF207 6355 // regulation
    Figure US20150132313A1-20150514-P00899
    		 5634 // nu
    Figure US20150132313A1-20150514-P00899
    		 3700 // tra
    Figure US20150132313A1-20150514-P00899
    		 —
    221505_at Hs.385913 acidic (leucine-rich) nucle
    Figure US20150132313A1-20150514-P00899
    		 ANP32E — 5634 // nu
    Figure US20150132313A1-20150514-P00899
    		 19212 // p
    Figure US20150132313A1-20150514-P00899
    		 —
    1554472_a
    Figure US20150132313A1-20150514-P00899
    		 Hs.304362 PHD finger protein 20-like
    Figure US20150132313A1-20150514-P00899
    		 PHF20L1 6355 // regulation
    Figure US20150132313A1-20150514-P00899
    		 — 5515 // pro
    Figure US20150132313A1-20150514-P00899
    		 —
    226345_at Hs.25362 ADP-ribosylation factor-li
    Figure US20150132313A1-20150514-P00899
    		 ARL8 6886 // intracellula
    Figure US20150132313A1-20150514-P00899
    		 — 166 // nuc
    Figure US20150132313A1-20150514-P00899
    		 —
    224862_at Hs.269782 Guanine nucleotide bindi
    Figure US20150132313A1-20150514-P00899
    		 GNAQ 6471 // protein am
    Figure US20150132313A1-20150514-P00899
    		 5737 // cyt
    Figure US20150132313A1-20150514-P00899
    		 166 // nuc
    Figure US20150132313A1-20150514-P00899
    		 G_Protein_
    Figure US20150132313A1-20150514-P00899
    207387_s_
    Figure US20150132313A1-20150514-P00899
    		 Hs.1466 glycerol kinase GK 5975 // carbohydr
    Figure US20150132313A1-20150514-P00899
    		 5737 // cyt
    Figure US20150132313A1-20150514-P00899
    		 166 // nuc
    Figure US20150132313A1-20150514-P00899
    		 Glycerolipi
    Figure US20150132313A1-20150514-P00899
    222633_at Hs.438970 transducin (beta)-like 1X-
    Figure US20150132313A1-20150514-P00899
    		 TBL1XR1 6350 // transcipti
    Figure US20150132313A1-20150514-P00899
    		 5634 // nu
    Figure US20150132313A1-20150514-P00899
    		 — —
    236224_at Hs.491234 Ras-like without CAAX 1 RIT1 6886 // intracellula
    Figure US20150132313A1-20150514-P00899
    		 5886 // pla
    Figure US20150132313A1-20150514-P00899
    		 166 // nuc
    Figure US20150132313A1-20150514-P00899
    		 —
    203080_s_
    Figure US20150132313A1-20150514-P00899
    		 Hs.470369 bromodomain adjacent to
    Figure US20150132313A1-20150514-P00899
    		 BAZ2B 6350 // transcipti
    Figure US20150132313A1-20150514-P00899
    		 5634 // nu
    Figure US20150132313A1-20150514-P00899
    		 3677 // DN
    Figure US20150132313A1-20150514-P00899
    		 —
    222587_s_
    Figure US20150132313A1-20150514-P00899
    		 Hs.127407 UDP-N-acetyl-alpha-D-ga
    Figure US20150132313A1-20150514-P00899
    		 GALNT7 5975 // carbohydr
    Figure US20150132313A1-20150514-P00899
    		 5795 // Go
    Figure US20150132313A1-20150514-P00899
    		 4653 // po
    Figure US20150132313A1-20150514-P00899
    		 O-Glycan
    Figure US20150132313A1-20150514-P00899
    235057_at Hs.472509 itchy homolog E3 ubiquiti
    Figure US20150132313A1-20150514-P00899
    		 ITCH 1558 // regulation
    Figure US20150132313A1-20150514-P00899
    		 5634 // nu
    Figure US20150132313A1-20150514-P00899
    		 3677 // DN
    Figure US20150132313A1-20150514-P00899
    		 —
    1554154_a
    Figure US20150132313A1-20150514-P00899
    		 Hs.310809 ganglioside induced differ
    Figure US20150132313A1-20150514-P00899
    		 GDAP2 — — — —
    226444_at Hs.413434 Solute carrier family 39 (z
    Figure US20150132313A1-20150514-P00899
    		 SLC39A10
    Figure US20150132313A1-20150514-P00899
    		 30001 // metal ion
    Figure US20150132313A1-20150514-P00899
    		 5634 // nu
    Figure US20150132313A1-20150514-P00899
    		 3676 // nu
    Figure US20150132313A1-20150514-P00899
    		 —
    204646_at Hs.335034 dihydropyrimidine dehydr
    Figure US20150132313A1-20150514-P00899
    		 DPYD 6118 // electron tr
    Figure US20150132313A1-20150514-P00899
    		 5737 // cy
    Figure US20150132313A1-20150514-P00899
    		 4152 // dih
    Figure US20150132313A1-20150514-P00899
    		 Pyrimidine
    Figure US20150132313A1-20150514-P00899
    205321_at Hs.539684 eukaryotic translation init
    Figure US20150132313A1-20150514-P00899
    		 EIF2S3 6412 // protein bio
    Figure US20150132313A1-20150514-P00899
    		 5843 // cy
    Figure US20150132313A1-20150514-P00899
    		 166 // nuc
    Figure US20150132313A1-20150514-P00899
    		 Translation
    Figure US20150132313A1-20150514-P00899
    202165_at Hs.535731 protein phosphatase 1, re
    Figure US20150132313A1-20150514-P00899
    		 PPP1R2 5975 // carbohydr
    Figure US20150132313A1-20150514-P00899
    		 — 4865 // typ
    Figure US20150132313A1-20150514-P00899
    		 —// KEG
    Figure US20150132313A1-20150514-P00899
    201668_x_
    Figure US20150132313A1-20150514-P00899
    		 Hs.519909 myristoylated alanine-rich
    Figure US20150132313A1-20150514-P00899
    		 MARCKS 6928 // cell motilit
    Figure US20150132313A1-20150514-P00899
    		 5886 // pla
    Figure US20150132313A1-20150514-P00899
    		 5516 // ca
    Figure US20150132313A1-20150514-P00899
    		 —
    213701_at Hs.494204 hypothetical protein DKF
    Figure US20150132313A1-20150514-P00899
    		 DKFZp434
    Figure US20150132313A1-20150514-P00899
    		 — — — —
    201110_s_
    Figure US20150132313A1-20150514-P00899
    		 Hs.164226 thrombospondin 1 THBS1 6928 // cell motilit
    Figure US20150132313A1-20150514-P00899
    		 5576 // ext
    Figure US20150132313A1-20150514-P00899
    		 4866 // en
    Figure US20150132313A1-20150514-P00899
    		 TGF_Beta
    Figure US20150132313A1-20150514-P00899
    224800_at Hs.368359 WD repeat and FYVE do
    Figure US20150132313A1-20150514-P00899
    		 WDFY1 — 5634 // nu
    Figure US20150132313A1-20150514-P00899
    		 5545 // ph
    Figure US20150132313A1-20150514-P00899
    		 —
    218396_at Hs.511668 vacuolar protein sorting 1
    Figure US20150132313A1-20150514-P00899
    		 VPS13C 8104 // protein loc
    Figure US20150132313A1-20150514-P00899
    		 — — —
    213737_x_
    Figure US20150132313A1-20150514-P00899
    		 Hs.146211 hypothetical LOC283768 LOC28376
    Figure US20150132313A1-20150514-P00899
    		 — — — —
    202973_x_
    Figure US20150132313A1-20150514-P00899
    		 Hs.97270 family with sequence sim
    Figure US20150132313A1-20150514-P00899
    		 FAM13A1 — — — —
    205198_s_
    Figure US20150132313A1-20150514-P00899
    		 Hs.496414 ATPase, Cu++ transporti
    Figure US20150132313A1-20150514-P00899
    		 ATP7A 6825 // copper ion
    Figure US20150132313A1-20150514-P00899
    		 5783 // en
    Figure US20150132313A1-20150514-P00899
    		 166 // nuc
    Figure US20150132313A1-20150514-P00899
    		 Oxidative
    Figure US20150132313A1-20150514-P00899
    208867_s_
    Figure US20150132313A1-20150514-P00899
    		 Hs.529862 casein kinase 1, alpha 1 CSNK1A1 6468 // protein am
    Figure US20150132313A1-20150514-P00899
    		 — 166 // nuc
    Figure US20150132313A1-20150514-P00899
    		 —
    Figure US20150132313A1-20150514-P00899
    vg.    		 Avg.
    Figure US20150132313A1-20150514-P00899
    LE]-    		 p
    Figure US20150132313A1-20150514-P00899
    SSR]-
    Figure US20150132313A1-20150514-P00899
    99R]-
    Figure US20150132313A1-20150514-P00899
    26CR]-
    Figure US20150132313A1-20150514-P00899
    KHR]-
    Figure US20150132313A1-20150514-P00899
    33XR]-
    Probe_ID Norma
    Figure US20150132313A1-20150514-P00899
    		 SLE
    Figure US20150132313A1-20150514-P00899
    		 [Avg.
    Figure US20150132313A1-20150514-P00899
    		 value [Avg
    Figure US20150132313A1-20150514-P00899
    		 [Avg
    Figure US20150132313A1-20150514-P00899
    		 [Avg
    Figure US20150132313A1-20150514-P00899
    		 [Avg
    Figure US20150132313A1-20150514-P00899
    		 Avg
    Figure US20150132313A1-20150514-P00899
    223674_s_
    Figure US20150132313A1-20150514-P00899
    		 2.355 6.012 3.657 1.20E−05 2.787 4.166 4.429 3.165 3.737
    204415_at 6.515 9.733 3.218 0.018746 1.626 1.102 2.325 5.854 5.183
    228220_at 4.381 7.361 2.980 0.023153 4.085 2.810 1.084 2.995 3.928
    226312_at 7.034 9.818 2.784 0.025167 3.163 2.487 1.045 3.274 3.953
    215245_x_
    Figure US20150132313A1-20150514-P00899
    		 6.070 8.828 2.758 0.032436 3.158 2.255 1.234 3.377 3.787
    202194_at 6.365 9.064 2.699 0.065615 3.433 2.392 1.051 2.553 4.064
    226641_at 7.476 10.170 2.694 0.030007 3.184 2.337 1.070 2.878 4.001
    212585_at 8.182 10.818 2.636 0.028512 3.093 2.358 1.163 2.445 4.120
    201237_at 6.438 9.060 2.622 0.026777 3.338 2.289 1.004 2.644 3.836
    226934_at 5.619 8.241 2.622 0.007781 2.441 2.553 1.672 2.505 3.940
    203983_at 5.522 8.141 2.619 0.018885 2.958 2.306 1.051 2.878 3.900
    221428_s_
    Figure US20150132313A1-20150514-P00899
    		 5.859 8.427 2.568 0.017844 3.004 2.258 1.524 2.398 3.654
    215838_at 6.647 9.190 2.543 0.000349 2.071 2.399 2.263 2.840 3.144
    209884_s_
    Figure US20150132313A1-20150514-P00899
    		 4.525 7.068 2.543 0.006683 2.579 2.292 1.432 2.495 3.918
    222605_at 5.249 7.775 2.526 0.032918 2.965 1.850 1.330 2.689 3.796
    202304_at 4.793 7.268 2.475 0.014487 3.070 2.013 1.088 2.696 3.510
    212579_at 8.996 11.436 2.440 0.014165 2.930 2.037 1.088 3.002 3.143
    206783_s_
    Figure US20150132313A1-20150514-P00899
    		 8.996 11.431 2.435 0.033522 3.161 2.327 1.100 2.518 3.068
    1555643_s 6.942 9.367 2.426 0.001163 2.004 2.163 1.967 2.854 3.140
    226617_at 4.385 6.781 2.395 0.07287 2.903 1.994 1.025 2.486 3.570
    229584_at 8.541 10.926 2.385 0.008927 2.872 1.812 1.216 2.938 3.087
    211967_at 8.352 10.735 2.383 0.032836 2.049 1.805 1.025 3.397 3.640
    212192_at 8.386 10.763 2.377 0.040801 2.993 1.615 1.076 2.365 3.838
    208719_s_
    Figure US20150132313A1-20150514-P00899
    		 4.196 6.546 2.349 0.009291 1.614 4.874 1.826 2.018 1.416
    201669_s_
    Figure US20150132313A1-20150514-P00899
    		 8.355 10.688 2.333 0.007803 2.738 2.177 1.128 3.141 2.479
    222572_at 5.355 7.664 2.329 0.069262 2.681 1.957 1.016 2.279 3.712
    212195_at 8.733 11.015 2.282 0.006803 2.104 2.242 1.440 2.020 3.605
    226711_at 7.581 9.859 2.278 0.016463 2.791 1.734 1.043 2.440 3.384
    222846_at 5.584 7.857 2.273 0.044318 2.897 1.665 1.193 2.829 2.779
    203566_s_
    Figure US20150132313A1-20150514-P00899
    		 4.862 7.131 2.269 0.041967 2.283 1.758 1.057 2.579 3.668
    207564_x_
    Figure US20150132313A1-20150514-P00899
    		 6.919 9.156 2.236 0.004017 2.212 2.086 1.479 2.355 3.048
    219237_s_
    Figure US20150132313A1-20150514-P00899
    		 6.022 8.229 2.207 0.004813 2.454 1.832 1.172 2.322 3.253
    214093_s_
    Figure US20150132313A1-20150514-P00899
    		 5.205 7.403 2.198 0.007941 1.994 1.644 1.199 2.491 3.661
    218589_at 6.422 8.576 2.154 0.011493 2.263 1.396 1.174 1.868 4.067
    217941_s_
    Figure US20150132313A1-20150514-P00899
    		 7.497 9.637 2.140 0.020564 2.313 2.026 1.112 2.354 2.895
    203603_s_
    Figure US20150132313A1-20150514-P00899
    		 4.781 6.915 2.143 0.021477 2.750 1.278 1.039 2.257 3.346
    213111_at 5.914 8.033 2.119 0.013802 2.394 1.869 1.048 2.315 2.968
    213070_at 4.886 6.996 2.111 0.043279 2.405 1.654 1.103 1.921 3.472
    218041_x_
    Figure US20150132313A1-20150514-P00899
    		 7.527 9.629 2.102 0.023894 2.417 1.890 1.140 1.927 3.136
    202033_s_
    Figure US20150132313A1-20150514-P00899
    		 7.096 9.178 2.082 0.018164 2.798 1.406 1.272 2.225 2.709
    200603_at 9.293 11.373 2.080 0.030496 2.651 2.062 1.004 2.031 2.653
    228996_at 4.366 6.436 2.070 0.004022 3.253 1.738 1.435 1.897 2.026
    1554479_at 7.947 10.012 2.065 0.023092 2.558 1.733 1.054 2.133 2.848
    203011_at 5.383 7.442 2.059 0.043964 2.487 1.447 1.001 2.187 3.173
    223940_x_
    Figure US20150132313A1-20150514-P00899
    		 4.166 6.212 2.046 0.003564 2.139 1.026 1.120 2.671 3.273
    222317_at 4.840 6.865 2.025 0.021022 2.593 1.664 1.155 1.901 2.812
    228157_at 6.352 8.371 2.019 0.043641 2.300 1.363 1.074 2.263 3.094
    221505_at 7.489 9.501 2.012 0.057164 2.070 1.656 1.053 2.251 3.028
    1554472_a
    Figure US20150132313A1-20150514-P00899
    		 4.062 6.074 2.012 0.000292 2.270 1.460 1.355 2.254 2.718
    226345_at 5.050 7.057 2.007 0.034947 2.308 1.707 1.169 1.898 2.953
    224862_at 6.663 8.665 2.002 0.046272 2.679 1.850 1.194 1.605 2.682
    207387_s_
    Figure US20150132313A1-20150514-P00899
    		 6.577 8.565 1.987 0.00655 2.663 1.071 1.146 2.292 2.765
    222633_at 5.358 7.324 1.966 3.89E−05 2.171 1.460 1.799 1.689 2.711
    236224_at 5.105 7.064 1.960 0.018708 2.825 2.017 1.110 2.178 1.669
    203080_s_
    Figure US20150132313A1-20150514-P00899
    		 7.254 9.212 1.959 0.008344 2.597 1.166 1.051 2.058 2.921
    222587_s_
    Figure US20150132313A1-20150514-P00899
    		 4.095 6.038 1.944 0.006624 2.585 1.283 1.121 2.393 2.336
    235057_at 3.238 5.161 1.923 0.001003 1.885 1.781 1.343 1.272 3.337
    1554154_a
    Figure US20150132313A1-20150514-P00899
    		 4.572 6.494 1.922 0.001031 2.092 1.729 1.615 1.761 2.413
    226444_at 5.668 7.583 1.915 0.024435 1.542 1.861 1.070 1.880 3.221
    204646_at 7.632 9.545 1.913 0.049899 2.288 1.489 1.263 1.806 2.719
    205321_at 6.682 8.563 1.881 0.030696 2.094 2.213 1.758 1.309 2.030
    202165_at 5.590 7.464 1.874 0.064575 2.078 1.532 1.055 1.763 2.943
    201668_x_
    Figure US20150132313A1-20150514-P00899
    		 4.137 5.987 1.850 0.001437 2.370 1.760 1.413 2.538 1.170
    213701_at 3.954 5.802 1.848 0.044061 1.883 1.388 1.137 1.485 3.345
    201110_s_
    Figure US20150132313A1-20150514-P00899
    		 4.265 6.106 1.841 0.000653 1.953 1.964 1.018 2.122 2.149
    224800_at 6.372 8.193 1.820 0.027641 2.080 1.251 1.067 2.247 2.457
    218396_at 7.271 9.069 1.798 0.020416 1.839 1.550 1.168 1.532 2.902
    213737_x_
    Figure US20150132313A1-20150514-P00899
    		 7.771 9.551 1.780 0.02147 1.892 1.274 1.120 1.602 3.013
    202973_x_
    Figure US20150132313A1-20150514-P00899
    		 5.718 7.492 1.774 0.010098 1.538 2.187 1.599 1.388 2.157
    205198_s_
    Figure US20150132313A1-20150514-P00899
    		 4.069 5.842 1.773 0.008607 2.038 1.332 1.003 1.660 2.833
    208867_s_
    Figure US20150132313A1-20150514-P00899
    		 5.746 7.514 1.768 0.007708 2.015 1.473 1.260 1.787 2.304
    Figure US20150132313A1-20150514-P00899
    indicates data missing or illegible when filed
  • TABLE 2
    Up-Regulation in Gene Expression for a Set of Genes for each of Five Lupus Patients
    Gene I29KHR.SLE I29KHR.SLE RH33XR.SLE RH33XR.SLE
    Probe_ID Symbol (TaqMan) (Affy) (TaqMan) (Affy)
    Figure US20150132313A1-20150514-P00899
    J9SSR
    Figure US20150132313A1-20150514-P00899
     (Ta
    Figure US20150132313A1-20150514-P00899
    228220_at FCHO2 3.24 39.86 3.30 76.15 33.05
    205483_s_at G1P3 86.13 146.74 80.55 92.15 4.45
    212195_at IL6ST 3.87 9.18 3.63 27.52 6.60
    203275_at IRF2 8.10 6.46 5.00 4.80 5.07
    1555643_s_at LILRA5 16.43 12.00 27.25 14.64 11.22
    205170_at STAT2 11.55 8.67 9.74 2.25 8.08
    Probe_ID
    Figure US20150132313A1-20150514-P00899
    OJ9SSR (
    Figure US20150132313A1-20150514-P00899
    Figure US20150132313A1-20150514-P00899
    499R (Ta
    Figure US20150132313A1-20150514-P00899
    Figure US20150132313A1-20150514-P00899
    4499R (
    Figure US20150132313A1-20150514-P00899
    Figure US20150132313A1-20150514-P00899
    I26CR(Ta
    Figure US20150132313A1-20150514-P00899
    Figure US20150132313A1-20150514-P00899
    MI26CR(
    Figure US20150132313A1-20150514-P00899
    228220_at 84.86 22.36 35.07 17.77 10.61
    205483_s_at 7.83 2.90 5.45 5.06 12.71
    212195_at 9.73 4.95 10.70 2.35 6.14
    203275_at 6.54 4.12 4.32 2.44 4.66
    1555643_s_at 6.66 6.82 7.44 4.86 6.49
    205170_at 2.16 6.37 2.92 4.12 2.62
    Figure US20150132313A1-20150514-P00899
    indicates data missing or illegible when filed
    • Example 1a Validation of Genes Identified as Up-Regulated Genes in Lupus Patients
  • To further identify candidate PD markers for anti-IFN-α mAb clinical trials in SLE, the Affymetrix Human Genome U133 Plus 2.0 GENECHIP® array platform was used to profile WB from 46 SLE patients and WB from 24 age- and sex-matched healthy donors. It was observed that 245 and 77 probe sets were upregulated and downregulated, respectively, in WB of SLE patients compared with that from healthy control donors.
  • Of the 245 probe sets upregulated in WB of SLE patients, 114 were type I IFN inducible. Table 30 lists the 50 most upregulated probe sets in WB of these SLE patients; 76% of them are type I IFN inducible. Table 30 also lists the prevalence of the overexpression of these genes in WB of SLE patients. The majority of these genes are overexpressed by at least 2-fold in 65% to 80% of the patients profiled. The robust and prevalent overexpression of a large number of type I IFN-inducible genes in SLE patients suggests that they might be suitable PD markers for clinical trials that investigate an anti-IFN-α mAb therapy for SLE.
  • TABLE 30
    50 most upregulated probe sets in whole blood of SLE patients
    Gene log2 q Value
    Probe ID Gene Title Symbol fc (FDR) Prevalence
    202411 — at interferon, alpha-inducible protein 27 IFI27 4.60 8.41E−07 73.91
    219519 — s — at sialic acid binding Ig-like lectin 1, SIGLEC1 3.52 7.28E−07 65.22
    sialoadhesin
    214059 — at Interferon-induced protein 44 IFI44 3.51 8.04E−07 73.91
    213797 — at radical S-adenosyl methionine domain RSAD2 3.29 9.86E−06 71.74
    containing 2
    204415 — at interferon, alpha-inducible protein 6 IFI6 3.21 2.25E−09 82.61
    242625 — at radical S-adenosyl methionine domain RSAD2 3.19 1.55E−06 69.57
    containing 2
    204439 — at interferon-induced protein 44-like IFI44L 3.14 4.99E−06 71.74
    219211 — at ubiquitin specific peptidase 18 USP18 2.84 2.23E−06 67.39
    214453 — s — at interferon-induced protein 44 IFI44 2.72 1.07E−05 71.74
    202145 — at lymphocyte antigen 6 complex, locus E LY6E 2.53 7.28E−07 63.04
    207329_at matrix metallopeptidase 8 (neutrophil MMP8 2.51 0.00111 60.87
    collagenase)
    202869 — at 2′,5′-oligoadenylate synthetase 1, OAS1 2.33 1.66E−06 69.57
    40/46 kDa
    222154 — s — at DNA polymerase-transactivated protein 6 DNAPTP6 2.32 1.14E−05 65.22
    44673 — at sialic acid binding Ig-like lectin 1, SIGLEC1 2.31 2.23E−06 58.70
    sialoadhesin
    242234 — at XIAP associated factor-1 BIRC4BP 2.31 8.41E−07 65.22
    203153 — at interferon-induced protein with IFIT1 2.25 9.53E−05 67.39
    tetratricopeptide repeats 1
    218400 — at 2′-5′-oligoadenylate synthetase 3, 100 kDa OAS3 2.24 1.23E−05 67.39
    212768_s_at olfactomedin 4 OLFM4 2.23 0.00608 60.87
    241869_at apolipoprotein L, 6 APOL6 2.22 0.00045 80.43
    235643 — at sterile alpha motif domain containing 9- SAMD9L 2.22 1.37E−06 84.78
    like
    231688_at Transcribed locus — 2.22 0.00248 63.04
    208470_s_at haptoglobin /// haptoglobin-related protein HP /// HPR 2.20 2.48E−05 80.43
    239979 — at Epithelial stromal interaction 1 (breast) EPSTI1 2.20 5.44E−06 65.22
    206697_s_at haptoglobin HP 2.19 2.96E−05 73.91
    205552 — s — at 2′,5′-oligoadenylate synthetase 1, OAS1 2.18 4.98E−07 65.22
    40/46 kDa
    205483 — s — at ISG15 ubiquitin-like modifier ISG15 2.16 2.73E−06 65.22
    227609 — at epithelial stromal interaction 1 (breast) EPSTI1 2.15 4.99E−06 67.39
    1555643_s_at leukocyte immunoglobulin-like receptor, LILRA5 2.14 8.41E−07 76.09
    subfamily A
    222816 — s — at zinc finger, CCHC domain containing 2 ZCCHC2 2.09 5.43E−05 80.43
    205569 — at lysosomal-associated membrane protein 3 LAMP3 2.08 2.74E−06 65.22
    226702 — at hypothetical protein LOC129607 LOC129607 2.07 5.96E−05 67.39
    215838_at leukocyte immunoglobulin-like receptor, LILRA5 2.07 1.87E−05 71.74
    subfamily A
    219863 — at hect domain and RLD 5 HERC5 2.03 1.53E−05 67.39
    204747 — at interferon-induced protein with IFIT3 2.01 1.55E−06 67.39
    tetratricopeptide repeats 3
    200986 — at serpin peptidase inhibitor, clade G (C1 SERPING1 1.98 0.00013 67.39
    inhibitor), member 1
    224225 — s — at ets variant gene 7 (TEL2 oncogene) ETV7 1.98 2.48E−05 58.70
    219684 — at receptor (chemosensory) transporter RTP4 1.96 2.74E−06 63.04
    protein 4
    206133 — at XIAP associated factor-1 BIRC4BP 1.96 7.28E−07 65.22
    206871_at elastase 2, neutrophil ELA2 1.95 0.00316 54.35
    217502 — at interferon-induced protein with IFIT2 1.95 4.86E−06 71.74
    tetratricopeptide repeats 2
    237340_at solute carrier family 26, member 8 SLC26A8 1.93 6.68E−06 60.87
    235276 — at — — 1.93 6.44E−06 65.22
    203757_s_at carcinoembryonic antigen-related cell CEACAM6 1.91 0.00124 47.83
    adhesion molecule 6
    202086 — at myxovirus (influenza virus) resistance 1, MX1 1.90 2.66E−05 67.39
    interferon-inducible protein p78 (mouse)
    /// myxovirus (influenza virus) resistance
    1, interferon-inducible protein p78 (mouse)
    241916 — at Phospholipid scramblase 1 PLSCR1 1.89 4.86E−06 73.91
    203595 — s — at interferon-induced protein with IFIT5 1.89 2.81E−08 69.57
    tetratricopeptide repeats 5
    205660 — at 2′-5′-oligoadenylate synthetase-like OASL 1.89 1.94E−05 65.22
    219352 — at hect domain and RLD 6 HERC6 1.87 9.79E−06 63.04
    211657_at carcinoembryonic antigen-related cell CEACAM6 1.86 0.00667 60.87
    adhesion molecule 6
    228439 — at basic leucine zipper transcription factor, BATF2 1.86 2.63E−05 63.04
    ATF-like 2
    Data were generated from 46 SLE patients and 24 healthy controls using SAM and FDR in R (see Methods). Type I IFN-inducible genes are highlighted in bold. FDR = false discovery rate; SAM = significance analysis of microarrays; SLE = systemic lupus erythematosus; WB = whole blood.
  • FIG. 80 (top panel) shows a heat map of the expression of the 114 upregulated type I IFN-inducible probe sets in SLE patients and healthy controls. A total of 32/46 of the SLE patients profiled showed significant overexpression of the type I IFN gene signature. To confirm the observation that type I IFN-inducible genes are overexpressed in WB of SLE patients, WB was procured from 54 SLE patients in a prospective study. FIG. 81A shows the PCA plot of the 46 SLE patients in the first study using the 114 overexpressed type I IFN-inducible probes. A clear difference was observed between SLE patients that had distinct overexpression of type I IFN gene signature from healthy donors and SLE patients that had weak or nondetectable type I IFN gene signature in WB. FIG. 81B shows the PCA plot from the 54 SLE patients in the prospective study using the same 114 type I IFN-inducible probe sets identified. A similar separation of SLE patients was observed based on type I IFN gene signature as in FIG. 81A. The distribution of the type I IFN gene signature scores in the prospective study was also similar to that of the first study (data not shown). The ability to use the overexpressed type I IFN-inducible genes identified to segregate SLE patients into 2 distinct groups—patients with or without type I IFN gene signature—validated the accurate identification of overexpression in the type I IFN gene signature in WB of SLE patients.
  • In addition to the overexpression of a type I IFN gene signature, the overexpression of a gene signature that is indicative of granulocyte activation in WB of SLE patients was observed. The granulocyte gene signature included (but was not limited to) the following genes: AZU, DEFA1, DEFA4, ELA2, MMP8, MMP9, RNAS2, MPO, CAMP, FCAR, and CYBB (FIG. 80, second panel). The granulocyte gene signature was present in about 50% of the SLE patients profiled.
  • The 50 most downregulated probe sets observed in WB of SLE patients are shown in Table 31. The downregulation of T, NK, and B cell gene signatures was observed in WB of SLE patients (FIG. 80, panels three, four, and five, respectively); this is in agreement with the observation of lymphopenia in SLE patients previously reported in the literature (Bennett L, Palucka A K, Arce E et al.: Interferon and granulopoiesis signatures in systemic lupus erythematosus blood. J Exp Med. 197(6), 711-723 (2003), Rivero S J, Diaz-Jouanen E and Alarcon-Segovia D: Lymphopenia in systemic lupus erythematosus. Clinical, diagnostic, and prognostic significance. Arthritis Rheum. 21(3), 295-305 (1978).
  • TABLE 31
    Top 50 most downregulated transcripts in whole blood of SLE patients
    Gene log2 q Value
    Probe ID Gene Title Symbol fc (FDR) Prevalence
    1552713_a_at solute carrier family 4, anion SLC4A1 −1.82 0.00021 69.57
    exchanger, member 1 (erythrocyte
    membrane protein band 3, Diego
    blood group)
    1552348_at protease, serine, 33 PRSS33 −1.71 0.00046 63.04
    211734_s_at Fc fragment of IgE, high affinity I, FCER1A −1.59 0.00083 54.35
    receptor for; alpha polypeptide ///
    Fc fragment of IgE, high affinity I,
    receptor for; alpha polypeptide
    236307_at BTB and CNC homology 1, basic BACH2 −1.51 0.00012 54.35
    leucine zipper transcription factor 2
    214470_at killer cell lectin-like receptor KLRB1 −1.50 0.00000 58.70
    subfamily B, member 1 /// killer
    cell lectin-like receptor subfamily
    B, member 1
    209570_s_at DNA segment on chromosome 4 D4S234E −1.46 0.00000 65.22
    (unique) 234 expressed sequence
    217143_s_at T cell receptor alpha locus /// T TRA@ /// −1.38 0.00001 58.70
    cell receptor delta locus TRD@
    203562_at fasciculation and elongation FEZ1 −1.36 0.00028 89.13
    protein zeta 1 (zygin I)
    227198_at AF4/FMR2 family, member 3 AFF3 −1.35 0.00046 45.65
    207840_at CD160 molecule CD160 −1.34 0.00079 47.83
    232286_at AF4/FMR2 family, member 3 AFF3 −1.34 0.00003 56.52
    209993_at ATP-binding cassette, sub-family ABCB1 −1.32 0.00002 63.04
    B (MDR/TAP), member 1
    209815_at patched homolog 1 (Drosophila) PTCH1 −1.29 0.00003 54.35
    241881_at olfactory receptor, family 2, OR2W3 −1.29 0.01736 50.00
    subfamily W, member 3
    213674_x_at immunoglobulin heavy constant IGHD −1.29 0.01801 50.00
    delta
    231798_at Noggin NOG −1.28 0.00234 73.91
    239673_at Nuclear receptor subfamily 3, NR3C2 −1.27 0.00004 56.52
    group C, member 2
    221748_s_at tensin 1 /// tensin 1 TNS1 −1.23 0.00953 50.00
    218864_at tensin 1 TNS1 −1.22 0.00718 50.00
    219630_at PDZK1 interacting protein 1 PDZK1IP1 −1.20 0.00528 56.52
    1553177_at SH2 domain containing 1B SH2D1B −1.20 0.00187 47.83
    229513_at Spermatid perinuclear RNA STRBP −1.20 0.00017 58.70
    binding protein
    243054_at Zinc finger, MYND domain ZMYND11 −1.20 0.00101 60.87
    containing 11
    236796_at BTB and CNC homology 1, basic BACH2 −1.20 0.00004 56.52
    leucine zipper transcription factor
    2
    203661_s_at tropomodulin 1 TMOD1 −1.19 0.00675 50.00
    239278_at CDNA clone IMAGE: 5301129 — −1.17 0.00002 65.22
    235400_at Fc receptor-like A FCRLA −1.17 0.00099 52.17
    240690_at Homolog of rat pragma of Rnd2 DKFZp761P0423 −1.17 0.00012 52.17
    210746_s_at erythrocyte membrane protein EPB42 −1.16 0.00552 45.65
    band 4.2 /// erythrocyte membrane
    protein band 4.2
    232478_at Nuclear receptor subfamily 6, NR6A1 −1.15 0.00004 47.83
    group A, member 1
    243810_at Similar to Heterogeneous nuclear LOC341333 −1.15 0.00014 47.83
    ribonucleoprotein A1 (Helix-
    destabilizing protein) (Single-
    strand RNA-binding protein)
    (hnRNP core protein A1)
    228599_at membrane-spanning 4-domains, MS4A1 −1.14 0.00454 45.65
    subfamily A, member 1
    212827_at immunoglobulin heavy constant IGHM −1.14 0.00324 45.65
    mu /// immunoglobulin heavy
    constant mu
    1552349_a_at protease, serine, 33 PRSS33 −1.13 0.02357 47.83
    216191_s_at T cell receptor alpha locus /// T TRA@ /// −1.12 0.01073 50.00
    cell receptor delta locus /// B-cell TRD@ ///
    CLL/lymphoma 11B (zinc finger BCL11B
    protein)
    232686_at sialic acid binding Ig-like lectin, SIGLECP3 −1.12 0.00003 58.70
    pseudogene 3
    211532_x_at killer cell immunoglobulin-like KIR2DS2 −1.10 0.04011 54.35
    receptor, two domains, short
    cytoplasmic tail, 2
    1563217_at Protein kinase (cAMP-dependent, PKIA −1.10 0.00024 58.70
    catalytic) inhibitor alpha
    243798_at Burkitt lymphoma receptor 1, GTP BLR1 −1.10 0.00044 54.35
    binding protein (chemokine (C-X-
    C motif) receptor 5)
    220751_s_at chromosome 5 open reading frame 4 C5orf4 −1.09 0.00531 50.00
    202555_s_at myosin, light chain kinase /// MYLK −1.09 0.00149 52.17
    myosin, light chain kinase
    230245_s_at hypothetical protein LOC283663 LOC283663 −1.09 0.00977 47.83
    233921_s_at MAD1 mitotic arrest deficient-like MAD1L1 −1.08 0.00001 41.30
    1 (yeast)
    214974_x_at chemokine (C-X-C motif) ligand 5 CXCL5 −1.08 0.00717 54.35
    209569_x_at DNA segment on chromosome 4 D4S234E −1.08 0.00005 58.70
    (unique) 234 expressed sequence
    235401_s_at Fc receptor-like A FCRLA −1.08 0.00173 50.00
    205900_at keratin 1 (epidermolytic KRT1 −1.08 0.04518 43.48
    hyperkeratosis)
    242509_at Chromosome 16 open reading C16orf74 −1.08 0.00016 47.83
    frame 74
    209994_s_at ATP-binding cassette, sub-family ABCB1 /// −1.08 0.00000 56.52
    B (MDR/TAP), member 1 /// ATP- ABCB4
    binding cassette, sub-family B
    (MDR/TAP), member 4
    204793_at G protein-coupled receptor GPRASP1 −1.08 0.00026 45.65
    associated sorting protein 1
    Data were generated from 46 SLE patients and 24 healthy controls using SAM and FDR in R (see Methods). FDR = false discovery rate; SLE = systemic lupus erythematosus; SAM = significance analysis of microarrays; WB = whole blood.
  • To further confirm the observation of overexpression of the type I IFN and granulocyte signatures and to identify other signaling pathways that may be altered in SLE, a pathway and network analysis was carried out with GeneGo software (see Methods). Overall, for SLE, this pathway analysis confirmed the activation of the type I IFN pathway, along with the activation of a granulocyte signature, and the underexpression of the T-cell signaling pathway. Additionally, in the patients profiled, the activation of the IL-10 signaling pathway was among the other notable pathways found to be altered. This may suggest B cell activation and be indicative of the abnormal apoptosis of T-cell subsets observed in SLE patients. (Diaz-Alderete A, Crispin J C, Vargas-Rojas M I and Alcocer-Varela J: IL-10 production in B cells is confined to CD154+ cells in patients with systemic lupus erythematosus. J Autoimmun. 23(4), 379-383 (2004), Wang H, Xu J, Ji X et al.: The abnormal apoptosis of T cell subsets and possible involvement of IL-10 in systemic lupus erythematosus. Cell Immunol. 235(2), 117-121 (2005)).
  • Confirmation of Overexpression of Type I IFN-Inducible Genes:
  • To confirm the overexpression of type I IFN-inducible genes in SLE that were observed in the microarray analyses, a BIOMARK™ 48.48 dynamic array was used to perform high throughput (HTP) TAQMAN QRT-PCR on 40 of the type I IFN-inducible genes (selected based on their magnitude and prevalence of overexpression in whole blood of SLE patients). TAQMAN QRT-PCR assays confirmed the overexpression of all 40 genes in whole blood of 35 of the originally profiled 46 SLE patients. The overexpression of 15 of the 40 type I IFN-inducible genes using TAQMAN QRT-PCR assays is shown in FIG. 83A. These genes were upregulated by an average of 8- to 92-fold, and all were significantly overexpressed (P<0.05). These observations provide evidence that type I IFN-inducible genes are significantly overexpressed in SLE patients. The consistency of the results among microarray and TAQMAN assays and the strong correlation (correlation coefficient >0.98) between microarray and TAQMAN assays for 21 IFN-inducible genes in 2 example SLE patients (FIGS. 83B and 4C) argues for their potential as PD and diagnostic markers in clinical trials that investigate anti-IFN-α approaches in the treatment of SLE.
    • Example 2 Potential PD Markers Selected from Genes Up-Regulated in Lupus Patients
  • Using the whole genome profiling data described in Example 1a, a group of candidate PD markers were selected. These candidate markers are provided in Table 3.
  • TABLE 3
    Candidate PD markers
    Probe_ID Gene Symbol Group
    204415_at HERC5
    1
    202411_at IFI27 1
    214453_s_at IFI44 1
    229450_at IFIT3 1
    1555643_s_at LILRA5 1
    205483_s_at G1P2 1
    204439_at IFI44L 1
    203153_at IFIT1 1
    202145_at LY6E 1
    202869_at OAS1 1
    218400_at OAS3 1
    242625_at RSAD2 1
    228220_at FCHO2 2
    205483_s_at G1P3 2
    212195_at IL6ST 2
    203275_at IRF2 2
    1555643_s_at LILRA5 2
    205170_at STAT2 2
    208436_s_at IRF7 3
    211967_at PORIMIN 3
    226312_at AVO3 3
    201669_s_at MARCKS 3
    222846_at RAB8B 3
    • Example 3 Candidate PD Markers Exhibit Minimal Variation in Healthy Donors
  • qPCR was conducted for a selected group of candidate PD markers to determine whether they exhibited variation at baseline in the whole blood of healthy volunteers. qPCR indicated that baseline variation was minimal. See Table 4, which provides the baseline qPCR data (healthy volunteers shown in shaded columns).
  • TABLE 4
    Baseline Variation of Candidate PD Markers
    Figure US20150132313A1-20150514-C00001
    • Example 4 IFNα Stimulates Up-Regulation in Expression of Candidate PD Markers in Whole Blood of Healthy Volunteers
  • A study was performed to determine whether IFNα could stimulate expression of candidate PD markers in whole blood of healthy volunteers. Whole blood of healthy volunteers was collected in heparinized tubes, transferred to the appropriate wells of 6-well culture plates, and incubated with leukocyte IFN doses of 3, 30, 100, and 300 I.U. and then incubated for 4 hours at 37° C., 5% CO2. Fold-induction of expression of candidate PD markers for genes IFI44, IRF2, RSAD2, G1P3, and HERC5 was determined using RNA isolated from PBMCs (Peripheral Blood Mononuclear Cells) with Qiagen's RNAeasy kit. As shown in Table 5 (IFI44 and IRF2), Table 6 (RSAD2), and Table 7 (G1P3 and HERC5) leukocyte IFN causes up-regulation in expression of each of these candidate PD markers. See also FIG. 1 (IFI44), FIG. 2 (IRF2), FIG. 3 (RSAD2), FIG. 4 (G1P3), and FIG. 5 (HERC5) for a graphical analysis of these candidate PD marker expression results.
  • A summary hierarchical clustering of all samples using 1384 genes differentially regulated by IFN type 1, IFN type 2, or TNFα obtained from a separate experiment is shown in FIG. 17. A heat map with a summary hierarchical clustering is also provided for 689 type I IFN inducible probe sets used on whole blood samples from healthy donors ex vivo stimulated with IFN type 1, IFN type 2, or TNFα. See FIG. 64.
  • TABLE 5
    Induced IFI44 and IRF2 Expression Following Leukocyte
    IFN Stimulation of Healthy Volunteer's Whole Blood
    Sample Gene Average FC StDev
    63A Media IFI44 1.00
    63A IFN3 IFI44 8.58 0.16
    63A IFN30 IFI44 8.27 0.07
    63A IFN100 IFI44 15.12 0.50
    63A IFN300 IFI44 12.42 0.04
    63A Media IRF2 1.00
    63A IFN3 IRF2 2.25 0.08
    63A IFN30 IRF2 1.96 0.06
    63A IFN100 IRF2 2.19 0.06
    63A IFN300 IRF2 3.75 0.10
  • TABLE 6
    Induced RSAD2 Expression Following Leukocyte IFN
    Stimulation of Healthy Volunteer′s Whole Blood
    Sample Gene Average FC StDev
    63A Media RSAD2 1.00
    63A IFN3 RSAD2 10.88 0.11
    63A IFN30 RSAD2 11.14 0.21
    63A IFN100 RSAD2 14.96 0.12
    63A IFN300 RSAD2 25.50 0.50
  • TABLE 7
    Induced G1P3 and HERC5 Expression Following Leukocyte
    IFN Stimulation of Healthy Volunteer's Whole Blood
    Sample Gene Average FC StDev
    63A Media G1P3 1.00
    63A IFN3 G1P3 42.88 1.03
    63A IFN30 G1P3 25.76 0.10
    63A IFN100 G1P3 21.72 0.48
    63A IFN300 G1P3 16.02 0.06
    63A Media HERC5 1.00
    63A IFN3 HERC5 14.17 0.12
    63A IFN30 HERC5 13.74 0.12
    63A IFN100 HERC5 18.51 0.58
    63A IFN300 HERC5 23.55 0.54
    • Example 5 IFNα Ab Neutralizes IFNα-Induced Candidate PD Marker Expression in Healthy Volunteers' Whole Blood Source of Interferon=IFNα2a
  • Because IFNα treatment of healthy volunteers' whole blood induced expression of candidate PD markers, it was determined whether IFNα Ab, MEDI-545, could neutralize the induction of expression of these markers.
  • Blood was drawn from each of three donors into heparin tubes. Aliquots of 2.5 ml of drawn blood were added to each of 4 wells of 6- or 24-well treatment plates. The 4 wells were designated for treatment as follows: (a) blood+vehicle, (b) blood+100 IU IFNα2a, (c) blood+100 IU IFNα2a+MEDI-545 (IFNα Ab), and (d) blood+100 IU IFNα2a+R347 (control Ab).
  • Wells containing blood to be treated with Ab were first incubated with either MEDI-545 (IFNα Ab; well (c)) or R347 (control Ab; well (d)) for 30 minutes. Following Ab treatment, vehicle (well (a)) or IFN α2a (wells (b), (c), and (d)) was added to the appropriate wells and was then incubated for an additional 4 hours at 37° C., 5% CO2. The samples were then transferred to PAXgene tubes and incubated at room temperature for 2 hr. Following the 2 hr incubation the tubes were transferred to −80° C. for storage.
  • Following, at least, an overnight incubation at −80° C. the total RNA of the cells was prepared according to the PAXgene protocol. First and second strand cDNA was prepared via Affy GRP methods and TAQMAN was conducted on the cDNA samples.
  • Expression of at least 11 candidate PD markers, previously identified as up-regulated in lupus patients, could be neutralized by MEDI-545 in the IFNα2a-stimulated whole blood. See Table 8 (RAB8B), Table 9 (IRF7), Table 10 (MARCKS), Table 11 (IL6ST), Table 12 (LY6E), Table 13 (IFIT3), Table 14 (IFIT1), Table 15 (HERC5), Table 16 (OAS1), Table 17 (OAS3), and Table 18 (RSAD2), which provide quantitative gene expression analysis for each of these 11 genes in the whole blood of each of the 3 healthy volunteers.
  • TABLE 8
    IFN α2a-Induced RAB8B Gene Expression
    is Neutralized by MEDI-545
    Sample Gene Average StDev
    107 VEH RAB8B 1.00
    107 IFN RAB8B 3.45 0.31
    107 IFN + 545 RAB8B 1.30 0.04
    107 IFN + R347 RAB8B 3.15 0.03
    163 VEH RAB8B 0.70 0.01
    163 IFN RAB8B 2.20 0.04
    163 IFN + 545 RAB8B 1.18 0.01
    163 IFN + R3437 RAB8B 3.71 0.02
    175 VEH RAB8B 0.64 0.01
    175 IFN RAB8B 2.63 0.04
    175 IFN + 545 RAB8B 1.15 0.02
    175 IFN + R347 RAB8B 2.51 0.05
  • TABLE 9
    IFN α2a-Induced IRF7 Gene Expression
    is Neutralized by MEDI-545
    Sample Gene Average StDev
    107 VEH IRF7 1.00
    107 IFN IRF7 18.53 3.32
    107 IFN + 545 IRF7 3.42 0.33
    107 IFN + R347 IRF7 19.48 1.67
    163 VEH IRF7 0.91 0.02
    163 IFN IRF7 17.16 1.39
    163 IFN + 545 IRF7 2.92 0.22
    163 IFN + R3437 IRF7 23.28 1.46
    175 VEH IRF7 1.25 0.10
    175 IFN IRF7 24.65 0.80
    175 IFN + 545 IRF7 2.43 0.08
    175 IFN + R347 IRF7 26.34 8.61
  • TABLE 10
    IFN α2a-Induced MARCKS Gene Expression
    is Neutralized by MEDI-545
    Sample Gene Average StDev
    107 VEH MARCKS 1.00
    107 FN MARCKS 3.97 0.09
    107 IFN + 545 MARCKS 1.30 0.08
    107 IFN + R347 MARCKS 2.99 0.10
    163 VEH MARCKS 0.56 0.01
    163 IFN MARCKS 2.59 0.12
    163 IFN + 545 MARCKS 1.55 0.05
    163 IFN + R3437 MARCKS 4.42 0.07
    175 VEH MARCKS 0.41 0.01
    175 IFN MARCKS 2.59 0.06
    175 IFN + 545 MARCKS 0.55 0.02
    175 IFN + R347 MARCKS 3.38 0.05
  • TABLE 11
    IFN α2a-Induced IL6ST Gene Expression is Neutralized by MEDI-545
    Sample Gene Average StDev
    107 VEH IL6ST 1.00
    107 IFN IL6ST 3.54 0.60
    107 IFN + 545 IL6ST 2.62 0.16
    107 IFN + R347 IL6ST 8.19 0.54
    163 VEH IL6ST 2.50 0.58
    163 IFN IL6ST 7.69 0.47
    163 IFN + 545 IL6ST 4.18 0.44
    163 IFN + R3437 IL6ST 13.24 0.12
    175 VEH IL6ST 1.37 0.09
    175 IFN IL6ST 7.62 0.56
    175 IFN + 545 IL6ST 2.95 0.38
    175 IFN + R347 IL6ST 23.91 2.77
  • TABLE 12
    IFN α2a-Induced LY6E Gene Expression is Neutralized by MEDI-545
    Sample Gene Average StDev
    107 VEH LY6E 1.00
    107 IFN LY6E 19.09 0.03
    107 IFN + 545 LY6E 3.50 0.15
    107 IFN + R347 LY6E 12.54 0.20
    163 VEH LY6E 1.02 0.04
    163 IFN LY6E 13.52 0.35
    163 IFN + 545 LY6E 4.80 0.18
    163 IFN + R3437 LY6E 22.56 0.35
    175 VEH LY6E 1.61 0.15
    175 IFN LY6E 19.32 0.68
    175 IFN + 545 LY6E 3.74 0.00
    175 IFN + R347 LY6E 15.57 0.44
  • TABLE 13
    IFN α2a-Induced IFIT3 Gene Expression is Neutralized by MEDI-545
    Sample Gene Average StDev
    107 VEH IFIT3 1.00
    107 IFN IFIT3 38.43 0.78
    107 IFN + 545 IFIT3 6.78 0.14
    107 IFN + R347 IFIT3 42.59 0.75
    163 VEH IFIT3 0.62 0.01
    163 IFN IFIT3 25.94 0.57
    163 IFN + 545 IFIT3 4.58 0.08
    163 IFN + R3437 IFIT3 44.83 0.44
    175 VEH IFIT3 1.32 0.02
    175 IFN IFIT3 35.02 0.48
    175 IFN + 545 IFIT3 5.28 0.05
    175 IFN + R347 IFIT3 29.71 0.79
  • TABLE 14
    IFN α2a-Induced IFIT1 Gene Expression is Neutralized by MEDI-545
    Sample Gene Average StDev
    107 VEH IFIT1 1.00
    107 IFN IFIT1 80.21 3.44
    107 IFN + 545 IFIT1 13.14 0.02
    107 IFN + R347 IFIT1 86.44 0.57
    163 VEH IFIT1 0.92 0.03
    163 IFN IFIT1 51.65 1.21
    163 IFN + 545 IFIT1 7.60 0.05
    163 IFN + R3437 IFIT1 86.63 2.67
    175 VEH IFIT1 1.47 0.17
    175 IFN IFIT1 82.98 2.94
    175 IFN + 545 IFIT1 8.40 0.24
    175 IFN + R347 IFIT1 58.50 1.47
  • TABLE 15
    IFN α2a-Induced HERC5 Gene Expression is Neutralized by MEDI-545
    Sample Gene Average StDev
    107 VEH HERC5 1.00
    107 IFN HERC5 41.12 2.87
    107 IFN + 545 HERC5 6.29 0.49
    107 IFN + R347 HERC5 55.04 0.69
    163 VEH HERC5 1.05 0.07
    163 IFN HERC5 75.81 0.50
    163 IFN + 545 HERC5 7.83 0.00
    163 IFN + R3437 HERC5 95.44 7.79
    175 VEH HERC5 1.19 0.06
    175 IFN HERC5 74.58 5.79
    175 IFN + 545 HERC5 6.89 0.13
    175 IFN + R347 HERC5 98.15 19.40
  • TABLE 16
    IFN α2a-Induced OAS1 Gene Expression is Neutralized by MEDI-545
    Sample Gene Average StDev
    107 VEH OAS1 1.00
    107 IFN OAS1 15.11 4.27
    107 IFN + 545 OAS1 3.45 1.03
    107 IFN + R347 OAS1 17.82 3.93
    163 VEH OAS1 0.77 0.22
    163 IFN OAS1 14.19 3.14
    163 IFN + 545 OAS1 3.05 0.75
    163 IFN + R3437 OAS1 22.44 3.49
    175 VEH OAS1 1.62 0.38
    175 IFN OAS1 22.09 0.97
    175 IFN + 545 OAS1 4.04 0.45
    175 IFN + R347 OAS1 15.22 4.48
  • TABLE 17
    IFN α2a-Induced OAS3 Gene Expression is Neutralized by MEDI-545
    Sample Gene Average StDev
    107 VEH OAS3 1.00
    107 IFN OAS3 49.04 13.74
    107 IFN + 545 OAS3 7.03 0.84
    107 IFN + R347 OAS3 76.88 13.69
    163 VEH OAS3 0.49 0.06
    163 IFN OAS3 42.01 10.01
    163 IFN + 545 OAS3 14.60 4.53
    163 IFN + R3437 OAS3 52.60 7.04
    175 VEH OAS3 1.27 0.14
    175 IFN OAS3 37.87 3.57
    175 IFN + 545 OAS3 3.92 0.06
    175 IFN + R347 OAS3 34.91 2.07
  • TABLE 18
    IFN α2a-Induced RSAD2 Gene Expression is Neutralized by MEDI-545
    Sample Gene Average StDev
    107 VEH RSAD2 1.00
    107 IFN RSAD2 109.64 36.65
    107 IFN + 545 RSAD2 9.88 0.32
    107 IFN + R347 RSAD2 107.32 35.38
    163 VEH RSAD2 0.56 0.11
    163 IFN RSAD2 71.47 21.17
    163 IFN + 545 RSAD2 4.39 0.60
    163 IFN + R3437 RSAD2 114.51 28.63
    175 VEH RSAD2 1.88 0.43
    175 IFN RSAD2 126.27 22.95
    175 IFN + 545 RSAD2 8.43 0.36
    175 IFN + R347 RSAD2 90.97 7.42
  • See also FIG. 6 (RAB8B), FIG. 7 (IRF7), FIG. 8 (MARCKS), FIG. 9 (IL6ST), FIG. 10 (LY6E), FIG. 11 (IFIT3), FIG. 12 (IFIT1), FIG. 13, (HERC5), FIG. 14 (OAS1), FIG. 15 (OAS3), and FIG. 16 (RSAD2) for graphical representations of the gene expression data for each of the 11 genes.
    • Source of Interferon=SLE Patient Serum
  • (a) Neutralization of type I IFN-induced genes by MEDI-545 could also be observed in whole blood of healthy volunteers that had been stimulated with serum obtained from lupus patients. Serum samples were obtained from SLE patients that had been tested in an IFN bioassay. Whole blood was collected from healthy donors in heparinized vacutainer tubes and PBMC were isolated using Ficoll gradient centrifugation method. PBMC were resuspended at 1×107 cells/mL in RPMI media with 10% fetal bovine serum (FBS) and 125 L of cells were aliquoted into each well of a 24 well flat bottom plate (1.25×106 cells/well). Serum from SLE patients was preincubated for one hour with MEDI-545 (0.1, 1, 10 μg/mL), anti-IFN-γ antibody (1 μg/mL) or control antibody (10 μg/mL). SLE serum was added to the PBMC at a final concentration 25% (62.5 μL per well). Additional volume of RPMI+10% FBS was added to the wells to obtain a final volume of 250 L per well. Plates were incubated at 37° C. for either 4 or 18 hours. Following the incubation, RNA was harvested by adding 750 μL of Trizol LS to each well. Samples were frozen at −70° C. until the time of RNA isolation. Table 21 provides the MEDI-545 blockade of 74 type I IFN genes in healthy volunteers' whole blood stimulated ex vivo with SLE patient serum.
  • TABLE 21
    MEDI-545 blocks overexpression of type I IFN genes in whole blood of healthy
    volunteers stimulated ex vivo with lupus patient serum
    Probe ID D1_002_545.10 D1_004_545.10 D1_17021_545.10 UniGene. ID Gene. Symbol
    219211_at −3.1949 −4.9995 −4.0543 Hs.38260 USP18
    217502_at −3.1886 −4.2648 −3.0247 Hs.437609 IFIT2
    218400_at −3.1235 −4.3204 −3.9594 Hs.528634 OAS3
    213797_at −3.0752 −3.3250 −2.5795 Hs.17518 RSAD2
    203153_at −2.8862 −4.6545 −4.7890 Hs.20315 IFIT1
    242625_at −2.8104 −2.9506 −2.2214 Hs.17518 RSAD2
    204747_at −2.7900 −3.6590 −2.9676 Hs.47338 IFIT3
    205483_s_at −2.5237 −2.9955 −3.1566 Hs.458485 ISG15
    204439_at −2.5133 −3.5887 −3.5926 Hs.389724 IFI44L
    202145_at −2.4809 −3.0198 −3.5950 Hs.521903 LY6E
    202869_at −2.4582 −3.5402 −3.2304 Hs.524760 OAS1
    235643_at −2.4535 −3.3586 −2.9115 Hs.489118 SAMD9L
    219352_at −2.4496 −3.5983 −3.8692 Hs.529317 HERC6
    204415_at −2.4417 −2.5228 −2.3149 Hs.523847 IFI6
    219684_at −2.4167 −2.8965 −2.1421 Hs.43388 RTP4
    236156_at −2.4160 −2.5440 −2.8885 Hs.127445 LIPA
    205552_s_at −2.3880 −3.3679 −2.7561 Hs.524760 OAS1
    206133_at −2.3139 −3.0772 −2.4787 Hs.441975 BIRC4BP
    214453_s_at −2.2965 −3.1707 −3.3204 Hs.82316 IFI44
    1556643_at −2.2666 −2.0429 −1.7120 Hs.515243 LOC93343
    228607_at −2.2597 −2.1659 −2.3234 Hs.414332 OAS2
    218943_s_at −2.2563 −2.4118 −2.6600 Hs.190622 DDX58
    242020_s_at −2.2542 −2.6436 −1.7975 Hs.302123 ZBP1
    204959_at −2.2501 −1.3731 −1.5559 Hs.153837 MNDA
    226757_at −2.2481 −2.9288 −2.3984 Hs.437609 IFIT2
    219863_at −2.2465 −3.0980 −3.8114 Hs.26663 HERC5
    229450_at −2.2281 −3.2200 −2.2151 — —
    214059_at −3.2929 −3.5281 Hs.82316 IFI44
    232517_s_at −2.1925 −2.2750 −2.4569 Hs.517180 PRIC285
    232666_at −2.1925 −1.9206 −1.4938 Hs.528634 OAS3
    230036_at −2.1654 −3.0256 −2.4879 Hs.489118 SAMD9L
    227609_at −2.1548 −2.5608 −1.1577 Hs.546467 EPSTI1
    226702_at −2.1420 −3.0150 −3.0155 Hs.7155 LOC129607
    226603_at −2.1183 −2.8672 −2.4103 Hs.489118 SAMD9L
    210397_at −2.1095 −0.5687 −2.0322 Hs.32949 DEFB1
    204994_at −2.0685 −3.2727 −3.6132 Hs.926 MX2
    202086_at −2.0661 −3.2741 −3.6406 Hs.517307 MX1
    228617_at −2.0596 −2.5832 −2.3139 Hs.441975 BIRC4BP
    219364_at −2.0583 −2.3774 −2.4651 Hs.55918 LGP2
    209417_s_at −2.0364 −2.5262 −2.4132 Hs.632258 IFI35
    222154_s_at −2.0330 −2.4542 −2.6425 Hs.120323 DNAPTP6
    228230_at −2.0323 −2.9621 −3.0255 Hs.517180 PRIC285
    242234_at −2.0161 −3.0047 −3.1633 Hs.441975 BIRC4BP
    219519_s_at −2.0077 −0.2596 −3.1621 Hs.31869 SIGLEC1
    207713_s_at −1.9940 −1.0134 −1.6345 Hs.247280 C20orf18
    218974_at −1.8904 −2.5122 −2.5244 Hs.445244 FLJ10159
    1552309_a_at −1.8820 −2.4284 −2.7221 Hs.632387 NEXN
    210873_x_at −1.8424 −1.2891 −1.2710 Hs.348983 APOBEC3A
    243271_at −1.8388 −2.2657 −2.0595 Hs.489118 SAMD9L
    202411_at −1.8385 −0.1345 −2.4757 Hs.532634 IFI27
    222793_at −1.8137 −2.4540 −2.6576 Hs.190622 DDX58
    235276_at −1.8007 −2.6121 −1.4780 — —
    203236_s_at −1.7926 −1.9069 −2.6425 Hs.81337 LGALS9
    225291_at −1.7801 −2.0167 −2.4613 Hs.388733 PNPT1
    44673_at −1.7547 −0.1337 −2.3913 Hs.31869 SIGLEC1
    213294_at −1.7361 −2.4393 −2.5907 Hs.546523 —
    211122_s_at −1.7296 −3.0816 −1.5743 Hs.632592 CXCL11
    224701_at −1.6827 −1.7880 −1.2356 Hs.583792 PARP14
    230314_at −1.6795 −2.2159 −2.3476 Hs.112420 —
    218986_s_at −1.6648 −2.1615 −2.0204 Hs.591710 FLJ20035
    205569_at −1.6647 −2.5741 −2.6878 Hs.518448 LAMP3
    219691_at −1.6420 −1.8434 −1.8310 Hs.65641 SAMD9
    204211_x_at −1.6244 −2.0612 −2.3379 Hs.131431 EIF2AK2
    220146_at −1.6033 −2.7419 −1.7471 Hs.443036 TLR7
    241916_at −1.6026 −1.5906 −1.3802 Hs.130759 PLSCR1
    229350_x_at −1.5906 −1.7395 −1.3577 Hs.348609 PARP10
    1555464_at −1.5866 −1.7397 −1.3101 Hs.163173 IFIH1
    204972_at −1.5822 −2.8402 −2.8355 Hs.414332 OAS2
    204698_at −1.5277 −1.5978 −1.6553 Hs.459265 ISG20
    203595_s_at −1.4853 −1.8724 −1.5442 Hs.252839 IFIT5
    220576_at −1.4834 −1.7834 −1.0040 Hs.229988 PGAP1
    1555491_a_at −1.4739 −1.0165 −1.4991 — FLJ11286
    1565752_at −1.4418 −0.0040 −1.0835 Hs.509664 FGD2
    203596_s_at −1.4389 −2.0356 −1.9284 Hs.252839 IFIT5
  • Analysis of the genes uniquely activated at the 18 hour time point revealed upregulation of genes involved in the innate immune response (TLR, NFκB), adaptive immune response (NFAT, IL-1/IL-6), complement activation as well as leukocyte chemotaxis and adhesion. It is possible that neutralization of the type IFN pathway has the potential to modify downstream pathways that may significantly impact the pathogenesis of SLE.
  • Heatmap analysis was also performed to examine induction of a type I IFN signature in PBMCs of a healthy donor by serum of an SLE patient and neutralization of the type I IFN signature by MEDI-545. See FIG. 67. The anti-IFN-α mAb treatment (lanes 4-6) demonstrated strong neutralization of a large number of genes stimulated with the serum of an SLE patient. Furthermore, neutralization by the anti-IFN-α mAb was dose-dependent, which suggests that these genes could be good candidates for PD. The reference mAb itself inhibited the overexpression of some of the genes upregulated when challenged with SLE patient sera; some of these were identified as type I IFN-inducible genes. However, the effect of anti-IFN-α mAb was much broader, with strong neutralization observed in a large number of genes of which neither the reference mAb nor anti-IFN-γ mAb had any significant effect (lane 2; lanes 4-6). It should be noted that treatment with anti-IFN-αR mAb (lane 7) induced more neutralization than anti-IFN-α mAb, which suggests the presence of other type I IFN family members in the serum of the SLE patients, in addition to IFN-α.
  • (b) Further investigation was conducted to identify early and late transcriptional responses in healthy donor PBMCs stimulated with SLE patient serum. In this study, four SLE patient serum samples, with varying levels of IFNα activity, were used to stimulate PBMCs isolated from a healthy donor. The varying levels of IFNα activity in the four SLE serum samples were determined in a luciferase reporter gene assay as described in Example 20. Briefly, HEK293H cells were stably transfected with a luciferase construct (Gaussia princeps) under the control of the IFN-stimulated response element (ISRE). Transfected cells were incubated with 50% patient sera and luciferase activity was detected in the culture supernatants 24 h later. Samples generating a signal greater than 1.5× negative control wells (normal human serum) were considered positive. To determine which class of type I IFN was responsible for the positive response, cells were treated with anti-type I and anti-type II IFN mAbs. FIG. 70 a shows the range of levels of type I IFN activity in each of the four SLE patient serum samples.
  • Each of the four SLE patient serum samples was co-incubated with PBMCs isolated from a healthy volunteer. The PBMCs from the healthy volunteer (previously determined to be IFN-signature negative) were isolated using Ficoll gradient centrifugation. Isolated PBMCs were incubated with 25% SLE patient serum or with 25% autologous patient serum (as a negative control). Following the incubation, cells were harvested with Trizol LS and stored at −70° C. for RNA isolation. Total RNA was extracted and RNA purity and concentration were determined spectrophotometrically (260/280>1.9). The generation and hybridization of biotin-labeled amplified complementary RNA (cRNA) were conducted according to manufacturer's instructions (Affymetrix, Santa Clara, Calif.). Data was generated by implementing a 3-fold (up-regulation) expression cutoff between SLE serum stimulation compared to autologous serum control samples (q value ≦0.05). FIG. 70 b shows the number of probes detected as 3-fold or more upregulated in the healthy volunteer PBMCs by each of the four SLE patient serum samples. The number of probes detected as 3-fold or more upregulated by an SLE patient serum sample correspondingly increased with the level of type I IFN activity detected in the SLE serum sample.
  • The role of type I IFNs in inducing the 3-fold or more upregulation of probes by the SLE patient serum samples was next investigated. PBMCs isolated from a healthy volunteer, discussed above, were incubated with 25% SLE patient serum in the presence or absence of neutralizing antibodies against IFN-α, or irrelevant mAb, for 4 or 18 hours. As a negative control, PBMC were incubated with 25% of autologous patient serum. Following the incubation, cells were harvested with Trizol LS and stored at −70° C. for RNA isolation. Total RNA was extracted and RNA purity and concentration were determined spectrophotometrically (260/280>1.9). The generation and hybridization of biotin-labeled amplified complementary RNA (cRNA) were conducted according to manufacturer's instructions (Affymetrix, Santa Clara, Calif.). ArrayAssist® Lite software was used to calculate probe-level summaries from the array cell intensity files and R packages were used to identify differentially regulated genes (3-fold or greater upregulation in expression between SLE serum stimulation compared to autologous serum control samples (q value ≦0.05); R Development Core Team, New Zealand). Percent neutralization was then determined by calculating the percent change for each upregulated probe treated with and without anti-IFNα antibody. FIG. 71 a provides heat maps showing the percent neutralization of probes that were identified as upregulated following anti-IFNα treatment for type I IFN genes (689 probes) and non-type I IFN genes (probes induced by SLE serum outside of type I IFN gene list) 4 and 18 h post incubation. FIG. 71 b shows, for each of the four SLE patient serum samples, the percentage of type I IFN gene signature or non-type I IFN gene signature probes that were neutralized by the anti-IFNα treatment following both the 4 and 18 hour incubations. It appears that the majority of genes neutralized by anti-IFNα treatment of SLE serum-treated healthy volunteer's PBMCs 4 hours post-incubation were type I IFN genes, while the majority of genes neutralized by anti-IFNα treatment of SLE serum-treated healthy volunteer's PBMCs 18 hours post-incubation were non-type I IFN genes.
  • Genes, whether type I IFN genes or non-type I IFN genes, that were both upregulated and neutralized by anti-IFNα treatment at 18 hours, but that were not upregulated at 4 hours (i.e., “unique genes”) were identified for each SLE patient serum sample. FIG. 72 provides the (a) type I IFN genes and (b) non-type I IFN genes that were identified as unique genes. Shaded areas indicate greater than 50% neutralization by anti-IFNα in that patient sample.
  • Cell pathways and processes neutralized by anti-IFNα treatment at the 18 hr time point are involved in cytokine and chemokine signaling pathways, immune regulation, cell adhesion, and cell survival. See FIG. 73, which provides a table showing the pathway analysis of altered genes and proteins at the 18 hr time point. Pathways highlighted in yellow were also significantly altered in SLE serum samples. The cell pathways and processes neutralized by anti-IFNα treatment at the 18 hr time point were analyzed with the MetaCore integrated software suite from GeneGo, Inc. using the identified unique genes. Only pathways with p-values S 0.05 were considered significant. The pathways shown were altered in at least 2 out of 4 SLE serum samples.
    • Example 6 Administering MEDI-545 to Lupus Patients Neutralizes the IFNα-Inducible Candidate PD Marker Expression Pattern
  • Whole blood of lupus patients receiving placebo, 0.3 mg/kg, 1.0 mg/kg, and 3.0 mg/kg MEDI-545 were analyzed for expression of IFNα-inducible PD markers over the course of 28 days. Whole blood (˜2.5 mL) was drawn into PAXgene RNA tubes and processed as outlined above. With increasing doses of MEDI-545, up-regulated expression of the top 25 PD markers was neutralized. See FIG. 18, FIG. 23, and FIG. 24 which provide graphical representations of neutralization of these top 25 PD markers following administration of varying concentrations of the MEDI-545 IFNα Ab over various lengths of time. The top 25 PD markers measured in this study are provided in Table 19.
  • TABLE 19
    Top 25 IFN-Induced PD Markers in Lupus Patients
    UniGene
    Probe ID ID Gene Title Gene Symbol
    202086_at Hs.517307 myxovirus (influenza virus) resistance 1, interferon- MX1
    inducible protein p78 (mouse) /// myxovirus (influenza
    virus) resistance 1, interferon-inducible protein p78
    (mouse)
    202145_at Hs.521903 lymphocyte antigen 6 complex, locus E LY6E
    202411_at Hs.532634 interferon, alpha-inducible protein 27 IFI27
    202869_at Hs.524760 2′,5′-oligoadenylate synthetase 1, 40/46 kDa OAS1
    203153_at Hs.20315 interferon-induced protein with tetratricopeptide IFIT1
    repeats 1 /// interferon-induced protein with
    tetratricopeptide repeats 1
    204415_at Hs.523847 interferon, alpha-inducible protein 6 IFI6
    204439_at Hs.389724 interferon-induced protein 44-like IFI44L
    205483_s_at Hs.458485 ISG15 ubiquitin-like modifier ISG15
    205569_at Hs.518448 lysosomal-associated membrane protein 3 LAMP3
    205660_at Hs.118633 2′-5′-oligoadenylate synthetase-like OASL
    213797_at Hs.17518 radical S-adenosyl methionine domain containing 2 RSAD2
    214059_at Hs.82316 Interferon-induced protein 44 IFI44
    217502_at Hs.437609 interferon-induced protein with tetratricopeptide IFIT2
    repeats 2
    218400_at Hs.528634 2′-5′-oligoadenylate synthetase 3, 100 kDa OAS3
    219211_at Hs.38260 ubiquitin specific peptidase 18 USP18
    219519_s_at Hs.31869 sialic acid binding Ig-like lectin 1, sialoadhesin /// sialic SIGLEC1
    acid binding Ig-like lectin 1, sialoadhesin
    219863_at Hs.26663 hect domain and RLD 5 HERC5
    222154_s_at Hs.120323 DNA polymerase-transactivated protein 6 DNAPTP6
    226702_at Hs.7155 hypothetical protein LOC129607 LOC129607
    227609_at Hs.546467 epithelial stromal interaction 1 (breast) EPSTI1
    229450_at — — —
    235276_at — — —
    239979_at Hs.546467 Epithelial stromal interaction 1 (breast) EPSTI1
    242234_at Hs.441975 XIAP associated factor-1 BIRC4BP
    44673_at Hs.31869 sialic acid binding Ig-like lectin 1, sialoadhesin SIGLEC1
  • The neutralization of IFN-induced PD markers by MEDI-545 for several individual lupus patients was examined and is presented in FIGS. 19-21. FIGS. 19 and 20 are heatmaps showing the neutralization of the top 25 PD markers (see Table 19) for two individual lupus patients (FIG. 19, patient 1541; and FIG. 20, patient 1449). Each of these lupus patients received 3 mg/kg MEDI-545. Each exhibited neutralization of the top 25 inducible PD markers at 7 and 14 days post-MEDI-545 treatment.
  • Neutralization of the top 25 type I IFN inducible genes in whole blood of an SLE patient treated with high dose (30 mg/kg) MEDI-545 was also examined. A heatmap of neutralization of the top 25 type I IFN inducible genes at 1, 4, 7, and 14 days following administration of MEDI-545 is presented in FIG. 25( a). Neutralization of all genes can be seen following administration of MEDI-545. FIG. 25( b) is a PCA of target modulation based on the top 25 type I IFN inducible genes. The PCA diagram shows the progression of the treated SLE patient from a position directly opposite that of normal healthy donors prior to administration of MEDI-545 to a position where it clusters with the healthy donors after administration of MEDI-545.
  • The neutralization of 165 PD markers by MEDI-545 was examined in a further lupus patient dosed with a lower, 0.3 mg/kg dose, of Ab. See FIG. 21. MEDI-545 neutralized most of the 165 candidate PD markers in this lupus patient. The 165 candidate PD markers are shown as the first 165 entries of Table 20.
  • The neutralization of type I IFN inducible probes sets was not observed in SLE patients treated with placebo control. Compare PCA plots of SLE patients before (a) and after (b) dosing with placebo in FIG. 26. Thus, the neutralization of the type-I IFN PD markers was due to the MEDI-545 antibody.
  • Table 22 provides a list of the 63 type I IFN inducible probes upregulated in whole blood of lupus patients and neutralized by MEDI-545 or placebo by at least 30% at day 7, day 14, or day 28 post administration. Each set of columns provides neutralization data for each of the indicated genes at 7, 14, and 28 days post-administration. The first set of columns provides percentage neutralization of each of the indicated genes for lupus patients having a type I IFN signature and that were treated with MEDI-545. It can be noted that for each of the indicated genes, neutralization ranged from 30% to 68% at day 7 post-administration. Meanwhile, at day 7 in the placebo treated group, neutralization of the same genes ranged from 0% to 27%.
  • TABLE 22
    Neutralization of 63 Type I IFN Inducible Probes in Whole Blood of Lupus by MEDI-545
    Figure US20150132313A1-20150514-P00899
    ol (type I
    Figure US20150132313A1-20150514-P00899
    5    		 Lupus Samples With IFN ALL Lupus Samples, (+)Medi-
    Figure US20150132313A1-20150514-P00899
    IFN indu
    Figure US20150132313A1-20150514-P00899
    		 neutralizab
    Figure US20150132313A1-20150514-P00899
    		 Day.7_Sig Day.14_Si
    Figure US20150132313A1-20150514-P00899
    		 Day.28_Si
    Figure US20150132313A1-20150514-P00899
    		 Day.7_All Day.14_All Day.28_All
    IFI44 214059_at 0.6871 0.6276 0.5047 0.3433 0.2657 0.2357
    IFI44L 204439_at 0.6621 0.6193 0.5515 0.6662 0.5561 0.492
    RSAD2 213797_at 0.6547 0.631 0.5213 0.6023 0.4611 0.4464
    G1P2 205483_s_at 0.6395 0.5954 0.5703 0.5404 0.4781 0.4148
    RSAD2 242625_at 0.6359 0.6123 0.4946 0.5607 0.541 0.3443
    USP18 219211_at 0.6305 0.6269 0.5577 0.4322 0.4423 0.4082
    IFI44 214453_s_at 0.626 0.5875 0.4223 0.4956 0.2741 0.2298
    IFIT1 203153_at 0.6224 0.6093 0.5376 0.5442 0.4586 0.4182
    IFIT3 204747_at 0.6213 0.5676 0.5638 0.5212 0.4174 0.3854
    SERPING1 200986_at 0.617 0.6214 0.5974 0.4617 0.4294 0.3673
    HERC6 219352_at 0.5996 0.531 0.5352 0.3581 0.3678 0.4335
    DNAPTP6 222154_s_at 0.5973 0.6223 0.5016 0.345 0.3819 0.2244
    OASL 210797_s_at 0.5968 0.5529 0.5815 0.4715 0.3853 0.4208
    HERC5 219863_at 0.5948 0.5552 0.4997 0.4651 0.4521 0.3816
    OAS3 218400_at 0.589 0.5792 0.5062 0.4846 0.4039
    IFRG28 219684_at 0.581 0.5218 0.4955 0.3014 0.3035 0.2441
    MX1 202086_at 0.5807 0.5329 0.5073 0.512 0.4831 0.4001
    OAS1 202869_at 0.5761 0.5148 0.5652 0.4345 0.429 0.4373
    OASL 205660_at 0.5681 0.5549 0.5494 0.4814 0.4415 0.4046
    OAS1 205552_s_at 0.5678 0.5193 0.56 0.4796 0.4115 0.4196
    LAMP3 205569_at 0.5531 0.6796 0.4871 0.3427 0.4182 0.2854
    MGC20410 228439_at 0.535 0.5085 0.5093 0.359 0.2949 0.332
    SN 219519_s_at 0.5321 0.5639 0.5307 0.307 0.3711 0.212
    HSXIAPAF1 228617_at 0.5317 0.503 0.4707 0.3942 0.3604 0.266
    IFIT5 203596_s_at 0.5257 0.4922 0.3314 0.3004 0.1997 0.0723
    IRF7 208436_s_at 0.5183 0.494 0.4717 0.4318 0.3509 0.301
    EPSTI1 227609_at 0.517 0.5298 0.4999 0.3142 0.2662 0.2798
    EPSTI1 239979_at 0.5074 0.4803 0.553 0.3738 0.3527 0.3674
    ETV7 224225_s_at 0.5057 0.5101 0.3596 0.2965 0.2389 0.0985
    IFIT5 203595_s_at 0.5056 0.4731 0.2902 0.2482 0.2263 0.028
    HES4 227347_x_at 0.4998 0.4746 0.4266 0.3377 0.3141 0.2703
    ZC3HDC1 218543_s_at 0.4812 0.4274 0.4076 0.3058 0.2935 0.2109
    C7orf6 230036_at 0.4636 0.4665 0.4025 0.3114 0.2848 0.2299
    C7orf6 226603_at 0.4578 0.4242 0.3425 0.264 0.1555 0.1794
    OAS3 232666_at 0.4557 0.3628 0.4828 0.3165 0.2457 0.3356
    OAS2 204972_at 0.4532 0.4503 0.3889 0.2963 0.3106 0.2084
    IFIT2 217502_at 0.4514 0.4519 0.1899 0.0857 −0.039 −0.4306
    CXCL10 204533_at 0.4476 0.4647 0.262 0.1834 0.1911 0.1282
    LY6E 202145_at 0.4463 0.4582 0.4113 0.3404 0.3294 0.2612
    HERC6 239988_at 0.4449 0.3726 0.3596 0.2951 0.2402 0.2433
    G1P3 204415_at 0.4421 0.3914 0.1018 0.152 0.3129 −0.3045
    C7orf6 243271_at 0.4419 0.4279 0.401 0.2663 0.2445 0.2165
    OAS2 206553_at 0.4377 0.3721 0.2965 0.3008 0.2379 0.1882
    APOL6 241869_at 0.4264 0.063 0.4352 −0.0787 −0.5482 −0.2042
    ZBP1 242020_s_at 0.4232 0.406 0.3729 0.0761 0.1281 0.2718
    PLSCR1 202446_s_at 0.4022 0.3948 0.2996 0.1919 0.1973 0.1063
    OAS2 228607_at 0.3989 0.3655 0.3374 0.2712 0.2174 0.1639
    TRIM6 223599_at 0.3896 0.3464 0.2669 0.2285 0.1987 0.1119
    ZCCHC2 233425_at 0.3891 0.4249 0.3925 0.2541 0.2965 0.2822
    PLSCR1 202430_s_at 0.3847 0.3858 0.2706 −0.2032 −0.0283 −0.1714
    CLEC4D 1552773_at 0.3782 0.2012 0.1293 −0.5127 −0.9029 −0.5568
    ECGF1 204858_s_at 0.3778 0.2403 0.2971 0.3178 0.1699 0.0019
    C17orf27 233880_at 0.3658 0.3508 0.2804 0.2913 0.2599 0.108
    SN 44673_at 0.3642 0.3373 0.3736 0.2344 0.2522 0.1405
    PRIC285 228230_at 0.3636 0.4131 0.3363 0.2701 0.2731 0.1074
    PARP14 224701_at 0.3611 0.3765 0.3718 0.2737 0.2855 0.2267
    DNAPTP6 241812_at 0.3448 0.3672 0.2896 0.2048 0.2134 0.108
    HSXIAPAF1 242234_at 0.3371 0.3793 0.1084 0.1586 0.1796 −0.2285
    TNFAIP6 206025_s_at 0.336 0.3559 0.3269 0.1913 0.1909 0.1164
    LGALS3BP 200923_at 0.3331 0.27 0.2644 −0.0457 0.1764 0.1032
    CKS2 204170_s_at 0.3215 0.0604 0.0634 −0.2323 −0.5787 −1.1884
    STAT2 205170_at 0.3176 0.1781 0.1852 0.1643 −0.0318 −0.051
    EIF2AK2 204211_x_at 0.3094 0.3621 0.2577 0.2165 0.286 0.1441
    Figure US20150132313A1-20150514-P00899
    ol (type I    		 Lupus Samples Without an IFN Samples Receiving Placebo
    IFN indu
    Figure US20150132313A1-20150514-P00899
    Figure US20150132313A1-20150514-P00899
    ay.7_NoSi
    Figure US20150132313A1-20150514-P00899
    Figure US20150132313A1-20150514-P00899
    ay.14_NoS
    Figure US20150132313A1-20150514-P00899
    Figure US20150132313A1-20150514-P00899
    ay.28_NoS
    Figure US20150132313A1-20150514-P00899
    Figure US20150132313A1-20150514-P00899
    ay.7_Place
    Figure US20150132313A1-20150514-P00899
    Figure US20150132313A1-20150514-P00899
    y.14_Place
    Figure US20150132313A1-20150514-P00899
    Figure US20150132313A1-20150514-P00899
    y.28_Place
    Figure US20150132313A1-20150514-P00899
    IFI44 −0.0799 −0.2278 −0.0088 −0.1325 −1.91* −0.4185
    IFI44L 0.6713 0.4698 0.4379 0.007 −2.1816 0.0035
    RSAD2 0.5377 0.2294 0.3783 −0.2332 −5.0172 −0.9617
    G1P2 0.4185 0.3181 0.2734 0.0423 −0.944 0.1706
    RSAD2 0.4681 0.4437 0.2077 −0.3537 −2.7176 −0.2632
    USP18 0.1882 0.1907 0.2723 −0.4424 −2.4219 −0.4972
    IFI44 0.3352 −0.1532 0.0547 −0.2833 −1.0524 −2.4006
    IFIT1 0.448 0.2532 0.3097 −0.1604 −1.1565 −0.436
    IFIT3 0.398 0.2124 0.2232 −5.9101 −9.7543 −7.4011
    SERPING1 0.2706 0.1676 0.1582 −0.5973 −2.7824 −0.4193
    HERC6 0.0609 0.1452 0.341 −0.9901 −4.4468 −1.6832
    DNAPTP6 0.0345 0.0543 −0.0276 0.028 −1.947 0.007
    OASL 0.3174 0.1569 0.2748 −0.1014 −1.6808 −0.1344
    HERC5 0.3054 0.3115 0.2742 −0.0955 −0.9446 −0.1306
    OAS3 0.3562 0.3065 0.311 −0.0945 −1.1786 −0.1744
    IFRG28 −0.0427 0.0058 0.0155 −2.1401 −2.8445 −3.3644
    MX1 0.4273 0.4152 0.3026 −0.0951 −0.7789 0.01
    OAS1 0.2603 0.3119 0.3211 0.0389 −0.6246 0.0692
    OASL 0.3746 0.2868 0.2729 −0.0675 −0.9765 0.0773
    OAS1 0.3711 0.2644 0.292 −0.1562 −1.7918 −0.395
    LAMP3 0.0838 0.0618 0.1021 0.007 −1.4332 0.045
    MGC20410 0.1424 0.0036 0.1709 −1.1629 −2.0558 −0.5523
    SN 0.03 0.1081 −0.0778 −0.1736 −4.8297 0.1133
    HSXIAPAF1 0.2249 0.1659 0.0799 −0.2206 −0.7607 −0.1053
    IFIT5 0.023 −0.1991 −0.1633 0.0791 −0.2048 −0.1939
    IRF7 0.3253 0.1557 0.1459 0.1162 −0.2791 0.2169
    EPSTI1 0.0646 −0.0932 0.0797 0.0161 −1.0185 −0.1578
    EPSTI1 0.2093 0.1786 0.1987 −0.6502 −1.8449 −0.4975
    ETV7 0.039 −0.1308 −0.1389 −0.5808 −1.3814 −0.6834
    IFIT5 −0.0685 −0.1102 −0.2105 −0.1956 −0.4059 −0.6195
    HES4 0.1383 0.0953 0.1283 0.0775 −0.3688 0.2619
    ZC3HDC1 0.0898 0.1109 0.0321 0.055 −0.1726 0.1826
    C7orf6 0.1241 0.037 0.073 0.0287 −0.4023 −0.002
    C7orf6 0.0253 −0.211 0.0312 −0.2153 −0.8023 −0.4988
    OAS3 0.1452 0.086 0.2018 −0.3754 −1.0637 −0.0014
    OAS2 0.1032 0.1202 0.0444 −0.1067 −0.9025 −0.1084
    IFIT2 −0.3643 −0.7083 −0.9948 −0.7316 −0.9653 −4.4123
    CXCL10 −0.1418 −0.1819 0.0066 −0.1664 −0.9562 −0.1939
    LY6E 0.21 0.1536 0.1247 −0.4715 −1.729 −0.5966
    HERC6 0.1108 0.0596 0.1376 0.2771 −0.098 0.0584
    G1P3 −0.205 0.2058 −0.6738 −0.3862 −0.3826 −0.4763
    C7orf6 0.0501 −0.0055 0.0488 1.00E−04 −0.2487 0.116
    OAS2 0.1323 0.0548 0.0897 −0.0861 −1.1845 −0.2322
    APOL6 −0.7003 −1.3816 −0.7855 −1.0548 −2.225 0.0949
    ZBP1 −0.3512 −0.2508 0.1799 0.0954 −0.6879 −0.0275
    PLSCR1 −0.0668 −0.0719 −0.0694 0.0049 −0.5041 −0.1826
    OAS2 0.114 0.0155 0.0061 −0.026 −0.5978 −0.0611
    TRIM6 0.0303 −0.0027 −0.0289 −0.4333 −1.2181 −0.76
    ZCCHC2 0.088 0.1213 0.182 −0.1376 −0.4844 −0.075
    PLSCR1 −0.9268 −0.5931 −0.5733 −0.091 −0.5114 −0.3841
    CLEC4D −1.6091 −2.4085 −1.1806 −0.0151 −0.298 −0.9965
    ECGF1 0.244 0.0741 −0.2665 0.0637 −0.2711 0.1519
    C17orf27 0.1996 0.136 −0.0488 −0.4266 −0.7606 −0.4247
    SN 0.0747 0.1362 −0.0714 −0.321 −1.2105 0.1766
    PRIC285 0.155 0.0822 −0.1008 −0.5711 −0.6313 −0.1671
    PARP14 0.1662 0.1614 0.0947 −0.0715 −0.3247 0.0835
    DNAPTP6 0.0325 0.0037 −0.0571 −0.134 −0.5147 0.0613
    HSXIAPAF1 −0.0612 −0.0927 −0.5347 −0.4102 −0.7359 0.0295
    TNFAIP6 0.0133 −0.034 −0.0751 −0.3457 −0.7114 −0.2343
    LGALS3BP −0.512 0.0487 −0.0434 0.111 −0.2857 0.3187
    CKS2 −0.914 −1.4502 −2.3265 −0.3697 0.1034 −1.5141
    STAT2 −0.0245 −0.318 −0.2657 0.0708 −0.6738 −0.8915
    EIF2AK2 0.1021 0.1822 0.0408 −0.2044 −0.3038 −0.2564
    Figure US20150132313A1-20150514-P00899
    indicates data missing or illegible when filed

    Table 33 provides the results of a separate study which determined the top 50 genes neutralized in SLE patient whole blood 7 days after MEDI-545 treatment. Only three genes of the 50 genes, ZCCHC2, REC8L1, and GCLM, were not IFN-α/β-inducible
  • TABLE 33
    Top 50 probes neutralized 7 days post-dose in SLE patients receiving MEDI-545
    treatment
    Avg Probe Rank (By %
    Probe ID UniGene ID Gene Title Gene Symbol Neutralization) Final Probe Rank
    219352_at Hs.529317 hect domain and RLD 6 HERC6 2277.0 1
    208436_s_at Hs.166120 interferon regulatory factor 7 IRF7 2497.5 2
    210797_s_at Hs.118633 2′-5′-oligoadenylate synthetase-like OASL 2708.2 3
    205483_s_at Hs.458485 ISG15 ubiquitin-like modifier ISG15 2735.7 4
    204439_at Hs.389724 interferon-induced protein 44-like IFI44L 3194.9 5
    219211_at Hs.38260 ubiquitin specific peptidase 18 USP18 3458.6 6
    218543_s_at Hs.12646 poly (ADP-ribose) polymerase family, member 12 PARP12 3472.3 7
    205241_at Hs.567405 SCO cytochrome oxidase deficient homolog 2 (yeast) SCO2 3825.7 8
    204747_at Hs.47338 interferon-induced protein with tetratricopeptide repeats 3 IFIT3 3987.2 9
    219519_s_at Hs.31869 sialic acid binding Ig-like lectin 1, sialoadhesin SIGLEC1 4207.2 10
    228230_at Hs.517180 peroxisomal proliferator-activated receptor A interacting PRIC285 4373.1 11
    complex 285
    235276_at — — — 4438.7 12
    214059_at Hs.82316 Interferon-induced protein 44 IFI44 4477.4 13
    222154_s_at Hs.120323 DNA polymerase-transactivated protein 6 DNAPTP6 4531.3 14
    202145_at Hs.521903 lymphocyte antigen 6 complex, locus E LY6E 4618.6 15
    223849_s_at Hs.514941 Mov10, Moloney leukemia virus 10, homolog (mouse) MOV10 4691.0 16
    219364_at Hs.55918 likely ortholog of mouse D11Igp2 LGP2 4717.4 17
    224503_s_at Hs.114191 zinc finger. CCHC domain containing 2 ZCCHC2 4926.5 18
    228617_at Hs.441975 XIAP associated factor-1 BIRC4BP 4942.0 19
    53720_at — hypothetical protein FLJ11286 FLJ11286 5046.2 20
    218400_at Hs.528634 2′-5′-oligoadenylate synthetase 3, 100 kDa OAS3 5136.7 21
    235508_at Hs.526464 promyelocytic leukemia PML 5328.7 22
    232155_at Hs.514554 KIAA1618 KIAA1618 5344.5 23
    202086_at Hs.517307 myxovirus (influenza virus) resistance 1, MX1 5484.4 24
    interferon-inducible protein p78 (mouse)
    242625_at Hs.17518 radical S-adenosyl methionine domain containing 2 RSAD2 5522.4 25
    209417_s_at Hs.632258 interferon-induced protein 35 IFI35 5529.4 26
    228439_at Hs.124840 basic leucine zipper transcription factor, ATF-like 2 BATF2 5563.0 27
    221766_s_at Hs.10784 family with sequence similarity 46, member A FAM46A 5607.1 28
    202446_s_at Hs.130759 phospholipid scramblase 1 PLSCR1 5911.3 29
    205660_at Hs.118633 2′-5′-oligoadenylate synthetase-like OASL 6001.3 30
    205875_s_at Hs.344812 three prime repair exonuclease 1 TREX1 6062.0 31
    34689_at Hs.344812 three prime repair exonuclease 1 TREX1 6097.0 32
    202869_at Hs.524760 2′,5′-oligoadenylate synthetase 1, 40/46 kDa OAS1 6101.5 33
    214453_s_at Hs.82316 interferon-induced protein 44 IFI44 6210.4 34
    1555491_a_at — hypothetical protein FLJ11286 FLJ11286 6235.7 35
    230036_at Hs.489118 sterile alpha motif domain containing 9-like SAMD9L 6254.1 36
    222217_s_at Hs.438723 solute carrier family 27 (fatty acid transporter), member 3 SLC27A3 6257.9 37
    201641_at Hs.118110 bone marrow stromal cell antigen 2 BST2 6371.4 38
    218599_at Hs.419259 REC8-like 1 (yeast) REC8L1 6423.3 39
    238327_at Hs.531314 glutamate-cysteine ligase, modifier subunit GCLM 6500.4 40
    225291_at Hs.388733 polyribonucleotide nucleotidyltransferase 1 PNPT1 6537.6 41
    208581_x_at Hs.374950 metallothionein 1X MT1X 6541.4 42
    212380_at Hs.520102 KIAA0082 KIAA0082 6547.1 43
    227347_x_at Hs.154029 hairy and enhancer of split 4 (Drosophila) HES4 6557.3 44
    1557116_at Hs.257352 apolipoprotein L, 6 APOL6 6571.1 45
    231769_at Hs.464419 F-box protein 6 FBXO6 6683.0 46
    200986_at Hs.384598 serpin peptidase inhibitor, clade G (C1 inhibitor), SERPING1 6688.7 47
    member 1, (angioedema, hereditary)
    33304_at Hs.459265 interferon stimulated exonuclease gene 20 kDa ISG20 6853.8 48
    209593_s_at Hs.252682 torsin family 1, member B (torsin B) TOR1B 6866.4 49
    202307_s_at Hs.352018 transporter 1, ATP-binding cassette, sub-family B TAP1 6909.0 50
    (MDR/TAP)
    • Example 7 The Majority of Lupus Patients Exhibit a Type I IFN-Inducible PD Marker Expression Pattern
  • Using 169 probe sets to detect expression of a number of PD markers, gene expression in whole blood samples of 35 lupus patients was analyzed using PCA (Principal Component Analysis). Principal component analysis is a statistical technique for simplifying a dataset, by reducing multidimensional datasets to lower dimensions for analysis. PCA was conducted on the filtered data set (169 probe sets) using the Spotfire statistical tool. The PCA determined that 24/35 of the lupus patients had a statistically significant PD marker signature. See FIG. 22 for PCA analysis results. The 169 probe sets used for this PCA analysis are provided in Table 20.
  • TABLE 20
    Gene Expression Detected by 169 Probe Sets in 35 SLE Patients (Table 20
    discloses “DEAD (Asp-Glu-Ala-Asp)” as SEQ ID NO: 1)
    Gene
    Probe ID UniGene ID Gene Title Symbol
    1552772_at Hs.351811 C-type lectin domain family 4, member D CLEC4D
    1554343_a_at Hs.435579 BCR downstream signaling 1 BRDG1
    1555464_at Hs.163173 interferon induced with helicase C domain 1 IFIH1
    1555728_a_at Hs.325960 membrane-spanning 4-domains, subfamily A, MS4A4A
    member 4
    1556643_at Hs.515243 Hypothetical protein BC011840 LOC93343
    1557236_at Hs.257352 apolipoprotein L, 6 APOL6
    1559585_at Hs.535011 hypothetical protein FLJ31033 FLJ31033
    200887_s_at Hs.565365 signal transducer and activator of transcription 1, STAT1
    91 kDa
    200923_at Hs.514535 lectin, galactoside-binding, soluble, 3 binding LGALS3BP
    protein
    200986_at Hs.384598 serpin peptidase inhibitor, clade G (C1 inhibitor), SERPING1
    member 1, (angioedema, hereditary)
    201015_s_at Hs.514174 junction plakoglobin JUP
    201324_at Hs.436298 epithelial membrane protein 1 EMP1
    201641_at Hs.118110 bone marrow stromal cell antigen 2 BST2
    201646_at Hs.349656 scavenger receptor class B, member 2 SCARB2
    201761_at Hs.469030 methylenetetrahydrofolate dehydrogenase (NADP+ MTHFD2
    dependent) 2, methenyltetrahydrofolate
    cyclohydrolase
    202086_at Hs.517307 myxovirus (influenza virus) resistance 1, MX1
    interferon-inducible protein p78 (mouse) ///
    myxovirus (influenza virus) resistance 1,
    interferon-inducible protein p78 (mouse)
    202145_at Hs.521903 lymphocyte antigen 6 complex, locus E LY6E
    202270_at Hs.62661 guanylate binding protein 1, interferon-inducible, GBP1
    67 kDa /// guanylate binding protein 1, interferon-
    inducible, 67 kDa
    202411_at Hs.532634 interferon, alpha-inducible protein 27 IFI27
    202430_s_at Hs.130759 phospholipid scramblase 1 PLSCR1
    202446_s_at Hs.130759 phospholipid scramblase 1 PLSCR1
    202759_s_at Hs.591908 A kinase (PRKA) anchor protein 2 /// PALM2- AKAP2 ///
    AKAP2 protein PALM2-
    AKAP2
    202863_at Hs.369056 SP100 nuclear antigen SP100
    202869_at Hs.524760 2′,5′-oligoadenylate synthetase 1, 40/46 kDa OAS1
    203153_at Hs.20315 interferon-induced protein with tetratricopeptide IFIT1
    repeats 1 /// interferon-induced protein with
    tetratricopeptide repeats 1
    203595_s_at Hs.252839 interferon-induced protein with tetratricopeptide IFIT5
    repeats 5
    203596_s_at Hs.252839 interferon-induced protein with tetratricopeptide IFIT5
    repeats 5
    203771_s_at Hs.488143 biliverdin reductase A BLVRA
    204211_x_at Hs.131431 eukaryotic translation initiation factor 2-alpha EIF2AK2
    kinase 2
    204224_s_at Hs.86724 GTP cyclohydrolase 1 (dopa-responsive dystonia) GCH1
    204326_x_at Hs.374950 metallothionein 1X MT1X
    204415_at Hs.523847 interferon, alpha-inducible protein 6 IFI6
    204439_at Hs.389724 interferon-induced protein 44-like IFI44L
    204533_at Hs.632586 chemokine (C—X—C motif) ligand 10 CXCL10
    204747_at Hs.47338 interferon-induced protein with tetratricopeptide IFIT3
    repeats 3
    204972_at Hs.414332 2′-5′-oligoadenylate synthetase 2, 69/71 kDa OAS2
    204994_at Hs.926 myxovirus (influenza virus) resistance 2 (mouse) MX2
    205098_at Hs.301921 chemokine (C-C motif) receptor 1 CCR1
    205099_s_at Hs.301921 chemokine (C-C motif) receptor 1 CCR1
    205170_at Hs.530595 signal transducer and activator of transcription 2, STAT2
    113 kDa
    205241_at Hs.567405 SCO cytochrome oxidase deficient homolog 2 SCO2
    (yeast)
    205483_s_at Hs.458485 ISG15 ubiquitin-like modifier ISG15
    205552_s_at Hs.524760 2′,5′-oligoadenylate synthetase 1, 40/46 kDa OAS1
    205569_at Hs.518448 lysosomal-associated membrane protein 3 LAMP3
    205660_at Hs.118633 2′-5′-oligoadenylate synthetase-like OASL
    206025_s_at Hs.437322 tumor necrosis factor, alpha-induced protein 6 TNFAIP6
    206026_s_at Hs.437322 tumor necrosis factor, alpha-induced protein 6 TNFAIP6
    206133_at Hs.441975 XIAP associated factor-1 BIRC4BP
    206332_s_at — interferon, gamma-inducible protein 16 IFI16
    206513_at Hs.281898 absent in melanoma 2 AIM2
    206553_at Hs.414332 2′-5′-oligoadenylate synthetase 2, 69/71 kDa OAS2
    206576_s_at Hs.512682 carcinoembryonic antigen-related cell adhesion CEACAM1
    molecule 1 (biliary glycoprotein)
    206715_at Hs.125962 transcription factor EC TFEC
    208087_s_at Hs.302123 Z-DNA binding protein 1 /// Z-DNA binding ZBP1
    protein 1
    208436_s_at Hs.166120 interferon regulatory factor 7 IRF7
    208581_x_at Hs.374950 metallothionein 1X MT1X
    208653_s_at Hs.591335 CD164 molecule, sialomucin CD164
    208966_x_at — interferon, gamma-inducible protein 16 IFI16
    209417_s_at Hs.632258 interferon-induced protein 35 IFI35
    209498_at Hs.512682 carcinoembryonic antigen-related cell adhesion CEACAM1
    molecule 1 (biliary glycoprotein)
    209593_s_at Hs.252682 torsin family 1, member B (torsin B) TOR1B
    210001_s_at Hs.50640 suppressor of cytokine signaling 1 SOCS1
    210705_s_at Hs.370515 tripartite motif-containing 5 TRIM5
    210797_s_at Hs.118633 2′-5′-oligoadenylate synthetase-like OASL
    210873_x_at Hs.348983 apolipoprotein B mRNA editing enzyme, catalytic APOBEC3A
    polypeptide-like 3A
    210985_s_at Hs.369056 SP100 nuclear antigen SP100
    211012_s_at Hs.498345 promyelocytic leukemia /// hypothetical protein PML ///
    LOC161527 /// similar to promyelocytic leukemia LOC161527
    protein isoform 9 ///
    LOC652671
    211456_x_at — hypothetical protein LOC650610 LOC650610
    211889_x_at Hs.512682 carcinoembryonic antigen-related cell adhesion CEACAM1
    molecule 1 (biliary glycoprotein)
    212185_x_at Hs.534330 metallothionein 2A MT2A
    212657_s_at Hs.81134 interleukin 1 receptor antagonist IL1RN
    212659_s_at Hs.81134 interleukin 1 receptor antagonist IL1RN
    212845_at Hs.98259 sterile alpha motif domain containing 4A SAMD4A
    213293_s_at Hs.501778 tripartite motif-containing 22 TRIM22
    213294_at Hs.546523 Full-length cDNA clone CS0DK002YF13 of HeLa —
    cells Cot 25-normalized of Homo sapiens (human)
    213361_at Hs.193842 tudor domain containing 7 TDRD7
    213469_at Hs.229988 GPI deacylase PGAP1
    213797_at Hs.17518 radical S-adenosyl methionine domain containing 2 RSAD2
    214059_at Hs.82316 Interferon-induced protein 44 IFI44
    214329_x_at Hs.478275 tumor necrosis factor (ligand) superfamily, member TNFSF10
    10 /// tumor necrosis factor (ligand) superfamily,
    member 10
    214453_s_at Hs.82316 interferon-induced protein 44 IFI44
    214511_x_at Hs.534956 Fc fragment of IgG, high affinity Ia, receptor FCGR1A ///
    (CD64) /// Fc-gamma receptor I B2 /// similar to LOC440607
    Fc-gamma receptor I B2 isoform b ///
    LOC652758
    216243_s_at Hs.81134 interleukin 1 receptor antagonist IL1RN
    216598_s_at Hs.303649 chemokine (C-C motif) ligand 2 CCL2
    217165_x_at Hs.513626 metallothionein 1F (functional) MT1F
    217502_at Hs.437609 interferon-induced protein with tetratricopeptide IFIT2
    repeats 2
    217933_s_at Hs.570791 leucine aminopeptidase 3 LAP3
    218400_at Hs.528634 2′-5′-oligoadenylate synthetase 3, 100 kDa OAS3
    218543_s_at Hs.12646 poly (ADP-ribose) polymerase family, member 12 PARP12
    218943_s_at Hs.190622 DEAD (Asp-Glu-Ala-Asp) box polypeptide 58 DDX58
    218986_s_at Hs.591710 hypothetical protein FLJ20035 FLJ20035
    219062_s_at Hs.631682 zinc finger, CCHC domain containing 2 ZCCHC2
    219209_at Hs.163173 interferon induced with helicase C domain 1 IFIH1
    219211_at Hs.38260 ubiquitin specific peptidase 18 USP18
    219352_at Hs.529317 hect domain and RLD 6 HERC6
    219364_at Hs.55918 likely ortholog of mouse D11lgp2 LGP2
    219519_s_at Hs.31869 sialic acid binding Ig-like lectin 1, sialoadhesin /// SIGLEC1
    sialic acid binding Ig-like lectin 1, sialoadhesin
    219607_s_at Hs.325960 membrane-spanning 4-domains, subfamily A, MS4A4A
    member 4
    219684_at Hs.43388 receptor transporter protein 4 RTP4
    219691_at Hs.65641 sterile alpha motif domain containing 9 SAMD9
    219863_at Hs.26663 hect domain and RLD 5 HERC5
    219885_at — schlafen family member 12 SLFN12
    220059_at Hs.435579 BCR downstream signaling 1 BRDG1
    220576_at Hs.229988 GPI deacylase PGAP1
    221680_s_at Hs.272398 ets variant gene 7 (TEL2 oncogene) ETV7
    221816_s_at Hs.369039 PHD finger protein 11 PHF11
    222154_s_at Hs.120323 DNA polymerase-transactivated protein 6 DNAPTP6
    222631_at Hs.443733 phosphatidylinositol 4-kinase type 2 beta PI4K2B
    222793_at Hs.190622 DEAD (Asp-Glu-Ala-Asp) box polypeptide 58 DDX58
    222816_s_at Hs.631682 zinc finger, CCHC domain containing 2 ZCCHC2
    223167_s_at Hs.473370 ubiquitin specific peptidase 25 USP25
    223220_s_at Hs.518200 poly (ADP-ribose) polymerase family, member 9 PARP9
    223434_at — guanylate binding protein 3 GBP3
    223501_at — — —
    223849_s_at Hs.514941 Mov10, Moloney leukemia virus 10, homolog MOV10
    (mouse)
    224225_s_at Hs.272398 ets variant gene 7 (TEL2 oncogene) ETV7
    224701_at Hs.583792 poly (ADP-ribose) polymerase family, member 14 PARP14
    225291_at Hs.388733 polyribonucleotide nucleotidyltransferase 1 PNPT1
    225415_at Hs.518201 deltex 3-like (Drosophila) DTX3L
    225636_at Hs.530595 signal transducer and activator of transcription 2, STAT2
    113 kDa
    225834_at Hs.599880 hypothetical protein LOC652689 /// family with LOC652689
    sequence similarity 72, member A /// similar to /// FAM72A
    family with sequence similarity 72, member A /// ///
    similar to family with sequence similarity 72, LOC653594
    member A ///
    LOC653820
    225869_s_at Hs.502989 unc-93 homolog B1 (C. elegans) UNC93B1
    226103_at Hs.632387 nexilin (F actin binding protein) NEXN
    226603_at Hs.489118 sterile alpha motif domain containing 9-like SAMD9L
    226702_at Hs.7155 hypothetical protein LOC129607 LOC129607
    226757_at Hs.437609 interferon-induced protein with tetratricopeptide IFIT2
    repeats 2
    227458_at — — —
    227609_at Hs.546467 epithelial stromal interaction 1 (breast) EPSTI1
    227697_at Hs.527973 suppressor of cytokine signaling 3 SOCS3
    228152_s_at Hs.535011 hypothetical protein FLJ31033 FLJ31033
    228230_at Hs.517180 peroxisomal proliferator-activated receptor A PRIC285
    interacting complex 285
    228439_at Hs.124840 basic leucine zipper transcription factor, ATF-like 2 BATF2
    228531_at Hs.65641 sterile alpha motif domain containing 9 SAMD9
    228607_at Hs.414332 2′-5′-oligoadenylate synthetase 2, 69/71 kDa OAS2
    228617_at Hs.441975 XIAP associated factor-1 BIRC4BP
    229450_at — — —
    230036_at Hs.489118 sterile alpha motif domain containing 9-like SAMD9L
    230314_at Hs.112420 Transcribed locus, strongly similar to XP_511805.1 —
    PREDICTED: hypothetical protein XP_511805
    [Pan troglodytes]
    231769_at Hs.464419 F-box protein 6 FBXO6
    232034_at Hs.599821 hypothetical protein LOC203274 LOC203274
    232155_at Hs.514554 KIAA1618 KIAA1618
    232375_at Hs.565365 Signal transducer and activator of transcription 1, STAT1
    91 kDa
    232666_at Hs.528634 2′-5′-oligoadenylate synthetase 3, 100 kDa OAS3
    233425_at Hs.631682 zinc finger, CCHC domain containing 2 ZCCHC2
    233880_at Hs.195642 chromosome 17 open reading frame 27 C17orf27
    235061_at Hs.291000 protein phosphatase 1K (PP2C domain containing) PPM1K
    235112_at Hs.533491 KIAA1958 KIAA1958
    235157_at Hs.583792 Poly (ADP-ribose) polymerase family, member 14 PARP14
    235276_at — — —
    235643_at Hs.489118 sterile alpha motif domain containing 9-like SAMD9L
    236156_at Hs.127445 lipase A, lysosomal acid, cholesterol esterase LIPA
    (Wolman disease)
    236692_at — — —
    238439_at Hs.217484 ankyrin repeat domain 22 ANKRD22
    238581_at Hs.513726 Guanylate binding protein 5 GBP5
    238743_at Hs.546523 Full-length cDNA clone CS0DK002YF13 of HeLa —
    cells Cot 25-normalized of Homo sapiens (human)
    239196_at Hs.217484 ankyrin repeat domain 22 ANKRD22
    239277_at — — —
    239979_at Hs.546467 Epithelial stromal interaction 1 (breast) EPSTI1
    241812_at Hs.120323 DNA polymerase-transactivated protein 6 DNAPTP6
    241916_at Hs.130759 Phospholipid scramblase 1 PLSCR1
    242020_s_at Hs.302123 Z-DNA binding protein 1 ZBP1
    242234_at Hs.441975 XIAP associated factor-1 BIRC4BP
    242625_at Hs.17518 radical S-adenosyl methionine domain containing 2 RSAD2
    242898_at — — —
    243271_at Hs.489118 Sterile alpha motif domain containing 9-like SAMD9L
    44673_at Hs.31869 sialic acid binding Ig-like lectin 1, sialoadhesin SIGLEC1
    AFFX- Hs.565365 signal transducer and activator of transcription 1, STAT1
    HUMISGF3A/M97935_3_at 91 kDa
    AFFX- Hs.565365 signal transducer and activator of transcription 1, STAT1
    HUMISGF3A/M97935_5_at 91 kDa
    AFFX- Hs.565365 signal transducer and activator of transcription 1, STAT1
    HUMISGF3A/M97935_MB_at 91 kDa
  • Similarly, using 25 highly upregulated IFN-inducible genes, expression in whole blood samples of lupus patients and normal healthy donors was analyzed using PCA (Principal Component Analysis). The PCA determined that approximately 66% of the lupus patients had a strong/moderate type I IFN inducible signature. See FIG. 68 a for PCA analysis results and 68 b for 25 genes used in the PCA analysis.
  • The overexpression of type I IFN genes in SLE patient whole blood for a larger number of patients, determined using an Affymetrix whole genome array, is provided in Table 23. Table 23 and FIG. 65 provide further evidence that a high percentage of SLE patients share at least 2-fold overexpression of each individual type I IFN genes.
  • TABLE 23
    Overexpressed Type-I IFN Genes in Whole Blood of Lupus Patients
    Number Of Samples
    Displaying A Fold-Change Average log2 Fold-
    Probe.ID Gene.Title Gene.Symbol >= 2 % of Samples Change
    222816_s_at zinc finger, CCHC domain containing 2 ZCCHC2 70 79.55 2.124
    204415_at interferon, alpha-inducible protein 6 IFI6 67 76.14 3.007
    217502_at interferon-induced protein with IFIT2 65 73.86 1.913
    tetratricopeptide repeats 2
    235643_at sterile alpha motif domain containing 9-like SAMD9L 65 73.86 2.020
    213797_at radical S-adenosyl methionine domain RSAD2 62 70.45 2.978
    containing 2
    214059_at interferon-induced protein 44 IFI44 61 69.32 3.050
    202411_at interferon, alpha-inducible protein 27 IFI27 60 68.18 3.937
    204439_at interferon-induced protein 44-like IFI44L 60 68.18 2.847
    242625_at radical S-adenosyl methionine domain RSAD2 59 67.05 2.861
    containing 2
    214453_s_at interferon-induced protein 44 IFI44 59 67.05 2.463
    203153_at interferon-induced protein with tetratricopeptide IFIT1 59 67.05 2.034
    repeats 1 /// in
    242234_at XIAP associated factor-1 BIRC4BP 59 67.05 2.066
    203595_s_at interferon-induced protein with IFIT5 59 67.05 1.603
    tetratricopeptide repeats 5
    202086_at myxovirus (influenza virus) resistance 1, MX1 58 65.91 1.777
    interferon-inducible p
    Figure US20150132313A1-20150514-P00899
    206133_at XIAP associated factor-1 BIRC4BP 58 65.91 1.803
    216243_s_at interleukin 1 receptor antagonist IL1RN 58 65.91 1.278
    219863_at hect domain and RLD 5 HERC5 57 64.77 1.795
    202869_at 2′,5′- oligoadenylate synthetase 1, 40/46 kDa OAS1 56 63.64 2.057
    226702_at hypothetical protein LOC129607 LOC129607 56 63.64 1.797
    205483_s_at ISG15 ubiquitin-like modifier ISG15 56 63.64 1.979
    204747_at interferon-induced protein with IFIT3 56 63.64 1.675
    tetratricopeptide repeats 3
    1555464_at interferon induced with helicase C domain 1 IFIH1 56 63.64 1.532
    218400_at 2′-5′- oligoadenylate synthetase 3, 100 kDa OAS3 55 62.50 1.932
    227609_at epithelial stromal interaction 1 (breast) EPSTI1 55 62.50 1.788
    200986_at serpin peptidase inhibitor, clade G (C1 inhibitor), SERPING1 55 62.50 1.503
    member 1, (a
    Figure US20150132313A1-20150514-P00899
    202145_at lymphocyte antigen 6 complex, locus E LY6E 54 61.36 2.242
    239979_at Epithelial stromal interaction 1 (breast) EPSTI1 54 61.36 1.895
    205552_s_at 2′-5′- oligoadenylate synthetase 1, 40/46 kDa OAS1 54 61.36 1.945
    225929_s_at chromosome 17 open reading frame 27 C17orf27 54 61.36 1.054
    222154_s_at DNA polymerase-transactivated protein 6 DNAPTP6 53 60.23 2.030
    205569_at lysosomal-associated membrane protein 3 LAMP3 53 60.23 1.813
    205660_at 2′-5′-oligoadenylate synthetase-like OASL 53 60.23 1.677
    219352_at hect domain and RLD 6 HERC6 52 59.09 1.663
    210797_s_at 2′-5′-oligoadenylate synthetase-like OASL 52 59.09 1.548
    241916_at Phospholipid scramblase 1 PLSCR1 52 59.09 1.396
    208087_s_at Z-DNA binding protein 1 /// Z-DNA ZBP1 52 59.09 1.438
    binding protein 1
    243271_at Sterile alpha motif domain containing 9-like SAMD9L 52 59.09 1.126
    219519_s_at sialic acid binding Ig-like lectin 1, SIGLEC1 51 57.95 3.019
    sialoadhesin /// sialic acid bin
    Figure US20150132313A1-20150514-P00899
    228617_at XIAP associated factor-1 BIRC4BP 51 57.95 1.473
    202446_s_at phospholipid scramblase 1 PLSCR1 51 57.95 1.307
    232095_at SLIT-ROBO Rho GTPase activating protein 2 SRGAP2 50 56.82 1.155
    232666_at 2′-5′-oligoadenylate synthetase 3, 100 kDa OAS3 49 55.68 1.862
    204972_at 2′-5′-oligoadenylate synthetase 2, 69/71 kDa OAS2 49 55.68 1.642
    202430_s_at phospholipid scramblase 1 PLSCR1 49 55.68 1.209
    224701_at poly (ADP-ribose) polymerase family, member 14 PARP14 49 55.68 1.098
    219211_at ubiquitin specific peptidase 18 USP18 48 54.55 2.365
    206553_at 2′-5′-oligoadanylate synthetase 2, 69/71 kDa OAS2 48 54.55 1.582
    219684_at receptor transporter protein 4 RTP4 48 54.55 1.534
    239900_at chromosome 17 open reading frame 27 C17orf27 47 53.41 0.936
    44673_at sialic acid binding Ig-like lectin 1, sialoadhesin SIGLEC1 47 53.41 1.975
    203596_s_at interferon-induced protein with IFIT5 47 53.41 1.327
    tetratricopeptide repeats 5
    218986_s_at hypothetical protein FLJ20035 FLJ20035 47 53.41 1.091
    242020_s_at Z-DNA binding protein 1 ZBP1 47 53.41 1.195
    212659_s_at interleukin 1 receptor antagonist IL1RN 47 53.41 1.196
    228439_at basic leucine zipper transcription factor, BATF2 46 52.27 1.180
    ATF-like 2
    226757_at interferon-induced protein with IFIT2 46 52.27 0.882
    tetratricopeptide repeats 2
    225291_at polyribonucleotide nucleotidyltransferase 1 PNPT1 46 52.27 0.957
    206026_s_at tumor necrosis factor, alpha-induced protein 6 TNFAIP6 46 52.27 0.942
    222858_s_at dual adaptor of phosphotryosine and 3- DAPP1 46 52.27 1.055
    phosphoinositides
    208436_s_at interferon regulatory factor 7 IRF7 45 51.14 1.146
    217933_s_at leucine aminopeptidase 3 LAP3 45 51.14 0.807
    228152_s_at hypothetical protein FLJ31033 FLJ31033 45 51.14 0.834
    230036_at sterile alpha motif domain containing 9-like SAMD9L 44 50.00 1.097
    228607_at 2′-5′-oligoadenylate synthetase 2, 69/71 kDa OAS2 44 50.00 1.113
    218543_s_at poly (ADP-ribose) polymerase family, member 12 PARP12 44 50.00 1.111
    226603_at sterile alpha motif domain containing 9-like SAMD9L 44 50.00 1.033
    204211_x_at eukaryotic translation initiation factor 2- EIF2AK2 44 50.00 1.050
    alpha kinase 2
    235157_at Poly (ADP-ribose) polymerase family, PARP14 44 50.00 0.940
    member 14
    209417_s_at interferon-induced protein 35 IFI35 44 50.00 0.957
    Figure US20150132313A1-20150514-P00899
    indicates data missing or illegible when filed
  • Based on the observations of different overexpressed type I IFN genes in SLE patients, described above, a set of 21 type I IFN genes in whole blood of lupus patients was identified as potentially useful. See Table 24.
  • TABLE 24
    Twenty one potential overexpressed type I IFN genes useful as PD markers
    Sample IFI44 IFI27 IFI44L DNAPTP6 LAMP3 LY6E RSAD2 HERC5 IFI6 ISG15 OAS3
    A_37329 23.67 3.34 23.45 7.63 6.75 7.25 28.21 8.12 5.53 7.47 4.82
    A13
    A_37330 5.31 4.33 6.28 2.80 4.23 1.44 8.14 2.76 2.39 3.44 3.48
    A13
    A_37343 10.70 1.41 10.31 2.51 2.23 2.94 11.76 2.52 1.25 1.97 2.63
    A13
    A_37345 37.55 30.71 28.86 5.28 3.94 4.30 35.61 1.88 1.85 3.73 2.26
    A16
    A_37360 10.72 4.62 7.36 2.42 1.34 3.38 14.35 2.07 3.34 2.46 2.55
    A13
    A_37361 4.19 0.83 5.32 2.51 4.13 1.27 7.01 3.64 4.67 3.08 4.16
    A13
    A_37365 24.79 8.25 26.45 15.76 18.11 11.33 54.51 13.72 15.37 16.02 10.79
    A13
    A_37373 0.88 0.96 0.53 0.63 0.65 0.85 0.27 0.39 0.48 0.70 0.25
    A13
    A_37375 0.85 0.17 0.67 0.89 0.14 0.36 0.36 0.32 0.18 0.27 0.42
    A11
    A_37376 1.25 4.20 0.83 2.71 2.19 2.82 0.95 1.97 0.70 1.78 0.93
    A15
    A_37377 0.78 17.78 0.54 0.37 0.40 2.26 0.11 0.28 0.65 1.99 0.28
    A11
    A_37378 1.53 5.56 0.98 1.90 2.24 1.89 0.82 1.65 0.71 2.89 0.50
    A14
    C_001 8.93 162.67 16.29 41.43 4.13 35.49 14.75 10.03 5.34 31.98 5.95
    C_002 30.64 135.38 53.11 15.25 6.78 7.33 20.98 4.88 6.52 8.78 6.28
    C_004 25.99 220.81 71.18 18.13 8.48 9.94 51.74 8.77 4.32 12.04 7.00
    C_005 11.39 324.78 63.12 44.63 6.71 14.93 50.68 11.58 7.46 22.37 11.03
    C_006b 0.48 0.57 0.47 0.55 0.25 0.73 0.27 0.33 1.20 0.70 0.21
    C_007 63.08 498.86 71.47 31.25 9.75 25.15 124.43 17.26 12.01 30.68 4.98
    C_009 30.12 209.75 46.29 15.45 6.63 11.07 32.35 8.07 4.71 10.17 6.77
    C_010 24.31 85.83 42.22 21.61 10.78 15.14 49.98 12.94 7.29 19.29 10.90
    C_011 26.17 160.53 30.34 57.41 32.45 29.58 45.36 35.18 2.66 14.93 44.32
    C_012 48.84 131.90 85.63 15.28 7.85 10.17 57.95 8.19 5.21 8.71 7.76
    C_013 3.14 2.21 4.97 1.84 1.79 0.73 6.65 2.66 1.34 1.02 1.85
    C_017 21.09 256.30 48.34 18.49 5.74 9.18 35.38 7.79 4.91 13.13 6.54
    C_018 71.14 177.60 97.17 41.72 11.95 28.82 98.76 16.75 10.97 27.33 18.71
    C_019 75.89 362.67 158.96 30.47 16.33 17.58 113.44 17.70 16.63 29.09 7.39
    C_020 49.27 149.00 96.50 40.29 13.89 23.41 77.48 16.52 10.21 30.40 6.26
    C_10721 100.31 153.10 123.21 46.69 25.19 19.63 95.12 17.61 8.08 42.37 3.38
    C_10722b 7.05 3.09 4.15 2.50 3.07 1.82 2.62 1.75 0.61 1.29 0.40
    C_129141 49.92 189.36 47.56 32.63 11.84 24.45 50.62 15.98 15.19 50.39 12.14
    C_19171 32.06 8.24 26.46 13.54 9.78 6.63 41.14 12.40 5.23 10.87 7.65
    C_325532 77.48 163.43 90.25 236.52 162.67 30.05 73.47 26.40 25.86 193.45 35.73
    C_45311 5.39 0.81 2.19 1.36 0.54 1.08 1.15 0.79 1.05 1.42 0.17
    C_71277 16.15 7.55 19.03 7.33 3.59 6.35 14.39 3.88 1.82 4.88 3.85
    C_72371 86.57 51.95 89.42 96.06 18.37 28.43 110.34 24.75 12.09 45.54 24.29
    median 23.67 30.71 26.46 15.25 6.63 7.33 32.35 8.07 4.71 8.78 4.98
    average 28.22 101.10 40.00 25.02 12.14 11.37 38.03 9.19 5.94 18.76 7.62
    Sample IFI44 IFI27 IFI44L DNAPTP6 LAMP3 LY6E RSAD2 HERC5 IFI6 ISG15 OAS3
    Sample SIGLEC1 OAS2 USP18 RTP4 IFIT1 MX1 OAS1 EPSTI1 PLSCR1 IFRG28
    A_37329 5.16 5.22 7.14 3.94 15.26 4.98 7.75 6.57 3.69 3.71
    A13
    A_37330 2.26 2.63 2.12 1.82 4.83 2.77 2.06 2.48 3.65 2.17
    A13
    A_37343 0.96 2.38 2.85 2.73 7.39 2.82 3.78 2.97 2.12 2.89
    A13
    A_37345 0.92 3.03 2.54 3.70 21.92 2.66 4.51 10.06 2.48 3.92
    A16
    A_37360 2.81 2.17 2.01 1.12 13.79 2.32 2.30 3.51 1.40 1.29
    A13
    A_37361 6.38 2.97 2.43 1.46 4.55 2.40 2.02 2.40 2.43 1.41
    A13
    A_37365 10.33 8.85 9.57 7.07 23.56 8.22 11.56 16.51 5.93 7.49
    A13
    A_37373 0.26 0.50 0.96 1.35 0.31 0.77 0.68 0.59 1.45 1.48
    A13
    A_37375 0.12 0.73 0.43 0.69 0.32 0.23 0.92 0.50 2.97 0.82
    A11
    A_37376 0.45 2.15 2.94 4.70 0.49 1.76 1.54 1.01 7.92 4.96
    A15
    A_37377 0.57 0.35 1.18 3.44 0.23 0.96 1.65 0.51 2.05 3.50
    A11
    A_37378 1.00 1.64 1.86 4.20 0.39 1.73 2.40 1.23 8.18 4.51
    A14
    C_001 13.14 6.35 15.81 13.08 0.65 18.84 10.75 9.42 8.16 14.58
    C_002 6.49 5.58 23.17 6.56 15.64 6.73 9.22 7.10 3.62 6.68
    C_004 6.60 7.87 32.60 11.21 21.06 9.69 8.07 11.63 7.62 10.31
    C_005 23.05 11.90 63.56 10.70 19.74 17.43 14.42 9.62 5.59 9.02
    C_006b 0.31 0.34 0.38 0.81 0.33 0.38 0.52 0.60 0.37 0.67
    C_007 4.68 11.92 37.94 14.21 32.73 13.92 12.20 14.28 14.35 11.18
    C_009 8.67 9.57 21.00 8.07 14.25 9.04 9.53 8.01 7.83 7.49
    C_010 7.34 10.34 18.34 7.80 12.47 8.32 11.58 12.30 7.21 7.03
    C_011 25.28 27.10 51.74 26.85 9.19 15.63 17.96 15.00 19.29 28.84
    C_012 4.55 10.17 31.27 10.46 27.35 8.32 7.66 12.35 6.33 9.08
    C_013 0.74 1.41 2.45 2.69 3.55 2.14 1.32 3.19 2.30 2.31
    C_017 4.77 6.67 16.58 4.91 18.66 5.69 10.37 8.29 5.62 5.43
    C_018 9.84 16.48 75.02 18.41 44.09 23.41 12.66 18.71 12.52 15.63
    C_019 5.29 15.13 61.50 21.00 22.61 21.25 19.06 18.93 12.46 19.78
    C_020 5.92 11.57 48.59 13.57 34.76 13.99 11.76 13.89 8.63 13.38
    C_10721 8.45 14.21 58.15 21.60 20.80 14.95 20.32 23.72 13.22 13.85
    C_10722b 0.58 1.55 5.30 1.56 3.31 1.98 1.87 4.22 3.40 1.54
    C_129141 6.27 13.98 26.94 12.80 33.17 10.47 17.41 16.85 8.43 13.63
    C_19171 8.53 8.22 12.46 5.35 25.74 11.90 5.68 8.13 6.33 5.56
    C_325532 130.31 28.23 71.63 23.96 33.26 13.14 20.71 25.62 12.29 27.39
    C_45311 0.30 0.88 1.08 2.50 1.43 1.29 2.19 2.02 2.02 2.80
    C_71277 3.76 4.75 7.64 3.43 7.76 4.15 3.10 6.32 2.90 3.76
    C_72371 12.46 25.62 54.29 17.10 51.00 13.86 21.64 25.98 14.28 17.42
    median 5.16 6.35 12.16 5.35 14.25 6.73 7.75 8.13 5.93 5.56
    average 9.39 8.07 22.10 8.17 15.62 7.95 8.32 9.27 6.55 8.16
    Sample SIGLEC1 OAS2 USP18 RTP4 IFIT1 MX1 OAS1 EPSTI1 PLSCR1 IFRG28

    Overexpression of these genes, as detected initially using the Affymetrix arrays, was confirmed by Fluidigm dynamic array, validating their overexpression. See FIG. 69.
    • Example 8 MEDI-545 Considerably Neutralizes the Type I IFN Gene Signature of SLE
  • Patients Having a Strong to Moderate Type I IFN Gene Signature Patients in a clinical trial were identified as having a strong/moderate type I IFN gene, a weak type I IFN gene signature, or no type I IFN gene signature. These patients were designated into one of these groups based on 149 genes. Table 25 shows the number of lupus patients in the clinical trial that were designated in each of these three groups and indicates the treatment protocol they received.
  • TABLE 25
    Patient distribution based on type-I IFN gene signature prior to treatment
    Group Strong & moderate signature Weak signature No signature
    PBO
    10 5 2
    0.3 mpk  5 0 1
     1 mpk 2 2 2
     3 mpk 3 2 1
    10 mpk 4 3 0
    30 mpk 3 2 1
    Total 27 14 7

    The SLE patients that were designated as having strong and moderate type-I IFN gene signatures all had: an average 4-fold increase in expression of the top 25 most upregulated type I IFN genes; an average 2-fold increase in expression of the top 50 most upregulated type I IFN genes; and a percentage of total examined disease genes being type I IFN inducible of 3.8. The average fold increase in the top 25 type I IFN inducible genes for each patient having a strong/moderate type I IFN signature or a weak signature in the trial is provided in FIG. 28.
  • Treatment of these different SLE patient groups provided evidence that neutralization of the type I IFN gene signature by MEDI-545 is drug specific. FIG. 29( a) shows that in a group of SLE patients having a type-I IFN gene signature, virtually all of the top 39 genes neutralized 14 days post-MEDI-545 treatment are type I IFN signature genes (see yellow highlighted genes; percentage inhibition of the type I IFN signature genes ranged from 30.5-64.7). By contrast, none of the top 39 neutralized genes in SLE patients who received placebo were type I IFN signature genes. See FIG. 29( c). The SLE patients who lacked a type I IFN signature and were treated with MEDI-545 displayed an intermediate neutralization pattern, with some type I IFN signature genes neutralized. (See FIG. 29( b); yellow highlighting indicates type I IFN signature genes, which were neutralized from 19%-44.9%).
  • Further break down of SLE patients into strong, moderate, and weak type-I IFN gene signatures was conducted. Briefly, the 25 most highly overexpressed type I IFN-inducible genes in individual SLE patients generated from the ex vivo stimulation of healthy donor WB with SLE patient sera study were selected and the median fold change of these 25 genes was used to construct a type I IFN gene signature score for each SLE patient. FIG. 84 shows the distribution of the type I IFN gene signature scores of the 46 SLE patients profiled. The SLE patients were profiled into 3 groups based on their type I IFN gene signature score: high type I IFN gene signature (score >10); moderate type I IFN gene signature (score 4-10); and weak type I IFN gene signature (score <4).
    • Selection of a Panel of 21 Type I IFN-Inducible Genes in WB of SLE Patients
  • To select a small, robust panel of type I IFN-inducible genes that could be developed into an HTP assay, the gene panel was narrowed to 21 genes. To identify the 21 potential PD and diagnostic markers, 807 IFN-α/β-inducible probes identified by ex vivo stimulation of healthy donor WB with 10 IFN-α subtypes (2a, 4b, 5, 6, 7, 8, 10, 14, 16, and 17) and IFN-β were used as a candidate marker starting point. The WB samples from a total of 46 SLE patients procured from commercial vendors and 24 healthy normal controls were used to determine the type I IFN-inducible probes that are upregulated in WB of SLE patients. 114 overexpressed probes (q≦0.05; fold change ≧2) were identified in WB of SLE patients were type I IFN-inducible using SAM and FDR.
  • To investigate whether these overexpressed type I IFN-inducible genes in WB of SLE patients were neutralizable by an anti-IFN-α mAb, one healthy donor PBMC was stimulated ex vivo with sera from six individual SLE patients. The healthy donor was prescreened to exclude those donors that might have viral infection. 161 type I IFN-inducible probes were upregulated by ≧2-fold in the PBMC of the healthy donor following stimulation with ≧1 SLE patient serum in which the overexpression of these genes was suppressed by ≧50% and ≧70% by an anti-IFN-α mAb and an anti-IFN-αR mAb, respectively.
  • The intersection between this list of 161 probes and previously determined list of 114 probes was 80 probes. Each of these 80 probes was ranked by both the average fold change magnitude across all SLE patients and the percentage of patients displaying a change ≧2-fold. Generally, the 21 most prevalently overexpressed type I IFN-inducible genes (that represent unique genes using the NetAffx annotation file for the Affymetrix U133 2.0 plus array; ESTs were excluded) from this ranking were retained for a static list of probes used to measure PD. The type I IFN signature score was then defined by the median of these 21 genes.
  • With these 21 genes, it was necessary to recalculate the thresholds that had been previously identified for partitioning SLE patients into type I IFN gene signature responses of strong, moderate, or weak (based on the Affymetrix platform) for a lower density platform (TAQMAN-based assay). A scaling method was required to convert the type I IFN signature score based on the top 25 differentially expressed genes (independent for each SLE patient) on the Affymetrix platform to the type I IFN signature score based on the 21 genes selected for the TAQMAN-based assay. This method was implemented to compensate for 3 primary differences between the 2 platforms: (1) the number of probes used for the type I IFN signature (25 genes dynamically determined for each patient on the Affymetrix platform versus a 21 static gene list on the TAQMAN-based assay), (2) the differences in sensitivity between the 2 platforms, and (3) the scales of the dynamic ranges within each platform. First, the fold change values were calculated (on a log2 scale) for the 155 type I-inducible probes between the 35 randomly selected SLE patients and the average of a set of normal healthy controls. The genes with the top 25-fold change values were determined for each patient on the Affymetrix platform (this gene set is allowed to vary from patient to patient depending on which type I IFN-inducible genes are most highly expressed). Next, the median fold change was calculated from the top 25 genes for each SLE patient. The same calculation was conducted across the same patients using the static 21 gene set on the TAQMAN-based assay. This gene set was identical for each patient and the median fold change was calculated based on 21 genes, rather than 25 dynamic genes, as was conducted for the Affymetrix platform. A simple regression model was then computed using these 2 vectors of equal length (35 median fold change values), and the coefficients from the model were used to calculate the conversion factor (from the Affymetrix platform to the TAQMAN-based assay) for the response threshold values to partition the SLE patients into a type I IFN gene signature category of strong (>10 on Affymetrix; >5.53 on TAQMAN), moderate (between 4 and 10 on Affymetrix; between 1.91 and 5.53 on TAQMAN), or weak (<4 on Affymetrix; <1.91 on TAQMAN). Using these scaled threshold values, for the purpose of stratifying SLE patients, the signature (ie, median fold change) that was calculated on the 21 genes from the TAQMAN-based assay was comparable to that from the top 25 upregulated type I IFN-inducible genes.
  • The prevalence and fold change (log2 based) of the 21 IFN α/β-inducible genes in whole blood of 111 SLE patients is provided in Table 32, below.
  • TABLE 32
    Prevalence and fold chance in expression of 21 IFN α/β-inducible genes in
    SLE patient whole blood
    Gene
    Probe Q value Fold Prevalence Gene name symbol
    204415_at qv <1e−16 9.38 78.20 interferon, alpha-inducible protein 6 IFI6
    213797_at 2.67E−12 8.27 71.80 radical S-adenosyl methionine domain RSAD2
    containing 2
    214059_at 7.18E−14 7.93 70.90 Interferon-induced protein 44 IFI44
    204439_at 5.85E−12 6.45 69.10 interferon-induced protein 44-like IFI44L
    202411_at 6.35E−12 14.42 67.30 interferon, alpha-inducible protein 27 IFI27
    202086_at 1.09E−09 3.26 66.40 myxovirus (influenza virus) resistance 1, MX1
    interferon-inducible protein p78 (mouse)
    203153_at 3.90E−07 3.52 65.50 interferon-induced protein with IFIT1
    tetratricopeptide repeats 1
    219863_at 8.05E−11 3.27 64.50 hect domain and RLD 5 HERC5
    205483_s_at 1.23E−13 3.71 63.60 ISG15 ubiquitin-like modifier ISG15
    205569_at qv <1e−16 3.91 62.70 lysosomal-associated membrane protein 3 LAMP3
    218400_at 1.01E−10 3.65 62.70 2′-5′-oligoadenylate synthetase 3, 100 kDa OAS3
    202869_at 4.95E−11 3.77 61.80 2′,5′-oligoadenylate synthetase 1, OAS1
    40/46 kDa
    227609_at 7.41E−10 3.16 60.90 epithelial stromal interaction 1 (breast) EPSTI1
    204747_at 9.78E−11 3.04 60.90 interferon-induced protein with IFIT3
    tetratricopeptide repeats 3
    202145_at qv <1e−16 4.65 60.90 lymphocyte antigen 6 complex, locus E LY6E
    204972_at qv <1e−16 3.06 58.20 2′-5′-oligoadenylate synthetase 2, OAS2
    69/71 kDa
    241916_at 6.29E−07 2.46 56.40 Phospholipid scramblase 1 PLSCR1
    44673_at qv <1e−16 3.91 55.50 sialic acid binding Ig-like lectin 1, SIGLEC1
    sialoadhesin
    219211_at 2.54E−13 4.83 55.50 ubiquitin specific peptidase 18 USP18
    219684_at 2.75E−07 2.47 50.00 receptor (chemosensory) transporter RTP4
    protein 4
    241812_at 5.25E−07 1.84 38.20 DNA polymerase-transactivated protein 6 DNAPTP6

    These 21 genes were neutralized in a dose-dependent dependent fashion by MEDI-545. See FIGS. 86 and 89. Heatmap (FIG. 87 a) and PCA calculations (FIG. 87 b) using these 21 genes showed neutralization of the upregulated IFN α/β gene signature in an SLE patient treated with 30 mg/kg MEDI-545, but not in placebo-treated SLE patients (FIG. 88). Thus, it is evident that these genes could be used as a PD marker set.
    • Stratification of 35 Patients, by Strength of Type I IFN Gene Signature Using the 21 Genes
  • FIG. 85 shows the stratification of 35 SLE patients into groups of high (20 patients), moderate (8 patients), and weak (7 patients) type I IFN gene signatures based on the distribution of fold change values (log2 scale) of all 21 type I IFN-inducible genes and partitioned into each group by the median fold change of this distribution of 21 genes for each patient (vertical dashed lines), as measured by the dynamic array from Fluidigm. From FIG. 85, it is apparent that each patient distribution exhibits slight differences in skewness and basic shape/form, as this indicates the diversity in the various severity levels of SLE, based on the 21 type IFN-inducible gene selected. In a PCA plot for all SLE patients profiled in this study (n=100) and for the 24 healthy control samples using the 21 type I IFN-inducible genes, a clear distinction between SLE patients with an overexpressed type I IFN gene signature and those with weak or nondetectable type I IFN gene signatures is observed (FIG. 82C). Furthermore, the SLE patients with weak or nondetectable type I IFN gene signatures were clustered together with healthy donors. Importantly, the partitioning between these groups using the 21-gene panel of type I IFN-inducible genes was similar to that observed with the larger 114-gene set (FIGS. 81A and 81B).
    • Example 9 Multiple Type-I IFN Subtypes are Up-Regulated in Whole Blood of SLE Patients
  • To identify the type-I IFN subtypes responsible for the induction of the type-I IFN signature of SLE patients, mRNA levels of type-I IFN genes in SLE patient whole blood were measured.
  • Gene expression analysis was performed using a TAQMAN Low Density Array (TLDA) from Applied Biosystems. Expression of type- I IFNα subtypes 1, 2, 5, 6, 7, 8, 14, 17, and 21 was monitored and compared in whole blood of SLE patients relative to healthy volunteers.
  • Double-stranded cDNA for each patient sample was pre-amplified using the TAQMAN PreAmp Master Mix kit (Applied Biosystems). cDNA was pre-amplified by conducting 10 cycles of PCR on each patient sample using a pooled solution of primers, a pair for each gene analyzed on the array. The pre-amplified cDNA were diluted 1:5 with TE. A 50 μL volume of the diluted pre-amplified cDNA was added to a 50 μL volume of 2×TAQMAN Universal PCR Master Mix (Applied Biosystems) and mixed. The array was loaded with the mixture using standard procedures and the loaded array was run on a 7900HT Fast Real-Time PCR System (Applied Biosystems). Data analysis of the resulting Ct values was conducted with the SDSv2.2.2 software tool (Applied Biosystems).
  • FIG. 27 shows the relative overexpression of mRNA of nine IFNα subtypes in the whole blood of lupus patients relative to healthy volunteers. Many of these IFNα subtypes were upregulated at the mRNA level in the whole blood of SLE patients.
  • FIG. 66 shows that IFNβ, IFNω and IFNAR1 and IFNAR2 genes are also overexpressed in whole blood of lupus patients relative to healthy volunteers.
  • FIG. 82 shows that TNF-α, IFN-γ, IFN-γR1, and IFN-γR2 transcripts were also upregulated in WB of SLE patients (FIG. 82). However, the relative magnitude of overexpression of these transcripts was less than that of the type I IFN family members, especially the IFN-α subtypes.
    • Example 10 Ex Vivo IFN-Stimulated Whole Blood and Keratinocytes of Healthy Individuals Identifies a Panel of Type I IFN-Inducible Genes Relevant to Psoriasis
  • To identify type-I IFN inducible genes over-expressed in keratinocytes of lesions of psoriatic patients, whole blood and keratinocytes of healthy donors were stimulated ex vivo with a panel of IFNα subtypes, as well as IFNβ, IFNγ, and TNFα.
    • Whole Blood
  • Whole blood was collected from healthy donors in heparinized tubes. The total blood volume collected from each donor was pooled into a single culture flask and 3 mL of the total volume was aliquoted into a single well of a 6-well culture plate. Individual wells of blood were then exposed to a variety of treatments, including: vehicle (1×PBS), a panel of IFNα subtypes (IFNα2a, -4b, -5, -6, -7, -8, -10, -16, -17), IFNβ, IFNω, IFNλ, IFNγ, leukocyte IFN, or TNFα. Following exposure, the blood was gently mixed by pipetting and incubated at 37° C., 5% CO2 for 4 hrs (TNFα treatment was conducted for both 2 hrs and 4 hrs). Following the incubation period, 2.5 mL of blood was transferred to a PAXgene RNA tube and inverted 8-10 times. The PAXgene tubes were incubated at room temperature for two hours and then frozen (−20° C. overnight, −70° C. for long term storage) until further processing was required. Induction of gene expression by exposure to each of the treatment conditions was performed using Affymetrix GENECHIP® human genome U133 plus v2.0 arrays.
  • The various IFNα subtypes and IFNβ up-regulated 900-1200 probe sets by at least 2 fold. Of these, 689 probe sets (approximately 1.3% of all probe sets on the Affymetrix human genome U133 plus v2.0 array) were uniformly up-regulated by at least 2 fold in all donors by all ten IFNα subtypes and IFNβ. Using the same approach, 336 probe sets were identified as down-regulated by IFNα/β in the ex vivo stimulated whole blood.
  • Alterations in gene expression in healthy patient whole blood stimulated with TNFα were also observed at both the two and four hour time points. In all, 234 and 72 probe sets were up-regulated and down-regulated, respectively, by at least 2 fold in all donors. Furthermore, IFNγ challenge of whole blood for 4 hrs induced up-regulation of 304 probe sets and down-regulation of 52 probe sets by at least 2 fold. Little overlap was observed in the probe sets up-regulated by IFNα/β and TNFα (40 probes). By contrast, greater overlap was observed in the probe sets up-regulated by IFNα/β and IFNγ. 198 probes were up-regulated by at least 2-fold by both IFNα/β and IFNγ. Of the 198 probes up-regulated by at least 2-fold by both IFNα/β and IFNγ, the magnitude of up-regulation by IFNα/β was greater for about ⅔ of these probes (p value less than 0.05) than IFNγ.
  • FIG. 30 provides the hierarchical clustering of 1384 probe sets differentially regulated by either IFNα/β, or IFNγ, or TNFα in ex vivo stimulated whole blood. From this hierarchical clustering the similar response of whole blood to challenge with IFNα subtypes and IFNβ can easily be observed, as can the similar but distinctly different effect of IFNγ from IFNα/β, and the drastically different effect of TNFα from IFNα/β.
  • FIG. 31 a provides the hierarchical clustering of the relative expression of only the top 25 type-I IFN inducible probe sets identified in the ex vivo stimulated whole blood.
    • Keratinocytes
  • Normal human keratinocytes (EpiDerm system, MatTek, Inc.) were grown under serum-free conditions according to the manufacturers instructions. Briefly, keratinocytes were maintained on tissue culture inserts at the air-liquid interface to maintain a multilayered, fully differentiated epithelial phenotype. Keratinocytes were stimulated with human leukocyte IFN (15, 50, 150, IU/mL, PBL Biomedical Labs), human IFNα2a (15-350 IU/ml, PBL Biomedical Labs), recombinant human TNFα (0.1 ng/ml, R+D Systems) or recombinant human IFNγ (3 ng/ml, R+D Systems). Epidermal cultures were harvested at 2, 4, or 18 hours post treatment for transcript analysis. Over 100 probe sets were identified as overexpressed in keratinocytes cultures stimulated with human IFNα2a and leukocyte IFN.
  • FIG. 31 b provides the hierarchical clustering of the relative expression of 25 type-I IFN inducible genes in ex vivo stimulated keratinocytes. The 25 type-I IFN inducible probe sets used to prepare the hierarchical clustering are the top 25 type-I IFN inducible probes identified in the ex vivo stimulated whole blood (those shown in FIG. 31 a). Many of the top 25 type-I IFN inducible probe sets in ex vivo stimulated whole blood are also induced in ex vivo stimulated keratinocytes. See, e.g., MX1, IFI27, OAS1, IFI6, IFI44L, etc.
  • In addition, many of these genes were among those most overexpressed in the lesional skin of psoriasis patients. See discussion in Example 11, below.
    • Example 11 Whole Genome Array Profiling Identified IFNα/β Signaling Pathway as the Most Significantly Activated Pathway in Lesional Skin of Psoriasis Patients
  • A comparison of gene expression profiles of skin samples from healthy donors and paired non-lesional/lesional skin samples from psoriasis patients was performed to identify a type-I interferon induced gene expression signature associated with psoriatic skin lesions. Briefly, skin samples of 21 normal healthy control donors (5 samples obtained from Biochain, 14 from ILSbio, and 2 from Dr. James Krueger's lab) and 26 paired non-lesional/lesional skin samples of 24 psoriatic patients (21 pairs obtained from Asterand, and 5 from Dr. James Krueger's lab) were obtained. Three additional lesional skin samples from 3 psoriatic patients were obtained. These 3 additional lesional skin samples lacked a paired non-lesional skin sample because the non-lesional skin sample either did not yield sufficient cRNA for hybridization or the scanned array for the non-lesional skin sample had high scaling factors that were more than 3-fold of average.
  • Total RNA from the samples was extracted using the Qiagen RNAeasy-Mini kit (Hilden, Germany). The purity and concentration of the extracted RNA were determined spectrophotometrically (260/280>1.9). RNA quality was assessed on an Agilent 2100 Bioanalyzer using the RNA 6000 NANO LABCHIP®. Generation of biotin-labeled amplified cRNA, from 2 μg of total RNA, was accomplished using the Affymetrix GENECHIP® One-Cycle cDNA Synthesis kit and the Affymetrix GENECHIP® IVT Labeling kit. Concentration and purity of the cRNA product were determined spectrophotometrically.
  • Twenty micrograms of each biotin-labeled cRNA was fragmented for hybridization on Affymetrix GENECHIP® human genome U133 plus v2.0 arrays. Fragmented cRNA was prepared for hybridization as outlined in the Affymetrix GENECHIP® manual. Hybridization was conducted overnight in a model 320 rotating hybridization oven set at 45° C. All GENECHIP® wash and staining procedures were performed on an Affymetrix Model 450 Fluidics station. Arrays were scanned on an Affymetrix GENECHIP® Scanner 3000. Data capture and initial array quality assessment were performed with the GENECHIP Operating Software (GCOS) tool.
  • Stratagene's (La Jolla, Calif.) ArrayAssist® Lite software was used to calculate probe-level summaries (GC-RMA normalization algorithm) from the array CEL files. R packages (R development core team) samr & qvalue were used to generate differentially regulated genes. PCA and hierarchical clustering analyses were performed in both SpotFire and R (R Development Core Team). SAM & FDR were used to select differentially regulated genes (pairwise comparison between lesional and non-lesional skin, lesional and normal skin, and non-lesional and normal skin). Probe sets with a fold-change of at least 2 and q value less than or equal to 0.05 were considered to be differentially regulated. PCA and hierarchical clustering were performed in both SpotFire and bioconductor R.
  • Overall, 1408 probe sets were up-regulated and 1465 probe sets were down-regulated in lesional skin compared to non-lesional skin. Although the downregulated genes outnumbered the upregulated genes in the lesional skin, the magnitude of differential regulation of the upregulated genes was much greater as a whole. For example, 318 probe sets were upregulated by at least four fold in the lesional skin, while only 84 probe sets were downregulated by at least four fold in the lesional skin. Among them, 96 probe sets were upregulated by at least eight fold in the lesional skin, while only six probe sets were downregulated by at least eight fold.
  • 463 probe sets were also up-regulated and 489 probe sets were down-regulated in non-lesional skin compared to normal skin. FIG. 45 provides a Venn diagram of the probe sets both upregulated (downregulated) in lesional skin and non-lesional skin relative to normal healthy skin. Only 70 of the 1408 upregulated probe sets in the lesional skin were also upregulated in non-lesional skin. Meanwhile, only 43 of the 1465 probe sets downregulated in the lesional skin were also downregulated in the non-lesional skin. These data suggested that the molecular events and biological changes from the non-lesional skin to lesional skin were quite different from those from the normal skin to the non-lesional skin.
  • To identify the most statistically significant signaling pathways altered in psoriasis, the list of differentially regulated genes were submitted to GeneGo for pathway and network analysis. Briefly, the pathway and network analysis was conducted with the MetaCore™ integrated software suite from GeneGo, Inc. (St. Joseph, Mich.). The significance, given a particular pathway or network, is approximated by a hypergeometric distribution where the p-value essentially represents the probability of a particular gene set mapping arising by chance, given the numbers of genes in the set of all genes on pathway maps, genes on a particular pathway map and genes in the experiment.
  • Fifty seven signaling pathways were significantly altered in lesional skin compared to non-lesional skin, a majority of which were involved in immune response and cell cycle. The IFNα/β signaling pathway was the most significantly altered in lesional skin with a p value of 3.8×1013. IFNα/β signaling pathway members such as IFNα, IFNβ, IFNAR1, IFNAR2, STAT1, IRF1, MPL, ISG15, IFI6 were all significantly overexpressed in lesional skin compared to uninvolved skin.
  • Overall, 22 signaling pathways were activated and 37 signaling pathways were inhibited (p<0.05) in the lesional skin compared to non-lesional skin. All the putative signaling pathways activated were either cytokine and chemokine mediated signaling pathways or were involved in immune responses. For example, IFNγ, TNFα and onconstatin M signaling pathways were activated in the lesional skin of psoriatic patients. Of all the signaling pathways altered in lesional and non-lesional skin, IFNα/β signaling pathway topped the list with a p value of 6.6×1026(FIG. 46). Components of the pathway like IFNα subtypes, IFNβ, IFNAR1, IFNAR2, STAT1, IRF1, MPL, ISG15, IFI6 were all significantly overexpressed in lesional skin compared to non-lesional skin of psoriatic patients.
  • Using the list of probe sets identified to be type-I IFN inducible in the whole blood and keratinocyte ex vivo stimulation studies (Example 10), 164 of the 1408 (approximately 11.7%) probe sets upregulated in lesional relative to non-lesional skin were identified as type-I IFN inducible. Fisher's exact test calculated a p value (one-tailed t test) less than 0.0001, suggesting that the observed overexpression of type-I IFN genes in lesional skin of psoriatic patients was statistically significant. The type-I IFN induced genes were also many of the most highly upregulated genes in the lesional relative to non-lesional psoriatic skin. Nineteen percent of the top 100 and 200 most upregulated probe sets in lesional skin relative to non-lesional skin were type-I IFN genes. See FIGS. 47 a and b for the top 100 upregulated probe sets in lesional skin. These genes included STAT1, a key component in forming the ISGF3 complex; IRF7, a master regulator of the IFNα/β mediated immune response; MYD88, which governs the induction of CD8+ T-cell responses with IRF7; IRF1, a transcriptional activator for the type-I IFN genes; OAS family members OAS1, OAS2, OAS3, mediators of resistance to virus infection; ISG15, a ubiquitin-like protein that becomes conjugated to many cellular proteins upon activation by IFNα/β; and members of the ISG15 signaling pathways such as USP18, UBE2L6, and HERC5. This enrichment of type I IFN genes indicated them as the most overexpressed genes in lesional skin of psoriatic patients.
  • Table 26 lists, in descending order, the top 50 IFN induced probes in lesional skin compared to non-lesional skin of psoriasis patients. Table 26 not only compares the log 2-based fold change (log 2 fc) and q value for each of the 50 most upregulated type I IFN inducible genes in lesional relative to non-lesional skin of psoriasis patients, it also compares the log 2-based fold change and q value for these 50 genes in non-lesional skin of psoriasis patients relative to healthy control patients.
  • TABLE 26
    The frequency of upregulation of the top 50 type-I IFN induced probes in lesional relative to non-lesional skin in psoriasis patients
    Lesional vs. Non-lesional Non-lesional vs. Normal
    Unigene Gene log2 q log2 q
    Probe ID ID Gene Title Symbol fc value fc value
    219403_s_at Hs.44227 heparanase HPSE 4.598 4.46E−22 0.226 0.23589
    204972_at Hs.414332 2′-5′-oligoadenylate synthetase 2, OAS2 4.098 8.57E−14 0.096 0.28896
    69/71 kDa
    205660_at Hs.118633 2′-5′-oligoadenylate synthetase-like OASL 4.030 1.34E−12 0.029 0.20341
    227609_at Hs.546467 epithelial stromal interaction 1 (breast) EPSTI1 4.002 1.14E−14 −0.254 0.10796
    227458_at — — — 3.859 9.31E−14 −0.591 0.05449
    219352_at Hs.529317 hect domain and RLD 6 HERC6 3.842 9.49E−16 −0.460 0.04810
    216834_at Hs.75256 regulator of G-protein signalling 1 RGS1 3.809 2.47E−17 −5.269 0.00000
    204533_at Hs.632586 chemokine (C-X-C motif) ligand 10 CXCL10 3.697 2.97E−12 0.338 0.13024
    226702_at Hs.7155 hypothetical protein LOC129607 LOC129607 3.572 2.37E−16 −0.156 0.26500
    242625_at Hs.17518 radical S-adenosyl methionine domain RSAD2 3.403 1.65E−12 −0.070 0.31309
    containing 2
    213797_at Hs.17518 radical S-adenosyl methionine domain RSAD2 3.243 3.36E−10 0.004 0.36209
    containing 2
    202086_at Hs.517307 myxovirus (influenza virus) resistance 1, MX1 3.235 5.28E−14 0.050 0.33453
    interferon-inducible protein p78 (mouse)
    205552_s_at Hs.524760 2′-5′-oligoadenylate synthetase 1, OAS1 3.222 2.41E−14 0.328 0.13669
    40/46 kDa
    210797_s_at Hs.118633 2′-5′-oligoadenylate synthetase-like OASL 3.216 1.63E−09 0.005 0.34940
    204439_at Hs.389724 interferon-induced protein 44-like IFI44L 3.205 4.73E−13 0.120 0.30073
    202411_at Hs.532634 interferon, alpha-inducible protein 27 IFI27 3.165 4.81E−12 −0.154 0.26878
    202869_at Hs.524760 2′-5′-oligoadenylate synthetase 1, OAS1 3.150 2.47E−14 0.248 0.21403
    40/46 kDa
    205483_s_at Hs.458485 ISG15 ubiquitin-like modifier ISG15 3.008 4.73E−13 −0.273 0.11013
    209969_s_at Hs.565365 signal transducer and activator of STAT1 2.993 7.95E−17 0.199 0.20072
    transcription 1, 91 kDa
    228531_at Hs.65641 sterile alpha motif domain containing 9 SAMD9 2.846 5.42E−14 −0.033 0.35359
    204415_at Hs.523847 interferon, alpha-inducible protein 6 IFI6 2.769 7.23E−09 −0.045 0.29074
    214453_s_at Hs.82316 interferon-induced protein 44 IFI44 2.679 1.94E−12 0.086 0.32618
    222838_at Hs.517265 SLAM family member 7 SLAMF7 2.659 1.60E−16 −0.046 0.31222
    219684_at Hs.43388 receptor transporter protein 4 RTP4 2.649 3.73E−11 0.497 0.04912
    203127_s_at Hs.435661 serine palmitoyltransferase, long chain SPTLC2 2.628 1.04E−20 −1.016 0.00017
    base subunit 2
    205569_at Hs.518448 lysosomal-associated membrane protein 3 LAMP3 2.569 2.64E−09 0.293 0.22865
    219691_at Hs.65641 stenile alpha motif domain containing 9 SAMD9 2.559 1.30E−13 0.011 0.37349
    223220_s_at Hs.518200 poly (ADP-ribose) polymerase family, PARP9 2.553 1.08E−15 0.069 0.31416
    member 9
    AFFX-HUMISG
    Figure US20150132313A1-20150514-P00899
    		 Hs.565365 signal transducer and activator of STAT1 2.525 1.64E−10 0.706 0.03338
    transcription 1, 91 kDa
    212268_at Hs.381167 serpin peptidase inhibitor, clade B SERPINB1 2.510 3.02E−15 −0.605 0.07749
    (ovalbumin), member 1
    216202_s_at Hs.435661 serine palmitoyltransferase, long chain SPTLC2 2.507 1.17E−13 −0.682 0.01693
    base subunit 2
    229450_at — — — 2.492 1.50E−14 0.224 0.20674
    208436_s_at Hs.166120 interferon regulatory factor 7 IRF7 2.448 6.90E−15 −0.578 0.01612
    AFFX-HUMISG
    Figure US20150132313A1-20150514-P00899
    		 Hs.565365 signal transducer and activator of STAT1 2.444 3.03E−10 0.516 0.05854
    transcription 1, 91 kDa
    204747_at Hs.47338 interferon-induced protein with IFIT3 2.424 2.15E−14 0.365 0.07219
    tetratricopeptide repeats 3
    229390_at Hs.381220 hypothetical protein LOC441168 RP1-93H18.5 2.400 2.59E−12 −369 0.11426
    218400_at Hs.528634 2′-5′-oligoadenylate synthetase 3, OAS3 2.397 3.83E−14 0.179 0.11631
    100 kDa
    235276_at — — — 2.386 3.61E−15 0.057 0.32771
    203153_at Hs.20315 interferon-induced protein with IFIT1 2.351 1.17E−10 0.054 0.34454
    tetratricopeptide repeats 1
    210873_x_at Hs.348983 apolipoprotein B mRNA editing enzyme, APOBEC3A 2.348 1.35E−07 −0.048 0.30119
    catalytic polypeptide-like 3A
    204698_at Hs.459265 interferon stimulated exonuclease gene ISG20 2.337 1.50E−12 −0.644 0.05052
    20 kDa
    232666_at Hs.528634 2′-5′-oligoadenylate synthetase 3, OAS3 2.236 4.50E−10 0.077 0.04816
    100 kDA
    222881_at Hs.44227 heparanase HPSE 2.230 3.47E−15 0.221 0.17127
    205241_at Hs.567405 SCO cytochrome oxidase deficient homolog 2 SCO2 2.208 1.90E−17 −0.285 0.08517
    (yeast)
    AFFX-HUMISG
    Figure US20150132313A1-20150514-P00899
    		 Hs.565365 signal transducer and activator of STAT1 2.205 5.29E−10 0.397 0.10218
    transcription 1, 91 kDA
    206553_at Hs.414332 2′-5′-oligoadenylate synthetase 2, OAS2 2.183 1.34E−09 0.043 0.14755
    69/71 kDa
    207387_s_at Hs.1466 glycerol kinase GK 2.160 9.38E−14 0.014 0.37488
    219716_at Hs.257352 apolipoprotein L, 6 APOL6 2.123 3.03E−11 −0.126 0.19251
    202270_at Hs.62661 guanylate binding protein 1, interferon- GBP1 2.113 4.67E−14 −0.053 0.31367
    inducible, 67 kDa
    Figure US20150132313A1-20150514-P00899
    indicates data missing or illegible when filed

    Removal of ESTs, hypothetical proteins, and duplications of genes due to identification by multiple probe sets produced Table 27. Table 27 provides, in descending order, the top 50 most upregulated type-I IFN genes in lesional skin compared to non-lesional skin. For genes identified by more than one probe set, only the probe set detected as most upregulated is provided.
  • TABLE 27
    Top 50 type-I IFN induced genes in lesional relative to non-lesional skin in psoriasis
    patients (Table 27 discloses “DEAD (Asp-Glu-Ala-Asp)” as SEQ ID NO: 1)
    Probe. ID Unigene. ID Gene. Title Gene. Symbol log2. fc q. value (fdr) % Prevalence
    219403_s_at Hs.44227 heparanase HPSE 4.60 4.46E−22 100.00
    204972_at Hs.414332 2′-5′-oligoadenylate synthetase 2, 69/71 kDa OAS2 4.10 8.57E−14 96.15
    205660_at Hs.118633 2′-5′-oligoadenylate synthetase-like OASL 4.03 1.34E−12 96.15
    227609_at Hs.546467 epithelial stromal interaction 1 (breast) EPSTI1 4.00 1.14E−14 92.31
    219352_at Hs.529317 hect domain and RLD 6 HERC6 3.84 9.49E−16 96.15
    216834_at Hs.75256 regulator of G-protein signalling 1 RGS1 3.81 2.47E−17 100.00
    204533_at Hs.632586 chemokine (C-X-C motif) ligand 10 CXCL10 3.70 2.97E−12 100.00
    242625_at Hs.17518 radical S-adenosyl methionine domain containing 2 RSAD2 3.40 1.65E−12 88.46
    202086_at Hs.517307 myxovirus (influenza virus) resistance 1, MX1 3.24 5.28E−14 92.31
    interferon-inducible protein p78 (mouse)
    205552_s_at Hs.524760 2′-5′-oligoadenylate synthetase 1, 40/46 kDa OAS1 3.22 2.41E−14 96.15
    204439_at Hs.389724 interferon-induced protein 44-like IFI44L 3.21 4.73E−13 88.46
    202411_at Hs.532634 interferon alpha-inducible protein 27 IFI27 3.17 4.81E−12 92.31
    205483_s_at Hs.458485 ISG15 ubiquitin-like modifier ISG15 3.09 4.73E−13 92.31
    209969_s_at Hs.565365 signal transducer and activator of transcription 1, 91 kDa STAT1 2.99 7.95E−17 96.15
    228531_at Hs.65641 sterile alpha motif domain containing 9 SAMD9 2.85 5.42E−14 92.31
    204415_at Hs.523847 interferon, alpha-inducible protein 6 IFI6 2.77 7.23E−09 84.62
    214453_s_at Hs.82316 interferon-induced protein 44 IFI44 2.68 1.94E−12 92.31
    222838_at Hs.517265 SLAM family member 7 SLAMF7 2.66 1.60E−16 92.31
    219684_at Hs.43388 receptor transporter protein 4 RTP4 2.65 3.73E−11 88.46
    203127_s_at Hs.435661 serine palmitoyltransferase, long chain base subunit 2 SPTLC2 2.63 1.04E−20 100.00
    205569_at Hs.518448 lysosomal-associated membrane protein 3 LAMP3 2.57 2.64E−09 96.15
    223220_s_at Hs.518200 poly (ADP-ribose) polymerase family, member 9 PARP9 2.55 1.08E−15 88.46
    212268_at Hs.381167 serpin peptidase inhibitor, clade B (ovalbumin), member 1 SERPINB1 2.51 3.02E−15 88.46
    208436_s_at Hs.166120 interferon regulatory factor 7 IRF7 2.45 6.90E−15 96.15
    204747_at Hs.47338 interferon-induced protein with tetratricopeptide repeats 3 IFIT3 2.42 2.15E−14 92.31
    218400_at Hs.528634 2′-5′-oligoadenylate synthetase 3, 100 kDa OAS3 2.40 3.83E−14 100.00
    203153_at Hs.20315 interferon-induced protein with tetratricopeptide repeats 1 IFIT1 2.35 1.17E−10 84.62
    210873_x_at Hs.348983 apolipoprotein B mRNA editing enzyme, APOBEC3A 2.35 1.35E−07 80.77
    catalytic polypeptide-like 3A
    204698_at Hs.459265 interferon stimulated exonuclease gene 20 kDa ISG20 2.34 1.50E−12 92.31
    205241_at Hs.567405 SCO cytochrome oxidase deficient homolog 2 (yeast) SCO2 2.21 1.90E−17 96.15
    207387_s_at Hs.1466 glycerol kinase GK 2.16 9.38E−14 92.31
    219716_at Hs.257352 apolipoprotein L, 6 APOL6 2.12 3.03E−11 92.31
    202270_at Hs.62661 guanylate binding protein 1, interferon-inducible, 67 kDa GBP1 2.11 4.67E−14 92.31
    229625_at Hs.513726 Guanylate binding protein 5 GBP5 2.07 7.52E−10 88.46
    228617_at Hs.441975 XIAP associated factor-1 BIRC4BP 2.05 3.41E−12 84.62
    206513_at Hs.281898 absent in melanoma 2 AIM2 2.04 2.32E−08 76.92
    218943_s_at Hs.190622 DEAD (Asp-Glu-Ala-Asp) box polypeptide 58 DDX58 2.00 1.39E−10 88.46
    203148_s_at Hs.575631 tripartite motif-containing 14 TRIM14 1.94 2.17E−17 96.15
    213293_s_at Hs.501778 tripartite motif-containing 22 TRIM22 1.89 1.36E−12 88.46
    214838_at — SFT2 domain containing 2 SFT2D2 1.88 5.30E−17 92.31
    231769_at Hs.464419 F-box protein 6 FBXO6 1.86 6.34E−14 88.46
    227697_at Hs.527973 suppressor of cytokine signalling 3 SOCS3 1.82 4.55E−10 88.46
    206632_s_at Hs.226307 apolipoprotein B mRNA editing enzyme, APOBEC3B 1.81 9.42E−10 92.31
    catalytic polypeptide-like 3B
    201649_at Hs.425777 ubiquitin-conjugating enzyme E2L 6 UBE2L6 1.81 2.15E−13 84.62
    204702_s_at Hs.404741 nuclear factor (erythroid-derived 2)-like 3 NFE2L3 1.80 1.71E−16 96.15
    202531_at Hs.436061 interferon regulator factor 1 IRF1 1.79 2.13E−13 80.77
    204994_at Hs.926 myxovirus (influenza virus) resistance 2 (mouse) MX2 1.75 7.99E−09 69.23
    215966_x_at — glycerol kinase pseudogene 3 GKP3 1.73 3.33E−11 80.77
    207655_s_at Hs.444049 B-cell linker BLNK 1.71 2.28E−14 96.15
    216598_s_at Hs.303649 chemokine (C-C motif) ligand 2 CCL2 1.71 4.80E−07 65.38

    The fold changes (log 2 fc) were calculated based on relative transcript level between paired lesional skin and non-lesional skin. Q values were calculated based on FDR. Prevalence tabulated the percentage of the 26 paired lesional and non-lesional skin that had at least 2-fold overexpression of the genes listed in the table.
  • These top 50 type-I IFN induced genes in lesional relative to non-lesional skin in psoriasis patients were overexpressed, on average, 3.2-fold (CCL2 and BLNK) to 24-fold (HPSE) more in the lesional skin. In addition, all of the genes in the table, except CCL2 and AIM2, were upregulated in at least 84% of the paired lesional/non-lesional skin biopsies (23 of the 26 pairs) of the psoriasis patients. This robust upregulation of a large panel of type-I IFN genes across lesional versus non-lesional skin samples of psoriasis patients provided a strong rationale for their use as PD markers.
  • As briefly alluded to, above, upregulation of type-I interferon inducible genes was consistently observed across psoriasis patients. Table 28 provides the average and median fold change of the top 25 most upregulated type-I IFN probe sets for each paired lesional/non-lesional skin sample. The top 25 most upregulated type-I IFN probe sets were consistently observed to detect elevated gene expression in the lesional relative to non-lesional skin of each individual psoriasis patient.
  • TABLE 28
    Average and median fold change of the top 25 most upregulated type-I IFN
    inducible genes in 26 pairs of lesional skin compared to lesional skin
    Probe ID Unigene ID Gene Symbol Pair 1 Pair 2 Pair 3 Pair 4 Pair 5 Pair 6 Pair 7 Pair 8 Pair 9 Pair 10 Pair 11
    219403_s_at Hs.44227 HPSE 67.78 24.31 35.28 27.91 37.31 28.56 236.24 128.77 10.29 7.12 19.62
    204972_at Hs.414332 OAS2 12.60 21.22 1.19 2.44 49.33 48.03 33.22 43.96 13.92 71.36 28.17
    205660_at Hs.118633 OASL 7.19 13.48 4.15 9.03 62.19 50.23 31.12 54.05 9.72 9.94 1.10
    227609_at Hs.546467 EPSTI1 11.25 20.34 −1.43 1.38 57.01 32.14 14.40 23.42 10.53 55.80 32.87
    227458_at — — 16.69 10.94 19.35 3.11 54.31 23.30 30.76 10.59 3.25 40.43 41.37
    219352_at Hs.529317 HERC6 7.86 15.70 2.38 1.45 49.25 51.01 11.64 19.63 20.95 21.72 15.84
    216834_at Hs.75256 RGS1 27.92 8.50 17.90 6.81 58.42 16.25 4.97 20.52 10.02 24.32 19.50
    204533_at Hs.632586 CXCL10 3.92 3.01 8.72 3.91 249.50 13.12 13.37 15.14 4.75 69.66 56.31
    226702_at Hs.7155 LOC129607 3.59 5.77 3.10 1.27 60.00 12.76 14.72 22.00 9.53 58.99 27.55
    242625_at Hs.17518 RSAD2 4.57 6.19 1.79 1.24 66.13 51.91 19.28 23.36 4.02 32.04 8.80
    213797_at Hs.17518 RSAD2 8.33 7.37 1.16 1.00 78.54 33.08 11.98 25.13 1.86 21.73 8.43
    202066_at Hs.517307 MX1 5.03 9.17 1.25 1.08 20.97 39.08 14.63 23.54 11.33 18.56 11.71
    205552_s_at Hs.524760 OAS1 5.93 11.05 1.19 2.76 21.03 29.00 11.76 27.37 7.71 19.23 20.14
    210797_s_at Hs.118633 OASL 2.04 6.90 1.32 1.34 45.94 31.06 16.86 66.61 9.25 1.69 1.73
    204439_at Hs.389724 IFI44L 4.52 6.71 −3.59 −1.06 14.49 58.16 9.25 32.21 6.68 37.49 31.82
    202411_at Hs.532634 IFI27 10.97 15.52 1.94 2.66 12.02 38.87 14.83 27.63 17.02 17.22 17.69
    202869_at Hs.524760 OAS1 5.34 7.99 2.04 2.09 16.23 32.48 13.29 30.47 12.75 49.00 10.15
    205483_s_at Hs.458485 ISG15 5.54 4.37 1.65 1.10 19.82 40.24 8.30 13.89 7.00 12.18 14.49
    209969_s_at Hs.565365 STAT1 6.14 6.12 2.85 2.00 38.39 16.50 10.35 7.10 12.90 17.32 12.41
    228531_at Hs.65541 SAMD9 5.07 5.24 2.52 1.79 12.56 12.67 5.76 15.63 9.88 12.94 20.85
    204415_at Hs.523847 IFI6 1.62 6.53 −2.01 1.00 13.90 25.74 5.59 16.68 4.65 11.65 6.45
    214453_s_at Hs.82316 IFI44 2.60 6.23 −2.89 1.22 14.76 10.55 4.43 9.99 2.67 12.32 25.67
    222838_at Hs.517265 SLAMF7 5.26 7.36 1.70 1.97 −19.55 8.75 5.56 9.97 6.78 10.62 15.91
    219684_at Hs.43388 RTP4 13.11 13.02 −3.07 −1.11 13.95 18.00 6.50 10.09 3.48 30.25 23.69
    203127_s_at Hs.435551 SPTLC2 6.06 5.07 4.11 3.50 8.18 5.50 11.49 8.25 2.73 4.53 6.24
    Average fold change 10.04 9.92 4.12 3.20 43.40 29.08 22.41 27.45 8.55 26.73 19.14
    Median fold change 5.93 7.37 1.79 1.79 37.31 29.00 11.98 22.00 9.25 19.23 17.69
    Probe ID Unigene ID Gene Symbol Pair 12 Pair 13 Pair 14 Pair 15 Pair 16 Pair 17 Pair 18 Pair 19 Pair 20
    219403_s_at Hs.44227 HPSE 25.78 30.21 24.01 56.80 10.70 35.20 11.42 5.86 12.73
    204972_at Hs.414332 OAS2 4.04 24.63 79.34 15.84 96.99 10.27 30.28 9.26 30.11
    205660_at Hs.118633 OASL 2.31 24.75 44.7 11.94 45.98 17.46 14.66 33.60 17.27
    227609_at Hs.546467 EPSTI1 8.86 59.54 47.71 33.84 78.12 14.34 25.86 33.41 12.06
    227458_at — — 6.70 26.83 23.19 37.88 70.78 75.98 19.04 26.19 49.50
    219352_at Hs.529317 HERC6 5.82 10.58 23.05 30.42 133.47 11.03 26.94 9.90 16.46
    216834_at Hs.75256 RGS1 9.91 94.41 14.83 23.00 15.64 13.95 31.90 100.03 8.02
    204533_at Hs.632586 CXCL10 22.30 12.75 8.30 16.61 28.11 12.95 30.79 65.10 17.72
    226702_at Hs.7155 LOC129607 2.99 5.99 39.75 25.66 225.99 19.79 30.96 4.88 45.30
    242625_at Hs.17518 RSAD2 1.76 5.64 16.36 15.97 94.85 9.47 14.58 4.64 33.67
    213797_at Hs.17518 RSAD2 2.73 3.23 31.91 12.04 49.52 8.11 12.51 11.92 24.02
    202066_at Hs.517307 MX1 3.08 8.93 20.03 8.68 86.72 11.04 19.60 7.24 4.00
    205552_s_at Hs.524760 OAS1 3.49 2.82 37.85 21.19 39.43 6.13 24.10 5.86 2.63
    210797_s_at Hs.118633 OASL 1.20 19.00 23.73 1.62 43.88 11.71 10.30 26.36 2.27
    204439_at Hs.389724 IFI44L 3.95 19.43 16.66 23.81 253.56 6.81 20.34 3.18 17.90
    202411_at Hs.532634 IFI27 5.81 9.36 26.00 15.85 38.94 2.01 30.69 4.59 −4.73
    202869_at Hs.524760 OAS1 5.52 2.31 18.94 19.52 36.57 4.58 16.19 4.81 8.96
    205483_s_at Hs.458485 ISG15 4.47 6.78 19.24 10.65 57.01 3.67 12.65 2.96 2.57
    209969_s_at Hs.565365 STAT1 3.77 14.31 7.49 25.00 18.73 5.45 9.63 9.18 17.30
    228531_at Hs.65541 SAMD9 1.97 4.70 24.24 15.22 20.12 10.49 10.39 5.60 14.30
    204415_at Hs.523847 IFI6 3.30 5.43 30.75 3.29 38.93 4.08 20.01 2.08 1.00
    214453_s_at Hs.82316 IFI44 3.56 8.26 18.22 2.57 61.65 6.49 20.83 8.32 10.75
    222838_at Hs.517265 SLAMF7 5.44 19.09 5.39 14.93 6.86 10.10 8.89 15.42 7.99
    219684_at Hs.43388 RTP4 8.83 5.66 16.47 10.87 18.65 3.40 17.35 5.96 1.92
    203127_s_at Hs.435551 SPTLC2 5.57 5.61 11.38 8.26 7.73 10.92 7.32 4.82 3.64
    Average fold change 6.13 17.25 25.18 18.49 63.16 13.02 19.09 16.49 14.30
    Median fold change 4.01 9.36 23.06 15.85 43.88 10.27 19.04 7.24 12.06
    Probe ID Unigene ID Gene Symbol Pair 21 Pair 22 Pair 23 Pair 24 Pair 25 Pair 26
    219403_s_at Hs.44227 HPSE 25.78 30.81 32.26 24.58 48.50 105.13
    204972_at Hs.414332 OAS2 16.38 24.27 60.43 25.32 132.09 9.07
    205660_at Hs.118633 OASL 84.97 24.22 92.12 45.44 54.96 39.66
    227609_at Hs.546467 EPSTI1 19.24 17.86 28.12 22.43 78.03 10.90
    227458_at — — 5.43 27.89 24.13 11.45 26.05 9.87
    219352_at Hs.529317 HERC6 19.06 33.32 27.98 19.09 26.56 8.66
    216834_at Hs.75256 RGS1 2.44 13.49 15.83 22.64 29.15 14.83
    204533_at Hs.632586 CXCL10 11.89 12.12 41.27 10.90 30.14 5.86
    226702_at Hs.7155 LOC129607 14.42 7.91 32.87 14.50 19.85 3.13
    242625_at Hs.17518 RSAD2 16.26 10.67 68.96 20.21 40.57 5.99
    213797_at Hs.17518 RSAD2 25.00 10.04 75.04 17.36 28.33 6.29
    202066_at Hs.517307 MX1 12.05 10.63 28.80 11.08 27.74 5.68
    205552_s_at Hs.524760 OAS1 4.18 13.46 21.42 9.30 32.15 16.09
    210797_s_at Hs.118633 OASL 78.51 15.88 65.78 33.47 35.32 18.92
    204439_at Hs.389724 IFI44L 12.16 7.60 18.42 4.52 25.93 1.12
    202411_at Hs.532634 IFI27 3.46 10.59 22.17 7.00 50.18 7.37
    202869_at Hs.524760 OAS1 4.73 11.05 11.67 7.13 18.20 7.39
    205483_s_at Hs.458485 ISG15 11.30 5.71 34.41 18.06 30.48 5.07
    209969_s_at Hs.565365 STAT1 7.10 9.27 11.03 10.91 12.19 4.37
    228531_at Hs.65541 SAMD9 6.80 6.38 16.24 12.46 13.49 6.75
    204415_at Hs.523847 IFI6 49.45 16.05 58.43 17.95 52.57 6.85
    214453_s_at Hs.82316 IFI44 4.93 5.55 13.27 8.02 26.71 2.03
    222838_at Hs.517265 SLAMF7 4.69 5.06 5.92 5.61 11.22 9.01
    219684_at Hs.43388 RTP4 5.90 8.90 4.55 4.92 28.75 3.91
    203127_s_at Hs.435551 SPTLC2 9.24 5.35 9.32 13.11 11.00 12.89
    Average fold change 18.21 13.65 32.82 15.94 35.61 13.07
    Median fold change 11.89 10.67 27.98 13.11 28.75 7.37
  • FIG. 32 provides a graphic of the distribution of the average and median fold changes among the different pairs of lesional and non-lesional skin. The prevalent and uniform upregulation of the most overexpressed type-I IFN genes in lesional skin of psoriatic patients verified their usefulness as PD markers.
  • Seventeen probe sets were also observed as underexpressed in lesional skin that were also down-regulated by IFN/3 in the ex vivo stimulation studies described in Example 10. These genes include CYP1B1, TGST1, RRAGD, IRS2, MGST1, TGFBR3, and RGS2.
    • Example 12 Expression of Type-I IFN Genes is not Significantly Altered in Normal Skin Relative to Non-Lesional Skin of Psoriatic Patients
  • Although the array data obtained in Example 11 identified overexpression of numerous type-I IFN-inducible genes in lesional relative to non-lesional skin, it identified only 5 probe sets overexpressed in non-lesional skin relative to normal control skin. The p value of Fisher's exact test (two-tailed t-test) was 0.581, which suggested that the overexpression of the type-I IFN genes is not statistically significant in the non-lesional skin of the psoriasis patients over normal skin.
  • As shown in Table 26 (Example 11), most of the genes identified as being top 50 type-I IFN-induced genes in lesional relative to non-lesional skin were comparably expressed in non-lesional skin relative to normal skin controls (several genes, e.g., RGS1, SPTLC2, are downregulated in the non-lesional skin compared to normal skin). FIG. 33 provides a graphical representation of the relative expression of 3 type-I IFN inducible genes (HPSE, OASL, and HERC6; included as top 50 type-I IFN-induced probe sets in lesional relative to non-lesional skin), and 1 non type-I IFN inducible gene (SERPINB4) in both (a) lesional skin compared to non-lesional skin and (b) non-lesional skin compared to normal skin. The overexpression of genes HPSE, OASL, and HERC6 in lesional skin compared to non-lesional skin is both statistically significant (as evidenced by the very small p value) and large in scale (between 12-250 fold overexpression on average). SERPINB4 is overexpressed in non-lesional skin by about 3-4 fold compared to normal skin, but upregulated by well over 200 fold in lesional skin compared to non-lesional skin.
  • Analysis of normal healthy, lesional psoriasis, and non-lesional psoriasis skin samples using the 164 probe sets identified in Example 11 as type-I IFN inducible, showed a clustering of lesional psoriasis samples and a clustering of non-lesional psoriasis and normal healthy skin samples. FIG. 34 a provides heatmap of unsupervised hierarchical clustering of all lesional, non-lesional, and normal skin samples profiled using the 164 type-I IFN-inducible probe sets in lesional skin compared to non-lesional skin of psoriasis patients. It can be observed that nearly all (all but three) of the lesional skin samples clustered together, while nearly all of the non-lesional and normal skin samples clustered together. FIG. 34 b provides a PCA plot of the skin samples using the same 164 upregulated type-I IFN inducible probe sets. Again, the normal skin samples and the non-lesional skin samples mostly clustered together, indicating similar levels of expression of the 164 genes. Also, the majority of the lesional skin samples were separated from the normal and non-lesional skin samples, indicating that the lesional samples exhibited a distinct overexpression of the type-I IFN inducible genes that was separable from the gene expression levels of the normal and non-lesional skin samples.
  • These observations were further confirmed by gene pathway analysis. GeneGo analysis showed that the possibility of an alteration in the IFNα/β signaling pathway of non-lesional skin of psoriasis patients relative to normal skin had a p value close to 1. A distinctive separation of lesional skin samples from non-lesional skin samples and normal skin samples was even observed when clustering samples based on the transcript profile of an entire genome array. See FIG. 47.
    • Example 13 Validation of Type-I IFN-Inducible Gene Up-Regulation in Psoriatic Lesional Skin Using TAQMAN-Based Assays
  • A BIOMARK™ 48.48 dynamic array (TAQMAN-based assay) from Fluidigm was used to validate the results of the Affymetrix GENECHIP® human genome U133 plus v2.0 arrays, results indicating that type-I IFN genes are up-regulated in lesional psoriatic relative to non-lesional psoriatic or normal skin samples.
  • Eighteen pairs of lesional and non-lesional skin samples from 18 psoriasis patients were used for the gene expression analysis. Twenty nine of these genes were type-I IFN inducible genes while 11 were highly upregulated in lesional skin but were not IFN-inducible genes, e.g., S100A9, S100A12, SERPINGB4, and KLK13. Each of these genes was selected based on prevalence and significance of overexpression in lesional skin. The overexpression of all genes in the lesional skin was confirmed by TAQMAN qRT-PCR, the majority of which showed very good correlation between microarray and TAQMAN assays. FIG. 35 provides TAQMAN data showing overexpression of each of ten (OAS2, OASL, EPSTI1, MX1, IFI44L, IFI44, HERC6, HPSE, ISG15, and STAT1) type-I IFN-inducible genes in lesional skin in the 18 paired lesional/non-lesional samples.
  • Overall, the TAQMAN-based assay and Affymetrix array results correlated well, validating the selected genes as overexpressed type-I IFN-induced genes in lesional psoriatic skin. The distribution of correlation coefficients between the TAQMAN-based assay and the Affymetrix array for the 40 overexpressed genes is provided in FIG. 36 a. Nineteen of the overexpressed genes had correlation coefficients greater than 0.85, indicating excellent correlation between the microarray and TAQMAN-based assay. Another 17 genes had high correlation coefficients between the microarray and TAQMAN-based assay of 0.5-0.85. FIG. 36 b provides the distribution of correlation coefficients between the TAQMAN-based assay and the Affymetrix array for the 29 type-I IFN-induced genes of the 18 psoriasis patients. Again, many of the genes had high correlation coefficients, greater than 0.90. These genes include, inter alia, IFI27, CXCL10, ISG15, and MX1.
  • FIGS. 37 a-37 d and 38 provide detailed gene expression data obtained from the microarray and TAQMAN-based assays for several type-I IFN-inducible genes in the paired lesional/non-lesional samples. These data evidence that similar levels of overexpression of type-I IFN-induced genes in lesional psoriatic skin is detected between the TAQMAN and array assays, and thus the high correlation coefficients discussed above. FIGS. 37 a and 37 b show similar overexpression of ISG15 in each of the 18 paired lesional/non-lesional skin samples as determined by TAQMAN (37 a) and microarray (37 b) analysis. FIGS. 37 c and 37 d show similar overexpression of MX1 in each of the 18 paired lesional/non-lesional skin samples as determined by TAQMAN (37 c) and microarray (37 d) analysis. The correlation coefficient between the TAQMAN and microarray was 0.9735 for ISG15 and 0.9836 for MX1. FIG. 38 shows measurement of similar overexpression of type-I IFN-inducible genes IFI27 and CXCL10 by TAQMAN and microarray analysis in each if the 18 paired lesional/non-lesional skin samples. The correlation coefficient between the TAQMAN and microarray results for IFI27 and CXCL10 was 0.9456 and 0.9455, respectively.
    • Example 14 IFNα Ab Neutralizes Type-I IFNα-Induced Gene Expression in Ex Vivo Stimulated Keratinocytes of Healthy Volunteers
  • Keratinocytes of healthy volunteers were isolated and stimulated ex vivo with escalating doses of IFNα2a and leukocyte IFN to induce an escalating type I IFNα-induced gene expression pattern. Anti-IFNα antibody was able to neutralize the type I IFNα-induced gene expression pattern in a dose-dependent manner.
  • Normal human keratinocytes (EpiDerm system, MatTek, Inc.) were grown under serum-free conditions according to manufacturer's instructions. Briefly, keratinocytes were maintained on tissue culture inserts at the air-liquid interface to maintain a multilayered, fully differentiated epithelial phenotype. Keratinocytes were stimulated with human leukocyte IFN (15-150 IU/ml, PBL Biomedical Labs) and human IFNα2a (15-350 IU/ml, PBL Biomedical Labs). In some wells a humanized anti-human IFNα monoclonal antibody (0.01-100 μg/ml; MEDI-545, MedImmune, Inc) or isotype matched control antibody of irrelevant specificity (R347, MedImmune, Inc) was added simultaneously with cytokine stimulus. Epidermal cultures were harvested at 2, 4, or 18 hours post treatment for transcript analysis. Expression of type-I IFN-induced genes was measured using a BIOMARK™ 48.48 dynamic array.
  • Expression of a majority of type-I IFN-induced genes was upregulated in the IFNα2a and leukocyte interferon stimulated keratinocytes in a dose-dependent manner. This upregulation of type-I IFN-induced genes, by either IFNα2a or leukocyte interferon, was likewise inhibited in a dose-dependent manner by IFNα monoclonal antibody (MEDI-545). Control antibody, R347, did not have a significant effect on neutralization of the type-I IFN-induced genes.
  • Dose-dependent neutralization of three type-I IFN-induced genes (ISG15, USP18, and IFIT2) by MEDI-545 in IFNα2a or leukocyte IFN stimulated keratinocytes is provided in FIG. 39. FIGS. 39 (a), (c), and (e) show that MEDI-545 neutralizes overexpression of type-I IFN induced genes ISG15, USP18, and IFIT2, respectively, in keratinocytes stimulated with 350 IU/mL IFNα2a. Each of these genes was neutralized 100% by MEDI-545. FIGS. 39 (b), (d), and (f), show that MEDI-545 neutralizes overexpression of type-I IFN induced genes ISG15, USP18, and IFIT2, respectively, in keratinocytes stimulated with 150 I.U./mL leukocyte IFN. Neutralization of these genes by MEDI-545 was between 70 and 100%, which is not surprising because leukocyte IFN contains both IFNα and IFNβ. MEDI-545 neutralizes a majority of IFNα subtypes efficiently, but not IFNβ. These neutralization data provide further evidence that the type-I IFN-inducible genes identified in ex vivo stimulated whole blood and keratinocytes (Example 10) are type-I IFN-inducible genes. It also provides further support that upregulated expression of these genes in lesional psoriatic skin relative to non-lesional skin due to type-I IFN induction.
    • Example 15 Multiple Type-I IFN Subtypes are Up-Regulated in Lesional Skin of Psoriasis Patients
  • To identify the type-I IFN subtypes responsible for the induction of the type-I IFN signature in lesional skin of psoriasis patients, mRNA levels of type-I IFN genes in psoriatic lesions were measured.
  • Gene expression analysis was performed using a TAQMAN Low Density Array (TLDA) from Applied Biosystems. Expression of 23 genes, including type- I IFNα subtypes 1, 2, 5, 6, 7, 8, 14, 17, and 21; type-I IFNs IFNβ, κ, and ω; IFNγ; IFNα receptors IFNAR1 and IFNAR2; IFNγ receptors IFNGR1 and IFNGR2; type-I IFNα inducible genes RSAD2, OAS3, IFI44, MX1, and CXCL10; and TNFα was monitored and compared in paired lesional and non-lesional skin of 18 psoriasis patients.
  • Double-stranded cDNA for each patient sample was pre-amplified using the TAQMAN PreAmp Master Mix kit (Applied Biosystems). cDNA was pre-amplified by conducting 10 cycles of PCR on each patient sample using a pooled solution of primers, a pair for each gene analyzed on the array. The pre-amplified cDNA were diluted 1:5 with TE. A 50 μL volume of the diluted pre-amplified cDNA was added to a 50 μL volume of 2×TAQMAN Universal PCR Master Mix (Applied Biosystems) and mixed. The array was loaded with the mixture using standard procedures and the loaded array was run on a 7900HT Fast Real-Time PCR System (Applied Biosystems). Data analysis of the resulting Ct values was conducted with the SDSv2.2.2 software tool (Applied Biosystems).
  • FIG. 40 a shows the relative overexpression of mRNA of nine IFNα subtypes in the lesional skin compared to either non-lesional skin or normal skin. With the exception of IFNα5 (upregulated by about 4.6 fold; median fold change, p<0.001), none of the IFNα subtypes were significantly altered at the mRNA level in the non-lesional skin compared to that in the normal skin (p<0.05). However, all of these IFNα subtypes were upregulated at the mRNA level in the lesional skin compared to that in the normal skin (or non-lesional skin), with the overexpression of IFNα1, IFNα5, IFNα8, IFNα14, IFNα17, IFNα21 being statistically significant (p<0.05). FIG. 40 b shows that the overexpression of other members of type I IFN family members, IFN β, -κ, and -ω mRNA in the lesional skin compared to either non-lesional skin or normal skin. The alterations of IFNβ and IFNω mRNAs in the non-lesional skin were not significant. However, the upregulation of these mRNAs were significant in the lesional skin compared to normal skin (p values of 0.022 and 0.049 respectively). IFNκ mRNA was upregulated by about 1.6 fold (median fold change, p=0.03) in the non-lesional skin, and was sharply upregulated by 62.6 fold (median fold change) in the lesional skin compared to normal skin (p<0.001). Additionally, the receptors for type I IFN, IFNAR1 and IFNAR2 were also significantly overexpressed in the lesional skin of psoriatic patients at transcript level (p values<0.001; FIG. 40 c). While IFNAR2 upregulation was significant in the non-lesional skin, IFNAR1 was not (FIG. 40 c). Collectively, these data provided strong evidence that mRNA levels of type I IFN family members were comparable between the non-lesional skin and healthy normal skin (with the exception of IFNα5 and IFNκ), and were uniformly overexpressed in the lesional skin of psoriatic patients.
  • Table 29, lists the correlation coefficients of the overexpression of type-I IFN family member (type- I IFNα subtypes 1, 2, 5, 6, 7, 8, 14, 17, and 21; and IFNβ, IFNκ, and IFNω) mRNAs in lesional skin compared to non-lesional skin of psoriatic patients. Of the 12 type-I IFN family members measured, overexpression of IFNα1, 2, 8, and 14 in lesional skin correlated most consistently with overexpression of other members in the type-I IFN family, with the exception of IFNα5 which showed the weakest correlation with other type-I IFN family members.
  • TABLE 29
    Correlation coefficient of overexpression of type-I IFN family members in lesional skin of psoriasis patients
    IFNA1 IFNA2 IFNA5 IFNA6 IFNA7 IFNA8 IFNA14 IFNA17 IFNA21 IFNB1 IFNK IFNW1
    INFA1
    1
    IFNA2 0.66 1
    IFNA5 0.11 0.20 1
    IFNA6 0.45 0.47 −0.01 1
    IFNA7 0.77 0.79 0.09 0.68 1
    IFNA8 0.64 0.99 0.19 0.49 0.84 1
    IFNA14 0.84 0.94 0.28 0.44 0.72 0.94 1
    IFNA17 1.00 0.96 0.15 0.07 0.77 0.97 0.94 1
    IFNA21 0.71 0.49 0.50 0.42 0.81 0.49 0.61 0.75 1
    IFNB1 0.54 0.86 0.28 0.33 0.69 0.96 0.80 0.93 0.54 1
    IFNK 0.78 0.73 0.09 0.59 0.27 0.73 0.77 0.03 0.22 0.54 1
    IFNW1 0.73 0.72 0.44 0.22 0.75 0.70 0.77 0.93 0.90 0.73 0.26 1
    • Example 16 Co-Overexpression of Type-I IFN, Type-II IFN, and TNFα and their Gene Signatures in Lesional Skin or Psoriasis Patients
  • The involvement of IFNγ and TNFα mRNA signaling pathways was also evaluated in the paired lesional/non-lesional psoriasis and normal skin samples. As discussed in Example 15, above, TLDA from Applied Biosciences was used to measure IFNγ, IFNGR1 and IFNGR2, and TNFα mRNA in lesional and non-lesional skin of psoriasis patients and in normal healthy skin.
  • Unlike the observations for type-I IFN mRNA expression levels, IFNγ, IFNGR1, IFNGR2, and TNFα mRNAs were significantly overexpressed in non-lesional skin compared to healthy normal skin (FIG. 41; p values of 0.02, <0.001, <0.001 and <0.001 respectively). TNFα mRNA was upregulated by about 5.7 fold, while IFNγ, IFNGR1 and IFNGR2 mRNAs were upregulated by about 1.5, 2.2, and 2.8 fold compared to that in the normal skin (median fold change; FIG. 41). However, like the type I IFNs, these genes were upregulated in the lesional skin compared to either non-lesional skin (p values of 0.04, 0.01, 0.001 and 0.007 respectively) or normal skin (p values<0.001 for all of them; FIG. 41). TNFα, IFNγ, IFNGR1 and IFNGR2 mRNAs were upregulated by about 33.5, 116.7, 11.6, and 8.4 fold in the lesional skin compared to that in the normal skin. These observations indicated that the mRNA expression patterns for IFNγ and TNFα are different from those of type I IFN family members, which were comparable between healthy skin and non-lesional skin (with the exception of IFNα5 and IFNκ), but upregulated in the lesional skin compared to non-lesional skin of psoriasis patients.
    • Example 17 Identification Genes Induced by Type II IFN and TNFα in Ex Vivo Stimulated Whole Blood and which are Induced in Skin Lesions of Psoriasis Patients
  • As described in Example 10, whole blood of healthy donors was stimulated ex vivo with a panel of IFNα subtypes, as well as IFNβ, IFNγ, and TNFα. Stimulating whole blood ex vivo with IFNγ or TNFα identified probe sets associated with potential IFNγ- or TNFα-inducible genes. Three hundred four probe sets were identified as at least 2-fold upregulated by IFNγ four hours post-stimulation. Two hundred thirty four probe sets were identified as at least 2-fold upregulated by TNFα both 2 and 4 hours post-stimulation.
  • The probe sets identified as associated with ex vivo IFNγ or TNFα induction were compared with the total 1408 probe sets (Example 11) found to be upregulated in lesional skin relative to non-lesional skin of psoriasis patients. Using this method, 106 and 35 of the probe sets included in the total 1408 upregulated in lesional skin were identified as IFNγ or TNFα inducible, respectively (FIG. 42). The 106 probe sets identified as IFNγ inducible are provided in FIG. 49. The 35 probe sets identified as TNFα inducible are provided in FIG. 50. The 164 probes sets shown in FIG. 42 as identified as type-I IFN inducible are provided in FIG. 51. The Fisher's exact test indicated that the p values (one-tailed t-test) of the overexpression of IFNγ or TNFα inducible genes in lesional skin were both less than 0.0001. The overexpression of IFNγ and TNFα inducible genes was significant.
  • Also using the list of probe sets identified to be type I IFN, IFNγ and TNFα inducible from the ex vivo studies, type I IFN, IFNγ and TNFα inducible genes upregulated at least 2-fold in each of the lesional relative to non-lesional skin sample were identified. FIG. 43 shows the number of type I IFN, IFNγ and TNFα inducible genes upregulated in each of the 26 paired lesional and non-lesional skin. The larger the number of type I IFN inducible genes upregulated in a particular lesional skin biopsy usually gave rise to the overexpression of larger numbers of IFNγ and TNFα inducible genes in the same lesional skin biopsy. This observation was confirmed by the strong correlation in the co-activation of these three sets of genes with correlation coefficients of 0.9811, 0.9179 and 0.9372 using two-tail paired t-test to compare the upregulation of type I IFN and IFNγ, type I IFN and TNFα, and IFNγ and TNFα inducible genes in lesional skin compared to non-lesional skin (FIG. 43 a).
  • Similar analysis was carried out for the downregulated genes in the lesional skin compared to the non-lesional skin of psoriatic patients (FIG. 42). Of the 1465 total probe sets downregulated in lesional relative to non-lesional skin, only 17, 5, and 5 of them were type I IFN, IFNγ and TNFα inducible.
  • Although IFNγ and TNFα mRNAs were found to be upregulated in the non-lesional skin of psoriatic patients when compared to healthy normal skin, IFNγ and TNFα inducible genes did not appear to be significantly overexpressed in the non-lesional skin (FIG. 42). The absence of type I IFN, IFNγ and TNFα inducible gene signatures in the non-lesional skin compared to normal skin, even when IFNγ and TNFα mRNAs are overexpressed in the non-lesional skin, suggested that either IFNγ and TNFα proteins were not made in the non-lesional skin, or other signaling molecules might have inhibitory effect on the IFNγ and TNFα pathways in the non-lesional skin of psoriatic patients.
    • Example 18 Immunohistochemical Analysis of Biopsies from Lesional Psoriatic Skin, Non-Lesional Psoriatic Skin, and Skin from Normal Donors Shows Increased Protein Levels of Type I IFN-Induced Genes
  • To determine whether some of the highly overexpressed type I IFN inducible genes in psoriatic skin gave rise to similar changes in the expression of the proteins, immunohistochemical analyses were carried out to assess the presence of STAT1 and ISG15 protein in the skin. Furthermore, analysis of the cellular infiltrates (pDCs, mDCs and CD4-positive cells) was carried to compare the number of IFN-producing cell types and inflammatory cells in the biopsies of the lesional vs. non-lesional and normal skin.
  • Snap-frozen lesional psoriatic, non-lesional psoriatic, and normal skin biopsies were divided in half. One-half of each sample was embedded in O.C.T., sectioned at 5 μM, placed on a “plus” slide, and fixed in cold acetone. The sectioned samples were incubated with primary antibodies (specific for BDCA2, CD83, CD4, STAT1, and ISG15) for 4 hours and washed with TBS. The slides were then incubated with peroxidase-labeled polymer conjugated to goat anti-mouse immunoglobulin antibody (Envision+; Dakocytomation, Carpenteria, Calif.) for 30 minutes and washed with Tris-buffered saline, pH 7.2. Detection was performed with 3,3′-diaminobenzidiine tetrahydrochloride (DAB+; DakoCytomation) as the chromogen. Slides were washed with dH2O), counterstained with hematoxylin, dehydrated and coverslipped.
  • In all psoriasis patients for which paired lesional/non-lesional samples could be evaluated, lesional skin contained increased numbers of pDCs, and/or mDCs, increased numbers of CD4+ cells, as well as the significant upregulation of STAT-1 and ISG15 protein in the epidermis and dermis compared to non-lesional biopsies. By contrast, skin biopsies from normal donors did not contain appreciable numbers of pDCs, mDCs or staining for STAT-1 and ISG15. See FIG. 44 for example immunohistochemistry slides.
    • Example 19 Immunohistochemical and Gene Expression Analysis of Biopsies from SLE Patient Skin Lesions Show Reduced Expression of Type I IFN-Induced Genes at the Protein and Transcript Level Following Treatment with MEDI-545
  • To determine whether transcripts of the top 25 type I IFN inducible genes in skin lesions of an SLE patient were neutralized by MEDI-545, biopsies from patients treated with 10 mg/kg MEDI-545 were examined. A heatmap of neutralization of the top 25 type I IFN inducible genes in skin lesions at 0 and 14 days post-treatment is provided in FIG. 58( a). All of the top 25 genes are neutralized 14 days following administration of MEDI-545. A PCA diagram of target modulation based on these top 25 type I IFN-inducible genes is provided in FIG. 58( b). The PCA diagram shows the progression of the treated SLE patient from a position directly opposite that of normal healthy donors prior to administration of MEDI-545 to a position nearing that of the healthy donors 14 days after administration of MEDI-545.
  • To determine whether levels of some of the proteins expressed from these highly overexpressed type I IFN inducible genes were also reduced by treatment with 10 mg/kg MEDI-545, immunohistochemical analyses were carried out to detect HERC5, ISG15, and IP10 protein in SLE skin lesions of patients treated with MEDI-545 and placebo. Furthermore, analysis of the cellular infiltrates (pDCs, mDCs and CD4-positive cells) was carried out to compare the number of IFN-producing cell types and inflammatory cells in the biopsies of the SLE skin lesions of MEDI-545 treated patients and placebo treated controls.
  • Snap-frozen skin lesion samples of MEDI-545 treated SLE patients and placebo treated SLE patients were divided in half. One-half of each sample was embedded in O.C.T., sectioned at 5 μM, placed on a “plus” slide, and fixed in cold acetone. The sectioned samples were incubated with primary antibodies (specific for BDCA2, CD83, CD4, IP10, and ISG15) for 4 hours and washed with TBS. The slides were then incubated with peroxidase-labeled polymer conjugated to goat anti-mouse immunoglobulin antibody (Envision+; Dakocytomation, Carpenteria, Calif.) for 30 minutes and washed with Tris-buffered saline, pH 7.2. Detection was performed with 3,3′-diaminobenzidiine tetrahydrochloride (DAB+; DakoCytomation) as the chromogen. Slides were washed with dH2O), counterstained with hematoxylin, dehydrated and coverslipped.
  • In placebo-treated SLE patients both cellular infiltrates and levels of proteins expressed from overexpressed type I IFN inducible genes increased (or worsened) over the course of 14 days. See FIG. 52 which shows an increase in (worsening of) mDC (CD83 staining) and T cell (CD4 staining) infiltration in skin lesions. FIG. 52 also shows no change in pDC (BDCA2 staining) infiltration in the placebo-treated SLE patient skin lesions over the 14 days. See also FIG. 53 which shows an increase in staining for proteins expressed from overexpressed type I IFN inducible genes HERC and IP10. No change in staining for ISG15 was observed.
  • By contrast, in patients treated with 10 mg/kg MEDI-545 levels of infiltrates and proteins expressed from overexpressed type I IFN inducible genes were decreased by varying degrees. See FIGS. 54 and 55, which provide immunohistochemical data from a first SLE patient treated with MEDI-545 and FIGS. 56 and 57, which provide immunohistochemical data from a second SLE patient treated with MEDI-545.
    • Example 20 Assay for Sensitive Detection of Type I and Type II IFNs
  • To devise an assay to sensitively detect type I and type II IFNs a construct containing the gene for a luciferase enzyme isolated from the marine organism Gaussia princeps (Targeting Systems; Santee, Calif.) under the control of an interferon-stimulated response element (ISRE) (TAGTITCACTITCCC)5 (SEQ ID NO: 2); Biomyx; San Diego, Calif.) was cloned. HEK293H cells were stably transfected with the construct and these cells were used for the IFN detection assays.
  • 25,000 of the stably transfected HEK293H cells were seeded per assay well in 50 uL of cell culture medium overnight in a CO2 incubator. The following day, patient serum samples (or normal pooled human serum spiked with the various sub-types of IFN alpha or IFN-beta, IFN-omega, IFN-gamma) were screened for detection of the various subtypes of IFN by adding 50 uL of undiluted patient or spiked serum to the assay wells containing the seeded cells (final concentration of 50% patient sera in the wells for 24 hours). IFN-induced luciferase activity was detected the following day, by observing chemiluminescence in the culture supernatants. Chemiluminescence was observed by transferring 50 uL of supernatant from the wells to a B&W Isoplate, adding 50 uL of chemiluminescent substrate, and detecting luminescence at 6 minutes. Samples generating a signal greater than 1.5-times the Negative Control wells on each assay plate are classified as Positive for IFN activity. See FIG. 59 a-d, which provide detected levels of type I and type II IFN activity in the IFN bioassay for different plates of cells treated with patient serum and spiked control serum. Each of panels a-d show that increased dose of IFN in the assay results in increased detection of IFN activity.
  • In samples where IFN activity is detected, antibodies that specifically neutralize various Type I and Type II IFNs can then be used to determine which IFN was responsible for the positive response. Anti-IFN-type specific antibodies are preincubated with either the positive serum sample(s) (in the case of MEDI 545, anti-IFN beta, anti-IFN gamma and anti-IFN omega that bind to the IFN ligand itself) or with the cells (in the case of MEDI 546 that binds to the Type I interferon receptor on the HEK293H cells) followed by addition of the samples to the cells and chemiluminescence determination as above. Spiked samples that demonstrate lower chemiluminescence following specific antibody treatment are considered to be positive for the presence of the particular IFN(s) that is neutralized by the IFN-specific antibodies.
  • FIG. 60( a) shows that increasing dose of MEDI-545 in the treated wells increasingly neutralizes of IFN activity as does increasing dose of MEDI-546 (FIG. 60( b)). FIGS. 61-63 show that IFNγ, IFNω, and IFNβ, respectively, are neutralized by antibodies specific for IFNγ, IFNω, and IFNβ, as expected.
    • Example 21 Alterations of Levels of Soluble Proteins in Serum of Lupus Patients
  • Serum was collected from SLE (n=40) and CLE (n=5) patients that had a history of at least 4 of 11 positive ACR classification criteria and demonstrated active disease manifestations at the time of sample collection. Ninety-five percent were female, with mean±SD age of 41±15 years. Seventy-six percent were currently receiving oral corticosteroids in doses ranging from 1 mg/d to 30 mg/d prednisone, with 2 SLE patients also receiving pulse intravenous steroids. Fifty-nine percent were receiving at least 1 potential disease-modifying medication other than corticosteroids. Luminex xMAP technology was used to detect changes in 89 analytes and was performed by Rules Based Medicine (see the world wide web at domain name rulesbasedmedicine.com). Results for each analyte were compared to the mean of a panel of normal human serum (n=17) and significance was determined using a paired t-test. FIG. 74 shows analytes whose levels were significantly (a) increased or (b) decreased from the mean of the normal serum (p value ≧0.05). Significant alterations in levels of cytokines chemokines, metabolic proteins, and other soluble mediators were detected in serum of lupus patients.
    • Example 22 Alternative Assay, Panomics OuantiGenePlex Assay, Verifies IFN-Induced Gene Expression Analysis Results
  • The QuantiGenePlex assay was first performed to assess the ability of QuantiGenePlex to detect 22 IFN-inducible transcripts in whole blood stimulated with IFNα2b. The 22 IFN-inducible transcripts detected by this initial QuantiGenePlex assay were selected based on their consistent up-regulation in SLE patients and are shown on the x-axis of the graphs shown in FIGS. 75 and 76.
  • Stimulation of the whole blood was performed by incubating freshly drawn Na-EDTA whole blood from 5 healthy donors with 20 IU/mL IFNα2b for 4 hours. Following this incubation, 2.5 mL of the stimulated whole blood was added to PAXgene tubes, mixed, and held overnight at room temperature. After overnight incubation, the samples were frozen at −80° C. These sample-handling procedures were selected to mimic those to be used during clinical trials.
  • PAXgene blood was analyzed for expression levels of the IFN-inducible transcripts. PAXgene blood (500 L) was pelleted and then lysed in 139 L of buffer according to the QuantiGenePlex PAXgene Blood Lysis Protocol. Processed blood from each donor was split into duplicate wells and hybridized overnight with a multiplex probe set for the 22 IFN-inducible genes. Gene expression was assessed the following day using a Luminex 100 instrument with BioRad BioPlex software. Fold changes were assessed for each individual based on the increase in signal observed between IFN-stimulated and PBS-stimulated control wells. FIG. 75 shows the fold-change in expression of each of the 22 IFN-inducible genes following IFN stimulation of each of the 5 healthy volunteer whole blood samples. The dashed line indicates a 2-fold change over PBS-stimulated control samples.
  • Whole blood of a single volunteer was further stimulated over a dose range of 0.2 to 200 IU/mL IFNα2b to determine whether upregulation of the IFN-inducible genes by IFNα2b was dose-dependent and could be detected by the QuantiGenePlex assay. For each of the 22 transcripts, a dose-dependent induction was observed. See FIG. 76, which provides the fold change in expression for each of the 22 transcripts at each IFNα2b dosage. Maximal transcript induction of nearly 100-fold was observed for RSAD2, IFIT3, and MX1. Using a 2-fold increase over baseline as a cutoff criterion, 19/22 genes were detected in samples spiked with 2 IU/mL of IFN and 5/22 were detected in samples spiked with 0.2 IU/mL IFN. Expression of SIGLEC1, LY6E, SERPING1, OAS3 and IFI27 transcripts were poorly induced by IFNα2b stimulation. These low levels of induction may indicate a lack of sensitivity of the assay to these targets or differences in gene expression between actual SLE disease (from which this panel of transcripts was chosen) and ex vivo stimulation with a single IFNα subtype, IFNα2b. Dashed line indicates a 2-fold change over PBS-stimulated control samples.
  • Next, the QuantiGenePlex assay was used to detect levels of IFN-inducible transcripts in whole blood of SLE patients. Twenty of the 22 probes from the original QuantiGenePlex kit, probes identified in FIGS. 75 and 76, were retained in the QuantiGenePlex assay used for this data analysis. Two probes, HSXIAPAF1 and GIP3, were substituted with different probes, XAF1 and IFI6. Using this panel of 22 probes, a baseline gene signature was established based on whole blood samples of ten healthy donors (blue bars in each panel). The baseline gene signature, based on the whole blood samples of the healthy donors, was compared to (1) the gene signature of an SLE patient that had detectable IFN serum activity and (2) the gene signature of an SLE patient that did not have detectable IFN serum activity. IFN serum activity was detected in the SLE patient serum samples using the assay described in Example 20. FIG. 77 a shows a comparison of the gene signature of an SLE patient (red bars) having no detectable serum IFNα activity (i.e. serum IFN activity <2.5 IU/mL) relative to the baseline gene signature (blue bars). With the exception of LAMP3, all transcript levels were detected as elevated in blood from the SLE patient with no IFN serum activity. FIG. 77 b shows a comparison of the gene signature of an SLE patient with high levels of serum IFNα activity (red bars) relative to the baseline gene signature (blue bars). All transcripts were elevated at least 2-fold in the blood of the patient with high IFN serum activity, with maximal inductions of nearly 80-fold for IFI27.
  • The data obtained from the QuantiGenePlex assay was next evaluated for its comparability to data obtained from a Fluidigm Real-Time PCR assay. QuantiGenePlex and Fluidigm methods were each used to analyze and compare transcript levels in PAXgene-preserved whole blood samples from 16 SLE patients participating in a Phase I clinical trial (of a monoclonal antibody against IFNα) relative to a composite median gene score from 10 healthy donors. Fluidigm analyses were carried out using a mixture of TAQMAN Gene Expression assays, including 4 reference control genes prepared using the TAQMAN PreAmp Master Mix Kit (Applied Biosystems). Dynamic arrays were loaded using a NanoFlex 4-IFC Controller (Fluidigm Corp) and real-time reactions were performed using a BIOMARK Real-Time PCR System. Results were analyzed using BIOMARK Real-Time PCR Analysis software. Delta-delta Cts (DDCt) were calculated using the mean of 4 reference genes (GAPDH, TFRC, b2M, and 18S) and a calibrator sample. The results obtained using whole blood samples from SLE patients demonstrated a high degree of correlation between QuantiGenePlex and Real-Time PCR approaches to detect disease-related gene expression profiles. FIG. 78 shows the (a) composite median and (b) mean-fold changes of all genes in the panels that were calculated and compared by Pearson's correlation analysis. Significant correlation was observed between QuantiGenePlex and Fluidigm when median (p=0.0002) and mean (p<0.0001) fold changes were compared for the panel of genes.
  • Data obtained from the QuantiGenePlex and Fluidigm Real-Time PCR assays were further compared in their ability to detect changes in transcript levels in SLE patient samples over the course of treatment in a clinical trial. For this comparison, SLE patient samples were collected directly into PAXgene tubes on Day 0 (pre-dose) and multiple subsequent time points following administration of a single dose of an anti-IFNα monoclonal antibody or placebo. For each sample, an aggregate median fold-change was calculated from the panel of 22 genes and compared to the pre-dose sample for that patient. FIG. 79 a shows the changes in gene signature for placebo- or antibody-treated SLE patients using Fluidigm technology. FIG. 79 b shows the changes in gene signature of the placebo- or antibody-treated SLE patients using QuantiGenePlex technology. For each non-placebo subject, a decrease in IFN gene signature is observed within 24 hours following drug administration and is consistent between Fluidigm and QuantiGenePlex. Subsequent changes in transcript levels post-administration were also highly similar between QuantiGenePlex and Fluidigm technologies.
    • Example 23 IFN-α/β-Inducible Genes Consistently Over-Expressed in Whole Blood of SLE, Myositis, and Rheumatoid Arthritis Patients
  • Overexpression of IFN-α/β-inducible genes in whole blood (WB) of SLE patients was observed as discussed in the Examples above. Affymetrix whole genome array (WGA) transcript profiling was used to quantify the abundance of over-expressed IFN-α/β-inducible genes in patients diagnosed with autoimmune disorders dermatomyositis (DM), polymyositis (PM), inclusion body myositis (IBM), and rheumatoid arthritis (RA) to see if there was a similar IFN-α/β-inducible gene over-expression pattern.
  • Whole blood from 24 healthy donors, 106 SLE, 14 IBM, 11 DM, 5 PM, and 12 RA patients was profiled using the Affymetrix human whole genome array (WGA) platform. To identify IFN-α/β-inducible probes, whole blood of healthy donors was challenged ex vivo with individual IFN-α subtypes to obtain 807 total probes. For each autoimmune disease, the abundance of these IFN-α/β-inducible probes was calculated on a patient-by-patient level. Two primary calculations were used for this evaluation: 1) a contingency table intersection between genes with a FC>3/FC≦3 and the presence/absence in the list of 807 IFN-α/β-inducible genes, and 2) a gene signature calculation based on the median fold change of the top 25 IFN-α/β-inducible genes, specific for each patient when compared to the average of 24 healthy donors. The total number of patients demonstrating this IFN-α/β-inducible gene signature for each method was summated for each autoimmune disease. Across all five autoimmune diseases, eight unique IFN-α/β-inducible genes were found to be consistently over-expressed in the WB of for all patients. These genes include: IFI44, IFI6, SAMD9L, GBP1, OAS1, BIRC4BP, SRGAP2, and RSAD2.
  • The prevalence of the overexpression of IFN-α/β-inducible genes in the WB of SLE, DM, PM, IBM, and RA patients provides evidence for type I IFN-inducible genes as pharmacodynamic markers across multiple autoimmune diseases.

Claims (13)

1-225. (canceled)
226. A method for treating myositis, comprising:
administering MEDI-546 to a subject identified as having an increase in the mRNA of at least two genes chosen from
interferon-induced protein 44 (IFI44),
interferon alpha-inducible protein 6 (IFI6),
radical S-adenosyl methionine domain containing 2 (RSAD2),
sterile alpha motif domain containing 9-like (SAMD9L),
interferon-inducible guanylate binding protein 1 (GBP1),
2′-5′-oligoadenylate synthetase 2 (OAS1),
XIAP associated factor-1 (BIRC4BP), and
SLIT-ROBO Rho GTPase activating protein 2 (SRGAP2)
in a biological sample, thereby treating the myositis.
227. The method of claim 226, wherein the increase in the mRNA of the at least two genes is an average increase in the mRNA for the at least two genes.
228. The method of claim 227, wherein the average increase is a mean increase or median increase.
229. The method of claim 226, wherein the at least two genes comprise IFI44 and RSAD2.
230. The method of claim 226, wherein an increase in the mRNA of at least three genes chosen from IFI44, IFI6, RSAD2, SAMD9L, GBP1, OAS1, BIRC4BP and SRBAP2, has been detected in the sample.
231. The method of claim 230, wherein the at least three genes comprise IFI44, IFI6 and RSAD2.
232. The method of claim 226, wherein the sample is whole blood or blood serum.
233. The method of claim 226, wherein the subject is in need of treatment of dermatomyositis (DM).
234. The method of claim 226, wherein the subject is in need of treatment of polymyositis (PM).
235. The method of claim 226, wherein the subject is in need of treatment of inclusion body myositis (IBM).
236. The method of claim 226, which comprises detecting the mRNA of the at least two genes in the sample from the subject.
237. The method of claim 236, comprising:
(i) isolating RNA from the sample;
(ii) synthesizing cDNA from the RNA;
(iii) hybridizing the cDNA with oligonucleotides that hybridize to the polynucleotides, and
(iv) amplifying the cDNA and detecting the amplified products.
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Families Citing this family (19)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
EP3779444A1 (en) 2008-01-18 2021-02-17 President and Fellows of Harvard College Methods of detecting signatures of disease or conditions in bodily fluids
DK2473636T3 (en) * 2009-09-03 2017-02-06 Medimmune Llc TYPE 1 INTERFERON DIAGNOSTICS
CN103237901B (en) 2010-03-01 2016-08-03 卡里斯生命科学瑞士控股有限责任公司 For treating the biomarker of diagnosis
JP2013526852A (en) 2010-04-06 2013-06-27 カリス ライフ サイエンシズ ルクセンブルク ホールディングス Circulating biomarkers for disease
CA2806293A1 (en) 2010-07-23 2012-01-26 President And Fellows Of Harvard College Methods of detecting autoimmune or immune-related diseases or conditions
EA201390149A1 (en) 2010-07-23 2013-08-30 Президент Энд Феллоуз Оф Гарвард Колледж METHODS FOR DETECTING DISEASES OR PATHOLOGICAL CONDITIONS USING PHAGOCYTARY CELLS
EP2596353A4 (en) 2010-07-23 2014-01-15 Harvard College Methods of detecting prenatal or pregnancy-related diseases or conditions
CN103119179A (en) 2010-07-23 2013-05-22 哈佛大学校长及研究员协会 Methods for detecting signatures of disease or conditions in bodily fluids
WO2012039161A1 (en) * 2010-09-22 2012-03-29 国立大学法人 千葉大学 Novel testing method and testing reagent for angiitis
GB201017520D0 (en) * 2010-10-15 2010-12-01 Sense Proteomic Ltd Biomarkers
US20140056889A1 (en) * 2011-04-26 2014-02-27 Genentech, Inc. Compositions and method for treating autoimmune diseases
AU2013204776A1 (en) * 2011-04-26 2013-05-09 Genentech, Inc. Compositions and method for treating autoimmune diseases
WO2014079966A1 (en) * 2012-11-23 2014-05-30 Medizinische Hochschule Hannover Analysis for adult-onset still's disease
NZ771629A (en) 2013-03-09 2022-12-23 Harry Stylli Methods of detecting cancer
WO2014164362A1 (en) 2013-03-09 2014-10-09 Harry Stylli Methods of detecting prostate cancer
US10626464B2 (en) 2014-09-11 2020-04-21 Cell Mdx, Llc Methods of detecting prostate cancer
MX2020002070A (en) 2017-08-22 2020-03-24 Sanabio Llc Soluble interferon receptors and uses thereof.
WO2020084591A1 (en) * 2018-10-26 2020-04-30 Janssen Biotech, Inc. Type i interferon signatures and methods of use
CN110747190B (en) * 2019-11-27 2021-03-09 浙江华睿生物技术有限公司 Maleic acid hydratase mutant and application thereof

Family Cites Families (29)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
JPS60500864A (en) 1983-02-04 1985-06-06 ワドリ、テクナラジズ、インコーパレイティド Production and characterization of hybridoma antibodies specific for common determinants present between closely related but distinct proteins
GB8303165D0 (en) 1983-02-04 1983-03-09 Secher D S Monoclonal antibody
DE3306060A1 (en) 1983-02-22 1984-08-23 Boehringer Ingelheim International GmbH, 6507 Ingelheim NEW IMMUNGLOBULIN-PRODUCING HYBRID CELL LINES, THEIR USE AND METHOD FOR THE PRODUCTION THEREOF
US4885166A (en) 1985-06-11 1989-12-05 Ciba-Geigy Corporation Hybrid interferons
US5143854A (en) 1989-06-07 1992-09-01 Affymax Technologies N.V. Large scale photolithographic solid phase synthesis of polypeptides and receptor binding screening thereof
US5744101A (en) 1989-06-07 1998-04-28 Affymax Technologies N.V. Photolabile nucleoside protecting groups
FR2692168B1 (en) 1992-06-16 1995-03-24 Centre Nat Rech Scient Preparation and use of new dispersible colloidal systems based on cyclodextrin, in the form of nanospheres.
US5888511A (en) * 1993-02-26 1999-03-30 Advanced Biotherapy Concepts, Inc. Treatment of autoimmune diseases, including AIDS
JP4285766B2 (en) 1994-03-23 2009-06-24 オハイオ ユニバーシティ Deliver to dense nucleic acids and cells
US6077835A (en) 1994-03-23 2000-06-20 Case Western Reserve University Delivery of compacted nucleic acid to cells
US5972901A (en) 1994-03-23 1999-10-26 Case Western Reserve University Serpin enzyme complex receptor--mediated gene transfer
AU749032B2 (en) 1997-06-13 2002-06-20 Johns Hopkins University, The Therapeutic nanospheres
US20050008683A1 (en) * 2000-06-29 2005-01-13 Becton Dickinson And Company Method for delivering interferons to the intradermal compartment
US20040265874A1 (en) * 2000-10-17 2004-12-30 Bio-Rad Laboratories, Inc. Pattern recognition method for diagnosis of systemic autoimmune diseases
MXPA03006100A (en) * 2001-01-09 2005-02-14 Baylor Reserch Inst Methods for treating autoimmune diseases in a subject and in vitro diagnostic assays.
US7087726B2 (en) 2001-02-22 2006-08-08 Genentech, Inc. Anti-interferon-α antibodies
EP1463761A1 (en) * 2001-11-30 2004-10-06 Innogenetics N.V. Therapeutic use of antibodies and fragments thereof binding primate ifn-gamma
EP2329827A3 (en) * 2002-11-21 2011-07-13 Bayhill Therapeutics, Inc. Methods and immune modulatory nucleic acid compositions for preventing and treating disease
EP1670931A2 (en) * 2003-09-05 2006-06-21 GTC Biotherapeutics, Inc. Method for the production of fusion proteins in transgenic mammal milk
ES2641831T3 (en) * 2003-12-10 2017-11-14 E. R. Squibb & Sons, L.L.C. Antibodies against interferon alfa and their uses
BRPI0607490A2 (en) * 2005-02-10 2009-09-08 Baylor Res Inst alpha interferon monoclonal antibodies and methods for use
US20070117105A1 (en) * 2005-05-12 2007-05-24 Crow Mary K Interferon assay
US20070065844A1 (en) * 2005-06-08 2007-03-22 Massachusetts Institute Of Technology Solution-based methods for RNA expression profiling
US20070092890A1 (en) * 2005-08-05 2007-04-26 Genentech, Inc. Methods and compositions for detecting autoimmune disorders
US7608395B2 (en) * 2005-09-15 2009-10-27 Baylor Research Institute Systemic lupus erythematosus diagnostic assay
NZ597082A (en) * 2005-10-13 2013-11-29 Human Genome Sciences Inc Methods and Compositions for Use in Treatment of Patients with Autoantibody Positive Diseases
US20100143372A1 (en) * 2006-12-06 2010-06-10 Medimmune, Llc Interferon alpha-induced pharmacodynamic markers
US20110287022A1 (en) * 2008-06-20 2011-11-24 Medlmmune, Llc Interferon alpha-induced pharmacodynamic markers
DK2473636T3 (en) * 2009-09-03 2017-02-06 Medimmune Llc TYPE 1 INTERFERON DIAGNOSTICS

Non-Patent Citations (1)

* Cited by examiner, † Cited by third party
Title
HighBeam Business (2004) *

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