AU2014200127A1 - Interferon alpha-induced pharmacodynamic markers - Google Patents

Abstract

The present invention encompasses type-I IFN and IFNa-induced PD marker expression profiles, kits, and methods for identifying such IFNa-induced PD marker 5 expression profiles. The type-I IFN and IFNa-induced PD marker expression profiles may also be used in, for example, methods of treating patients having a type-I IFN or IFNa mediated disorder, methods of monitoring disease progression of patients receiving treatment with a therapeutic agent that binds to and modulates IFNa activity, identifying patients as candidates to receive a therapeutic that binds to and neutralizes IFNc activity, and in 10 diagnosing or providing a prognosis to patients having IFNa-induced disorders. C:\poi\word\SPEC-854193[1 ].docx

Description

1 INTERFERON ALPHA-INDUCED PHARMACODYNAMIC MARKERS The present application is a divisional application from Australian Patent Application number 2007327995, the entire disclosure of which is incorporated herein by reference. FIELD OF THE INVENTION 5 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 10 The present invention encompasses PD markers that are induced by IFNa. The PD markers can be used in methods of treating patients with a therapeutic agent that binds to and modulates IFNa activity, methods that identify patients as candidates for a therapeutic agent that binds to and modulates IFNa activity, methods of diagnosing a patient as having a disorder associated with increased IFNa levels, methods of monitoring disease progression of 15 a patient receiving treatment with a therapeutic agent that binds to and modulates IFNa activity, and methods of identifying a candidate therapeutic for treating IFNa-mediated disorders SUMMARY OF THE INVENTION 20 One embodiment of the invention encompasses a method of identifying a patient as a candidate for a therapeutic agent that binds to and modulates IFNa activity. Presence or absence of an IFNa-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 25 having a type I IFN or IFNa-mediated disease or disorder. An agent that binds to and modulates type I IFN or IFNa activity is administered to the patient. The agent neutralizes a type I IFN or IFNa-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 IFNa PD 30 marker profile. An agent that binds to and modulates type I IFN or IFNa activity is administered to the patient. The agent neutralizes the type I IFN or IFNa-inducible PD marker expression profile of the patient. A further embodiment of the invention encompasses a method of neutralizing a type I IFN or IFNa-inducible PD marker expression profile in a patient in need thereof. An agent C:\poi\word\SPEC-8541 93[1].dox 2 that binds to and modulates type I IFN or IFNa activity is administered to the patient. The agent neutralizes the type I IFN or IFNa-inducible PD marker expression profile of the patient. Another embodiment of the invention encompasses a method of diagnosing a patient as 5 having a disorder associated with increased IFNa levels. Presence or absence of an IFNa 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 IFNa activity. A first IFNa-inducible PD marker expression profile is obtained in a 10 first sample from the patient. A therapeutic agent that binds to and modulates IFNa activity is administered to the patient. A second IFNa-inducible PD marker expression profile is obtained from a second sample from the patient. The first and the second IFNa-inducible PD marker expression profiles are compared. Yet another embodiment of the invention encompasses a method of identifying a 15 candidate therapeutic for treating IFNa-mediated disorders. Cells comprising an IFNa inducible PD marker expression profile are contacted with an agent. Presence or absence of a change in the IFNa-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. 20 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. 25 BRIEF DESCRIPTION OF THE FIGURES Figure 1: TaqMan qPCR IF144 gene expression analysis of IFNa-stimulated whole blood of healthy donors. Figure 2: TaqMan qPCR IRF2 gene expression analysis of IFNa-stimulated whole blood of healthy donors. 30 Figure 3: TaqMan qPCR RSAD2 gene expression analysis of IFNa-stimulated whole blood of healthy donors. C:\poi\word\SPEC-8541 93[1].dox 3 Figure 4: TaqMan qPCR G1P3 gene expression analysis of IFNa-stimulated whole blood of healthy donors. Figure 5: TaqMan qPCR HERC5 gene expression analysis of IFNa-stimulated whole blood of healthy donors. 5 Figure 6: MEDI-545 neutralization of RAB8B gene expression induced by IFN-a in whole blood of healthy donors. Figure 7: MEDI-545 neutralization of IRF7 gene expression induced by IFN-a in whole blood of healthy donors. Figure 8: MEDI-545 neutralization of MARCKS gene expression induced by IFN-a in whole 10 blood of healthy donors. Figure 9: MEDI-545 neutralization of IL6ST gene expression induced by IFN-a in whole blood of healthy donors. Figure 10: MEDI-545 neutralization of Ly6E gene expression induced by IFN-a in whole blood of healthy donors. 15 Figure 11: MEDI-545 neutralization of IFIT3 gene expression induced by IFN-a in whole blood of healthy donors. Figure 12: MEDI-545 neutralization of IFIT1 gene expression induced by IFN-a in whole blood of healthy donors. Figure 13: MEDI-545 neutralization of HERC5 gene expression induced by IFN-a in whole 20 blood of healthy donors. Figure 14: MEDI-545 neutralization of OAS 1 gene expression induced by IFN-a in whole blood of healthy donors. Figure 15: MEDI-545 neutralization of OAS3 gene expression induced by IFN-a in whole blood of healthy donors. 25 Figure 16: MEDI-545 neutralization of RSAD2 gene expression induced by IFN-a in whole blood of healthy donors. Figure 17: Ex vivo stimulation in whole blood identifies genes inducible by type I IFN. Figure 18: MEDI-545 neutralization of top 25 type I IFN inducible genes in individual lupus patients' whole blood. C:\poi\word\SPEC-8541 93[1].docx 4 Figure 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. Figure 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. 5 Figure 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. Figure 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. Figure 23: MEDI-545 neutralizes the top 25 most upregulated type I IFN inducible probe sets 10 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. Figure 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 15 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. Figure 25a and 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. 20 Figure 26a and 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. Figure 27: Type-I IFNa subtypes are upregulated in the whole blood of individual lupus patients. 25 Figure 28: Distribution of average fold-change of top 25 type I IFN inducible probe sets in whole blood of individual lupus patients. Figure 29a-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; (b) SLE patients not having a 30 type I IFN gene signature at 14 days following MEDI-545 treatment; and (c) SLE patients 14 C:\poi\word\SPEC-8541 93[1].docx 5 days following treatment with placebo. Genes highlighted in yellow are genes identified as having a type-I IFN signature. Figure 30: Hierarchical clustering of 1384 probe sets differentially regulated by IFNa subtypes, IFN3, IFNy, and TNFa in ex vivo stimulated whole blood. Each row corresponds to 5 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 10 change. Figure 3 1a-3 1b: 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 IFNa subtypes, IFN3, IFNy, and TNFa. b. Heatmap of the relative expression of the same 25 probe sets compared to no-treatment control in keratinocyte ex vivo challenged with 15 IFNa2a, IFN3, IFNy, and TNFa. 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. Figure 32a-32c: The distribution of the average (a) and median (b) fold change of the top 25 20 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. Figure 33a-33d: 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 25 (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; 30 0.0002, <0.00001. Figure 34a-34b: (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 C:\poi\word\SPEC-8541 93[1].docx 6 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 5 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 10 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). Figure 35: Overexpression of selected type-I IFN inducible genes in 18 pairs of lesional and 15 non-lesional skin from 18 psoriatic patients based on taqMan QRT-PCR assays using Fluidigm's BioMark T M 48.48 dynamic array. Figure 36a-36b: 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) 20 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. Figure 37a-37d: Comparison of taqMan QRT-PCR based assay using BioMarkTM 48.48 dynamic array and Affymetrix@ genechip results for selected type-I IFN inducible genes 25 ISG15 and MX1. Figure 38: TaqMan QRT-PCR validation of Affymetrix@ genechip results of overexpression of type-I IFN inducible genes IFI27 and CXCL10. Figure 39a-39f: Ex vivo stimulation of normal keratinocytes with leukocyte IFN and IFNa2a and dose-dependent neutralization of type-I IFN induced genes by IFNa antibody. (a) 30 neutralization of ISG15 overexpression in response to 350 I.U./mL IFNa2a, (b) neutralization of ISG15 overexpression in response to 150 I.U./mL leukocyte IFN, (c) neutralization of USP18 overexpression in response to 350 I.U./mL IFNa2a, (d) neutralization of USP18 C:\poi\word\SPEC-8541 93[1].docx 7 overexpression in response to 150 I.U./mL leukocyte IFN, (e) neutralization of IFIT2 overexpression in response to 350 I.U./mL IFNa2a, 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 IFNa 5 antibody is normalized to 1. Figure 40a-40c: Relative expression of mRNA and median fold changes of type-I IFNa subtypes (Figure 40a), other members of the type-I IFNs (Figure 40b), and IFNa receptors (Figure 40c) 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 10 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 15 to healthy normal skin (listed in pairs) are as follows: IFNal, 0.303, <0.001; IFNa2, 0.389, 0.072; IFNa5, <0.001, 0.002; IFNa6, 0.664, 0.093; IFNa7, 0.586, 0.077; IFNa8, 0.430, 0.049; IFNaI4, 0.224, 0.049; IFNaI7, 0.552, 0.0203; IFNa2l, 0.113, 0.003; IFN3, 0.255, 0.022; IFNK, 0.03, <0.001; IFNo, 0.516, 0.049; IFNAR1, 0.192, <0.001; IFNAR2, <0.001, <0.001, respectively. 20 Figure 41: Relative expression of mRNA and median fold changes of IFNy, TNFa, and IFNy 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 25 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: IFNy, 0.02, <0.001; IFNGR1, <0.001, <0.001; IFNGR2, <0.001, <0.001; TNFa, <0.001, <0.001, respectively. 30 Figure 42: A Venn diagram illustrating both the number of probe sets that are altered by type I IFN, IFNy, and TNFa 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 C:\poi\word\SPEC-8541 93[1].docx 8 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. Figure 43a and 43b: Co-overexpression type-I IFN, type-II IFN, and TNF-inducible genes in 5 lesional/non-lesional skin of psoriatic patients based on Affymetrix genechip@ results. The type-I IFN, type-II IFN, and TNFa 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, IFNy, and TNFa inducible genes in the lesional skin shows strong correlation. (b) the 10 number of type I IFN, IFNy, and TNFa inducible genes in the lesional skin were significantly different amongst pairwise comparisons. Figure 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. 15 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. 20 Figure 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 25 common to both comparisons. Figure 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, 30 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. C:\poi\word\SPEC-8541 93[1].dox 9 Figure 47a and 47b: Table providing fold change (fc; log2 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 log2 transformed fold change and q values of these genes when comparing non-lesional skin with healthy normal skin controls. Type I IFN 5 inducible genes are listed in bold font. Figure 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. Figure 49: Probe sets identified as IFNy inducible by overlap in Figure 42. 10 Figure 50: Probe sets identified as TNFa inducible by overlap in Figure 42. Figure 51: Probe sets identified as type I IFN inducible by overlap in Figure 42. Figure 52: Immunohistochemical analysis of biopsies from skin lesions of a placebo-treated SLE patient to detect pDC, mDC, and T cell infiltrates. Figure 53: Immunohistochemical analysis of biopsies from skin lesions of a placebo-treated 15 SLE patient to detect HERC5, ISG15, and IP10 proteins, proteins expressed from type I IFN induced genes. Figure 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. Figure 55: Immunohistochemical analysis of biopsies from skin lesions of an SLE patient 20 treated with 10 mg/kg MEDI-545 to detect HERC5, ISG15, and IP10 proteins, proteins expressed from type I IFN-induced genes. Figure 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. Figure 57: Immunohistochemical analysis of biopsies from skin lesions of an SLE patient 25 treated with 10 mg/kg MEDI-545 to detect HERC5, ISG15, and IP10 proteins, proteins expressed from type I IFN-induced genes. Figure 58a and 58b: 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. 30 Figure 59a-d: Detection of type I and type II IFN activity in an IFN bioassay. C:\poi\word\SPEC-8541 93[1].docx 10 Figure 60a and 60b: Detection of MEDI-545 (a) and MEDI-546 (b)-mediated neutralization of IFNa activity in the IFN bioassay. Figure 61: Detection of anti-IFNy-mediated neutralization of IFNy activity in the IFN bioassay. Figure 62: Detection of anti-IFNo-mediated neutralization of IFNo activity in the IFN 5 bioassay. Figure 63: Detection of anti-IFNp -mediated neutralization of IFNs activity in the IFN bioassay. Figure 64: Heat map showing modulation of gene expression in whole blood from healthy donors ex vivo stimulated with IFNy, TNFa, or IFNa/p. Negative control (NT). 10 Figure 65: Type I IFN-inducible genes were among the most upregulated genes in whole blood of SLE patients. Figure 66: IFNy, IFNo, IFNAR1 and IFNAR2 mRNAs are upregulated in whole blood of lupus patients. Figure 67: Heat map showing modulation of gene expression in healthy donor PBMCs ex vivo 15 stimulated with lupus patient serum. Figure 68a and 68b: (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. Figure 69: Confirmation of overexpression of selected type-I IFN inducible genes in lupus 20 patients based on taqMan QRT-PCR assays using Fluidigm's BioMark T M 48.48 dynamic array. Figure 70a and 70b: (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 25 hour co-incubation. Figure 71a and 71b: The majority of genes neutralized by an anti-IFNa 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-IFNa 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 30 and represented (b) in bar graphs. C:\poi\word\SPEC-8541 93[1].docx 11 Figure 72a and 71b: Provides the (a) type I IFN genes and (b) non-type I IFN genes that were upregulated and neutralized by an anti-IFNa 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. 5 Figure 73: Provides pathways and cell processes neutralized by an anti-IFNa Ab 18 hours following co-incubation of SLE patient serum and healthy human PBMCs. Figure 74a and 74b: Detection of (a) increased and (b) decreased levels of specific proteins in serum of lupus patients. Figure 75: QuantiGenePlex 1.0 analysis of IFN-inducible gene signatures from whole blood 10 of 5 healthy donors stimulated with 20 IU/mL IFNa2b. Figure 76: Dose-dependent changes in gene expression in blood from a single healthy donor treated with multiple concentrations of IFNa2b. Figure 77: Detection of IFN-inducible transcripts in PAXgene-preserved whole blood samples from SLE subjects with and without detectable serum IFNa activity. 15 Figure 78: Correlation between QuantiGenePlex and Fluidigm technologies in SLE PAXgene-preserved whole blood samples. Figure 79: Longitudinal testing of SLE samples following administration of an anti-IFNa monoclonal antibody: comparison of QuantiGenePlex 2.0 and Fluidigm technologies. Figure 80: Representative heat map visualizing the (in descending order) overexpression of 20 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. 25 Figure 81a-81c: 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 C:\poi\word\SPEC-8541 93[1].docx 12 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 5 sample (blue dots, healthy normals; red dots, SLE patients). IFN=interferon; PCA=principal components analysis; SLE=systemic lupus erythematosus. Figure 82: Relative expression of mRNAs and median fold changes (horizontal bars) of TNF a, IFN-y, and IFN-y 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 10 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. Figure 83a-83c: 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 15 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 20 genome array. The relative overexpression of 21 type I IFN-inducible genes in 2 SLE patients is shown via microarray (left) and TaqMan (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. 25 Figure 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 30 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. C:\poi\word\SPEC-8541 93[1].docx 13 Figure 85a-85c: 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 5 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; 10 SLE=systemic lupus erythematosus. Figure 86: Dose-dependent neutralization of 21 upregulated IFN-a/p-inducible genes in SLE patients by MEDI-545. Figure 87a and 87b: Heatmap (a) and PCA (b) showing neutralization of 21 upregulated IFN a/p-inducible genes in whole blood of an SLE patient treated with 30 mg/kg MEDI-545 (0, 1, 15 4, 7, and 14 days post-dose). Figure 88a and 88b: PCA plots prepared using the 21 upregulated IFN-a/p-inducible probe sets do not show IFN signature neutralization in placebo-treated patients. Figure 89: Neutralization of the 21 upregulated IFN-a/p-inducible probe sets in patients treated with 0.3, 1.0, 3.0, 10.0, and 30.0 mg/kg MEDI-545. 20 Figure 90: Methodology for calculating target neutralization for Figure 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 IFNa-inducible disease, disorder, or condition. The patient may have the disease, disorder, 25 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 IFNa-inducible PD marker expression 30 profile. The type I IFN or IFNa-inducible PD marker expression profile may be a strong C:\poi\word\SPEC-8541 93[1].dox 14 profile, a moderate profile, or a weak profile. The type I IFN or IFNa-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 IFNa-inducible PD marker expression profile of the patient, (e.g., the fold increase in expression of upregulated type I IFN or IFNa-inducible PD 5 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 IFNa-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 IFNa-inducible PD marker expression profile may comprise 10 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 15 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 IFNa-inducible PD 20 marker expression profile of the patient may be MX1, LY6E, IFI27, OAS1, IFIT1, IF16, IF144L, ISG15, LAMP3, OASL, RASD2, and IF144. The genes or genes detected by the probes may include IF144, IF127, IF144L, DNAPTP6, LAMP3, LY6E, RSAD2, HERC5, IF16, ISG15, OAS3, SIGLEC1, OAS2, USP18, RTP4, IFIT1, MX1, OAS1, EPSTI1, PLSCR1, and IFRG28. 25 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 30 any at least 28, or any at least 29, or any at least 30 of LAMP3, DNAPTP6, FLJ31033, HERC6, SERPING1, EPSTl1, RTP4, OASL, FBXO6, IFIT2, IF144, OAS3, BATF2, ISG15, IRF7, RSAD2, IF135, OAS1, LAP3, IFIT1, IFIT5, PLSCR1, IF144L, MS4A4A, GALM, UBE2L6, TOR1B, SAMD9L, HERC5, TDRD7, TREX1, PARP12, and AXUD1. C:\poi\word\SPEC-8541 93[1].docx 15 The type I IFN or IFNa-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 Figure 72. The 5 type I IFN or IFNa-inducible PD marker expression profile may include upregulation of all the genes identified in Table 24. The type I IFN or IFNa-inducible PD marker expression profile may include upregulation of the genes identified in figure 72 A or figure 72b, or figure 72a and figure 72b. The patient comprising the type I IFN or IFNa-inducible PD marker expression profile 10 may further comprise downregulated type I IFN or IFNa 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. 15 The patient comprising the type I IFN or IFNa-inducible PD marker expression profile may further comprise upregulation of expression of any number of IFNa or type-I IFN subtypes. The IFNa 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 IFNa or type-I IFN subtypes. These subtypes may 20 include IFNal, IFNa2, IFNa4, IFNa5, IFNa6, IFNa7, IFNa8, IFNa1O, IFNa14, IFNa17, IFNa21, IFNP, or IFNo. The patient may comprise upregulation of expression of IFN subtypes IFNa1I, IFNa2, IFNa8, and IFNa14. 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 25 expression of any number of IFNa or type-I IFN subtypes. The IFNa 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 IFNa or type-I IFN subtypes. These subtypes may include IFNa1, IFNa2, IFNa4, IFNa5, IFNa6, IFNa7, IFNa8, IFNa10, IFNa14, IFNa17, IFNa21, IFNP, or IFNo. These subtypes may 30 include IFNa1, IFNa2, IFNa8, and IFNa 14. The patient comprising the type I IFN or IFNa-inducible PD marker expression profile may further comprise upregulation of expression of IFNa receptors, either IFNAR1 or IFNAR2, or both, or TNFa, or IFNy, or IFNy receptors (either IFNGR1, IFNGR2, or both IFNGR1 and IFNGR2). The patient may simply be identified as one who comprises C:\poi\word\SPEC-8541 93[1]. docx 16 upregulation of expression of IFNa receptors, either IFNAR1 or IFNAR2, or both, or TNFa, or IFNy, or IFNy receptors (either IFNGR1, IFNGR2, or both IFNGR1 and IFNGR2). The upregulation or downregulation of the type I IFN or IFNa-inducible PD markers in the patient's expression profile may be by any degree relative to that of a sample from a 5 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 10 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 15 500% that of the control. The type I IFN subtype may be any one of IFNa1I, IFNa2, IFNa4, IFNa5, IFNa6, IFNa7, IFNa8, IFNa1O, IFNa14, IFNa17, IFNa21, IFNP, or IFNo. The type I IFN subtypes may include all of IFNa1, IFNa2, IFNa8, and IFNa14. 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 20 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-Ira, 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, o22, 23, 24, 25, or 26 of these proteins in serum. 25 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 30 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 C:\poi\word\SPEC-8541 93[1].docx 17 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; 5 (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, 10 alpha/beta subcomplex 1, 8 kDa; (k) NudE nuclear distribution gene E homolog 1 (A. nidulans); (1) 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, 15 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 20 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 entitled "Auto-antibody markers of autoimmune disease" to be filed November 6, 2007 (for example, but not limited to, those described on 25 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 IFNa-inducible disease, disorder, or condition is any that exhibits a 30 type I IFN or an IFNa 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, C:\poi\word\SPEC-8541 93[1].docx 18 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. 5 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 April 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 10 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 = 15 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, 20 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. 25 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 30 type I IFN or an IFNa-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 IFNa activity. The therapeutic agent may C:\poi\word\SPEC-8541 93[1].docx 19 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 IFNa. For instance, the antibody may be specific for any one of 5 IFNa1, IFNa2, IFNa4, IFNa5, IFNa6, IFNa7, IFNa8, IFNa10, IFNa14, IFNa17, IFNa21, IFNP, or IFNo. 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 IFNa subtypes. If the antibody is specific for more than one type I IFN subtype, the antibody may be specific for IFNal, IFNa2, IFNa4, IFNa5, IFNa8, IFNa10, and 10 IFNa21; or it may be specific for IFNal, IFNa2, IFNa4, IFNa5, IFNa8, and IFNa10; or it may be specific for IFNa1, IFNa2, IFNa4, IFNa5, IFNa8, and IFNa21; or it may be specific for IFNa1, IFNa2, IFNa4, IFNa5, IFNa10, and IFNa21. Antibodies specific for type I IFN or IFNa include MEDI-545, any biologic or antibody other than MEDI-545, antibodies described in U.S. patent applications 11/009,410 filed December 10, 2004 and 11/157,494 filed June 20, 15 2005, 9F3 and other antibodies described in U.S. Patent 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. Patent 4,902,618), 144 BS (U.S. Patent 4,885,166), and EBI-1, EBI-2, and EBI-3 (EP 119476). A therapeutic agent that modulates IFNa activity may neutralize IFNa activity. One 20 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 25 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 30 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. C:\poi\word\SPEC-8541 93[1].docx 20 In the methods of treatment a second agent other than the agent that binds to modulates IFNa 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 5 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 TNFa, such as, Enbrel, Remicade, and Humira. 10 Treatment with the agent may result in neutralization of the type I IFN or IFNa inducible profile. Treatment with the agent may result in a decrease in one or more symptoms of the type I IFN or an IFNa-mediated disease or disorder. Treatment with the agent may result in fewer flare-ups related to the type I IFN or an IFNa-mediated disease or disorder. Treatment with the agent may result in improved prognosis for the patient having the type I 15 IFN or an IFNa-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 IFNa-mediated disease or disorder. 20 The agent that binds to and modulates type I IFN or IFNa activity may neutralize a type I IFN or IFNa-inducible profile. Neutralization of the type I IFN or IFNa-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 25 up-regulated by type I IFN or IFNa. The genes upregulated by type I IFN or IFNa 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 IFNa-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%, 30 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 IFNa-inducible profile. Alternatively, neutralization of the type I IFN or IFNa-inducible profile refers to a reduction of expression of C:\poi\word\SPEC-8541 93[1].dox 21 up-regulated type I IFN or IFNa-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 IFNa-inducible genes in a control sample. If the agent that binds to and 5 modulates type I IFN or IFNa activity is a biologic agent, such as an antibody, the agent may neutralize the type I IFN or IFNa 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 IFNa-inducible profile may be increased expression 10 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 IFNa. The genes whose expression is reduced by type I IFN or IFNa may be any group of genes in Table 30. Neutralization of down-regulated genes in a type I IFN or 15 IFNa-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% 20 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 IFNa-inducible profile. Alternatively, neutralization of the type I IFN or IFNa-inducible profile refers to an increase in expression of type I IFN or IFNa-inducible genes to within at most 50%, at most 45%, at most 40%, at most 25 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 IFNa inducible (downregulated) genes in a control sample. If the agent that binds to and modulates type I IFN or IFNa activity is a biologic agent, such as an antibody, the agent may neutralize the type I IFN or IFNa profile at doses of 0.3 to 30 mg/kg, 0.3 to 10 mg/kg, 0.3 to 3 mg/kg, 30 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 IFNa activity may further or alternatively neutralize expression of one or more type I IFN or IFNa subtypes. The IFNa or type-I IFN subtypes may include any more than one, more than two, more than three, more C:\poi\word\SPEC-8541 93[1].docx 22 than four, more than five, more than six, more than seven, more than eight, more than nine, or more than ten IFNa or type-I IFN subtypes. These subtypes may include IFNa1, IFNa2, IFNa4, IFNa5, IFNa6, IFNa7, IFNa8, IFNa1O, IFNa14, IFNa17, IFNa21, IFNP, or IFNo. These subtypes may include all of IFNa1, IFNa2, IFNa8, and IFNa14. Alternatively, these 5 subtypes may include IFNal, IFNa2, IFNa4, IFNa5, IFNa8, IFNa1O, IFNa21. Neutralization of the IFNa 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 10 least seven, at least eight, or at least ten of the subtypes. Neutralization of the IFNa or type-I IFN subtypes may be a reduction in expression of IFNa 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 IFNa or type I IFN subtypes in a control sample. If the 15 agent that binds to and modulates IFNa activity or type I IFN activity is a biologic agent, such as an antibody, the agent may neutralize the IFNa 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 IFNa activity may further or 20 alternatively neutralize expression of IFNa receptors, either IFNAR1 or IFNAR2, or both, or TNFa, or IFNy, or IFNy receptors (either IFNGR1, IFNGR2, or both IFNGR1 and IFNGR2). Neutralization of expression of IFNa receptors, either IFNAR1 or IFNAR2, or both, or TNFa, or IFNy, or IFNy 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 25 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 IFNa receptors, either IFNAR1 or IFNAR2, or TNFa, or IFNy, or IFNy receptors (either IFNGR1, IFNGR2, or both IFNGR1 and IFNGR2) is a reduction of 30 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 IFNa activity is a biologic agent, such as an antibody, the agent may neutralize expression of IFNa receptors IFNAR1 or IFNAR2, or TNFa, or C:\poi\word\SPEC-8541 93[1].docx 23 IFNy, or IFNy 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 IFNa activity may further or 5 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, 10 ferritin, IL-10, IL-12p70, IL-16, IL-18, IL-lra, 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 15 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 IFNa activity is a biologic agent, such as an 20 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-lra, 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, 25 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 IFNa activity may further or alternatively reduce number or level of auto-antibodies that bind to any one, any at least 2, any 30 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); C:\poi\word\SPEC-8541 93[1].docx 24 (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. 5 nidulans); (1) 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 10 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) 15 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 November 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 20 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 IFNa activity is a biologic agent, such as an antibody, the agent may reduce number or level or auto-antibodies 25 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 IFNa activity may not neutralize expression of genes that are not included in an interferon-inducible signature or PD marker profile. 30 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. C:\poi\word\SPEC-8541 93[1].docx 25 IFNa-inducible PD marker expression profiles may include up-regulated expression or activity of genes in cells exposed to elevated IFNa 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 5 encoded by a gene. The expression or activity of the genes may be up-regulated as a direct or indirect response to IFNa. The up-regulated expression or activity of any gene detected in a sample, by probes, or by probes in kits in an IFNa-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 10 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 IFNa in culture. All of the genes in the IFNa 15 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 IFNa-inducible PD marker expression profile may be at least 5%, at 20 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 least97%, 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 IFNa in culture. All of the genes in the IFNa 25 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 IFNa-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 30 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 Figures 72, 74, 75, or 77. The genes included in IFNa-inducible PD C:\poi\word\SPEC-8541 93[1].docx 26 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 IFNa-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 5 and/or 28 and/or 30 and/or 31 and/or any of the genes identified in Figures 72, 74, 75, or 77. The genes included in the IFNa-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 10 26 and/or 28 and/or 30 and/or 31 and/or any of the genes identified in Figures 72, 74, 75, or 77. The IFNa-inducible PD markers in an expression profile may include any at least 5 genes such as, for example: MX1, LLY6E, IF127, OAS1, IFIT1; or MX1, LLY6E, IF127, OAS1, IF16; or MX1, LLY6E, IF127, OAS1, IF144L; or MX1, LLY6E, IF127, OAS1, ISG15; 15 or MX1, LLY6E, IF127, OAS1, LAMP3; or MX1, LLY6E, IF127, OAS1, OASL; or MX1, LLY6E, IF127, OAS1, RSAD2; or MX1, LLY6E, IF127, OAS1, IF144; or MX1, LLY6E, IF127, OAS1, IFIT2; or MX1, LLY6E, IF127, OAS1, OAS3; or MX1, LLY6E, IF127, OAS1, USP18; or MX1, LLY6E, IF127, OAS 1, SIGLECl; or MX1, LLY6E, IF127, OAS 1, HERC5; or MX1, LLY6E, IF127, OAS 1, DNAPTP6; or MX1, LLY6E, IF127, OAS 1, LOC129607; or 20 MX1, LLY6E, IF127, OAS1, EPST1l; or MX1, LLY6E, IF127, OAS1, BIRC4BP; or MX1, LLY6E, IF127, OAS1, SIGLEC1; or MX1, LLY6E, IF127, OAS1, gene detected by probe 229450_at; or MX1, LLY6E, IF127, OAS1, gene detected by probe 235276_at; or LLY6E, IF127, OAS 1, IFIT1, IF16; or LLY6E, IF127, OAS 1, IFIT 1, IF144L; or LLY6E, IF127, OAS 1, IFIT1, ISG15; or LLY6E, IF127, OAS1, IFIT1, LAMP3; or LLY6E, IF127, OAS1, IFIT1, 25 OASL; or LLY6E, IF127, OAS1, IFIT1, RSAD2; or LLY6E, IF127, OAS1, IFIT1, IF144; or LLY6E, IF127, OAS1, IFIT1, IFIT2; or LLY6E, IF127, OAS1, IFIT1, OAS3; or LLY6E, IF127, OAS1, IFIT1, USP18; or LLY6E, IF127, OAS1, IFIT1, SIGLECl; or LLY6E, IF127, OAS 1, IFIT1, HERC5; or LLY6E, IF127, OAS 1, IFIT1, DNAPTP6; or LLY6E, IF127, OAS 1, IFIT1, LOC129607; or LLY6E, IF127, OAS1, IFIT1, EPST1l; or LLY6E, IF127, OAS1, 30 IFIT1, BIRC4BP; or LLY6E, IF127, OAS1, IFIT1, SIGLECl; or LLY6E, IF127, OAS1, IFIT1, gene detected by probe 229450_at; or LLY6E, IF127, OAS 1, IFIT1, gene detected by probe 235276_at; or IF127, OAS1, IFIT1, IF16, IF144L, ISG15; or IF127, OAS1, IFIT1, IF16, LAMP3; or IF127, OAS 1, IFIT1, IF16, OASL; or IF127, OAS 1, IFIT 1, IF16, RSAD2; or IF127, OAS 1, IFIT1, IF16, IF144; or IF127, OAS 1, IFIT1, IF16, IFIT2; or IF127, OAS 1, IFIT1, IF16, C:\poi\word\SPEC-8541 93[1].docx 27 OAS3; or IF127, OAS1, IFIT1, IF16, USP18; or IF127, OAS1, IFIT1, IF16, SIGLECl; or IF127, OAS1, IFIT 1, IF16, HERC5; or IF127, OAS1, IFIT 1, IF16, DNAPTP6; or IF127, OAS1, IFIT1, IF16, LOC129607; or IF127, OAS 1, IFIT1, IF16, EPSTI1; or IF127, OAS 1, IFIT1, IF16, BIRC4BP; or IF127, OAS1, IFIT1, IF16, SIGLECl; or IF127, OAS1, IFIT1, IF16, gene 5 detected by probe 229450_at; or IF127, OAS 1, IFIT1, IF16, gene detected by probe 235276_at; or OAS1, IFIT1, IF16, IF144L, ISG15; or OAS1, IFIT1, IF16, IF144L, LAMP3; or OAS1, IFIT1, IF16, IF144L, OASL; or OAS1, IFIT1, IF16, IF144L, RSAD2; or OAS1, IFIT1, IF16, IF144L, IF144; or OAS 1, IFIT1, IF16, IF144L, IFIT2; or OAS 1, IFIT1, IF16, IF144L, OAS3; or OAS1, IFIT1, IF16, IF144L, USP18; or OAS1, IFIT1, IF16, IF144L, SIGLECl; or OAS1, 10 IFIT1, IF16, IF144L, HERC5; or OAS1, IFIT1, IF16, IF144L, DNAPTP6; or OAS1, IFIT1, IF16, IF144L, LOC129607; or OAS1, IFIT1, IF16, IF144L, EPST1l; or OAS1, IFIT1, IF16, IF144L, BIRC4BP; or OAS1, IFIT1, IF16, IF144L, SIGLEC1; or OAS1, IFIT1, IF16, IF144L, gene detected by probe 229450_at; or OAS1, IFIT1, IF16, IF144L, gene detected by probe 235276_at; or IFIT1, IF16, IF144L, ISG15, LAMP3; or IFIT1, IF16, IF144L, ISG15, OASL; or 15 IFIT1, IF16, IF144L, ISG15, RSAD2; or IFIT1, IF16, IF144L, ISG15, IF144; or IFIT1, IF16, IF144L, ISG15, IFIT2 or IFIT1, IF16, IF144L, ISG15, OAS3; or IFIT1, IF16, IF144L, ISG15, USP18; or IFIT1, IF16, IF144L, ISG15, SIGLECl; or IFIT1, IF16, IF144L, ISG15, HERC5; or IFIT1, IF16, IF144L, ISG15, DNAPTP6; or IFIT1, IF16, IF144L, ISG15, LOC129607; or IFIT1, IF16, IF144L, ISG15, EPST1l; or IFIT1, IF16, IF144L, ISG15, BIRC4BP; or IFIT1, 20 IF16, IF144L, ISG15, gene detected by probe 229450_at; or IFIT1, IF16, IF144L, ISG15, gene detected by probe 235276_at; or IF16, IF144L, ISG15, LAMP3, HERC5; or IF16, IF144L, ISG15, LAMP3, DNAPTP6; or IF16, IF144L, ISG15, LAMP3, LOC129607; or IF16, IF144L, ISG15, LAMP3, EPST1l; or IF16, IF144L, ISG15, LAMP3, BIRC4BP; or IF16, IF144L, ISG15, LAMP3, gene detected by probe 229450_at; or IF16, IF144L, ISG15, LAMP3, gene 25 detected by probe 235276_at; or IF16, IF144L, ISG15, LAMP3, SIGLECl; or IF16, IF144L, ISG15, LAMP3, USP18; or IF16, IF144L, ISG15, LAMP3, OAS3; or IF16, IF144L, ISG15, LAMP3, IFIT2; or IF16, IF144L, ISG15, LAMP3, IF144; or IF16, IF144L, ISG15, LAMP3, RSAD2; or IF16, IF144L, ISG15, LAMP3, OASL; or IF144L, ISG15, LAMP3, OASL, RSAD2; or IF144L, ISG15, LAMP3, OASL, IF144; or IF144L, ISG15, LAMP3, OASL, IFIT2; 30 or IF144L, ISG15, LAMP3, OASL, OAS3; or IF144L, ISG15, LAMP3, OASL, USP18; or IF144L, ISG15, LAMP3, OASL, SIGLECl; or IF144L, ISG15, LAMP3, OASL, HERC5; or IF144L, ISG15, LAMP3, OASL, DNAPTP6; or IF144L, ISG15, LAMP3, OASL, LOC129607; or IF144L, ISG15, LAMP3, OASL, EPST1;or IF144L, ISG15, LAMP3, OASL, BIRC4BP; or IF144L, ISG15, LAMP3, OASL, gene detected by probe 229450at; or IF144L, ISG15, C:\poi\word\SPEC-8541 93[1].docx 28 LAMP3, OASL, gene detected by probe 235276_at; or ISG15, LAMP3, OASL, RSAD2, IF144; or ISG15, LAMP3, OASL, RSAD2, IFIT2; or ISG15, LAMP3, OASL, RSAD2, OAS3; or ISG15, LAMP3, OASL, RSAD2, USP18; or ISG15, LAMP3, OASL, RSAD2, SIGLECl; or ISG15, LAMP3, OASL, RSAD2, HERC5; or ISG15, LAMP3, OASL, RSAD2, DNAPTP6; 5 or ISG15, LAMP3, OASL, RSAD2, LOC129607; or ISG15, LAMP3, OASL, RSAD2, EPST1l; or ISG15, LAMP3, OASL, RSAD2, BIRC4BP; or ISG15, LAMP3, OASL, RSAD2, gene detected by probe 229450_at; or ISG15, LAMP3, OASL, RSAD2, gene detected by probe 235276_at; or LAMP3, OASL, RSAD2, IF144, IFIT2; or LAMP3, OASL, RSAD2, IF144, OAS3; or LAMP3, OASL, RSAD2, IF144, USP18; or LAMP3, OASL, RSAD2, IF144, 10 SIGLECl; or LAMP3, OASL, RSAD2, IF144, HERC5; or LAMP3, OASL, RSAD2, IF144, DNAPTP6; or LAMP3, OASL, RSAD2, IF144, LOC129607; or LAMP3, OASL, RSAD2, IF144, EPST1l; or LAMP3, OASL, RSAD2, IF144, BIRC4BP; or LAMP3, OASL, RSAD2, IF144, gene detected by probe 229450at; or LAMP3, OASL, RSAD2, IF144, gene detected by probe 235276at; or OASL, RSAD2, IF144, IFIT2, OAS3; or OASL, RSAD2, IF144, 15 IFIT2, USP18; or OASL, RSAD2, IF144, IFIT2, SIGLECl; or OASL, RSAD2, IF144, IFIT2, HERC5; or OASL, RSAD2, IF144, IFIT2, DNAPTP6; or OASL, RSAD2, IF144, IFIT2, LOC129607; or OASL, RSAD2, IF144, IFIT2, EPST1l; or OASL, RSAD2, IF144, IFIT2, BIRC4BP; or OASL, RSAD2, IF144, IFIT2, gene detected by probe 229450at; or OASL, RSAD2, IF144, IFIT2, gene detected by probe 235276at; or RSAD2, IF144, IFIT2, OAS3, 20 USP18; or RSAD2, IF144, IFIT2, OAS3, SIGLECl; or RSAD2, IF144, IFIT2, OAS3, HERC5; or RSAD2, IF144, IFIT2, OAS3, DNAPTP6; or RSAD2, IF144, IFIT2, OAS3, LOC129607; or RSAD2, IF144, IFIT2, OAS3, EPST1l; or RSAD2, IF144, IFIT2, OAS3, BIRC4BP; or RSAD2, IF144, IFIT2, OAS3, gene detected by probe 229450_at; or RSAD2, IF144, IFIT2, OAS3, gene detected by probe 235276_at; or IF144, IFIT2, OAS3, USP18, SIGLECl; or 25 IF144, IFIT2, OAS3, USP18, HERC5; or IF144, IFIT2, OAS3, USP18, DNAPTP6; or IF144, IFIT2, OAS3, USP18, LOC129607; or IF144, IFIT2, OAS3, USP18, EPST1l; or IF144, IFIT2, OAS3, USP18, BIRC4BP; or IF144, IFIT2, OAS3, USP18, gene detected by probe 229450_at; or IF144, IFIT2, OAS3, USP18, gene detected by probe 235276_at; or IFIT2, OAS3, USP18, SIGLEC1, HERC5; or IFIT2, OAS3, USP18, SIGLEC1, DNAPTP6; or IFIT2, OAS3, USP18, 30 SIGLEC1, LOC129607; or IFIT2, OAS3, USP18, SIGLEC1, EPST1l; or IFIT2, OAS3, USP18, SIGLEC1, BIRC4BP; or IFIT2, OAS3, USP18, SIGLEC1, gene detected by probe 229450at; or IFIT2, OAS3, USP18, SIGLEC1, gene detected by probe 235276_at; or OAS3, USP18, SIGLEC1, HERC5, DNAPTP6; or OAS3, USP18, SIGLEC1, HERC5, LOC129607; or OAS3, USP18, SIGLEC1, HERC5, EPST1l; or OAS3, USP18, SIGLEC1, HERC5, C:\poi\word\SPEC-8541 93[1]. docx 29 BIRC4BP; or OAS3, USP18, SIGLEC1, HERC5, gene detected by probe 229450_at; or OAS3, USP18, SIGLEC1, HERC5, gene detected by probe 235276_at; or USP18, SIGLEC1, HERC5, DNAPTP6, LOC129607; or USP18, SIGLEC1, HERC5, DNAPTP6, EPST1l; or USP18, SIGLEC1, HERC5, DNAPTP6, BIRC4BP; or USP18, SIGLEC1, HERC5, 5 DNAPTP6, gene detected by probe 229450_at; or USP18, SIGLEC1, HERC5, DNAPTP6, gene detected by probe 235276_at; or SIGLEC1, HERC5, DNAPTP6, LOC129607, EPST1; or SIGLEC1, HERC5, DNAPTP6, LOC129607, BIRC4BP; or SIGLEC1, HERC5, DNAPTP6, LOC129607, gene detected by probe 229450_at; or SIGLEC1, HERC5, DNAPTP6, LOC129607, gene detected by probe 235276_at; or HERC5, DNAPTP6, 10 LOC 129607, EPSTI1, BIRC4BP; or HERC5, DNAPTP6, LOC 129607, EPSTI1, gene detected by probe 229450_at; or HERC5, DNAPTP6, LOC129607, EPSTI1, gene detected by probe 235276_at; or DNAPTP6, LOC129607, EPSTI1, BIRC4BP, gene detected by probe 229450_at; or DNAPTP6, LOC129607, EPSTI1, BIRC4BP, gene detected by probe 235276_at; or LOC129607, EPSTI1, BIRC4BP, gene detected by probe 229450_at, gene 15 detected by probe 235276_at. The IFNa-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 IFNa-inducible PD markers in an expression profile may include any at least 6 genes such as, for example: MX1, LLY6E, IF127, OAS1, IFIT1, IF16; or MX1, LLY6E, 20 IF127, OAS1, IFIT1, IF144L; or MX1, LLY6E, IF127, OAS1, IFIT1, ISG15; or MX1, LLY6E, IF127, OAS1, IFIT1, LAMP3; or MX1, LLY6E, IF127, OAS1, IFIT1, OASL; or MX1, LLY6E, IF127, OAS1, IFIT1, RSAD2; or MX1, LLY6E, IF127, OAS1, IFIT1, IF144; or MX1, LLY6E, IF127, OAS1, IFIT1, IFIT2; or MX1, LLY6E, IF127, OAS1, IFIT1, OAS3; or MX1, LLY6E, IF127, OAS1, IFIT1, USP18; or MX1, LLY6E, IF127, OAS1, IFIT1, SIGLECl; or 25 MX1, LLY6E, IF127, OAS1, IFIT1, HERC5; or MX1, LLY6E, IF127, OAS1, IFIT1, DNAPTP6; or MX1, LLY6E, IF127, OAS1, IFIT1, LOC129607; or MX1, LLY6E, IF127, OAS1, IFIT1, EPST1l; or MX1, LLY6E, IF127, OAS1, IFIT1, BIRC4BP;or MX1, LLY6E, IF127, OAS1, IFIT1, gene detected by probe 229450_at; or MX1, LLY6E, IF127, OAS1, IFIT1, gene detected by probe 235276_at; or LLY6E, IF127, OAS1, IFIT1, IF16, IF144L; or 30 LLY6E, IF127, OAS1, IFIT1, IF16, ISG15; or LLY6E, IF127, OAS1, IFIT1, IF16, LAMP3; or LLY6E, IF127, OAS 1, IFIT1, IF16, OASL ; or LLY6E, IF127, OAS 1, IFIT1, IF16, RSAD2; or LLY6E, IF127, OAS 1, IFIT1, IF16, IF144; or LLY6E, IF127, OAS 1, IFIT1, IF16, IFIT2; or LLY6E, IF127, OAS1, IFIT1, IF16, OAS3; or LLY6E, IF127, OAS1, IFIT1, IF16, USP18; or LLY6E, IF127, OAS 1, IFIT1, IF16, SIGLECl; or LLY6E, IF127, OAS 1, IFIT1, IF16, HERC5; C:\poi\word\SPEC-8541 93[1].docx 30 or LLY6E, IF127, OAS1, IFIT1, IF16, DNAPTP6; or LLY6E, IF127, OAS1, IFIT1, IF16, LOC 129607; or LLY6E, IF127, OAS 1, IFIT1, IF16, EPST1l; or LLY6E, IF127, OAS 1, IFIT1, IF16, BIRC4BP; or LLY6E, IF127, OAS 1, IFIT 1, IF16, gene detected by probe 229450_at; or LLY6E, IF127, OAS 1, IFIT1, IF16, gene detected by probe 235276_at; or IF127, OAS 1, IFIT1, 5 IF16, IFI44L, ISG15; or IF127, OAS1, IFIT1, IF16, IFI44L, LAMP3; or IF127, OAS1, IFIT1, IF16, IFI44L, OASL; or IF127, OAS 1, IFIT1, IF16, IFI44L, RSAD2; or IF127, OAS 1, IFIT1, IF16, IFI44L, IF144; or IF127, OAS 1, IFIT1, IF16, IFI44L, IFIT2; or IF127, OAS 1, IFIT1, IF16, IFI44L, OAS3; or IF127, OAS1, IFIT1, IF16, IFI44L, USP18; or IF127, OAS1, IFIT1, IFI6, IFI44L, SIGLEC1; or IF127, OAS1, IFIT1, IF16, IFI44L, HERC5; or IF127, OAS1, IFIT1, 10 IF16, IFI44L, DNAPTP6; or IF127, OAS 1, IFIT1, IF16, IFI44L, LOC 129607; or IF127, OAS 1, IFIT1, IF16, IFI44L, EPST1l; or IF127, OAS1, IFIT1, IF16, IFI44L, BIRC4BP; or IFI27, OAS 1, IFIT1, IF16, IFI44L, gene detected by probe 229450_at; or IF127, OAS 1, IFIT1, IF16, IFI44L, gene detected by probe 235276_at; or OAS 1, IFIT1, IF16, IFI44L, ISG15, LAMP3; or OAS1, IFIT1, IF16, IFI44L, ISG15, OASL; or OAS1, IFIT1, IF16, IFI44L, ISG15, RSAD2; or 15 OAS1, IFIT1, IF16, IFI44L, ISG15, IF144; or OAS1, IFIT1, IF16, IFI44L, ISG15, IFIT2; or OAS1, IFIT1, IF16, IFI44L, ISG15, OAS3; or OAS1, IFIT1, IF16, IFI44L, ISG15, USP18; or OAS1, IFIT1, IF16, IFI44L, ISG15, SIGLECl; or OAS1, IFIT1, IF16, IFI44L, ISG15, HERC5; or OAS1, IFIT1, IF16, IFI44L, ISG15, DNAPTP6; or OAS1, IFIT1, IF16, IFI44L, ISG15, LOC129607; or OAS1, IFIT1, IF16, IFI44L, ISG15, EPST1l; or OAS1, IFIT1, IF16, 20 IFI44L, ISG15, BIRC4BP; or OAS1, IFIT1, IF16, IFI44L, ISG15, gene detected by probe 229450at; or OAS1, IFIT1, IF16, IFI44L, ISG15, gene detected by probe 235276_at; or IFIT1, IF16, IFI44L, ISG15, LAMP3, OASL; or IFIT1, IF16, IFI44L, ISG15, LAMP3, RSAD2; or IFIT1, IF16, IFI44L, ISG15, LAMP3, IF144; or IFIT1, IF16, IFI44L, ISG15, LAMP3, IFIT2; or IFIT1, IF16, IFI44L, ISG15, LAMP3, OAS3; or IFIT1, IF16, IFI44L, 25 ISG15, LAMP3, USP18; or IFIT1, IF16, IFI44L, ISG15, LAMP3, SIGLECl; or IFIT1, IF16, IFI44L, ISG15, LAMP3, HERC5; or IFIT1, IF16, IFI44L, ISG15, LAMP3, DNAPTP6; or IFIT1, IF16, IFI44L, ISG15, LAMP3, LOC129607; or IFIT1, IF16, IFI44L, ISG15, LAMP3, EPST1l; or IFIT1, IF16, IFI44L, ISG15, LAMP3, BIRC4BP; or IFIT1, IF16, IFI44L, ISG15, LAMP3, gene detected by probe 229450_at; or IFIT1, IF16, IFI44L, ISG15, LAMP3, gene 30 detected by probe 235276_at; or IF16, IFI44L, ISG15, LAMP3, OASL, RSAD2; or IF16, IFI44L, ISG15, LAMP3, OASL, IF144; or IF16, IFI44L, ISG15, LAMP3, OASL, IFIT2; or IF16, IFI44L, ISG15, LAMP3, OASL, OAS3; or IF16, IFI44L, ISG15, LAMP3, OASL, USP18; or IF16, IFI44L, ISG15, LAMP3, OASL, SIGLECl; or IF16, IFI44L, ISG15, LAMP3, OASL, HERC5; or IF16, IFI44L, ISG15, LAMP3, OASL, DNAPTP6; or IF16, IFI44L, ISG15, C:\poi\word\SPEC-8541 93[1]. docx 31 LAMP3, OASL, LOC129607; or IF16, IF144L, ISG15, LAMP3, OASL, EPST1l; or IF16, IF144L, ISG15, LAMP3, OASL, BIRC4BP; or IF16, IF144L, ISG15, LAMP3, OASL, gene detected by probe 229450_at; or IF16, IF144L, ISG15, LAMP3, OASL, gene detected by probe 235276_at; or IF144L, ISG15, LAMP3, OASL, RSAD2, IF144; or IF144L, ISG15, LAMP3, 5 OASL, RSAD2, IFIT2; or IF144L, ISG15, LAMP3, OASL, RSAD2, OAS3; or IF144L, ISG15, LAMP3, OASL, RSAD2, USP18; or IF144L, ISG15, LAMP3, OASL, RSAD2, SIGLECl; or IF144L, ISG15, LAMP3, OASL, RSAD2, HERC5; or IF144L, ISG15, LAMP3, OASL, RSAD2, DNAPTP6; or IF144L, ISG15, LAMP3, OASL, RSAD2, LOC129607; or IF144L, ISG15, LAMP3, OASL, RSAD2, EPST1l; or IF144L, ISG15, LAMP3, OASL, RSAD2, 10 BIRC4BP; or IF144L, ISG15, LAMP3, OASL, RSAD2, gene detected by probe 229450_at; or IF144L, ISG15, LAMP3, OASL, RSAD2, gene detected by probe 235276at; or ISG15, LAMP3, OASL, RSAD2, IF144, IFIT2; or ISG15, LAMP3, OASL, RSAD2, IF144, OAS3; or ISG15, LAMP3, OASL, RSAD2, IF144, USP18; or ISG15, LAMP3, OASL, RSAD2, IF144, SIGLEC1; or ISG15, LAMP3, OASL, RSAD2, IF144, HERC5; or ISG15, LAMP3, OASL, 15 RSAD2, IF144, DNAPTP6; or ISG15, LAMP3, OASL, RSAD2, IF144, LOC129607; or ISG15, LAMP3, OASL, RSAD2, IF144, EPST1l; or ISG15, LAMP3, OASL, RSAD2, IF144, BIRC4BP; or ISG15, LAMP3, OASL, RSAD2, IF144, gene detected by probe 229450_at; or ISG15, LAMP3, OASL, RSAD2, IF144, gene detected by probe 235276at; or LAMP3, OASL, RSAD2, IF144, IFIT2, OAS3; or LAMP3, OASL, RSAD2, IF144, IFIT2, USP18; or 20 LAMP3, OASL, RSAD2, IF144, IFIT2, SIGLECl; or LAMP3, OASL, RSAD2, IF144, IFIT2, HERC5; or LAMP3, OASL, RSAD2, IF144, IFIT2, DNAPTP6; or LAMP3, OASL, RSAD2, IF144, IFIT2, LOC129607; or LAMP3, OASL, RSAD2, IF144, IFIT2, EPST1l; or LAMP3, OASL, RSAD2, IF144, IFIT2, BIRC4BP; or LAMP3, OASL, RSAD2, IF144, IFIT2, gene detected by probe 229450_at; or LAMP3, OASL, RSAD2, IF144, IFIT2, gene detected by 25 probe 235276at; or OASL, RSAD2, IF144, IFIT2, OAS3, USP18; or OASL, RSAD2, IF144, IFIT2, OAS3, SIGLECl; or OASL, RSAD2, IF144, IFIT2, OAS3, HERC5; or OASL, RSAD2, IF144, IFIT2, OAS3, DNAPTP6; or OASL, RSAD2, IF144, IFIT2, OAS3, LOC129607; or OASL, RSAD2, IF144, IFIT2, OAS3, EPST1l; or OASL, RSAD2, IF144, IFIT2, OAS3, BIRC4BP; or OASL, RSAD2, IF144, IFIT2, OAS3, gene detected by probe 30 229450at; or OASL, RSAD2, IF144, IFIT2, OAS3, gene detected by probe 235276_at; or RSAD2, IF144, IFIT2, OAS3, USP18, SIGLECl; or RSAD2, IF144, IFIT2, OAS3, USP18, HERC5; or RSAD2, IF144, IFIT2, OAS3, USP18, DNAPTP6; or RSAD2, IF144, IFIT2, OAS3, USP18, LOC129607; or RSAD2, IF144, IFIT2, OAS3, USP18, EPST1l; or RSAD2, IF144, IFIT2, OAS3, USP18, BIRC4BP; or RSAD2, IF144, IFIT2, OAS3, USP18, gene C:\poi\word\SPEC-8541 93[1]. docx 32 detected by probe 229450_at; or RSAD2, IF144, IFIT2, OAS3, USP18, gene detected by probe 235276_at; or IF144, IFIT2, OAS3, USP18, SIGLEC1, HERC5; or IF144, IFIT2, OAS3, USP18, SIGLEC1, DNAPTP6; or IF144, IFIT2, OAS3, USP18, SIGLEC1, LOC129607; or IF144, IFIT2, OAS3, USP18, SIGLEC1, EPST1l; or IF144, IFIT2, OAS3, USP18, SIGLEC1, 5 BIRC4BP; or IF144, IFIT2, OAS3, USP18, SIGLEC1, gene detected by probe 229450_at; or IF144, IFIT2, OAS3, USP18, SIGLEC1, gene detected by probe 235276_at; or IFIT2, OAS3, USP18, SIGLEC1, HERC5, DNAPTP6; or IFIT2, OAS3, USP18, SIGLEC1, HERC5, LOC129607; or IFIT2, OAS3, USP18, SIGLEC1, HERC5, EPST1l; or IFIT2, OAS3, USP18, SIGLEC1, HERC5, BIRC4BP; or IFIT2, OAS3, USP18, SIGLEC1, HERC5, gene detected by 10 probe 229450_at; or IFIT2, OAS3, USP18, SIGLEC1, HERC5, gene detected by probe 235276_at; or OAS3, USP18, SIGLEC1, HERC5, DNAPTP6, LOC129607; or OAS3, USP18, SIGLEC1, HERC5, DNAPTP6, EPST1l; or OAS3, USP18, SIGLEC1, HERC5, DNAPTP6, BIRC4BP; or OAS3, USP18, SIGLEC1, HERC5, DNAPTP6, gene detected by probe 229450_at; or OAS3, USP18, SIGLEC1, HERC5, DNAPTP6, gene detected by probe 15 235276_at; or USP18, SIGLEC1, HERC5, DNAPTP6, LOC129607, EPST1l; or USP18, SIGLEC1, HERC5, DNAPTP6, LOC129607, BIRC4BP; or USP18, SIGLEC1, HERC5, DNAPTP6, LOC129607, gene detected by probe 229450_at; or USP18, SIGLEC1, HERC5, DNAPTP6, LOC129607, gene detected by probe 235276_at; or SIGLEC1, HERC5, DNAPTP6, LOC129607, EPSTI1, BIRC4BP; or SIGLEC1, HERC5, DNAPTP6, LOC129607, 20 EPSTI1, gene detected by probe 229450_at; or SIGLEC1, HERC5, DNAPTP6, LOC129607, EPSTI1, gene detected by probe 235276_at ; or HERC5, DNAPTP6, LOC129607, EPSTI1, BIRC4BP, gene detected by probe 229450_at; or HERC5, DNAPTP6, LOC129607, EPSTI1, BIRC4BP, gene detected by probe 235276_at; or DNAPTP6, LOC129607, EPSTI1, BIRC4BP, gene detected by probe 229450_at, gene detected by probe 235276_at. The IFNa 25 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 IFNa-inducible PD markers in an expression profile may include any at least 7 genes such as, for example: MX1, LLY6E, IF127, OAS1, IFIT1, IF16, IF144L; or MX1, 30 LLY6E, IF127, OAS1, IFIT1, IF16, ISG15; or MX1, LLY6E, IF127, OAS1, IFIT1, IF16, LAMP3; or MX1, LLY6E, IF127, OAS1, IFIT1, IF16, OASL; or MX1, LLY6E, IF127, OAS1, IFIT1, IF16, RSAD2; or MX1, LLY6E, IF127, OAS1, IFIT1, IF16, IF144; or MX1, LLY6E, IF127, OAS1, IFIT1, IF16, IFIT2; or MX1, LLY6E, IF127, OAS1, IFIT1, IF16, OAS3; or MX1, LLY6E, IF127, OAS1, IFIT1, IF16, USP18; or MX1, LLY6E, IF127, OAS1, IFIT1, C:\poi\word\SPEC-8541 93[1].docx 33 IF16, SIGLECl; or MX1, LLY6E, IF127, OAS1, IFIT1, IF16, HERC5; or MX1, LLY6E, IF127, OAS1, IFIT1, IF16, DNAPTP6; or MX1, LLY6E, IF127, OAS1, IFIT1, IF16, LOC129607; or MX1, LLY6E, IF127, OAS1, IFIT1, IF16, EPST1l; or MX1, LLY6E, IF127, OAS1, IFIT1, IF16, BIRC4BP; or MX1, LLY6E, IF127, OAS1, IFIT1, IF16, gene detected by 5 probe 229450_at; or MX1, LLY6E, IF127, OAS1, IFIT1, IF16, gene detected by probe 235276_at; or LLY6E, IF127, OAS1, IFIT1, IF16, IFI44L, ISG15; or LLY6E, IF127, OAS1, IFIT1, IF16, IFI44L, LAMP3; or LLY6E, IF127, OAS1, IFIT1, IF16, IFI44L, OASL; or LLY6E, IF127, OAS1, IFIT1, IF16, IFI44L, RSAD2; or LLY6E, IF127, OAS1, IFIT1, IF16, IFI44L, IF144; or LLY6E, IF127, OAS 1, IFIT 1, IF16, IFI44L, IFIT2; or LLY6E, IF127, OAS 1, 10 IFIT1, IF16, IFI44L, OAS3; or LLY6E, IF127, OAS 1, IFIT1, IF16, IFI44L, USP18; or LLY6E, IF127, OAS1, IFIT1, IF16, IFI44L, SIGLECl; or LLY6E, IF127, OAS1, IFIT1, IF16, IFI44L, HERC5; or LLY6E, IF127, OAS 1, IFIT1, IF16, IFI44L, DNAPTP6; or LLY6E, IF127, OAS 1, IFIT1, IF16, IFI44L, LOC129607; or LLY6E, IF127, OAS1, IFIT1, IF16, IFI44L, EPST1l; or LLY6E, IF127, OAS1, IFIT1, IF16, IFI44L, BIRC4BP; or LLY6E, IF127, OAS1, IFIT1, IF16, 15 IFI44L, gene detected by probe 229450_at; or LLY6E, IF127, OAS1, IFIT1, IF16, IFI44L, gene detected by probe 235276_at; or IFI27, OAS 1, IFIT1, IF16, IFI44L, ISG15, LAMP3; or IF127, OAS1, IFIT1, IF16, IFI44L, ISG15, OASL; or IF127, OAS1, IFIT1, IF16, IFI44L, ISG15, RSAD2; or IF127, OAS1, IFIT1, IF16, IFI44L, ISG15, IF144; or IF127, OAS1, IFIT1, IF16, IFI44L, ISG15, IFIT2; or IF127, OAS1, IFIT1, IF16, IFI44L, ISG15, OAS3; or IF127, 20 OAS1, IFIT1, IF16, IFI44L, ISG15, USP18; or IF127, OAS1, IFIT1, IF16, IFI44L, ISG15, SIGLECl; or IF127, OAS1, IFIT1, IF16, IFI44L, ISG15, HERC5; or IF127, OAS1, IFIT1, IF16, IFI44L, ISG15, DNAPTP6; or IF127, OAS1, IFIT1, IF16, IFI44L, ISG15, LOC129607; or IF127, OAS1, IFIT1, IF16, IFI44L, ISG15, EPST1l; or IF127, OAS1, IFIT1, IF16, IFI44L, ISG15, BIRC4BP; or IF127, OAS1, IFIT1, IF16, IFI44L, ISG15, gene detected by probe 25 229450at; or IF127, OAS1, IFIT1, IF16, IFI44L, ISG15, gene detected by probe 235276_at; or OAS1, IFIT1, IF16, IFI44L, ISG15, LAMP3, OASL; or OAS1, IFIT1, IF16, IFI44L, ISG15, LAMP3, RSAD2; or OAS1, IFIT1, IF16, IFI44L, ISG15, LAMP3, IF144; or OAS1, IFIT1, IF16, IFI44L, ISG15, LAMP3, IFIT2; or OAS1, IFIT1, IF16, IFI44L, ISG15, LAMP3, OAS3; or OAS1, IFIT1, IF16, IFI44L, ISG15, LAMP3, USP18; or OAS1, IFIT1, IF16, IFI44L, 30 ISG15, LAMP3, SIGLECl; or OAS1, IFIT1, IF16, IFI44L, ISG15, LAMP3, HERC5; or OAS1, IFIT1, IF16, IFI44L, ISG15, LAMP3, DNAPTP6; or OAS1, IFIT1, IF16, IFI44L, ISG15, LAMP3, LOC129607; or OAS1, IFIT1, IF16, IFI44L, ISG15, LAMP3, EPST1l; or OAS1, IFIT1, IF16, IFI44L, ISG15, LAMP3, BIRC4BP; or OAS1, IFIT1, IF16, IFI44L, ISG15, LAMP3, gene detected by probe 229450_at; or OAS1, IFIT1, IF16, IFI44L, ISG15, C:\poi\word\SPEC-8541 93[1].docx 34 LAMP3, gene detected by probe 235276_at; or IFIT1, IF16, IF144L, ISG15, LAMP3, OASL, RSAD2; or IFIT1, IF16, IF144L, ISG15, LAMP3, OASL, IF144; or IFIT1, IF16, IF144L, ISG15, LAMP3, OASL, IFIT2; or IFIT1, IF16, IF144L, ISG15, LAMP3, OASL, OAS3; or IFIT1, IF16, IF144L, ISG15, LAMP3, OASL, USP18; or IFIT1, IF16, IF144L, ISG15, LAMP3, 5 OASL, SIGLECl; or IFIT1, IF16, IF144L, ISG15, LAMP3, OASL, HERC5; or IFIT1, IF16, IF144L, ISG15, LAMP3, OASL, DNAPTP6; or IFIT1, IF16, IF144L, ISG15, LAMP3, OASL, LOC129607; or IFIT1, IF16, IF144L, ISG15, LAMP3, OASL, EPST1l; or IFIT1, IF16, IF144L, ISG15, LAMP3, OASL, BIRC4BP; or IFIT1, IF16, IF144L, ISG15, LAMP3, OASL, gene detected by probe 229450_at; or IFIT1, IF16, IF144L, ISG15, LAMP3, OASL, gene detected 10 by probe 235276_at; or IF16, IF144L, ISG15, LAMP3, OASL, RSAD2, IF144; or IF16, IF144L, ISG15, LAMP3, OASL, RSAD2, IFIT2; or IF16, IF144L, ISG15, LAMP3, OASL, RSAD2, OAS3; or IF16, IF144L, ISG15, LAMP3, OASL, RSAD2, USP18; or IF16, IF144L, ISG15, LAMP3, OASL, RSAD2, SIGLECl; or IF16, IF144L, ISG15, LAMP3, OASL, RSAD2, HERC5; or IF16, IF144L, ISG15, LAMP3, OASL, RSAD2, DNAPTP6; or IF16, IF144L, 15 ISG15, LAMP3, OASL, RSAD2, LOC129607; or IF16, IF144L, ISG15, LAMP3, OASL, RSAD2, EPST1l; or IF16, IF144L, ISG15, LAMP3, OASL, RSAD2, BIRC4BP; or IF16, IF144L, ISG15, LAMP3, OASL, RSAD2, gene detected by probe 229450_at; or IF16, IF144L, ISG15, LAMP3, OASL, RSAD2, gene detected by probe 235276_at; or IF144L, ISG15, LAMP3, OASL, RSAD2, IF144, IFIT2; or IF144L, ISG15, LAMP3, OASL, RSAD2, IF144, 20 OAS3; or IF144L, ISG15, LAMP3, OASL, RSAD2, IF144, USP18; or IF144L, ISG15, LAMP3, OASL, RSAD2, IF144, SIGLECl; or IF144L, ISG15, LAMP3, OASL, RSAD2, IF144, HERC5; or IF144L, ISG15, LAMP3, OASL, RSAD2, IF144, DNAPTP6; or IF144L, ISG15, LAMP3, OASL, RSAD2, IF144, LOC129607; or IF144L, ISG15, LAMP3, OASL, RSAD2, IF144, EPST1l; or IF144L, ISG15, LAMP3, OASL, RSAD2, IF144, BIRC4BP; or 25 IF144L, ISG15, LAMP3, OASL, RSAD2, IF144, gene detected by probe 229450at; or IF144L, ISG15, LAMP3, OASL, RSAD2, IF144, gene detected by probe 235276_at; or ISG15, LAMP3, OASL, RSAD2, IF144, IFIT2, OAS3; or ISG15, LAMP3, OASL, RSAD2, IF144, IFIT2, USP18; or ISG15, LAMP3, OASL, RSAD2, IF144, IFIT2, SIGLEC1; or ISG15, LAMP3, OASL, RSAD2, IF144, IFIT2, HERC5; or ISG15, LAMP3, OASL, RSAD2, IF144, 30 IFIT2, DNAPTP6; or ISG15, LAMP3, OASL, RSAD2, IF144, IFIT2, LOC129607; or ISG15, LAMP3, OASL, RSAD2, IF144, IFIT2, EPST1l; or ISG15, LAMP3, OASL, RSAD2, IF144, IFIT2, BIRC4BP; or ISG15, LAMP3, OASL, RSAD2, IF144, IFIT2, gene detected by probe 229450at; or ISG15, LAMP3, OASL, RSAD2, IF144, IFIT2, gene detected by probe 235276_at; or LAMP3, OASL, RSAD2, IF144, IFIT2, OAS3, USP18; or LAMP3, OASL, C:\poi\word\SPEC-8541 93[1].docx 35 RSAD2, IF144, IFIT2, OAS3, SIGLECl; or LAMP3, OASL, RSAD2, IF144, IFIT2, OAS3, HERC5; or LAMP3, OASL, RSAD2, IF144, IFIT2, OAS3, DNAPTP6; or LAMP3, OASL, RSAD2, IF144, IFIT2, OAS3, LOC129607; or LAMP3, OASL, RSAD2, IF144, IFIT2, OAS3, EPST1l; or LAMP3, OASL, RSAD2, IF144, IFIT2, OAS3, BIRC4BP; or LAMP3, OASL, 5 RSAD2, IF144, IFIT2, OAS3, gene detected by probe 229450_at; or LAMP3, OASL, RSAD2, IF144, IFIT2, OAS3, gene detected by probe 235276at; or OASL, RSAD2, IF144, IFIT2, OAS3, USP18, SIGLECl; or OASL, RSAD2, IF144, IFIT2, OAS3, USP18, HERC5; or OASL, RSAD2, IF144, IFIT2, OAS3, USP18, DNAPTP6; or OASL, RSAD2, IF144, IFIT2, OAS3, USP18, LOC129607; or OASL, RSAD2, IF144, IFIT2, OAS3, USP18, EPST1l; or 10 OASL, RSAD2, IF144, IFIT2, OAS3, USP18, BIRC4BP; or OASL, RSAD2, IF144, IFIT2, OAS3, USP18, gene detected by probe 229450_at; or OASL, RSAD2, IF144, IFIT2, OAS3, USP18, gene detected by probe 235276_at; or RSAD2, IF144, IFIT2, OAS3, USP18, SIGLEC1, HERC5; or RSAD2, IF144, IFIT2, OAS3, USP18, SIGLEC1, DNAPTP6; or RSAD2, IF144, IFIT2, OAS3, USP18, SIGLEC1, LOC129607; or RSAD2, IF144, IFIT2, 15 OAS3, USP18, SIGLEC1, EPST1l; or RSAD2, IF144, IFIT2, OAS3, USP18, SIGLEC1, BIRC4BP; or RSAD2, IF144, IFIT2, OAS3, USP18, SIGLEC1, gene detected by probe 229450at; or RSAD2, IF144, IFIT2, OAS3, USP18, SIGLEC1, gene detected by probe 235276_at; or IF144, IFIT2, OAS3, USP18, SIGLEC1, HERC5, DNAPTP6; or IF144, IFIT2, OAS3, USP18, SIGLEC1, HERC5, LOC129607; or IF144, IFIT2, OAS3, USP18, SIGLEC1, 20 HERC5, EPST1l; or IF144, IFIT2, OAS3, USP18, SIGLEC1, HERC5, BIRC4BP; or IF144, IFIT2, OAS3, USP18, SIGLEC1, HERC5, gene detected by probe 229450_at; or IF144, IFIT2, OAS3, USP18, SIGLEC1, HERC5, gene detected by probe 235276_at; or IFIT2, OAS3, USP18, SIGLEC1, HERC5, DNAPTP6, LOC129607; or IFIT2, OAS3, USP18, SIGLEC1, HERC5, DNAPTP6, EPST1l; or IFIT2, OAS3, USP18, SIGLEC1, HERC5, DNAPTP6, 25 BIRC4BP; or IFIT2, OAS3, USP18, SIGLEC1, HERC5, DNAPTP6, gene detected by probe 229450at ; or IFIT2, OAS3, USP18, SIGLEC1, HERC5, DNAPTP6, gene detected by probe 235276_at; or OAS3, USP18, SIGLEC1, HERC5, DNAPTP6, LOC129607, EPST1l; or OAS3, USP18, SIGLEC1, HERC5, DNAPTP6, LOC129607, BIRC4BP; or OAS3, USP18, SIGLEC1, HERC5, DNAPTP6, LOC129607, gene detected by probe 229450at; or OAS3, 30 USP18, SIGLEC1, HERC5, DNAPTP6, LOC129607, gene detected by probe 235276_at; or USP18, SIGLEC1, HERC5, DNAPTP6, LOC129607, EPSTI1, BIRC4BP; or USP18, SIGLEC1, HERC5, DNAPTP6, LOC129607, EPSTI1, gene detected by probe 229450_at; or USP18, SIGLEC1, HERC5, DNAPTP6, LOC129607, EPSTI1, gene detected by probe 235276at; or SIGLEC1, HERC5, DNAPTP6, LOC129607, EPSTI1, BIRC4BP, gene C:\poi\word\SPEC-8541 93[1].docx 36 detected by probe 229450_at; or SIGLEC1, HERC5, DNAPTP6, LOC129607, EPSTJ1, BIRC4BP, gene detected by probe 235276_at; or HERC5, DNAPTP6, LOC129607, EPSTJ1, BIRC4BP, gene detected by probe 229450_at, gene detected by probe 235276_at. The IFNa inducible PD markers in such an expression profile may further include at least one or more 5 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 IFNa-inducible PD markers in an expression profile may include any at least 8 genes such as, for example: MX1, LLY6E, IF127, OAS1, IFIT1, IF16, IF144L, ISG15; or MX1, LLY6E, IF127, OAS 1, IFIT1, IFI6, IF144L, LAMP3; or MX1, LLY6E, IF127, OAS 1, 10 IFIT1, IF16, IF144L, OASL; or MX1, LLY6E, IF127, OAS1, IFIT1, IF16, IF144L, RSAD2; or MX1, LLY6E, IF127, OAS1, IFIT1, IF16, IF144L, IF144; or MX1, LLY6E, IF127, OAS1, IFIT1, IF16, IF144L, IFIT2; or MX1, LLY6E, IF127, OAS1, IFIT1, IF16, IF144L, OAS3; or MX1, LLY6E, IF127, OAS1, IFIT1, IF16, IF144L, USP18; or MX1, LLY6E, IF127, OAS1, IFIT1, IF16, IF144L, SIGLEC1; or MX1, LLY6E, IF127, OAS1, IFIT1, IF16, IF144L, HERC5; 15 or MX1, LLY6E, IF127, OAS1, IFIT1, IF16, IF144L, DNAPTP6; or MX1, LLY6E, IF127, OAS 1, IFIT 1, IF16, IF144L, LOC129607; or MX1, LLY6E, IF127, OAS 1, IFIT 1, IF16, IF144L, EPSTJ1; or MX1, LLY6E, IF127, OAS1, IFIT1, IF16, IF144L, BIRC4BP; or MX1, LLY6E, IF127, OAS1, IFIT1, IF16, IF144L, gene detected by probe 229450_at; or MX1, LLY6E, IF127, OAS1, IFIT1, IF16, IF144L, gene detected by probe 235276_at; or LLY6E, IF127, 20 OAS1, IFIT1, IF16, IF144L, ISG15, LAMP3; or LLY6E, IF127, OAS1, IFIT1, IF16, IF144L, ISG15, OASL; or LLY6E, IF127, OAS1, IFIT1, IF16, IF144L, ISG15, RSAD2; or LLY6E, IF127, OAS1, IFIT1, IF16, IF144L, ISG15, IF144; or LLY6E, IF127, OAS1, IFIT1, IF16, IF144L, ISG15, IFIT2; or LLY6E, IF127, OAS1, IFIT1, IF16, IF144L, ISG15, OAS3; or LLY6E, IF127, OAS1, IFIT1, IF16, IF144L, ISG15, USP18; or LLY6E, IF127, OAS1, IFIT1, 25 IF16, IF144L, ISG15, SIGLECl; or LLY6E, IF127, OAS1, IFIT1, IF16, IF144L, ISG15, HERC5; or LLY6E, IF127, OAS 1, IFIT1, IF16, IF144L, ISG15, DNAPTP6; or LLY6E, IF127, OAS1, IFIT1, IF16, IF144L, ISG15, LOC129607; or LLY6E, IF127, OAS1, IFIT1, IF16, IF144L, ISG15, EPSTJ1; or LLY6E, IF127, OAS 1, IFIT1, IF16, IF144L, ISG15, BIRC4BP; or LLY6E, IF127, OAS1, IFIT1, IF16, IF144L, ISG15, gene detected by probe 229450_at; or 30 LLY6E, IF127, OAS1, IFIT1, IF16, IF144L, ISG15, gene detected by probe 235276_at; orIFJ27, OAS1, IFIT1, IF16, IF144L, ISG15, LAMP3, OASL; or IF127, OAS1, IFIT1, IF16, IF144L, ISG15, LAMP3, RSAD2; or IF127, OAS1, IFIT1, IF16, IF144L, ISG15, LAMP3, IF144; or IF127, OAS1, IFIT1, IF16, IF144L, ISG15, LAMP3, IFIT2; or IF127, OAS1, IFIT1, IF16, IF144L, ISG15, LAMP3, OAS3; or IF127, OAS1, IFIT1, IF16, IF144L, ISG15, LAMP3, C:\poi\word\SPEC-8541 93[1].dox 37 USP18; or IF127, OAS1, IFIT1, IF16, IF144L, ISG15, LAMP3, SIGLECl; or IF127, OAS1, IFIT1, IF16, IF144L, ISG15, LAMP3, HERC5; or IF127, OAS1, IFIT1, IF16, IF144L, ISG15, LAMP3, DNAPTP6; or IF127, OAS1, IFIT1, IF16, IF144L, ISG15, LAMP3, LOC129607; or IF127, OAS1, IFIT1, IF16, IF144L, ISG15, LAMP3, EPST1l; or IF127, OAS1, IFIT1, IF16, 5 IF144L, ISG15, LAMP3, gene detected by probe 229450at; or IF127, OAS1, IFIT1, IF16, IF144L, ISG15, LAMP3, BIRC4BP; or IF127, OAS1, IFIT1, IF16, IF144L, ISG15, LAMP3, gene detected by probe 235276_at; or OAS1, IFIT1, IF16, IF144L, ISG15, LAMP3, OASL, RSAD2; or OAS1, IFIT1, IF16, IF144L, ISG15, LAMP3, OASL, IF144; or OAS1, IFIT1, IF16, IF144L, ISG15, LAMP3, OASL, IFIT2; or OAS1, IFIT1, IF16, IF144L, ISG15, LAMP3, 10 OASL, OAS3; or OAS1, IFIT1, IF16, IF144L, ISG15, LAMP3, OASL, USP18; or OAS1, IFIT1, IF16, IF144L, ISG15, LAMP3, OASL, SIGLECl; or OAS1, IFIT1, IF16, IF144L, ISG15, LAMP3, OASL, HERC5; or OAS1, IFIT1, IF16, IF144L, ISG15, LAMP3, OASL, DNAPTP6; or OAS1, IFIT1, IF16, IF144L, ISG15, LAMP3, OASL, LOC129607; or OAS1, IFIT1, IF16, IF144L, ISG15, LAMP3, OASL, EPST1l; or OAS1, IFIT1, IF16, IF144L, ISG15, 15 LAMP3, OASL, BIRC4BP; or OAS1, IFIT1, IF16, IF144L, ISG15, LAMP3, OASL, gene detected by probe 229450_at; or OAS1, IFIT1, IF16, IF144L, ISG15, LAMP3, OASL, gene detected by probe 235276_at; or IFIT1, IF16, IF144L, ISG15, LAMP3, OASL, RSAD2, IF144; or IFIT1, IF16, IF144L, ISG15, LAMP3, OASL, RSAD2, IFIT2; or IFIT1, IF16, IF144L, ISG15, LAMP3, OASL, RSAD2, OAS3; or IFIT1, IF16, IF144L, ISG15, LAMP3, OASL, 20 RSAD2, USP18; or IFIT1, IF16, IF144L, ISG15, LAMP3, OASL, RSAD2, SIGLECl; or IFIT1, IF16, IF144L, ISG15, LAMP3, OASL, RSAD2, HERC5; or IFIT1, IF16, IF144L, ISG15, LAMP3, OASL, RSAD2, DNAPTP6; or IFIT1, IF16, IF144L, ISG15, LAMP3, OASL, RSAD2, LOC129607; or IFIT1, IF16, IF144L, ISG15, LAMP3, OASL, RSAD2, EPST1l; or IFIT1, IF16, IF144L, ISG15, LAMP3, OASL, RSAD2, BIRC4BP; or IFIT1, IF16, IF144L, 25 ISG15, LAMP3, OASL, RSAD2, gene detected by probe 229450_at; or IFIT1, IF16, IF144L, ISG15, LAMP3, OASL, RSAD2, gene detected by probe 235276_at; or IF16, IF144L, ISG15, LAMP3, OASL, RSAD2, IF144, IFIT2; or IF16, IF144L, ISG15, LAMP3, OASL, RSAD2, IF144, OAS3; or IF16, IF144L, ISG15, LAMP3, OASL, RSAD2, IF144, USP18; or IF16, IF144L, ISG15, LAMP3, OASL, RSAD2, IF144, SIGLECl; or IF16, IF144L, ISG15, LAMP3, 30 OASL, RSAD2, IF144, HERC5; or IF16, IF144L, ISG15, LAMP3, OASL, RSAD2, IF144, DNAPTP6; or IF16, IF144L, ISG15, LAMP3, OASL, RSAD2, IF144, LOC129607; or IF16, IF144L, ISG15, LAMP3, OASL, RSAD2, IF144, EPST1l; or IF16, IF144L, ISG15, LAMP3, OASL, RSAD2, IF144, BIRC4BP; or IF16, IF144L, ISG15, LAMP3, OASL, RSAD2, IF144, gene detected by probe 229450_at; or IF16, IF144L, ISG15, LAMP3, OASL, RSAD2, IF144, C:\poi\word\SPEC-8541 93[1].docx 38 gene detected by probe 235276_at; or IF144L, ISG15, LAMP3, OASL, RSAD2, IF144, IFIT2, OAS3; or IF144L, ISG15, LAMP3, OASL, RSAD2, IF144, IFIT2, USP18; or IF144L, ISG15, LAMP3, OASL, RSAD2, IF144, IFIT2, SIGLECl; or IF144L, ISG15, LAMP3, OASL, RSAD2, IF144, IFIT2, HERC5; or IF144L, ISG15, LAMP3, OASL, RSAD2, IF144, IFIT2, 5 DNAPTP6; or IF144L, ISG15, LAMP3, OASL, RSAD2, IF144, IFIT2, LOC129607; or IF144L, ISG15, LAMP3, OASL, RSAD2, IF144, IFIT2, EPST1l; or IF144L, ISG15, LAMP3, OASL, RSAD2, IF144, IFIT2, BIRC4BP; or IF144L, ISG15, LAMP3, OASL, RSAD2, IF144, IFIT2, gene detected by probe 229450_at; or IF144L, ISG15, LAMP3, OASL, RSAD2, IF144, IFIT2, gene detected by probe 235276_at; or ISG15, LAMP3, OASL, RSAD2, IF144, IFIT2, 10 OAS3, USP18; or ISG15, LAMP3, OASL, RSAD2, IF144, IFIT2, OAS3, SIGLECl; or ISG15, LAMP3, OASL, RSAD2, IF144, IFIT2, OAS3, HERC5; or ISG15, LAMP3, OASL, RSAD2, IF144, IFIT2, OAS3, DNAPTP6; or ISG15, LAMP3, OASL, RSAD2, IF144, IFIT2, OAS3, LOC129607; or ISG15, LAMP3, OASL, RSAD2, IF144, IFIT2, OAS3, EPST1l; or ISG15, LAMP3, OASL, RSAD2, IF144, IFIT2, OAS3, BIRC4BP; or ISG15, LAMP3, OASL, 15 RSAD2, IF144, IFIT2, OAS3, gene detected by probe 229450_at; or ISG15, LAMP3, OASL, RSAD2, IF144, IFIT2, OAS3, gene detected by probe 235276_at; or LAMP3, OASL, RSAD2, IF144, IFIT2, OAS3, USP18, SIGLECl; or LAMP3, OASL, RSAD2, IF144, IFIT2, OAS3, USP18, HERC5; or LAMP3, OASL, RSAD2, IF144, IFIT2, OAS3, USP18, DNAPTP6; or LAMP3, OASL, RSAD2, IF144, IFIT2, OAS3, USP18, LOC129607; or LAMP3, OASL, 20 RSAD2, IF144, IFIT2, OAS3, USP18, EPST1l; or LAMP3, OASL, RSAD2, IF144, IFIT2, OAS3, USP18, BIRC4BP; or LAMP3, OASL, RSAD2, IF144, IFIT2, OAS3, USP18, gene detected by probe 229450_at; or LAMP3, OASL, RSAD2, IF144, IFIT2, OAS3, USP18, gene detected by probe 235276_at; or OASL, RSAD2, IF144, IFIT2, OAS3, USP18, SIGLEC1, HERC5; or OASL, RSAD2, IF144, IFIT2, OAS3, USP18, SIGLEC1, DNAPTP6; or OASL, 25 RSAD2, IF144, IFIT2, OAS3, USP18, SIGLEC1, LOC129607; or OASL, RSAD2, IF144, IFIT2, OAS3, USP18, SIGLEC1, EPST1l; or OASL, RSAD2, IF144, IFIT2, OAS3, USP18, SIGLEC1, BIRC4BP; or OASL, RSAD2, IF144, IFIT2, OAS3, USP18, SIGLEC1, gene detected by probe 229450_at; or OASL, RSAD2, IF144, IFIT2, OAS3, USP18, SIGLEC1, gene detected by probe 235276_at; or RSAD2, IF144, IFIT2, OAS3, USP18, SIGLEC1, 30 HERC5, DNAPTP6; or RSAD2, IF144, IFIT2, OAS3, USP18, SIGLEC1, HERC5, LOC129607; or RSAD2, IF144, IFIT2, OAS3, USP18, SIGLEC1, HERC5, EPST1l; or RSAD2, IF144, IFIT2, OAS3, USP18, SIGLEC1, HERC5, gene detected by probe 229450_at; or RSAD2, IF144, IFIT2, OAS3, USP18, SIGLEC1, HERC5, BIRC4BP; or RSAD2, IF144, IFIT2, OAS3, USP18, SIGLEC1, HERC5, gene detected by probe 235276_at; or IF144, IFIT2, C:\poi\word\SPEC-8541 93[1]. docx 39 OAS3, USP18, SIGLEC1, HERC5, DNAPTP6, LOC129607; or IF144, IFIT2, OAS3, USP18, SIGLEC1, HERC5, DNAPTP6, EPST1l; or IF144, IFIT2, OAS3, USP18, SIGLEC1, HERC5, DNAPTP6, BIRC4BP; or IF144, IFIT2, OAS3, USP18, SIGLEC1, HERC5, DNAPTP6, gene detected by probe 229450_at; or IF144, IFIT2, OAS3, USP18, SIGLEC1, HERC5, DNAPTP6, 5 gene detected by probe 235276_at; or IFIT2, OAS3, USP18, SIGLEC1, HERC5, DNAPTP6, LOC129607, EPST1l; or IFIT2, OAS3, USP18, SIGLEC1, HERC5, DNAPTP6, LOC129607, BIRC4BP; or IFIT2, OAS3, USP18, SIGLEC1, HERC5, DNAPTP6, LOC129607, gene detected by probe 229450_at; or IFIT2, OAS3, USP18, SIGLEC1, HERC5, DNAPTP6, LOC129607, gene detected by probe 235276_at; or OAS3, USP18, SIGLEC1, HERC5, 10 DNAPTP6, LOC129607, EPSTI1, BIRC4BP; or OAS3, USP18, SIGLEC1, HERC5, DNAPTP6, LOC129607, EPSTI1, gene detected by probe 229450_at; or OAS3, USP18, SIGLEC1, HERC5, DNAPTP6, LOC129607, EPSTI1, gene detected by probe 235276_at; or USP18, SIGLEC1, HERC5, DNAPTP6, LOC129607, EPSTI1, BIRC4BP, gene detected by probe 229450_at; or USP18, SIGLEC1, HERC5, DNAPTP6, LOC129607, EPSTI1, 15 BIRC4BP, gene detected by probe 235276_at; or SIGLEC1, HERC5, DNAPTP6, LOC129607, EPSTI1, BIRC4BP, gene detected by probe 229450_at, gene detected by probe 235276_at. The IFNa-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. 20 The IFNa-inducible PD markers in an expression profile may include any at least 12 genes such as, for example: MX1, LLY6E, IF127, OAS1, IFIT1, IF16, IF144L, ISG15, LAMP3, OASL, RSAD2, IF144; or MX1, LLY6E, IF127, OAS1, IFIT1, IF16, IF144L, ISG15, LAMP3, OASL, RSAD2, IFIT2; or MX1, LLY6E, IF127, OAS 1, IFIT1, IF16, IF144L, ISG15, LAMP3, OASL, RSAD2, OAS3; or MX1, LLY6E, IF127, OAS1, IFIT1, IF16, IF144L, ISG15, 25 LAMP3, OASL, RSAD2, USP18; or MX1, LLY6E, IF127, OAS1, IFIT1, IF16, IF144L, ISG15, LAMP3, OASL, RSAD2, SIGLECl; or MX1, LLY6E, IF127, OAS1, IFIT1, IF16, IF144L, ISG15, LAMP3, OASL, RSAD2, HERC5; or MX1, LLY6E, IF127, OAS1, IFIT1, IF16, IF144L, ISG15, LAMP3, OASL, RSAD2, DNAPTP6; or MX1, LLY6E, IF127, OAS1, IFIT1, IF16, IF144L, ISG15, LAMP3, OASL, RSAD2, LOC129607; or MX1, LLY6E, IF127, 30 OAS1, IFIT1, IF16, IF144L, ISG15, LAMP3, OASL, RSAD2, EPST1l; or MX1, LLY6E, IF127, OAS1, IFIT1, IF16, IF144L, ISG15, LAMP3, OASL, RSAD2, BIRC4BP; or MX1, LLY6E, IF127, OAS1, IFIT1, IF16, IF144L, ISG15, LAMP3, OASL, RSAD2, gene detected by probe 229450at; or MX1, LLY6E, IF127, OAS1, IFIT1, IF16, IF144L, ISG15, LAMP3, OASL, RSAD2, gene detected by probe 235276_at; or LLY6E, IF127, OAS1, IFIT1, IF16, C:\poi\word\SPEC-8541 93[1].docx 40 1FI44L, ISG15, LAMP3, GASL, RSAD2, 1F144, JFJT2; or LLY6E, 1F127, GAS 1, IFITi, 1F16, 1FI44L, ISG15, LAMP3, OASL, RSAD2, 1F144, GAS3; or LLY6E, 1F127, GAS 1, IFITi, 1F16, 1FI44L, JSG15, LAMP3, OASL, RSAD2, 1F144, USP18; or LLY6E, 1F127, QASi, IFIT1, 1F16, 1FI44L, JSG15, LAMP3, OASL, RSAD2, 1F144, SIGLECi; or LLY6E, 1F127, GASi, 5 IFITi, 1F16, 1FI44L, JSG15, LAMP3, OASL, RSAD2, 1F144, HERC5; or LLY6E, 1F127, GAS 1, IFITi, 1F16, 1FI44L, JSG15, LAMP3, OASL, RSAD2, 1F144, DNAPTP6; or LLY6E, 1F127, GAS 1, IFITi, 1F16, 1FI44L, JSG15, LAMP3, GASL, RSAD2, 1F144, LGC129607; or LLY6E, 1F127, GASi, IFITi, 1F16, 1FI44L, ISG15, LAMP3, GASL, RSAD2, 1F144, EPSTJ1; or LLY6E, 1F127, GAS 1, IFITi, 1F16, 1FI44L, JSG15, LAMP3, GASL, RSAD2, 1F144, 10 BJRC4BP; or LLY6E, 1F127, GASi, IFIT1, 1F16, 1FI44L, JSG15, LAMP3, GASL, RSAD2, 1F144, gene detected by probe 229450_at; or LLY6E, 1F127, GAS 1, IFITi, 1F16, 1FI44L, JSG15, LAMP3, GASL, RSAD2, 1F144, gene detected by probe 235276_at; or 1F127, GAS 1, IFIT1, 1F16, 1FI44L, JSG15, LAMP3, GASL, RSAD2, 1F144, IFIT2, GAS; or 1F127, GAS 1, IFIT1, 1F16, 1FI44L, JSG15, LAMP3, GASL, RSAD2, 1F144, IFIT2, USP18; or 1F127, OASi1, 15 IFITi, 1F16, 1FI44L, JSG15, LAMP3, GASL, RSAD2, 1F144, IFIT2, SIGLECi; or 1F127, GAS 1, IFITi1, 1F16, 1FI44L, IS G15, LAMP3, GASL, RSAD2, 1F144, IFIT2, HERC5; or 1F127, GAS 1, IFITi, 1F16, 1FI44L, I5G15, LAMP3, GASL, RSAD2, 1F144, IFIT2, DNAPTP6; or 1F127, GAS 1, IFITi, 1F16, 1FI44L, ISGiS, LAMP3, GASL, RSAD2, 1F144, IFIT2, LGC129607; or 1F127, GASi, IFIT1, 1F16, 1FI44L, ISGiS, LAMP3, GASL, RSAD2, 1F144, 20 IFIT2, EPSTJ1; or 1F127, GAS 1, IFITi, 1F16, 1FI44L, ISGiS, LAMP3, GASL, RSAD2, 1F144, IFIT2, BJRC4BP; or 1F127, GASi, IFIT1, 1F16, 1FI44L, ISGiS, LAMP3, GASL, RSAD2, 1F144, IFIT2, gene detected by probe 229450at; or 1F127, GAS 1, IFITi1, 1F16, 1FI44L, IS G15, LAMP3, GASL, RSAD2, 1F144, IFIT2, gene detected by probe 235 276_at; or GAS 1, IFITi, 1F16, 1FI44L, ISGiS, LAMP3, GASL, RSAD2, 1F144, IFIT2, GAS3, USP18; or GASi, IFIT1, 25 1F16, 1FI44L, ISGiS, LAMP3, GASL, RSAD2, 1F144, IFIT2, GAS3, SIGLECi; or GASi, IFITi, 1F16, 1FI44L, ISGiS, LAMP3, GASL, RSAD2, 1F144, IFIT2, GAS3, HERC5; or GAS 1, IFITi, 1F16, 1FI44L, ISGiS, LAMP3, GASL, RSAD2, 1F144, IFIT2, GAS3, DNAPTP6; or GAS 1, IFITi, 1F16, 1FI44L, ISGiS, LAMP3, GASL, RSAD2, 1F144, IFIT2, GAS3, LGC129607; or GASi, IFIT1, 1F16, 1FI44L, ISGiS, LAMP3, GASL, RSAD2, 1F144, 30 IFIT2, GAS3, EPSTJ1; or GASi, IFIT1, 1F16, 1FI44L, ISGiS, LAMP3, GASL, RSAD2, 1F144, IFIT2, GAS3, BJRC4BP; or GASi, IFIT1, 1F16, 1FI44L, ISGiS, LAMP3, GASL, RSAD2, 1F144, IFIT2, GAS3, gene detected by probe 229450_at; or GAS 1, IFITi, 1F16, 1FI44L, ISGiS, LAMP3, GASL, RSAD2, 1F144, IFIT2, GAS3, gene detected by probe 235276 at; or IFIT1, 1F16, 1FI44L, ISGiS, LAMP3, GASL, RSAD2, 1F144, IFIT2, GAS3, C:\poiwor\S P EC-8541 93[l ]. doc 41 USP18, SIGLECl; or IFIT1, IF16, IF144L, ISG15, LAMP3, OASL, RSAD2, IF144, IFIT2, OAS3, USP18, HERC5; or IFIT1, IF16, IF144L, ISG15, LAMP3, OASL, RSAD2, IF144, IFIT2, OAS3, USP18, DNAPTP6; or IFIT1, IF16, IF144L, ISG15, LAMP3, OASL, RSAD2, IF144, IFIT2, OAS3, USP18, LOC129607; or IFIT1, IF16, IF144L, ISG15, LAMP3, OASL, 5 RSAD2, IF144, IFIT2, OAS3, USP18, EPST1l; or IFIT1, IF16, IF144L, ISG15, LAMP3, OASL, RSAD2, IF144, IFIT2, OAS3, USP18, BIRC4BP; or IFIT1, IF16, IF144L, ISG15, LAMP3, OASL, RSAD2, IF144, IFIT2, OAS3, USP18, gene detected by probe 229450_at; or IFIT1, IF16, IF144L, ISG15, LAMP3, OASL, RSAD2, IF144, IFIT2, OAS3, USP18, gene detected by probe 235276_at; or IF16, IF144L, ISG15, LAMP3, OASL, RSAD2, IF144, IFIT2, 10 OAS3, USP18, SIGLEC1, HERC5; or IF16, IF144L, ISG15, LAMP3, OASL, RSAD2, IF144, IFIT2, OAS3, USP18, SIGLEC1, DNAPTP6; or IF16, IF144L, ISG15, LAMP3, OASL, RSAD2, IF144, IFIT2, OAS3, USP18, SIGLEC1, LOC129607; or IF16, IF144L, ISG15, LAMP3, OASL, RSAD2, IF144, IFIT2, OAS3, USP18, SIGLEC1, EPST1l; or IF16, IF144L, ISG15, LAMP3, OASL, RSAD2, IF144, IFIT2, OAS3, USP18, SIGLEC1, BIRC4BP; or IF16, 15 IF144L, ISG15, LAMP3, OASL, RSAD2, IF144, IFIT2, OAS3, USP18, SIGLEC1, gene detected by probe 229450_at; or IF16, IF144L, ISG15, LAMP3, OASL, RSAD2, IF144, IFIT2, OAS3, USP18, SIGLEC1, gene detected by probe 235276_at; or IF144L, ISG15, LAMP3, OASL, RSAD2, IF144, IFIT2, OAS3, USP18, SIGLEC1, HERC5, DNAPTP6; or IF144L, ISG15, LAMP3, OASL, RSAD2, IF144, IFIT2, OAS3, USP18, SIGLEC1, HERC5, 20 LOC129607; or IF144L, ISG15, LAMP3, OASL, RSAD2, IF144, IFIT2, OAS3, USP18, SIGLEC1, HERC5, EPST1l; or IF144L, ISG15, LAMP3, OASL, RSAD2, IF144, IFIT2, OAS3, USP18, SIGLEC1, HERC5, BIRC4BP; or IF144L, ISG15, LAMP3, OASL, RSAD2, IF144, IFIT2, OAS3, USP18, SIGLEC1, HERC5, gene detected by probe 229450at; or IF144L, ISG15, LAMP3, OASL, RSAD2, IF144, IFIT2, OAS3, USP18, SIGLEC1, HERC5, 25 gene detected by probe 235276_at; or ISG15, LAMP3, OASL, RSAD2, IF144, IFIT2, OAS3, USP18, SIGLEC1, HERC5, DNAPTP6, LOC129607; or ISG15, LAMP3, OASL, RSAD2, IF144, IFIT2, OAS3, USP18, SIGLEC1, HERC5, DNAPTP6, EPST1l; or ISG15, LAMP3, OASL, RSAD2, IF144, IFIT2, OAS3, USP18, SIGLEC1, HERC5, DNAPTP6, BIRC4BP; or ISG15, LAMP3, OASL, RSAD2, IF144, IFIT2, OAS3, USP18, SIGLEC1, HERC5, 30 DNAPTP6, gene detected by probe 229450_at; or ISG15, LAMP3, OASL, RSAD2, IF144, IFIT2, OAS3, USP18, SIGLEC1, HERC5, DNAPTP6, gene detected by probe 235276_at; or LAMP3, OASL, RSAD2, IF144, IFIT2, OAS3, USP18, SIGLEC1, HERC5, DNAPTP6, LOC129607, EPST1l; or LAMP3, OASL, RSAD2, IF144, IFIT2, OAS3, USP18, SIGLEC1, HERC5, DNAPTP6, LOC129607, BIRC4BP; or LAMP3, OASL, RSAD2, IF144, IFIT2, C:\poi\word\SPEC-8541 93[1]. docx 42 OAS3, USP18, SIGLEC1, HERC5, DNAPTP6, LOC129607, gene detected by probe 229450_at; or LAMP3, OASL, RSAD2, IF144, IFIT2, OAS3, USP18, SIGLEC1, HERC5, DNAPTP6, LOC129607, gene detected by probe 235276_at; or OASL, RSAD2, IF144, IFIT2, OAS3, USP18, SIGLEC1, HERC5, DNAPTP6, LOC129607, EPSTI1, BIRC4BP; or OASL, 5 RSAD2, IF144, IFIT2, OAS3, USP18, SIGLEC1, HERC5, DNAPTP6, LOC129607, EPSTI1, gene detected by probe 229450_at; or OASL, RSAD2, IF144, IFIT2, OAS3, USP18, SIGLEC1, HERC5, DNAPTP6, LOC129607, EPSTI1, gene detected by probe 235276_at; or RSAD2, IF144, IFIT2, OAS3, USP18, SIGLEC1, HERC5, DNAPTP6, LOC129607, EPSTI1, BIRC4BP, gene detected by probe 229450_at; or RSAD2, IF144, IFIT2, OAS3, USP18, 10 SIGLEC1, HERC5, DNAPTP6, LOC129607, EPSTI1, BIRC4BP, gene detected by probe 229450_at; or IF144, IFIT2, OAS3, USP18, SIGLEC1, HERC5, DNAPTP6, LOC129607, EPSTI1, BIRC4BP, gene detected by probe 229450at gene detected by probe 235276_at. The IFNa-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 15 26, and/or 28 and/or 30. The IFNa-inducible PD markers in an expression profile may include at least genes IF127, SIGLEC1, RSAD2, IF16, IF144L, IF144, USP18, IFIT2, SAMD9L, BIRC4BP, DNAPTP6, OAS3, LY6E, IFIT1, LIPA, LOC129607, ISG15, PARP14, MX1, OAS2, OASL, CCL2, HERC5, OAS 1. The IFNa-inducible PD markers in such an expression profile may 20 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 IFNa-inducible PD markers in an expression profile may include at least genes IFIT1, IFIT3, IRF7, IF16, IL6ST, IRF2, LY6E, MARCKS, MX1, MX2, OAS1, EIF2AK2, ISG15, STAT2, OAS3, IF144, IF144L, HERC5, RAB8B, LILRA5, RSAD2, and FCHO2. The 25 IFNa-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 IFNa-inducible PD markers in an expression profile may include at least genes SERPING1, IFIT2, IFIT3, IF16, LY6E, MX1, OAS1, ISG15, IF127, OAS3, IF144, LAMP3, 30 DNAPTP6, ETV7, HERC5, OAS2, USP18, XAF1, RTP4, SIGLEC1, and EPSTIl. The IFNa 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. C:\poi\word\SPEC-8541 93[1].docx 43 The IFNa-inducible PD markers in an expression profile may include at least genes SERPING1, IFIT2, IFIT3, IF16, LY6E, MX1, OAS1, ISG15, IF127, OAS3, IF144, LAMP3, DNAPTP6, ETV7, HERC5, OAS2, USP18, XAF1, RTP4, SIGLEC1, EPSTI1, and RSAD2. The IFNa-inducible PD markers in such an expression profile may further include at least one 5 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 IFNa-inducible PD markers in an expression profile may include at least genes BCL2, BAK1, BAD, BAX, and BCL2L1. The IFNa-inducible PD markers in such an expression profile may further include at least one or more gene listed in Table 19 and/or 20 10 and/or 21, and/or 22, and/or 23, and/or 24, and/or 26, and/or 28 and/or 30. The IFNa-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, IF127, DNAPTP6, LAMP3, EPSTI1, IF144, OAS2, IFIT2, and ISG15. The IFNa-inducible PD markers in such an expression profile may further include 15 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 IFNa-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, IF16, USP18, RSAD2, IF144, LY6E, ISG15, and IF127. 20 The IFNa-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 IFNa-inducible PD markers in an expression profile may include at least genes DNAPTP6, EPSTI1, HERC5, IF127, IF144, IF144L, IF16, IFIT1, IFIT3, ISG15, LAMP3, 25 LY6E, MX1, OAS1, OAS2, OAS3, PLSCR1, RSAD2, RTP4, SIGLEC1, and USP18. The IFNa-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 IFNa-inducible PD markers in an expression profile may include at least genes 30 SAMD9L, IF16, IF144, IFIT2, ZC3HAV1, ETV6, DAPP1, IL1RN, CEACAM1, OAS1, IF127, OAS3, IF144L, HERC5, IFIT1, EPSTI1, ISG15, SERPING1, OASL, GBP1, and MX1. The IFNa-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. C:\poi\word\SPEC-8541 93[1].docx 44 The IFNa-inducible PD markers in an expression profile may include at least genes IF16, RSAD2, IF144, IF144L, IF127, MX1, IFIT1, ISG15, LAMP3, OAS3, OAS1, EPSTI1, IFIT3, OAS2, SIGLEC1, and USP18. The IFNa-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, 5 and/or 22, and/or 23, and/or 24, and/or 26, and/or 28 and/or 30. The IFNa-inducible PD markers in an expression profile may include at least genes IF16, RSAD2, IF144, IF144L, IF127, MX1, IFIT1, HERC5, ISG15, LAMP3, OAS3, OAS1, EPSTI1, IFIT3, OAS2, LY6E, SIGLEC1, and USP18. The IFNa-inducible PD markers in such an expression profile may further include at least one or more gene listed in Table 19 10 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 IFNa-inducible PD markers in an expression profile may include at least genes IF16, RSAD2, IF144, IF144L, IF127, MX1, and IFIT1. The IFNa-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. 15 The IFNa-inducible PD markers in an expression profile may include at least genes IF16, RSAD2, IF144, IF144L, and IF127. The IFNa-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 IFNa-inducible PD markers in an expression profile may include at least genes 20 SAMD9L, IF16, IF144, IFIT2, OAS1, IF127, OAS3, IF144L, HERC5, IFIT1, EPSTI1, ISG15, SERPING1, OASL, GBP1, and MX1. The IFNa-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 IFNa-inducible PD markers in an expression profile may include at least genes 25 IF127, 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 IFNa-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 30 22, and/or 23, and/or 24, and/or 26, and/or 28 and/or 30. The IFNa-inducible PD markers in an expression profile may include at least genes complement factor B, insulin-like growth factor (IGF2BP3), cyclin Al, neuropilin 2, complement lqB, complement lqC, CD80, CD47, MMP14, toll-like receptor 3 (TLR3), TLR adaptor molecule 2 (TICAM2), macrophage scavenger receptor-1 (MSR1), desmoplakin, C:\poi\word\SPEC-8541 93[1].docx 45 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 IFNa-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, 5 and/or 28 and/or 30. The IFNa-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-lra, IL-3, MCP-1, MMP-3, myoglobin, SGOT, 10 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 IFNa-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, 15 beta-2 microglobulin, cancer antigen 125, cancer antigen 19-9, eotaxin, FABP, factor VII, ferritin, IL-10, IL-12p70, IL-16, IL-18, IL-lra, IL-3, MCP-1, MMP-3, myoglobin, SGOT, tissue factor, TIMP-1, TNF RII, TNF-alpha, VCAM-1, or vWF. The IFNa-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. 20 The IFNa-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 IFNa 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 25 28 and/or 30. An IFNa-inducible PD marker expression profile may further include genes whose expression or activity is down-regulated in cells exposed to non-baseline IFNa 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, 30 FCER1A, BACH2, KLRB 1, D4S234E, T cell receptor alpha locus/T cell receptor delta locus, FEZ1, AFF3, CD160, ABCB1, PTCH1, OR2W3, IGHD, NOG, NR3C2, TNS1, PDZK1IP1, SH2D1B, STRBP, ZMYND11, TMOD1, FCRLA, DKFZp761PO423, EPB42, NR6A1, LOC341333, MS4A1, IGHM, SIGLECP3, KIR2DS2, PKIA, BLR1, C5orf4, MYLK, LOC283663, MAD1L1, CXCL5, D4S234E, FCRLA, KRT1, cl6orf74, ABCB4, or C:\poi\word\SPEC-8541 93[1]. docx 46 GPRASPl. Any number of these genes may serve as PD markers in an IFNa-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 5 included in the IFNa-inducible PD marker expression profile. The IFNa-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 IFNa-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, 10 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 IFNa-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. 15 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 20 or cells not exposed to IFNa in culture. Up- or down-regulation of gene expression or activity of IFNa-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 25 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 IFNa-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, 30 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-lra, IL-3, MCP-1, MMP-3, myoglobin, SGOT, tissue factor, TIMP-1, TNF RII, TNF-alpha, VCAM-1, vWF, BDNK, complement 3, CD40 ligand, C:\poi\word\SPEC-8541 93[1]. docx 47 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 IFNa-inducible PD marker expression profile may comprise a profile of protein 5 activity. Up- or down-regulation of gene expression or activity of IFNa-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 IFNa-inducible PD markers may be determined by detecting any combination of these gene expression levels or activities. 10 A candidate therapeutic for treating IFNa-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 15 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 IFNa-inducible 20 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 IFNa-inducible PD marker expression profile, commercially available immortalized cell lines that have been treated with IFNa to induce an IFNa-inducible PD marker expression profile, cells isolated from a patient having an IFNa-inducible PD marker expression profile, or cells isolated from a 25 healthy patient and treated with IFNa to induce an IFNa-inducible PD marker expression profile. Presence or absence of a change in the IFNa-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 IFNa-inducible PD marker expression profile including at least a 10% 30 decrease in up-regulated expression or activity of at least 1 gene in the IFNa-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 C:\poi\word\SPEC-8541 93[1].docx 48 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 5 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 IFNa-inducible PD marker expression profile including at least a 10% increase in expression or activity of at least 1 down-regulated 10 gene in the IFNa-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 15 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 20 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 IFNa activity, or an agent that binds to and does not modulate type I 25 IFN or IFNa activity, or a combination of agents that may or may not include an agent that binds to and modulates type I IFN or IFNa activity. Type I IFN or IFNa inducible PD marker expression profiles are obtained in the (before and after agent administration) samples. The type I IFN or IFNa inducible PD marker expression profiles in the samples are compared. Comparison may be of the number of type I IFN or IFNa inducible PD markers present in the 30 samples or may be of the quantity of type I IFN or IFNa 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 IFNa inducible PD markers decreases in the sample obtained after administration of the therapeutic agent relative to the sample obtained before administration of the therapeutic C:\poi\word\SPEC-8541 93[1].docx 49 agent. The number of up-regulated type I IFN or IFNa 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 IFNa 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 5 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 IFNa 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 IFNa inducible PD markers may 10 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 IFNa 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 IFNa inducible PD markers may decrease by at least 1, at least 15 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 IFNa 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 IFNa inducible PD markers with increased levels may be at least 1, at 20 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 IFNa inducible PD markers may indicate efficacy. The sample obtained from the patient may be obtained prior to a first administration of 25 the agent, i.e., the patient is naive 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 IFNa inducible PD markers in the samples are compared. The samples may 30 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 IFNa 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 C:\poi\word\SPEC-8541 93[1].docx 50 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 5 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 10 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 15 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 20 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. 25 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 IFNa inducible PD markers increases in a later-obtained sample relative to an earlier obtained sample. The number of type I IFN or IFNa inducible PD markers may increase by at least 1, 30 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 IFNa 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 C:\poi\word\SPEC-8541 93[1].docx 51 I IFN or IFNa 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 IFNa inducible PD markers with increased levels may be at least 1, at least 2, at least 3, at least 4, at least 5, at 5 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 IFNa 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 IFNa 10 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 IFNa 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 IFNa inducible PD markers 15 decreases in a later-obtained sample relative to an earlier obtained sample. The number of type I IFN or IFNa 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 IFNa inducible PD marker decreases by at least 10%, at least 20%, at least 25%, at least 30%, at least 35%, at least 40%, 20 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 IFNa 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 IFNa inducible PD markers with 25 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 IFNa 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 30 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, C:\poi\word\SPEC-8541 93[1].docx 52 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. 5 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 IFNa-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 10 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, 15 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 20 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. 25 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. 30 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., C:\poi\word\SPEC-8541 93[1].dox 53 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). 5 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 10 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 15 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 TM (Invitrogen), GENEJUICE@ (Novagen), GENEJAMMER@ (Stratagene), FUGENE@ HD (Roche), MEGAFECTIN T M (Qbiogene), SUPERFECT@ (Qiagen), and EFFECTENE@ (Qiagen). 20 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. Patents 5,972,901, 6,008,336, and 6,077,835. Nanospheres are described in U.S. Patent 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 25 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 30 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 C:\poi\word\SPEC-8541 93[1].docx 54 transferase, p-galactosidase, green fluorescent protein, p-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 5 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). 10 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 15 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. 20 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 IFNa-mediated 25 disease or disorder comprising: administering an agent that binds to and modulates type I IFN or IFNa activity; wherein the patient comprises a type I IFN or IFNa-inducible PD marker expression profile; and wherein the agent neutralizes the type I IFN or IFNa-inducible PD marker 30 expression profile of the patient. Embodiment 2. The method of 1 further comprising detecting neutralization of the type I IFN or IFNa-inducible PD marker expression profile of the patient. C:\poi\word\SPEC-8541 93[1].docx 55 Embodiment 3. The method of embodiment 1 wherein the type I IFN or IFNa-inducible PD marker expression profile comprises up-regulated expression or activity of genes MX1, LY6E, IF127, OAS 1 IFIT1, IF16, IF144L, ISG15, LAMP3, OASL, RSAD2, and IF144. Embodiment 4. The method of embodiment 1 wherein the agent is a biologic agent. 5 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 IFNa subtype but is not MEDI-545. Embodiment 8. The method of embodiment 1 wherein the administering the agent alleviates 10 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 .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. 15 Embodiment 11. The method of embodiment 10 wherein the antibody is administered at a dose between .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 IFNa-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 20 or IFNa-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 IFNa-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 IFNa-inducible PD marker expression profile of the patient by at least 40%. 25 Embodiment 16. The method of embodiment 15 wherein the agent neutralizes the type I IFN or IFNa-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 IFNa-mediated disease or disorder is one of lupus, psoriasis, vasculitis, sarcoidosis, Sjogren's syndrome, or idiopathic inflammatory myositis. C:\poi\word\SPEC-8541 93[1].docx 56 Embodiment 18. The method of embodiment 17 wherein the type I IFN or an IFNa-mediated disease or disorder is lupus. Embodiment 19. The method of embodiment 17 wherein the type I IFN or an IFNa-mediated disease or disorder is psoriasis. 5 Embodiment 20. The method of embodiment 1 wherein the type I IFN or IFNa-inducible PD marker expression profile comprises up-regulated expression or activity of at least IFNa subtypes 1, 2, 8, and 14. Embodiment 21. The method of embodiment 1 wherein the type I IFN or IFNa-inducible PD marker expression profile comprises transcripts of PD marker genes. 10 Embodiment 22. The method of embodiment 1 wherein the type I IFN or IFNa-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 IFNa-inducible PD marker expression profile comprises up-regulated expression or activity of genes IFI27, SIGLEC1, RSAD2, IF16, IF144L, IF144, USP18, IFIT2, SAMD9L, BIRC4BP, DNAPTP6, 15 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 IFNa-inducible PD marker expression profile comprises up-regulated expression or activity of genes IFIT1, IFIT3, IRF7, IF16, IL6ST, IRF2, LY6E, MARCKS, MX1, MX2, OAS1, EIF2AK2, ISG15, STAT2, 20 OAS3, IF144, IF144L, HERC5, RAB8B, LILRA5, RSAD2, and FCHO2 Embodiment 25. The method of embodiment 1 wherein the type I IFN or IFNa-inducible PD marker expression profile comprises up-regulated expression or activity of genes SERPING1, IFIT2, IFIT3, IF16, LY6E, MX1, OAS1, ISG15, IF127, OAS3, IF144, LAMP3, DNAPTP6, ETV7, HERC5, OAS2, USP18, XAF1, RTP4, SIGLEC1, and EPSTIl. 25 Embodiment 26. The method of embodiment 1 wherein the type I IFN or IFNa-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, IF127, DNAPTP6, LAMP3, EPSTI1, IF144, OAS2, IFIT2, and ISG15. Embodiment 27. The method of embodiment 1 wherein the type I IFN or IFNa-inducible PD 30 marker expression profile comprises up-regulated expression or activity of genes LAMP3, C:\poi\word\SPEC-8541 93[1].docx 57 SIGLEC1, DNAPTP6, IFIT2, ETV7, RTP4, SERPING1, HERC5, XAF1, MX1, EPSTI1, OAS2, OAS 1, OAS3, IFIT3, IF16, USP18, RSAD2, IF144, LY6E, ISG15, and IF127. Embodiment 28. The method of embodiment 1 wherein the type I IFN or IFNa-inducible PD marker expression profile comprises up-regulated expression or activity of genes DNAPTP6, 5 EPSTI1, HERC5, IF127, IF144, IF144L, IF16, 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 IFNa-inducible PD marker expression profile comprises up-regulated expression or activity of genes SAMD9L, IF16, IF144, IFIT2, ZC3HAV1, ETV6, DAPP1, IL1RN, CEACAM1, OAS1, IF127, OAS3, 10 IFI44L, HERC5, IFIT1, EPSTI1, ISG15, SERPING1, OASL, GBP1, and MX1. Embodiment 30. The method of embodiment 1 wherein the type I IFN or IFNa-inducible PD marker expression profile comprises up-regulated expression or activity of genes SAMD9L, IFI6, IFI44, IFIT2, OAS 1, IFI27, OAS3, IFI44L, HERC5, IFIT1, EPSTI1, ISG15, SERPING1, OASL, GBP1, and MX1. 15 Embodiment 31. The method of embodiment 1 wherein the type I IFN or IFNa-inducible PD marker expression profile comprises up-regulated expression or activity of genes IF16, RSAD2, IF144, IF144L, IF127, 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 IFNa-inducible PD 20 marker expression profile comprises up-regulated expression or activity of genes IF16, RSAD2, IF144, IF144L, and IF127. Embodiment 33. The method of embodiment 32 wherein the type I IFN or IFNa-inducible PD marker expression profile further comprises up-regulated expression or activity of genes MX1 and IFIT1. 25 Embodiment 34. The method of embodiment 33 wherein the type I IFN or IFNa-inducible PD marker expression profile further comprises up-regulated expression or activity of genes OAS2 and OAS 1. Embodiment 35. The method of any one of embodiments 3 or 23-33 wherein the type I IFN or IFNa-inducible PD marker expression profile further comprises down-regulated expression or 30 activity of genes NOG, SLC4A1, PRSS33, and FEZ1. C:\poi\word\SPEC-8541 93[1].docx 58 Embodiment 36. The method of embodiment 1 wherein the type I IFN or IFNa-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 5 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. 10 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 IFNa PD marker profile comprising: administering an agent that binds to and modulates type I IFN or IFNa activity; 15 wherein the agent neutralizes the type I IFN or IFNa-inducible PD marker expression profile of the patient. Embodiment 42. The method of 41 further comprising detecting neutralization of the type I IFN or IFNa-inducible PD marker expression profile of the patient. Embodiment 43. The method of embodiment 41 wherein the type I IFN or IFNa-inducible PD 20 marker expression profile comprises up-regulated expression or activity of genes MX1, LY6E, IFI27, OAS 1 IFIT1, IF16, IF144L, ISG15, LAMP3, OASL, RSAD2, and IF144. Embodiment 44. The method of embodiment 41 wherein the type I IFN or IFNa-inducible PD marker expression profile comprises up-regulated expression or activity of genes IF127, SIGLEC1, RSAD2, IF16, IF144L, IF144, USP18, IFIT2, SAMD9L, BIRC4BP, DNAPTP6, 25 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 IFNa-inducible PD marker expression profile comprises up-regulated expression or activity of genes IFIT1, IFIT3, IRF7, IF16, IL6ST, IRF2, LY6E, MARCKS, MX1, MX2, OAS1, EIF2AK2, ISG15, STAT2, 30 OAS3, IF144, IF144L, HERC5, RAB8B, LILRA5, RSAD2, and FCHO2 C:\poi\word\SPEC-8541 93[1].docx 59 Embodiment 46. The method of embodiment 41 wherein the type I IFN or IFNa-inducible PD marker expression profile comprises up-regulated expression or activity of genes SERPING1, IFIT2, IFIT3, IF16, LY6E, MX1, OAS1, ISG15, IF127, OAS3, IF144, LAMP3, DNAPTP6, ETV7, HERC5, OAS2, USP18, XAF1, RTP4, SIGLEC1, and EPSTIl. 5 Embodiment 47. The method of embodiment 41 wherein the type I IFN or IFNa-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 IFNa-inducible PD 10 marker expression profile comprises up-regulated expression or activity of genes LAMP3, SIGLEC1, DNAPTP6, IFIT2, ETV7, RTP4, SERPING1, HERC5, XAF1, MX1, EPSTI1, OAS2, OAS 1, OAS3, IFIT3, IFI6, USP18, RSAD2, IFI44, LY6E, ISG15, and IFI27. Embodiment 49. The method of embodiment 41 wherein the type I IFN or IFNa-inducible PD marker expression profile comprises up-regulated expression or activity of genes DNAPTP6, 15 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 IFNa-inducible PD marker expression profile comprises up-regulated expression or activity of genes SAMD9L, IF16, IF144, IFIT2, ZC3HAV1, ETV6, DAPP1, IL1RN, CEACAM1, OAS1, IF127, OAS3, 20 IF144L, HERC5, IFIT1, EPSTI1, ISG15, SERPING1, OASL, GBP1, and MX1. Embodiment 51. The method of embodiment 41 wherein the type I IFN or IFNa-inducible PD marker expression profile comprises up-regulated expression or activity of genes SAMD9L, IF16, IF144, IFIT2, OAS 1, IF127, OAS3, IF144L, HERC5, IFIT1, EPSTI1, ISG15, SERPING1, OASL, GBP1, and MX1. 25 Embodiment 52. The method of embodiment 41 wherein the type I IFN or IFNa-inducible PD marker expression profile comprises up-regulated expression or activity of genes IF16, RSAD2, IF144, IF144L, IF127, 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 IFNa-inducible PD 30 marker expression profile comprises up-regulated expression or activity of genes IF16, RSAD2, IF144, and IF127. C:\poi\word\SPEC-8541 93[1].docx 60 Embodiment 54. The method of embodiment 53 wherein the type I IFN or IFNa-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 IFNa-inducible PD 5 marker expression profile comprises up-regulated expression or activity of at least IFNa 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. 10 Embodiment 59. The method of embodiment 57 wherein the antibody is specific for one or more type I IFN or IFNa 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 15 dose between approximately .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 .03 and 1 mg/kg. 20 Embodiment 64. The method of embodiment 41 wherein the wherein the agent neutralizes the type I IFN or IFNa-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 IFNa-inducible PD marker expression profile by at least 20%. Embodiment 66. The method of embodiment 65 wherein the agent neutralizes the type I IFN 25 or IFNa-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 IFNa-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 IFNa-inducible PD marker expression profile by at least 50%. C:\poi\word\SPEC-8541 93[1].docx 61 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. 5 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 IFNa-inducible PD marker expression profile in a patient in need thereof, comprising: administering an agent that binds to and modulates type I IFN or IFNa activity to the patient; 10 wherein the agent neutralizes the type I IFN or IFNa-inducible PD marker expression profile of the patient. Embodiment 73. The method of 72 further comprising detecting neutralization of the type I IFN or IFNa-inducible PD marker expression profile of the patient. Embodiment 74. The method of embodiment 72 wherein the type I IFN or IFNa-inducible PD 15 marker expression profile comprises up-regulated expression or activity of genes MX1, LY6E, IFI27, OAS 1 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. 20 Embodiment 78. The method of embodiment 76 wherein the antibody is specific for one or more type I IFN or IFNa 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 25 dose between approximately .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 .03 and 1 mg/kg. C:\poi\word\SPEC-8541 93[1].docx 62 Embodiment 83. The method of any one of embodiments 80-82 wherein the agent neutralizes the type I IFN or IFNa-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 IFNa-inducible PD marker expression profile of the patient by at least 20%. 5 Embodiment 85. The method of embodiment 84 wherein the agent neutralizes the type I IFN or IFNa-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 IFNa-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 10 or IFNa-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. 15 Embodiment 91. The method of embodiment 72 wherein the type I IFN or IFNa-inducible PD marker expression profile comprises up-regulated expression or activity of at least IFNa subtypes 1, 2, 8, and 14. Embodiment 92. The method of embodiment 72 wherein the type I IFN or IFNa-inducible PD marker expression profile comprises transcripts of PD marker genes. 20 Embodiment 93. The method of embodiment 72 wherein the type I IFN or IFNa-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 IFNa-inducible PD marker expression profile comprises up-regulated expression or activity of genes IF127, SIGLEC1, RSAD2, IF16, IF144L, IF144, USP18, IFIT2, SAMD9L, BIRC4BP, DNAPTP6, 25 OAS3, LY6E, IFIT1, LIPA, LOC129607, ISG15, PARP14, MX1, OAS2, OASL, CCL2, HERC5, OAS 1. Embodiment 95. The method of embodiment 72 wherein the type I IFN or IFNa-inducible PD marker expression profile comprises up-regulated expression or activity of genes IFIT1, IFIT3, IRF7, IF16, IL6ST, IRF2, LY6E, MARCKS, MX1, MX2, OAS1, EIF2AK2, ISG15, STAT2, 30 OAS3, IF144, IF144L, HERC5, RAB8B, LILRA5, RSAD2, and FCHO2. C:\poi\word\SPEC-8541 93[1].docx 63 Embodiment 96. The method of embodiment 72 wherein the type I IFN or IFNa-inducible PD marker expression profile comprises up-regulated expression or activity of genes SERPING1, IFIT2, IFIT3, IF16, LY6E, MX1, OAS1, ISG15, IF127, OAS3, IF144, LAMP3, DNAPTP6, ETV7, HERC5, OAS2, USP18, XAF1, RTP4, SIGLEC1, and EPSTIl. 5 Embodiment 97. The method of embodiment 72 wherein the type I IFN or IFNa-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 IFNa-inducible PD 10 marker expression profile comprises up-regulated expression or activity of genes LAMP3, SIGLEC1, DNAPTP6, IFIT2, ETV7, RTP4, SERPING1, HERC5, XAF1, MX1, EPSTI1, OAS2, OAS 1, OAS3, IFIT3, IFI6, USP18, RSAD2, IFI44, LY6E, ISG15, and IFI27. Embodiment 99. The method of embodiment 72 wherein the type I IFN or IFNa-inducible PD marker expression profile comprises up-regulated expression or activity of genes DNAPTP6, 15 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 IFNa-inducible PD marker expression profile comprises up-regulated expression or activity of genes SAMD9L, IF16, IF144, IFIT2, ZC3HAV1, ETV6, DAPP1, IL1RN, CEACAM1, OAS 1, IF127, 20 OAS3, IF144L, HERC5, IFIT1, EPSTI1, ISG15, SERPING1, OASL, GBP1, and MX1. Embodiment 101. The method of embodiment 72 wherein the type I IFN or IFNa-inducible PD marker expression profile comprises up-regulated expression or activity of genes SAMD9L, IF16, IF144, IFIT2, OAS1, IF127, OAS3, IF144L, HERC5, IFIT1, EPSTI1, ISG15, SERPING1, OASL, GBP1, and MX1. 25 Embodiment 102. The method of embodiment 72 wherein the type I IFN or IFNa-inducible PD marker expression profile comprises up-regulated expression or activity of genes IF16, RSAD2, IF144, IF144L, IF127, 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 IFNa-inducible 30 PD marker expression profile comprises up-regulated expression or activity of genes IF16, RSAD2, IF144, IF144L, and IF127. C:\poi\word\SPEC-8541 93[1].docx 64 Embodiment 104. The method of embodiment 103 wherein the type I IFN or IFNa-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 5 IFN or IFNa-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 IFNa-inducible PD marker expression profile comprises down-regulated expression or activity of genes NOG, SLC4A1, PRSS33, and FEZ1. 10 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 15 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: 20 obtaining a first IFNa-inducible PD marker expression profile in a first sample from a patient. Embodiment 112. The method of embodiment 111 wherein the first IFNa-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 25 and the progression is an SLE flare. Embodiment 114. The method of embodiment 111 wherein the first IFNa-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 IFNa-inducible PD marker expression profile in a second sample 30 from a patient; C:\poi\word\SPEC-8541 93[1].docx 65 wherein an increase in number or level of type I IFN or IFNa 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 IFNa inducible PD markers in the second relative to the first expression profile prognoses disease regression. 5 Embodiment 116. A method of monitoring disease progression of a patient receiving treatment with a therapeutic agent that binds to and modulates IFNa activity comprising: obtaining a first IFNa-inducible PD marker expression profile in a first sample from the patient; administering a therapeutic agent that binds to and modulates IFNa activity; 10 obtaining a second IFNa-inducible PD marker expression profile in a second sample from the patient; and comparing the first and the second IFNa-inducible PD marker expression profiles, wherein a variance in the first and the second IFNa-inducible PD marker expression profiles indicates a level of efficacy of the therapeutic agent that binds to 15 and modulates IFNa activity. Embodiment 117. The method of embodiment 116 wherein the first IFNa-inducible PD marker expression profile comprises up-regulated expression or activity of genes MX1, LY6E, IF127, OAS 1, IFIT1, IFI6, IFI44L, ISG15, LAMP3, OASL, RSAD2, and IFI44 Embodiment 118. The method of embodiment 116 wherein the first type I IFN or IFNa 20 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, OAS 1. Embodiment 119. The method of embodiment 116 wherein the first type I IFN or IFNa 25 inducible PD marker expression profile comprises up-regulated expression or activity of genes IFIT1, IFIT3, IRF7, IF16, IL6ST, IRF2, LY6E, MARCKS, MX1, MX2, OAS1, EIF2AK2, ISG15, STAT2, OAS3, IF144, IF144L, HERC5, RAB8B, LILRA5, RSAD2, and FCHO2. Embodiment 120. The method of embodiment 116 wherein the first type I IFN or IFNa inducible PD marker expression profile comprises up-regulated expression or activity of genes 30 SERPING1, IFIT2, IFIT3, IF16, LY6E, MX1, OAS1, ISG15, IF127, OAS3, IF144, LAMP3, DNAPTP6, ETV7, HERC5, OAS2, USP18, XAF1, RTP4, SIGLEC1, and EPSTIl. C:\poi\word\SPEC-8541 93[1].docx 66 Embodiment 121. The method of embodiment 116 wherein the first type I IFN or IFNa 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, IF127, DNAPTP6, LAMP3, EPSTI1, IF144, OAS2, IFIT2, 5 and ISG15. Embodiment 122. The method of embodiment 116 wherein the first type I IFN or IFNa 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. 10 Embodiment 123. The method of embodiment 116 wherein the first type I IFN or IFNa 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 IFNa 15 inducible PD marker expression profile comprises up-regulated expression or activity of genes SAMD9L, IF16, IF144, IFIT2, ZC3HAV1, ETV6, DAPP1, IL1RN, CEACAM1, OAS 1, IF127, OAS3, IF144L, HERC5, IFIT1, EPSTI1, ISG15, SERPING1, OASL, GBP1, and MX1. Embodiment 125. The method of embodiment 116 wherein the first type I IFN or IFNa inducible PD marker expression profile comprises up-regulated expression or activity of genes 20 SAMD9L, IF16, IF144, IFIT2, OAS1, IF127, OAS3, IF144L, HERC5, IFIT1, EPSTI1, ISG15, SERPING1, OASL, GBP1, and MX1. Embodiment 126. The method of embodiment 116 wherein the first type I IFN or IFNa inducible PD marker expression profile comprises up-regulated expression or activity of genes IF16, RSAD2, IF144, IF144L, IF127, MX1, IFIT1, ISG15, LAMP3, OAS3, OAS1, EPSTI1, 25 IFIT3, OAS2, SIGLEC1, and USP18. Embodiment 127. The method of embodiment 116 wherein the first type I IFN or IFNa inducible PD marker expression profile comprises up-regulated expression or activity of genes IF16, RSAD2, IF144, IF144L, and IF127. Embodiment 128. The method of embodiment 116 wherein the variance is a decrease in up 30 regulated expression of activity levels of the genes. C:\poi\word\SPEC-8541 93[1].docx 67 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 5 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 IFNa-inducible PD marker expression profile is obtained prior to administration of the therapeutic agent. 10 Embodiment 135. The method of embodiment 116 wherein the first IFNa-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 IFNa 15 inducible PD marker expression profile in a third sample from the patient. Embodiment 138. The method of 137 further comprising obtaining a fourth IFNa-inducible PD marker expression profile in a fourth sample from the patient. Embodiment 139. The method of 138 further comprising obtaining a fifth IFNa-inducible PD marker expression profile in a fifth sample from the patient. 20 Embodiment 140. The method of 139 further comprising obtaining a sixth IFNa-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. 25 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 30 least two months following obtaining the third sample. C:\poi\word\SPEC-8541 93[1].docx 68 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 5 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%. 10 Embodiment 147. A method of identifying a patient as a candidate for a therapeutic agent that binds to and modulates IFNa activity comprising: detecting presence or absence of an IFNa-inducible PD marker expression profile in a sample from the patient, wherein detecting presence of the IFNa-induced PD marker expression profile 15 identifies the patient as a candidate for the therapeutic agent that binds to and modulates IFNa activity. Embodiment 148. The method of embodiment 147 wherein the IFNa-inducible PD marker expression profile comprises up-regulated expression or activity of genes MX1, LY6E, IF127, OAS 1, IFIT1, IF16, IF144L, ISG15, LAMP3, OASL, RSAD2, and IF144. 20 Embodiment 149. The method of embodiment 147 wherein type I IFN or IFNa-inducible PD marker expression profile comprises up-regulated expression or activity of genes IF127, SIGLEC1, RSAD2, IF16, IF144L, IF144, USP18, IFIT2, SAMD9L, BIRC4BP, DNAPTP6, OAS3, LY6E, IFIT1, LIPA, LOC129607, ISG15, PARP14, MX1, OAS2, OASL, CCL2, HERC5, OAS 1. 25 Embodiment 150. The method of embodiment 147 wherein the type I IFN or IFNa-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 IFNa-inducible 30 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 EPSTIl. C:\poi\word\SPEC-8541 93[1]. docx 69 Embodiment 152. The method of embodiment 147 wherein the type I IFN or IFNa-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, IF127, DNAPTP6, LAMP3, EPSTI1, IF144, OAS2, IFIT2, and ISG15. 5 Embodiment 153. The method of embodiment 147 wherein the type I IFN or IFNa-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, OAS 1, OAS3, IFIT3, IFI6, USP18, RSAD2, IFI44, LY6E, ISG15, and IFI27. Embodiment 154. The method of embodiment 147 wherein the type I IFN or IFNa-inducible 10 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 IFNa-inducible PD marker expression profile comprises up-regulated expression or activity of genes 15 SAMD9L, IF16, IF144, IFIT2, ZC3HAV1, ETV6, DAPP1, IL1RN, CEACAM1, OAS1, IF127, OAS3, IF144L, HERC5, IFIT1, EPSTI1, ISG15, SERPING1, OASL, GBP1, and MX1. Embodiment 156. The method of embodiment 147 wherein the type I IFN or IFNa-inducible PD marker expression profile comprises up-regulated expression or activity of genes SAMD9L, IF16, IF144, IFIT2, OAS1, IF127, OAS3, IF144L, HERC5, IFIT1, EPSTI1, ISG15, 20 SERPING1, OASL, GBP1, and MX1. Embodiment 157. The method of embodiment 147 wherein the type I IFN or IFNa-inducible PD marker expression profile comprises up-regulated expression or activity of genes IF16, RSAD2, IF144, IF144L, IF127, MX1, IFIT1, ISG15, LAMP3, OAS3, OAS1, EPSTI1, IFIT3, OAS2, SIGLEC1, and USP18. 25 Embodiment 158. The method of embodiment 147 wherein the type I IFN or IFNa-inducible PD marker expression profile comprises up-regulated expression or activity of genes IF16, RSAD2, IF144, IF144L, and IF127. 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 30 myositis, Sjogren's syndrome, vasculitis, sarcoidosis, and psoriasis. Embodiment 160. The method of embodiment 159 wherein the disorder is lupus. C:\poi\word\SPEC-8541 93[1].docx 70 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. 5 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 10 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. 15 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 IFNa-inducible 20 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 IFNa-inducible PD marker expression profile comprises increased serum levels of polypeptides cancer antigen 125, ferritin, tissue factor, and MMP-3. 25 Embodiment 172. The method of embodiment 147 wherein the type I IFN or IFNa-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 IFNa levels comprising: C:\poi\word\SPEC-8541 93[1].docx 71 detecting presence or absence of an IFNa-inducible PD marker expression profile in a sample from the patient, wherein detecting presence of the IFNa-induced PD marker expression profile identifies the patient as having a disorder associated with increased IFNa levels. 5 Embodiment 174. The method of embodiment 173 wherein the IFNa-inducible PD marker expression profile comprises up-regulated expression or activity of genes MX1, LY6E, IF127, OAS 1, IFIT1, IF16, IF144L, ISG15, LAMP3, OASL, RSAD2, and IF144. Embodiment 175. The method of embodiment 173 wherein the IFNa-inducible PD marker expression profile comprises up-regulated expression or activity of genes IF127, SIGLEC1, 10 RSAD2, IF16, IF144L, IF144, 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 IFNa-inducible PD marker expression profile comprises up-regulated expression or activity of genes IFIT1, IFIT3, IRF7, IF16, IL6ST, IRF2, LY6E, MARCKS, MX1, MX2, OAS1, EIF2AK2, ISG15, STAT2, OAS3, 15 IF144, IF144L, HERC5, RAB8B, LILRA5, RSAD2, and FCHO2. Embodiment 177 The method of embodiment 173 wherein the IFNa-inducible PD marker expression profile comprises up-regulated expression or activity of genes SERPING1, IFIT2, IFIT3, IF16, LY6E, MX1, OAS1, ISG15, IF127, OAS3, IF144, LAMP3, DNAPTP6, ETV7, HERC5, OAS2, USP18, XAF1, RTP4, SIGLEC1, and EPSTIl. 20 Embodiment 178. The method of embodiment 173 wherein the IFNa-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, IF127, DNAPTP6, LAMP3, EPSTI1, IF144, OAS2, IFIT2, and ISG15. Embodiment 179. The method of embodiment 173 wherein the IFNa-inducible PD marker 25 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, IF16, USP18, RSAD2, IF144, LY6E, ISG15, and IF127. Embodiment 180. The method of embodiment 173 wherein the IFNa-inducible PD marker expression profile comprises up-regulated expression or activity of genes DNAPTP6, EPSTI1, 30 HERC5, IF127, IF144, IF144L, IF16, IFIT1, IFIT3, ISG15, LAMP3, LY6E, MX1, OAS1, OAS2, OAS3, PLSCR1, RSAD2, RTP4, SIGLEC1, and USP18. C:\poi\word\SPEC-8541 93[1].docx 72 Embodiment 181. The method of embodiment 173 wherein the IFNa-inducible PD marker expression profile comprises up-regulated expression or activity of genes SAMD9L, IF16, IF144, IFIT2, ZC3HAV1, ETV6, DAPP1, IL1RN, CEACAM1, OAS1, IF127, OAS3, IF144L, HERC5, IFIT1, EPSTI1, ISG15, SERPING1, OASL, GBP1, and MX1. 5 Embodiment 182. The method of embodiment 173 wherein the IFNa-inducible PD marker expression profile comprises up-regulated expression or activity of genes SAMD9L, IF16, IF144, IFIT2, OAS1, IF127, OAS3, IF144L, HERC5, IFIT1, EPSTI1, ISG15, SERPING1, OASL, GBP1, and MX1. Embodiment 183. The method of embodiment 173 wherein the IFNa-inducible PD marker 10 expression profile comprises up-regulated expression or activity of genes IF16, RSAD2, IF144, IF144L, IF127, MX1, IFIT1, ISG15, LAMP3, OAS3, OAS1, EPSTI1, IFIT3, OAS2, SIGLEC1, and USP18. Embodiment 184. The method of embodiment 173 wherein the IFNa-inducible PD marker expression profile comprises up-regulated expression or activity of genes IF16, RSAD2, IF144, 15 IF144L, and IF127. 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 20 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. 25 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 30 expression or activity comprises an increase in enzymatic activity of a protein expressed from one or more of the genes. C:\poi\word\SPEC-8541 93[1].docx 73 Embodiment 192. The method of any one of embodiments 174-184 wherein the type I IFN or IFNa-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 5 IFNa-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 IFNa-inducible PD marker expression profile further comprises decreased serum levels of polypeptides EGF, thrombopoietin, and CD40 ligand. 10 Embodiment 195. A method of identifying a candidate therapeutic for treating IFNa-mediated disorders comprising: contacting cells comprising an IFNa-inducible PD marker expression profile with an agent; and detecting presence or absence of a change in the IFNa-induced PD marker expression 15 profile of the cells, wherein the presence of a change comprising a reduction in the up-regulation of the genes of the IFNa-inducible PD marker expression profile indicates the agent is a candidate therapeutic agent. Embodiment 196. The method of embodiment 195 wherein the IFNa-inducible PD marker 20 expression profile comprises up-regulated expression or activity of genes MX1, LY6E, IFI27, OAS 1, IFIT1, IFI6, IFI44L, ISG15, LAMP3, OASL, RSAD2, and IFI44. Embodiment 197. The method of embodiment 195 wherein the IFNa-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, 25 IFIT1, LIPA, LOC129607, ISG15, PARP14, MX1, OAS2, OASL, CCL2, HERC5, and OAS1. Embodiment 198. The method of embodiment 195 wherein the IFNa-inducible PD marker expression profile comprises up-regulated expression or activity of genes IFIT1, IFIT3, IRF7, IF16, IL6ST, IRF2, LY6E, MARCKS, MX1, MX2, OAS1, EIF2AK2, ISG15, STAT2, OAS3, IF144, IF144L, HERC5, RAB8B, LILRA5, RSAD2, and FCHO2. 30 Embodiment 199 The method of embodiment 195 wherein the IFNa-inducible PD marker expression profile comprises up-regulated expression or activity of genes SERPING1, IFIT2, C:\poi\word\SPEC-8541 93[1].docx 74 IFIT3, IF16, LY6E, MX1, OAS1, ISG15, IF127, OAS3, IF144, LAMP3, DNAPTP6, ETV7, HERC5, OAS2, USP18, XAF1, RTP4, SIGLEC1, and EPSTIl. Embodiment 200. The method of embodiment 195 wherein the IFNa-inducible PD marker expression profile comprises up-regulated expression or activity of genes RTP4, RSAD2, 5 HERC5, SIGLEC1, USP18, LY6E, ETV7, SERPING1, IFIT3, OAS1, HSXIAPAF1, G1P3, MX1, OAS3, IF127, DNAPTP6, LAMP3, EPSTI1, IF144, OAS2, IFIT2, and ISG15. Embodiment 201. The method of embodiment 195 wherein the IFNa-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, 10 OAS3, IFIT3, IF16, USP18, RSAD2, IF144, LY6E, ISG15, and IF127. Embodiment 202. The method of embodiment 195 wherein the IFNa-inducible PD marker expression profile comprises up-regulated expression or activity of genes DNAPTP6, EPSTI1, HERC5, IF127, IF144, IF144L, IF16, IFIT1, IFIT3, ISG15, LAMP3, LY6E, MX1, OAS1, OAS2, OAS3, PLSCR1, RSAD2, RTP4, SIGLEC1, and USP18. 15 Embodiment 203. The method of embodiment 195 wherein the IFNa-inducible PD marker expression profile comprises up-regulated expression or activity of genes SAMD9L, IF16, IF144, IFIT2, ZC3HAV1, ETV6, DAPP1, IL1RN, CEACAM1, OAS1, IF127, OAS3, IF144L, HERC5, IFIT1, EPSTI1, ISG15, SERPING1, OASL, GBP1, and MX1. Embodiment 204. The method of embodiment 195 wherein the IFNa-inducible PD marker 20 expression profile comprises up-regulated expression or activity of genes SAMD9L, IF16, IF144, IFIT2, OAS1, IF127, OAS3, IF144L, HERC5, IFIT1, EPSTI1, ISG15, SERPING1, OASL, GBP1, and MX1. Embodiment 205. The method of embodiment 195 wherein the IFNa-inducible PD marker expression profile comprises up-regulated expression or activity of genes IF16, RSAD2, IF144, 25 IF144L, IF127, MX1, IFIT1, ISG15, LAMP3, OAS3, OAS1, EPSTI1, IFIT3, OAS2, SIGLEC1, and USP18. Embodiment 206. The method of embodiment 195 wherein the IFNa-inducible PD marker expression profile comprises up-regulated expression or activity of genes IF16, RSAD2, IF144, IF144L, and IF127. 30 Embodiment 207. The method of embodiment 195 wherein the cells obtained from a patient comprising a disorder associated with increased IFNa levels. C:\poi\word\SPEC-8541 93[1].docx 75 Embodiment 208. The method of embodiment 195 wherein the cells are cells treated with IFNa to induce the IFNa-inducible PD marker expression profile. Embodiment 209. The method of embodiment 195 wherein the up-regulation of the genes of the IFNa-inducible PD marker expression profile is at least a 2-fold increase in expression of 5 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 IFNa-inducible PD marker expression profile is at least a 3-fold increase in expression of one or more of the genes of the IFNa-inducible PD marker expression profile. Embodiment 211. The method of embodiment 195 wherein the up-regulation of the genes of 10 the IFNa-inducible PD marker expression profile comprises an increase in mRNA levels of one or more of the genes of the IFNa-inducible PD marker expression profile. Embodiment 212. The method of embodiment 195 wherein the up-regulation of the genes of the IFNa-inducible PD marker expression profile comprises an increase in protein levels of one or more of the genes of the IFNa-inducible PD marker expression profile. 15 Embodiment 213. The method of embodiment 195 wherein the up-regulation of the genes of the IFNa-inducible PD marker expression profile comprises an increase in enzymatic activity of a protein expressed from one or more of the genes of the IFNa-inducible PD marker expression profile. Embodiment 214. The method of any one of embodiments 196-206 wherein the type I IFN or 20 IFNa-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 25 IFNa-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 30 IFNa-inducible PD marker expression profile further comprises decreased serum levels of polypeptides EGF, thrombopoietin, and CD40 ligand C:\poi\word\SPEC-8541 93[1].docx 76 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: 5 (a) MX1, LY6E, IF127, OAS1, IFIT1, IF16, IF144L, ISG15, LAMP3, OASL, RSAD2, and IF144; or (b) IF127, SIGLEC1, RSAD2, IF16, IF144L, IF144, USP18, IFIT2, SAMD9L, BIRC4BP, DNAPTP6, OAS3, LY6E, IFIT1, LIPA, LOC129607, ISG15, PARP14, MX1, OAS2, OASL, CCL2, HERC5, OAS 1; or 10 (c) IFIT1, IFIT3, IRF7, IF16, IL6ST, IRF2, LY6E, MARCKS, MX1, MX2, OAS1, EIF2AK2, ISG15, STAT2, OAS3, IF144, IF144L, HERC5, RAB8B, LILRA5, RSAD2, and FCHO2; or (d) SERPING1, IFIT2, IFIT3, IF16, LY6E, MX1, OAS1, ISG15, IF127, OAS3, IF144, LAMP3, DNAPTP6, ETV7, HERC5, OAS2, USP18, XAF1, RTP4, SIGLEC1, and 15 EPST1;or (e) RTP4, RSAD2, HERC5, SIGLEC1, USP18, LY6E, ETV7, SERPING1, IFIT3, OAS1, HSXIAPAF1, G1P3, MX1, OAS3, IF127, DNAPTP6, LAMP3, EPSTI1, IF144, OAS2, IFIT2, and ISG15; or (f) LAMP3, SIGLEC1, DNAPTP6, IFIT2, ETV7, RTP4, SERPING1, HERC5, XAF1, 20 MX1, EPSTI1, OAS2, OAS1, OAS3, IFIT3, IF16, USP18, RSAD2, IF144, LY6E, ISG15, and IF127; or (g) DNAPTP6, EPSTI1, HERC5, IF127, IF144, IF144L, IF16, IFIT1, IFIT3, ISG15, LAMP3, LY6E, MX1, OAS1, OAS2, OAS3, PLSCR1, RSAD2, RTP4, SIGLEC1, and USP18; or 25 (h) SAMD9L, IF16, IF144, IFIT2, ZC3HAV1, ETV6, DAPP1, IL1RN, CEACAM1, OAS1, IF127, OAS3, IF144L, HERC5, IFIT1, EPSTI1, ISG15, SERPING1, OASL, GBP1, and MX1; or (i) SAMD9L, IF16, IF144, IFIT2, OAS1, IF127, OAS3, IF144L, HERC5, IFIT1, EPSTI1, ISG15, SERPING1, OASL, GBP1, and MX1; or 30 () IF16, RSAD2, IF144, IF144L, IF127, MX1, IFIT1, ISG15, LAMP3, OAS3, OAS1, EPSTI1, IFIT3, OAS2, SIGLEC1, and USP18; or (k) IF16, RSAD2, IF144, IF144L, and IF127; or (1) NOGSLC4A1, PRSS33, and FEZ1. C:\poi\word\SPEC-8541 93[1].docx 77 Embodiment 218. A kit comprising any of the set of probes recited in embodiment 217. Embodiment 219. 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 5 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, p-galactosidase, green fluorescent protein, p 10 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 15 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 20 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 Serial No. 60/873,008 filed December 6, 2006, U.S. Provisional Application Serial No. 60/907,762 25 filed April 16, 2007, U.S. Provisional Application Serial No. 60/924,219 filed May 3, 2007, U.S. Provisional Application Serial No. 60/924,584 filed May 21, 2007, U.S. Provisional Application Serial No. 60/960,187 filed September 19, 2007, and U.S. Provisional Application Serial No. 60/996,176 filed November 5, 2007, herein incorporated by reference for all purposes. This application also claims the benefit of priority of U.S. Provisional Application 30 Serial No. 60/924,220 filed May 3, 2007, U.S. Provisional Application entitled "Auto Antibody Markers of Autoimmune Disease" filed November 6, 2007 (Attorney docket no. C:\poi\word\SPEC-8541 93[1].docx 78 IA201P2), and U.S. Provisional Application entitled "Auto-Antibody Markers of Autoimmune Disease" filed December 6, 2007 (Attorney docket no. IA201P3), herein incorporated by reference for all purposes. This application further claims the benefit of priority of U.S. Provisional Application Serial No. 60/907,767 filed April 16, 2007, U.S. Provisional 5 Application Serial No. 60/996,174 filed November 5, 2007, and PCT application entitled "Methods of Treating Systemic Lupus Erythematosus", filed December 6, 2007 (Attorney docket no. IA21OPCT), 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. 10 C:\poi\word\SPEC-8541 93[1].docx 79 EXAMPLES Example la: 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 5 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 10 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 and TaqMan (i.e. qPCR)). 15 C:\poi\word\SPEC-8541 93[1].docx 80 Table 1: Genes Identified as Up-Regulated at Least 2-Fold in Whole Blood of Lupus Patients Probe ID UniGene l[.Gene Title Gene SymGene Ontology 3i: Gene OntGene ontcPathway j.NomniAj SLE LE]-[A 5.5 p ~Alue99R]-[ANN6ON][NelHl-[A433RN-Ad 223674 s Hs.22065 CDC42 small effector 1 CDC42SE 7165// signal tran 5886// pla5095// GT-- 2.355 6.012 3.657 1.20E-05 2.787 4.166 4.429 3.165 3.737 204415 at Hs.523847intereon, alpha-inoucibleGlP3 6955 immune re 16021 in 6. 515 9.733 3.218 0.018746 1.626 1.102 2.325 5.854 5.183 228220 at Hs.165762 FCH domain only 2 FCH(2 4 -- - 4381 7.36t 2.980 0.023153 4.085 2.810 1.084 2.995 3.928 226312 at Hs.40792ET(RC2-specific protein A:AV(3 : 5488 bin 7034 9.818 2.784 0.025167 3.163 2.487 1.045 3.274 3.953 215245 x t i :9 m x ? K 324% 3(Sej 2:2I:: Mf 33? 3[ 202194 at :-148? 18 1 Ft ... Nr ISm .. ... M3$ .. 4 M .3. O Mf 3 A. 2 32..2 3 -.. 226641 at Hs.432706 Ankynn repeat domain 44 LOC91526--- 7476 10.170 2.694 0.030007 3.184 2.337 1.070 2.878 4.001 212585 at Hs.43084S oxysterol binding protein- OSBP L8 6869 1ipi transr--- 8.182 10.818 2.636 0.028512 3.093 2.358 1.163 2.445 4.120 201237 aT Hs.446123 capping protein (actin filaiCAPZA2 '6461 protein cor 8290 F 43779 act 6.438 9.060 2.622 0.026777 3.338 2.289 1.004 2.644 3.836 226934Mat Hs.36960C Cleavage and polyaoeny1kCPSF6 6397/ mRNA pro5634 nuf166/ nucl 5.619 8.241 2.622 0.007781 2.441 2.553 1.672 2.505 3.940 203983 a1 Hs.9(624~' 11anslin-as socialed 111 TSNlAX :5634 nu3677 / D\ 5522 8.1 41 2.619 0.018885 2.958 2.306 1.051 2878 300 221428 s Hs4389~C11ansouin.bl:ike1XITBL1XR1.6350..t1ansc11p11<534 nur 5.859 8.427 2.568 0.017844 3.004 2.258 1.524 2.398 3.654 215838 at Hs.512231eukocyte immunoglobulin LILRA5 -6.647 9.190 2.543 0.000349 2.071 2.399 2.263 2.840 3.144 209884 s Hs.2500~'solute career family 4, soSLC4A7 6820 anion tran 16020 n5452 ino 4.525 7068 2.543 0006683 2.579 2.292 1 432 2.495 3.918 222605at Hs.35639S REST corepressor 3 RCOR3 45449 regulatiors634 niu36' DR 5249 7775 2.526 0.032918 2.965 1 850 1 330 2.689 3796 202304 at Hs.50801C ilbronectin type III comair FNDC3A 4.793 7268 2.475 0.014487 307 2.013 1 088 2.696 3.510 212579 atHs.8118 structural maintenance oiSMCHD1 51276 chromos5s694 chr5515 pro 8996 11436 2440 0014165: 2930 2037 1.088 3002 3143 20fij::J:0pirytttt~qdg~ t S M(2 W mripiq 5%i;-pWA? :Mt I$9 ttA4t 43 0 2353?2 331 2 39E SM 24% M 1555643 s Hs.512233leukocyte immunoglobulin LILRA5 6 942 9.367 2.426 0.001163 2.004 2.163 1 967 2.854 3.140 226617 at Hs.47023 ADP-ribosylation factor-li[ARL5 6886 intracellulk 166 nucl 4.385 6.781 2.395 0.07287 2.903 1 994 1 025 2.486 3.570 229584 at Hs.18763Eleucine-nch repeat kinasE LRRK2 6468 protein am 462 pro 8541 10926 2385 0.008927 282 1 812 1 216 2938 3087 211967~'_a1 Hs.503~'06 piooncosis 16ceploiindn PORI :1021 in 4872 rec 8.352 10.735 2.383 0.032836 2.049 1 805 1 025 3.397 3.640 21 1H 43T12 6813 potassium 807 ' r5249 rl- 8.386 107 63 2.377 0.040801 2.993 1 615 1 076 2.365 3.838 208719 s Hs.52830 :DEAD (Asp-GluAla-Asp DDX17 6396/ RNA proces5634 nu166// nucl 4.196 6.546 2.349 0.009291 1.614 4.874 1 826 2.018 1 416 201669 s Hs.51990o myristoylate alanine-nel MARCKS 6928 cell motilit 5886 plal5516 cal 8.355 10.688 2.333 0.007803 2.738 2.177 1.128 3.141 2.479 222572 at Hs.22265 protein phosphatase 2C, PPM2C 6470/ protein an5739 mif287 mag Krebs TCA 5.335 7664 2.329 :0.069262: 2.681 1 957 1 016 2.279 3.712 212195 at Hs.532082 Interleukin 6 signal transc IL6ST 6955 immune re 5886 pla 4872 rec Ribosomal 8.733 11.015 2.282 0.006803 2.104 2.242 1 440 2.020 3.605 2267~11 a1 Hs.4(84~' human T-cell leukemia Al HTLF 6350 transcripts634. nu3'0 trai 7581 9.859 2.278 0.016463 2.791 1 734 1 043 2.440 3.384 222846 at Hs.389~' RAB8B member 8B886t iacellul - :166 . nul 5.584 7 857 2.273 0.044318 2.897 1 665 1.193 2.829 2779 203566 s- Hs.904 amylo-1, 6-glucosicase, 'AGL 5975 carbohyor43033 is:4134 4-a GIly cogen 4 862 7131 2.269 0.041967 2.283 1 758 1 057 2.579 3.668 207564 x Hs.40541C0-linke N-acetylglucosa OGT 6493 protein an5634 nul5515 pi- 6.919 9.156 2.236 0.004017 2.212 2.086 1 479 2.355 3.048 219237 s Hs.512743DnaJ (Hsp40) homolog, DNAJB14 6457 protein 1l.--- :31072 hE-- 6022 8.229 2.207 0.004813 2.454 1 832 1.172 2.322 3.253 214093 s Hs.567~'25~131

.

ps11eam 4 element,.FL:FUBP1 (350 11anscuplo 5634 mu 3(70-in 5.205 7403 2.198 0.007941 1 994 1 144 1.199 2.491 3.661 2 8 1 11 signal 11an 16021.in84.he (PCRDB 6422 815 2154 0011493 2263 1 396 1174 1.868 4.067 217941 s Hs.51934e erbb2interacting protein E RBB21P 7049 cell cycle 5634 nui.5176 Et 7497 9.637 2.140 0.020564 2.313 2.026 1:112 2.354 2895 203603 s Hs.34871 zinc linger homeobox lb ZFHX1B 6355 regulation 5634 nud3700 trai TGF Beta 4.781 6.915 2.134 0:021477 2.750 1 278 1 039 2.257 3.346 213111 at Hs.17393 phosphatiylinositol-3-ph PIP5K3 7242 intracellul 45121 lil5515 pro-- 5914 8.033 2.119 0.013802 2.394 1 869 1 048 2.315 2.968 :2130~'0 1Hs.17534Phos phoinositiet-3kinas PlK3C2A 6661t phospha1i(5634 nu4428 ino Inositol ph' 4.886 6.996 2.111 *0043279 2405 1 654 1.103 1.921 3.472 218041 x Hs.22184 solute corner family 38, nSLC38A2 6865 amino acic16020 n15279 am '.52' 9.629 2.102 0.023894 2.417 1 890 1.140 1.927 3.136 .02039 H 19102RB1 inducible coilec-coil RB1CC1 6350 1ranscupli(5634 nul6301 ki -096 9178 2082 0.018164 2.798 1 406 1 272 2.225 2709 200603 at Hs. 280342 protein kinase cA MP -de PRKAR1A 6357 regulation 5952 cA 166 / nucl G Protein 9.293 11.373 2.080 0.030496 26151 2 062 1 004 2 031 26*53 228996 at Hs.49509~-fnng finger and CCCH-typ RC3H1 16567 protein ul 151 ubiq 3723 RN 4.366 6.436 2070 0 0.004022 3.253 1 738 1 435 1897 2026 1554479 e Hs.44614&caspase recruitment oom CARD8 42981 regulation 5634 nul5515 pro 7 947 10.012 2.065 0.023092 2.558 1 733 1 054 2.133 2.848 203011 1 Hs.49212C inositolmyo) 1(01 4)lmon. IMPA1 5975 carbohyor. 287 mag1Streptomy 5.383 7442 2.059 0.043964 2.487 1 447 1 001 2.187 3.173 2239 H18~19meastasis associated luI MALAT1 4.166 6212 2.046 0.003564 2.139 1 026 1.120 267 1k' 3273 222317 at Hs.445711 Phosphociesterase 3B, c PDE3B 7165 signal Iran 16020 r4119 cG 4.840 6.865 2.025 0.021022 2.593 1 664 1.155 1.901 2.812 228157 at Hs.50077" zinc finger protein 207 ZNF207 6355 regulation 5634 nui3700 trai 6.352 8.371 2.019 0.043641 2300 1 363 1 074 2.263 3.094 221505 at Hs.38591' aciic .leucine-rich) nucleAlP32E :5634 nut19212 7pl '489 9.501 2.012 0.057 164 2070 1 656 1 053 2.251 3.028 1.5544~'2 H3td..04362 PHD finger protein 20-like PHF2OL1 6355 regulation: 515 4.062 6.074 2.012 0.000292 2.270 1 460 1 355 2.254 2.718 226345 a1 Hs.25362 ADP rbosylation factor-i[ARL8 6886 intracellul; 166 nucl 5 050 05 7 2 007 0.034947 2.308 1 707 1169 1 898 2 953 2248132 -1H2(9~8d canine nucleotice biniGA( 64~'1 protein am573~9yt 1.t uePi Protein 66 .. 3 8.665 2.002 0.04627'2 2 679 1 850 1.194 1.605 2.682 20~'38~' . Hs.1466 glycrol kinase . 5975 carbohyor 5737 cy166 nucl Glycerolipi 6577 8.565 1 987 00655 2.663 1 071 1:146 2.292 2765 222633 at Hs.43897Cra.nsucin (beta)-like 1XI TBL1)1 6350 1ranscripti5s634 nu- 5.358 7324 1 966 3 89E 05 2.171 1 460 1 799 1.689 2.711 236224 at Hs.491234 Ras like without CAAX 1 RIT1 886 initracellulk5886 pla:166 nu-l 5.105 7064 1 960 0.018708 2.825 2.017 1.110 2.178 1 669 :203080 s Hs4~03cbromoomain adjacent toBAZ2B ,6350 transcripti6 5634. nu37. D\. _ 7254 9.212 1 959 0008344 2.597' 1 1i66 1 051 2.058 2.921 222-8~ H12~'40~- UDP \N acetyl alphaDa(ALlT.597'5 carbohyr ~ 43. l ((lycan : 4 095 6038 1 944 0 006624 2585 1 283 1.121 2.393 2 336 235057 at Hs.472501tchy homolog E3 ubiquitiTrICH 1558 regulation 5634 nui:3677 D\ 3238 5161 1 923 0.001003 1 885 1 781 1 343 1 272 3.337 1554154 a Hs.31080 0 gangliosioe induced differ GDAP2 4.572 6.494 1 922 0:001031 2.092 1 729 1 615 1.761 2.413 226444 at Hs.413434 Solute camera family 39 (zSLC39A1C 30001 metal ion 5634 nun3676 nui- 5.668 7583 1 915 0.024435 1.542 1 861 1 070 1.880 3.221 204646_31 Hs.335034 dihyd opyuimline dehyd DPYID _6118 electron 1r,5737 cy f4l52 oih Pynmioine 7632 9.545 1 913 0.049899 2.288 1 489 1 263 1 806 2719 205321 at Hs.539684eukaryotic translation in1iEIF2S3 6412 protein bi6 5843 cytl 66 nucl Translatior 6.682 8.563 1 881 0.030696 2.094 2.213 1 758 1.309 2.030 597'5 carbohy9rq 4865 yr KE( 5.590 7464 1 874 0.064575 2.078 1 532 1 055 1 763 2.943 201668 x Hs.51990Emyristoylate alanine-c neMARCKS 6928 cell motilit 5886 pla5516 cal 4.137 5987 1 850 0 001437' 2370 1 760 1 413 2.538 1.170 213701 at Hs.494204 hypothetical protein DKF; DKFZp434 3.954 5.802 1 848 0.044061 1.883 1 388 1.137 1.485 3.345 201110 s Hs.16422thrombosponoin 1 THBS1 6928 cell motilit 5576 exf4866 en;TGF Beta 4.265 6.106 1 841 0.000653 1 953 1 964 1 018 2.122 2.149 224800 at Hs.36835c WD repeatano FYiVE.dolWDFY15634 nu6.43 phi 6372 8.193 1 820 0.027641 2.080 1 251 1~ 067 2.247 2.457 218396 1Hs1166Eacuolaipioleisor11ng1VP13C 8104 protein lc ~' 2~ 9.069 1 798 0.020416 1.839 1 550 1168 1532 2902 213737 x Hs 146211 hypothetical L(C283768 L(C28376 9551 180 0 10214 1892 1.274 1120 1.602 3.013 202973 x Hs.9727'O family with sequence sim FAM13A1 5 718 7 492 1 7 74 0.010098 1.538 2.18 7 1 599 1.388 2.157 205198 - Hs.496414ATPase Cu++ transportiiATP7A 6825 copper ion 5783 en166.. nucl ()xioatle r 4.069 5.842 1 773 0.008607 2.038 1 332 1 003 1.660 2.833 208867 5 Hs.529862casein kinase , alpha1 C\K1A1 6468 protein am 166 nucl 5.746 :7514 1 768 0.007708 2.015 1 473 1 260 1787 2.304 C:\poT\word\SPEC-854193[1].docx 81 Table 2: Up-Regulation in Gene Expression for a Set of Genes for each of Five Lupus Patients 129KHR.SLE |129KHR.S RH33XR.SLE RH33XR.S 5 Probe ID Gene Symbol (TaqMan) :LE (Affy): (TaqMan) LE (Affy) )J9SSR (TaOJ9SSR (I499R (Tal4499R (26CR(TM26CR(A 228220 at FCHO2 3.24 39.86 3.30 76.15 33.05 84.86 22.36 35.07 17.77 10.61 205483 s at G1P3 86.13 146.74 80.55 92.15 4.45 7.83 2.90 5.45 5.06 12.71 212195 at IL6ST 3.87 9.18 3.63 27.52 6.60 9.73 4.95 10.70 2.35 6.14 203275 at IRF2 8.10 6.46 5.00 4.80 5.07 6.54 4.12 4.32 2.44 4.66 1555643_s at LILRA5 16.43 12.00 27.25 14.64 11.22 6.66 6.82 -/44 4.86 6.49 205170 at STAT2 11.55 8.67 9.74 2.25 8.08 2.6 6.37 2.92 4.12 2.62 10 Example la: Validation of Genes Identified as Up-Regulated Genes in Lupus Patients To further identify candidate PD markers for anti-IFN-a 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 15 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 20 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-a mAb therapy for SLE. Table 30: 50 most upregulated probe sets in whole blood of SLE patients Gene q Value Probe ID Gene Title Symbol log 2 fc (FDR) Prevalence 202411_at interferon, alpha-inducible protein 27 IF127 4.60 8.41E-07 73.91 sialic acid binding Ig-like lectin 1, 219519_s_at sialoadhesin SIGLECI 3.52 7.28E-07 65.22 214059_at Interferon-induced protein 44 IF144 3.51 8.04E-07 73.91 radical S-adenosyl methionine domain 213797_at containing 2 RSAD2 3.29 9.86E-06 71.74 204415_at interferon, alpha-inducible protein 6 IF16 3.21 2.25E-09 82.61 radical S-adenosyl methionine domain 242625_at containing 2 RSAD2 3.19 1.55E-06 69.57 204439_at interferon-induced protein 44-like IF144L 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 IF144 2.72 1.07E-05 71.74 202145_at lymphocyte antigen 6 complex, locus E LY6E 2.53 7.28E-07 63.04 matrix metallopeptidase 8 (neutrophil 207329_at collagenase) MMP8 2.51 0.00111 60.87 202869_at 2',5'-oligoadenylate synthetase 1, 40/46kDa OAS1 2.33 1.66E-06 69.57 222154_s_at DNA polymerase-transactivated protein 6 DNAPTP6 2.32 1.14E-05 65.22 sialic acid binding Ig-like lectin 1, 44673_at sialoadhesin SIGLEC1 2.31 2.23E-06 58.70 242234_at XIAP associated factor-i BIRC4BP 2.31 8.41E-07 65.22 interferon-induced protein with 203153_at tetratricopeptide repeats 1 IFITI 2.25 9.53E-05 67.39 C:\poi\word\SPEC-8541 93[1].docx 82 218400_at 2'-5'-oligoadenylate synthetase 3, 1OOkDa 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-like SAMD9L 2.22 1.37E-06 84.78 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, 40/46kDa OAS1 2.18 4.98E-07 65.22 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 leukocyte immunoglobulin-like receptor, 1555643_s_at subfamily A LILRA5 2.14 8.41E-07 76.09 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 LOC12960 226702_at hypothetical protein LOC129607 7 2.07 5.96E-05 67.39 leukocyte immunoglobulin-like receptor, 215838_at subfamily A LILRA5 2.07 1.87E-05 71.74 219863_at hect domain and RLD 5 HERC5 2.03 1.53E-05 67.39 interferon-induced protein with 204747_at tetratricopeptide repeats 3 IFIT3 2.01 1.55E-06 67.39 serpin peptidase inhibitor, clade G (Cl SERPING 200986_at inhibitor), member 1 1 1.98 0.00013 67.39 224225_s_at ets variant gene 7 (TEL2 oncogene) ETV7 1.98 2.48E-05 58.70 receptor (chemosensory) transporter 219684_at protein 4 RTP4 1.96 2.74E-06 63.04 206133_at XIAP associated factor-i BIRC4BP 1.96 7.28E-07 65.22 206871_at elastase 2, neutrophil ELA2 1.95 0.00316 54.35 interferon-induced protein with 217502_at tetratricopeptide repeats 2 IFIT2 1.95 4.86E-06 71.74 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 carcinoembryonic antigen-related cell 203757_s_at adhesion molecule 6 CEACAM6 1.91 0.00124 47.83 myxovirus (influenza virus) resistance 1, interferon-inducible protein p78 (mouse) / myxovirus (influenza virus) resistance 1, 202086_at interferon-inducible protein p78 (mouse) MX1 1.90 2.66E-05 67.39 241916_at Phospholipid scramblase 1 PLSCR1 1.89 4.86E-06 73.91 interferon-induced protein with 203595_s_at tetratricopeptide repeats 5 IFIT5 1.89 2.81E-08 69.57 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 carcinoembryonic antigen-related cell 211657_at adhesion molecule 6 CEACAM6 1.86 0.00667 60.87 basic leucine zipper transcription factor, 228439 at ATF-like 2 BATF2 1.86 2.63E-05 63.04 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. Figure 80 (top panel) shows a heat map of the expression of the 114 upregulated type I 5 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 C:\poi\word\SPEC-8541 93[1].docx 83 patients, WB was procured from 54 SLE patients in a prospective study. Figure 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 5 weak or nondetectable type I IFN gene signature in WB. Figure 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 Figure 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 10 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 15 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 (Figure 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 20 Table 31. The downregulation of T, NK, and B cell gene signatures was observed in WB of SLE patients (Figure 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 AK, Arce E et al.: Interferon and granulopoiesis signatures in systemic lupus erythematosus blood. J Exp Med. 197(6), 711-723 (2003), Rivero SJ, Diaz-Jouanen E and 25 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 q Value Probe ID Gene Title Gene Symbol log 2 fc (FDR) Prevalence solute carrier family 4, anion exchanger, member 1 (erythrocyte membrane protein band 3, Diego 1552713_a_at blood group) SLC4A1 -1.82 0.00021 69.57 1552348 at protease, serine, 33 PRSS33 -1.71 0.00046 63.04 Fc fragment of IgE, high affinity I, receptor for; alpha polypeptide /// Fc fragment of IgE, high affinity I, 211734 s at receptor for; alpha polypeptide FCER1A -1.59 0.00083 54.35 C:\poi\word\SPEC-8541 93[1].docx 84 BTB and CNC homology 1, basic 236307 at leucine zipper transcription factor 2 BACH2 -1.51 0.00012 54.35 killer cell lectin-like receptor subfamily B, member 1 /// killer cell lectin-like receptor subfamily B, 214470_at member 1 KLRB1 -1.50 0.00000 58.70 DNA segment on chromosome 4 209570_s_at (unique) 234 expressed sequence D4S234E -1.46 0.00000 65.22 T cell receptor alpha locus /// T cell TRA@ // 217143 s at receptor delta locus TRD@ -1.38 0.00001 58.70 fasciculation and elongation protein 203562_at zeta 1 (zygin I) FEZI -1.36 0.00028 89.13 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 ATP-binding cassette, sub-family B 209993 at (MDR/TAP), member 1 ABCB1 -1.32 0.00002 63.04 209815_at patched homolog 1 (Drosophila) PTCH1 -1.29 0.00003 54.35 olfactory receptor, family 2, 241881_at subfamily W, member 3 OR2W3 -1.29 0.01736 50.00 immunoglobulin heavy constant 213674_x_at delta IGHD -1.29 0.01801 50.00 231798 at Noggin NOG -1.28 0.00234 73.91 Nuclear receptor subfamily 3, group 239673_at C, member 2 NR3C2 -1.27 0.00004 56.52 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 lB SH2D1B -1.20 0.00187 47.83 Spermatid perinuclear RNA binding 229513_at protein STRBP -1.20 0.00017 58.70 Zinc finger, MYND domain 243054_at containing 11 ZMYND11 -1.20 0.00101 60.87 BTB and CNC homology 1, basic 236796 at leucine zipper transcription factor 2 BACH2 -1.20 0.00004 56.52 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 DKFZp761PO 240690 at Homolog of rat pragma of Rnd2 423 -1.17 0.00012 52.17 erythrocyte membrane protein band 4.2 /// erythrocyte membrane protein 210746 s at band 4.2 EPB42 -1.16 0.00552 45.65 Nuclear receptor subfamily 6, group 232478 at A, member 1 NR6A1 -1.15 0.00004 47.83 Similar to Heterogeneous nuclear ribonucleoprotein Al (Helix destabilizing protein) (Single-strand RNA-binding protein) (hnRNP core 243810 at protein Al) LOC341333 -1.15 0.00014 47.83 membrane-spanning 4-domains, 228599 at subfamily A, member 1 MS4A1 -1.14 0.00454 45.65 immunoglobulin heavy constant mu 212827_at // immunoglobulin heavy constant IGHM -1.14 0.00324 45.65 C:\poi\word\SPEC-8541 93[1].docx 85 mu 1552349 a at protease, serine, 33 PRSS33 -1.13 0.02357 47.83 T cell receptor alpha locus /// T cell receptor delta locus // B-cell TRA@ // CLL/lymphoma 11 B (zinc finger TRD@ // 216191 s at protein) BCL11B -1.12 0.01073 50.00 sialic acid binding Ig-like lectin, 232686 at pseudogene 3 SIGLECP3 -1.12 0.00003 58.70 killer cell immunoglobulin-like receptor, two domains, short 211532 x at cytoplasmic tail, 2 KIR2DS2 -1.10 0.04011 54.35 Protein kinase (cAMP-dependent, 1563217_at catalytic) inhibitor alpha PKIA -1.10 0.00024 58.70 Burkitt lymphoma receptor 1, GTP binding protein (chemokine (C-X-C 243798 at motif) receptor 5) BLR1 -1.10 0.00044 54.35 220751_s_at chromosome 5 open reading frame 4 C5orf4 -1.09 0.00531 50.00 myosin, light chain kinase /// myosin, 202555_s_at light chain kinase MYLK -1.09 0.00149 52.17 230245 s at hypothetical protein LOC283663 LOC283663 -1.09 0.00977 47.83 MADI mitotic arrest deficient-like 1 233921 s at (yeast) MADIL1 -1.08 0.00001 41.30 214974 x at chemokine (C-X-C motif) ligand 5 CXCL5 -1.08 0.00717 54.35 DNA segment on chromosome 4 209569_x_at (unique) 234 expressed sequence D4S234E -1.08 0.00005 58.70 235401 s at Fc receptor-like A FCRLA -1.08 0.00173 50.00 keratin 1 (epidermolytic 205900 at hyperkeratosis) KRT1 -1.08 0.04518 43.48 Chromosome 16 open reading frame 242509 at 74 Cl6orf74 -1.08 0.00016 47.83 ATP-binding cassette, sub-family B (MDR/TAP), member 1 /// ATP binding cassette, sub-family B ABCB1 I// 209994 s at (MDR/TAP), member 4 ABCB4 -1.08 0.00000 56.52 G protein-coupled receptor 204793 at associated sorting protein 1 GPRASP1 -1.08 0.00026 45.65 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 5 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 10 indicative of the abnormal apoptosis of T-cell subsets observed in SLE patients. (Diaz Alderete A, Crispin JC, Vargas-Rojas MI 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), C:\poi\word\SPEC-8541 93[1].docx 86 379-383 (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 5 overexpression of type I IFN-inducible genes in SLE that were observed in the microarray analyses, a 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 10 originally profiled 46 SLE patients. The overexpression of 15 of the 40 type I IFN-inducible genes using TaqMan assays is shown in Figure 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 15 strong correlation (correlation coefficient >0.98) between microarray and TaqMan assays for 21 IFN-inducible genes in 2 example SLE patients (Figures 83B and 4C) argues for their potential as PD and diagnostic markers in clinical trials that investigate anti-IFN-a approaches in the treatment of SLE. 20 Example 2: Potential PD Markers Selected from Genes Up-Regulated in Lupus Patients Using the whole genome profiling data described in Example la, a group of candidate PD markers were selected. These candidate markers are provided in Table 3. C:\poi\word\SPEC-8541 93[1].docx 87 Table 3: Candidate PD markers Probe ID Gene Symbol Group 204415_at . . 202411_at ~ ~ 214453_s_at ~ 4 229450_at1 1555643 s at LA1 205483_s at 204439_at 5F555 15 203153_at 5555T 5 15 202145_at LY6E 15 202869_at CS 218400_at O& 242625_at AD 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 IPR 3 211967_at PORI|MIN 3 226312_at AVO3 3 201669_s at MARCKS 3 222846_at RAB8B 3 5 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 1 0 data (healthy volunteers shown in shaded columns). C:\poI~word\SPEC-8541 93[1].docx 88 Table 4: Baseline Variation of Candidate PD Markers Gene 102-PAX 129-PAX 129KHR-SLE H33XR-SLE CDC42SE1 0.589 1.000 2.622 1.996 FCHO2 0.872 1.000 3.235 3.298 GIP3 2.059 1.000 86.130 80.545 HERC5 3.638 1.000 638.073 159.621 IF127 0.246 1.000 508.346 14.012 IF144 5.194 1.000 636.965 338.921 IFIT3 1.413 1.000 104.166 59.344 IL6ST 0.337 1.000 3.873 3.628 IRF2 1.486 1.000 8.096 4.998 LILRA5 1.48177 1.000 16.433182 27.248745 BAFF 0.433 1.000 2.478 4.679 GIP2 0.571 1.000 22.168 13.634 IF144L 2.581 1.000 407.035 259.517 IFIT1 4.018 1.000 128.164 151.301 LY6E 0.442 1.000 10.095 5.181 OAS1 0.817 1.000 16.650 10.379 OAS3 2.517 1.000 75.542 32.355 RSAD2 2.425 1.000 310.575 217.885 STAT2 1.526 1.000 11.551 9.735 5 Example 4. IFNa Stimulates Up-Regulation in Expression of Candidate PD Markers in Whole Blood of Healthy Volunteers A study was performed to determine whether IFNa could stimulate expression of candidate PD markers in whole blood of healthy volunteers. Whole blood of healthy 10 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 0 C, 5% CO 2 . Fold-induction of expression of candidate PD markers for genes IF144, IRF2, RSAD2, G1P3, and HERC5 was determined using RNA isolated from PBMCs (Peripheral Blood Mononuclear Cells) with Qiagen's RNAeasy kit. As shown in 15 Table 5 (IF144 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 Figure 1 (IF144), Figure 2 (IRF2), Figure 3 (RSAD2), Figure 4 (G1P3), and Figure 5 (HERC5) for a graphical analysis of these candidate PD marker expression results. A summary hierarchical clustering of all samples using 1384 genes differentially 20 regulated by IFN type 1, IFN type 2, or TNFa obtained from a separate experiment is shown in Figure 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 TNFa. See figure 64. Table 5: Induced IF144 and IRF2 Expression Following Leukocyte IFN Stimulation of 25 Healthy Volunteer's Whole Blood C:\poi\word\SPEC-8541 93[1].docx 89 Sample Gene :Averae ~FC: StDev 63A Media IF144 1.00 63A IFN3 IF144 8.58 0.16 63A IFN30 IF144 8.27 0.07 63A IFN100 IF144 15.12 0.50 63A IFN300 IF144 12.42 0.04 Sample Gene Average FC StDev 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 5 Volunteer's Whole Blood Sample Gene :Averae ~FC: StDev 63A Media RSAD2 1.00 63A IFN3 RSAD2 10.88 0.11 63AIFN30 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 10 Healthy Volunteer's Whole Blood Sample Gene :Average FC: StDev 63A Media G1P3 1.00 63A IFN3 G1 P3 42.88 1.03 63AIFN30 G1 P3 25.76 0.10 63A IFN100 G1 P3 21.72 0.48 63A IFN300 G1P3 16.02 0.06 Sample Gene Average FC StDev 63A Media HERC5 1.00 63A IFN3 HERC5 14.17 0.12 63AIFN30 HERC5 13.74 0.12 63A IFN100 HERC5 18.51 0.58 63A IFN300 HERC5 23.55 0.54 C:\poi\word\SPEC-8541 93[1 .docx 90 Example 5. IFNa Ab Neutralizes IFNa-Induced Candidate PD Marker Expression in Healthy Volunteers' Whole Blood Source of Interferon= IFNa2a 5 Because IFNa treatment of healthy volunteers' whole blood induced expression of candidate PD markers, it was determined whether IFNa 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 10 designated for treatment as follows: (a) blood + vehicle, (b) blood + 100 IU IFNa2a, (c) blood + 100 IU IFNa2a + MEDI-545 (IFNa Ab), and (d) blood + 100 IU IFNa2a + R347 (control Ab). Wells containing blood to be treated with Ab were first incubated with either MEDI 545 (IFNa Ab; well (c)) or R347 (control Ab; well (d)) for 30 minutes. Following Ab 15 treatment, vehicle (well (a)) or IFN a2a (wells (b), (c), and (d)) was added to the appropriate wells and was then incubated for an additional 4 hours at 37 0 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. Following, at least, an overnight incubation at -80C the total RNA of the cells was 20 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 IFNa2a-stimulated whole blood. See Table 8 (RAB8B), Table 9 (IRF7), Table 10 (MARCKS), Table 11 (IL6ST), Table 12 25 (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. C:\poi\word\SPEC-8541 93[1].docx 91 Table 8: IFN a2a-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 5 Table 9: IFN a2a-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 10 107 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 15 163 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 20 175 IFN+545 IRF7 2.43 0.08 175 IFN+R347 IRF7 26.34 8.61 C:\poi\word\SPEC-8541 93[1].dox 92 Table 10: IFN a2a-Induced MARCKS Gene Expression is Neutralized by MEDI-545 Sample Gene :Average: StDev: 107 VEH MARKS 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 5 Table 11: IFN a2a-Induced IL6ST Gene Expression is Neutralized by MEDI-545 Samle Gene Avrg 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 C:\poi\word\SPEC-8541 93[1].docx 93 Table 12: IFN a2a-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 5 Table 13: IFN a2a-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 C:\poi\word\SPEC-8541 93[1].dox 94 Table 14: IFN a2a-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 5 Table 15: IFN a2a-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 C:\poi\word\SPEC-8541 93[1].dox 95 Table 16: IFN a2a-Induced OAS 1 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 5 Table 17: IFN a2a-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 C:\poi\word\SPEC-8541 93[1].docx 96 Table 18: IFN a2a-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 5 See also Figure 6 (RAB8B), Figure 7 (IRF7), Figure 8 (MARCKS), Figure 9 (IL6ST), Figure 10 (LY6E), Figure 11 (IFIT3), Figure 12 (IFIT1), Figure 13, (HERC5), Figure 14 (OAS1), Figure 15 (OAS3), and Figure 16 (RSAD2) for graphical representations of the gene expression data for each of the 11 genes. Source of Interferon= SLE patient serum 10 (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 15 1x107 cells/mL in RPMI media with 10% fetal bovine serum (FBS) and 125 [tL of cells were aliquoted into each well of a 24 well flat bottom plate (1.25x106cells/well). Serum from SLE patients was preincubated for one hour with MEDI-545 (0.1, 1, 10 [tg/mL), anti-IFN-y antibody (1 [tg/mL) or control antibody (10 tg/mL). SLE serum was added to the PBMC at a final concentration 25% (62.5 [tL per well). Additional volume of RPMI + 10% FBS was 20 added to the wells to obtain a final volume of 250 [tL per well. Plates were incubated at 37 0 C for either 4 or 18 hours. Following the incubation, RNA was harvested by adding 750 [tL of Trizol LS to each well. Samples were frozen at -70C 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. 25 Table 21: MEDI-545 blocks overexpression of type I IFN genes in whole blood of healthy volunteers stimulated ex vivo with lupus patient serum C:\poi\word\SPEC-8541 93[1].docx 97 Probe ID D1_002_545.10 D1_004_545.10 D1_17021_545.10 UniGene.ID Gene.Symbol 219211 at -4.D541 Hs.38260 USP18 217502 at 13.0247 Hs.437609 IFIT2 218400_at -,25304 Hs.528634 OAS3 213797_at 5 325 Hs.17518 RSAD2 203153 at Hs.20315 IFITI 242625 at -2.12.22 Hs.17518 RSAD2 204747_at -. 3.0 Hs.47338 IFIT3 205483_s at -52323 Hs.458485 ISG15 204439_at 2, S3.5887 -2 Hs.389724 IF144L 202145 at 2 -5 Hs.521903 LY6E 202869 at A Hs.524760 OASI 235643_at Hs.489118 SAMD9L 219352_at 44% 3.' Hs.529317 HERC6 204415 at - 1 22-2.3" Hs.523847 IF16 219684_at '2 16 2622 Hs.43388 RTP4 236156_at 2,41 0 Hs.127445 LIPA 205552 s at 2 33'2 1 Hs.524760 OASI 206133_at -2Hs.441975 BIRC4BP 214453 s at - - Hs.82316 IF144 1556643_at Hs.515243 LOC93343 228607 at -12.3'23 Hs.414332 OAS2 218943_s at Hs.190622 DDX58 242020 s at Hs.302123 ZBP1 204959_at 1 Hs.153837 MNDA 226757_at '2.24 2 R2.384 Hs.437609 IFIT2 219863 at ',539 Hs.26663 HERC5 229450 at 22 -- 214059 at Hs.82316 IF144 232517_s at -2.192 27 2A. Hs.517180 PRIC285 232666 at ... Hs.528634 OAS3 230036 at Hs.489118 SAMD9L 227609 at Hs.546467 EPST11 226702_at '2.1<2 3.1 S3.156 Hs.7155 LOC129607 226603 at 72 4 Hs.489118 SAMD9L 210397_at -0.5687 Hs.32949 DEFBI 204994_at - Hs.926 MX2 202086_at Hs.517307 MX1 228617_at Hs.441975 BIRC4BP 219364_at 2. *4N 2. Hs.55918 LGP2 209417 s at 4 Hs.632258 IF135 222154 s at 22 4542 2.6 Hs.120323 DNAPTP6 228230_at Hs.517180 PRIC285 242234 at - Hs.441975 BIRC4BP 219519_s at -0.2596 Hs.31869 SIGLECI 207713 s at -14.0 Hs.247280 C20orf18 218974 at -2. Hs.445244 FLJ10159 1552309 a at Hs.632387 NEXN 210873 x at 14 Hs.348983 APOBEC3A 243271 at -2 -2 Hs.489118 SAMD9L 202411 at -0.1345 -. 4'.57 Hs.532634 IF127 222793_at Hs.190622 DDX58 235276_at -- - 203236 s at 1.2 Hs.81337 LGALS9 225291 at 1.13 Hs.388733 PNPT1 44673 at -0.1337 1 Hs.31869 SIGLECI 213294_at 1.3 2 45 2) Hs.546523 - 211122 s at ",2 k3.1 3 Hs.632592 CXCLI 1 224701 at -17 1 Hs.583792 PARP14 230314_at Hs.112420 - 218986 s at 2. Hs.591710 FLJ20035 205569 at Hs.518448 LAMP3 219691 at Hs.65641 SAMD9 204211 x at 1 2. 2 Hs.131431 EIF2AK2 220146_at 1 2 Hs.443036 TLR7 241916 at ,5906 '3 Hs.130759 PLSCRI 229350 x at - 7 Hs.348609 PARPIO 1555464 at -1.586 Hs.163173 IFIHI 204972 at Hs.414332 OAS2 204698_at 17 G Hs.459265 ISG20 203595_s at Hs.252839 IFIT5 220576 at 4$Z4 1173 4 Hs.229988 PGAPI 1555491_a at 1 7 S1 --- FLJ11286 1565752 at -0.0040 S Hs.509664 FGD2 203596 s at - 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, NFiB), adaptive immune response (NFAT, IL-1/IL-6), complement activation as well as leukocyte chemotaxis 5 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. C:\poi\word\SPEC-854193[1].docx 98 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 Figure 67. The anti-IFN-a mAb treatment (lanes 4-6) demonstrated strong neutralization of a large number of genes stimulated with the serum of an 5 SLE patient. Furthermore, neutralization by the anti-IFN-a 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 a mAb was much broader, with strong neutralization observed in a large number of genes of 10 which neither the reference mAb nor anti-IFN-y mAb had any significant effect (lane 2; lanes 4-6). It should be noted that treatment with anti-IFN-aR mAb (lane 7) induced more neutralization than anti-IFN-a mAb, which suggests the presence of other type I IFN family members in the serum of the SLE patients, in addition to IFN-a. (b) Further investigation was conducted to identify early and late transcriptional responses 15 in healthy donor PBMCs stimulated with SLE patient serum. In this study, four SLE patient serum samples, with varying levels of IFNa activity, were used to stimulate PBMCs isolated from a healthy donor. The varying levels of IFNa 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 20 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 1.5X 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. Figure 25 70a 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 30 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 C:\poi\word\SPEC-8541 93[1].docx 99 according to manufacturer's instructions (Affymetrix, Santa Clara, CA). 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). Figure 70b shows the number of probes detected as 3-fold or more upregulated in the healthy volunteer PBMCs by each of 5 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, 10 discussed above, were incubated with 25% SLE patient serum in the presence or absence of neutralizing antibodies against IFN-a, 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 15 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, CA). 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 20 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-IFNa antibody. Figure 71a provides heat maps showing the percent neutralization of probes that were identified as upregulated following anti-IFNa treatment for type I IFN genes (689 probes) and 25 non-type I IFN genes (probes induced by SLE serum outside of type I IFN gene list) 4 and 18 h post incubation. Figure 71b 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-IFNa treatment following both the 4 and 18 hour incubations. It appears that the majority of genes neutralized by anti-IFNa treatment of SLE serum-treated 30 healthy volunteer's PBMCs 4 hours post-incubation were type I IFN genes, while the majority of genes neutralized by anti-IFNa 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-IFNa treatment at 18 hours, but that were not upregulated at 4 hours C:\poi\word\SPEC-8541 93[1].docx 100 (i.e., "unique genes") were identified for each SLE patient serum sample. Figure 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-IFNa in that patient sample. Cell pathways and processes neutralized by anti-IFNa treatment at the 18 hr time point 5 are involved in cytokine and chemokine signaling pathways, immune regulation, cell adhesion, and cell survival. See Figure 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-IFNa treatment at the 18 hr time point were analyzed with the MetaCore 10 integrated software suite from GeneGo, Inc. using the identified unique genes. Only pathways with p-values < 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 IFNa-Inducible Candidate PD Marker Expression Pattern 15 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 IFNa-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 Figure 18, Figure 23, and Figure 24 which provide graphical 20 representations of neutralization of these top 25 PD markers following administration of varying concentrations of the MEDI-545 IFNa 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 25 UniGene Probe ID ID Gene Title Gene Symbol myxovirus (influenza virus) resistance 1, interferon inducible protein p78 (mouse) /// myxovirus (influenza virus) resistance 1, interferon-inducible protein p78 202086_at Hs.517307 (mouse) MX1 202145_at Hs.521903 lymphocyte antigen 6 complex, locus E LY6E 202411_at Hs.532634 interferon, alpha-inducible protein 27 IF127 202869_at Hs.524760 2',5'-oligoadenylate synthetase 1, 40/46kDa OAS1 interferon-induced protein with tetratricopeptide repeats 1 /// interferon-induced protein with 203153_at Hs.20315 tetratricopeptide repeats 1 IFIT1 204415_at Hs.523847 interferon, alpha-inducible protein 6 IF16 204439_at Hs.389724 interferon-induced protein 44-like IF144L 205483_s_at Hs.458485 ISG15 ubiquitin-like modifier ISG15 205569_at Hs.518448 lysosomal-associated membrane protein 3 LAMP3 C:\poi\word\SPEC-8541 93[1].docx 101 205660_at Hs.1 18633 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 IF144 interferon-induced protein with tetratricopeptide 217502_at Hs.437609 repeats 2 IFIT2 218400_at Hs.528634 2'-5'-oligoadenylate synthetase 3, 1 00kDa OAS3 219211_at Hs.38260 ubiquitin specific peptidase 18 USP18 sialic acid binding Ig-like lectin 1, sialoadhesin / sialic 219519_s_at Hs.31869 acid binding Ig-like lectin 1, sialoadhesin SIGLEC1 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) EPST11 229450_at --- ---

--

235276_at --- ---

--

239979_at Hs.546467 Epithelial stromal interaction 1 (breast) EPST11 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 Figures 19-21. Figures 19 and 20 are heatmaps showing the neutralization of the top 25 PD markers (see Table 19) for two 5 individual lupus patients (Figure 19, patient 1541; and Figure 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 10 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 Figure 25(a). Neutralization of all genes can be seen following administration of MEDI-545. Figure 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 15 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 Figure 21. MEDI-545 neutralized most of the 165 candidate PD markers in this lupus patient. The 165 candidate PD markers 20 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 C:\poi\word\SPEC-8541 93[1].docx 102 (b) dosing with placebo in Figure 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 5 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. 10 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 C:\poi\word\SPEC-8541 93[1].dox 103 Lupus Samples With IFN ALL Lupus Samples, (+)Medi- Lupus Samples Without an IFN Samples Receiving Placebo sol (type I IFN indud5 neutralizab Day.7_Sig Day.1 4SigDay.28_Sic Day.7_All Day.1 4_All Day.28_AII)ay.7_NoSiay.1 4NoSay.28_NoSiy.7_Placey.1 4Placey.28_Place 0.6871 0.6276 0.5047 03433 02657 02357 -0.0799 -0.2278 -0.0088 !Ia2 I 0____ 062 0.13 0.5515 0.6662 0.S561 0.492 0.67-13 0.4698 0.4379 5 05 0.6547 0.631 0.5213 0.6023 0.4611 0.4464 0.5377 0.2294 0.3783 222 2 09t 0.6395 0.5954 0.5703 0.5404 0.4781 0.4148 0.4185 0.3181 0.2734 4 0.6359 0.6123 0.4946 0.5607 0.541 0.3443 0.4681 0.4437 0.207 W57 2 X,7In -o+632 2 0.6305 0.6269 0.5577 0.4322 0.4423 0.4082 0.1882 0.1907 0.2723 - -2 E - A 0.626 0.5875 0.4223 0.4956 0.2741 0.2298 0.3352 -0.1532 0.0547 2863 1A 2.AOcS 3 0.6224 0.6093 0.5376 0.5442 0.4586 0.4182 0.448 0.2532 0.3097 W .. .4A 5676 0.5638 0.5212 0.4174 0.3854 0.398 0.2124 0.2232 X +:: 0.617 0.6214 0.5974 0.4617 0.4294 0.3673 0.2706 0.1676 0.1582 S 2 0.5996 0.531 0.5352 0.3581 0.3678 0.4335 0.0609 0.1452 0.341 x x, 0.5973 0.6223 0.5016 0.345 0.3819 0.2244 0.0345 0.0543 0.0276 0.5968 0.5529 0.5815 0.4 15 0.3853 0.4208 0.3174 0.1569 0.2748 X -6 l44+++:+ 0.5948 0.5552 0.4997 0.4651 0.4521 0.3816 0.3054 0.3115 0.2742 -OLOS M44 - 3 Yi 0.589 0.5792 0.5062 0.4846 0.4039 0.3562 0.3065 0.31 54 :1+66 1744 0.581 0.5218 0.4955 0.3014 0.3035 0.2441 -0.0427 0.0058 0.0155 0.5807 0.5329 0.5073 0.512 0.4831 0.4001 0.4273 0.4152 0.3026 X0O& - S7 T 0.5761 0.51 48 0.5652 0.4345 0.429 0.4373 0.2603 0.3119 0.3211 i3 -245 O06 0.5681 0.5549 0.5494 0.4814 0.4415 0.4046 0.3746 0.2868 0.2729 .. .... ..... 0.5678 0.5193 0.56 0.4796 0.4115 0.4196 0.3711 0.2644 0.292 2, 0.5531 0.6796 0.4871 0.3427 0.4182 0.2854 0.0838 0.0618 0.1021 T 4 3-1a: G 0 5 0.535 0.5085 0.5093 0.359 0.2949 0.332 0.1424 0.0036 0.1709 2 -SSR -OSS$ 0.5321 0.5639 0.5307 0.307 0.3711 0.212 0.03 0.1081 -0.078 7...3. ....... 0.5317 0.503 0.4707 0.3942 0.3604 0.266 0.2249 0.1659 0.0799 ::,22:: %7+7 53 0.5257 0.4922 0.3314 0.3004 0.1997 0.0723 0.023 -0.1991 -0.1633 7 X X39 0.5183 0.494 0.4717 0.4318 0.3509 0.301 0.3253 0.1557 0.1459 99i O2i 2i5 0.517 0.5298 0.4999 0.3142 0.2662 0.2798 0.0646 -0.0932 0.0797 X+ :15+ 0.5074 0.4803 0.553 0.3738 0.3527 0.3674 0.2093 0.1786 0.1987-, 0.5057 0.5101 0.3596 0.2965 0.2389 0.0985 0.039 -0.1308 -0.1389 X X53% 0 634 z 0.5056 0.4731 0.2902 0.2482 0.2263 0.028 -0.0685 -0.1102 -0.2105 X66 - 64$ 0.4998 0.4746 0.4266 0.3377 0.3141 0.2703 0.1383 0.0953 0.1283 5 0.4812 0.4274 0.4076 0.3058 0.2935 0.2109 0.0898 0.1109 0.0321 0.4636 0.4665 0.4025 0.3114 0.2848 0.2299 0.1241 0.037 0.073 +2OZ -4U2 992 0.4578 0.4242 0.3425 0.264 0.1555 0.1794 0.0253 -0.211 0.0312 -15S -&23 -. & 0.4557 0.3628 0.4828 0.3165 0.2457 0.3356 0.1452 0.086 0.2018 X 0 2 0.4532 0.4503 0.3889 0.2963 0.3106 0.2084 0.1032 0.1202 0.0444 I+Q067 2 l 0.4514 0.4519 0.1899 0.0857 -0.039 -0.4306 -0.3643 -0.7083 -0.9948 -U.79l565 - 2 0.4476 0.4647 0.262 0.1834 0.1911 0.1282 -0.1418 -0.1819 0.0066 -5 0.4463 0.4582 0.4113 0.3404 0.3294 0.2612 0.21 0.1536 0.1247 0.4449 0.3726 0.3596 0.2951 0.2402 0.2433 0.1108 0.0596 0376 0.4421 0.3914 0.1018 0.152 0.3129 -0.3045 -0.205 0.2058 -0.6738 -ThQ3 2 :: .4+: 3 0.4419 0.4279 0.401 0.2663 0.2445 0.2165 0.0501 -0.0055 0.0488 ijOiE-O4 M : 0.4377 0.3721 0.2965 0.3008 0.2379 0.1882 0.1323 -00548 0 0897 4 0.4264 0.063 0.4352 -0.0787 -0.5482 -0.2042 -0.7003 -1.3816 -0.7855 0.4232 0.406 0.3729 0.0761 0.1281 0.2718 -0.3512 -0.2508 0.1799 +4:: :::7: a7++ z 0.4022 0.3948 0.2996 0.1919 0.1973 0.1063 -0.0668 -0.0719 -0.0694 ThOQMS :I4q -O82 0.3989 0.3655 0.3374 002712 0.2174 0.1639 0.114 0.0155 0.0061 U: 0.3896 0.3464 0.2669 0.2285 0.1987 0.1119 0.0303 -0.0027 -0.0289 :O:4:3 x1.21+ -p.7 C - 2 0.3891 0.4249 0.3925 0.2541 0.2965 0.2822 0.088 0.1213 0.182 -S7 4 0.3847 0.3858 0.2706 -0.2032 -0.0283 -0.1714 -0.9268 -0.5931 -0.5733 - 1 S 0.3782 0.2012 0.1293 -0.5127 -0.9029 -0.5568 -1.6091 -2.4085 -1. 16 X X 0.3778 0.2403 0.2971 0.3178 0.699 0.0019 0.244 0.0741 -0.2665 TI: Q: C n 0.3658 0.3508 0.2804 0.2913 02599 0.108 0.1996 0.136 -0.0488 26 - A#2 0.3642 0.3373 0.3736 0.2344 02522 0.1405 0.0747 0.1362 -0.0714 :+ i - 6 0.3636 0.4131 0.3363 0.2701 0.2731 0.1074 0.155 0.0822 -0.1008 :O,71I +41:7 0.3611 0.3765 0.3718 0.2737 0.2855 0.2267 0.1662 0.1614 0.0947 RO+7:: 47+:++:+ 0.3448 0.3672 0.2896 0.2048 0.2134 0.108 0.0325 0.0037 -0.0571 Q +S17 + + 0.3371 0.3793 0.1084 0.1586 0.1796 -0.2285 -0.0612 -0.0927 -0.5347 - 5 0.336 0.3559 0.3269 0.1913 0.1909 0.1164 0.0133 -0.034 -0.0751 0 0'++2+243+++++ 0.3331 0.27 0.2644 -0.0457 0.1764 0032 -0.512 0.0487 -0.0434 0111 + +++. 0.3215 0.0604 0.0634 -0.2323 -0.5787 -1.1884 -0.914 -1.4502 -2.3265 -U.+7 +++ -+514+ 0.3176 0.1781 0.1852 0.1643 -0.0318 -0.051 -0.0245 -0.318 -0.2657 ODS EG7 - $91 0.3094 0.3621 0.2577 0.2165 0.286 0.1441 0.1021 0.1822 0.0408 +O:244 + OA++:+________ 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-a/p-inducible 5 Table 33: Top 50 probes neutralized 7 days post-dose in SLE patients receiving MEDI-545 treatment C:\poi\word\SPEC-854193[1].docx 104 Avg Probe Rank (By % e ID UniGene ID Gene Title Gene Symbol Neutralization) Final Probe Rank 52_at Hs.529317 hect domain and RLD 6 HERC6 2277.0 1 36 s-at Hs.166120 interferon regulatory factor 7 IRF7 2497.5 2 97 s at Hs.118633 2-5'-oligoadenylate synthetase-like OASL 2708.2 3 83 s-at Hs.458485 ISG15 ubiquitin-like modifier ISG15 2735.7 4 39_at Hs.389724 interferon-induced protein 44-like IF144L 3194.9 5 11 at Hs.38260 ubiguitin specific peptidase 18 USP18 3458.6 6 43 s at Hs.12646 poly (ADP-ribose) polymerase family, member 12 PARP12 3472.3 7 41_at Hs.567405 SCO cytochrome oxidase deficient homolog 2 (yeast) SC02 3825.7 8 47_at Hs.47338 interferon-induced protein with tetratricopeptide repeats 3 IFIT3 3987.2 9 19 s-at Hs.31869 sialic acid binding Ig-like lectin 1, sialoadhesin SIGLEC1 4207.2 10 30_at Hs.517180 peroxisomal proliferator-activated receptor A interacting complex 285 PRIC285 4373.1 11 76_at --- --- --- 4438.7 12 59_at Hs.82316 Interferon-induced protein 44 IF144 4477.4 13 54 s-at Hs.120323 DNA polymerase-transactivated protein 6 DNAPTP6 4531.3 14 45_at Hs.521903 lymphocyte antigen 6 complex, locus E LY6E 4618.6 15 49 s-at Hs.514941 Movl0, Moloney leukemia virus 10, homolog (mouse) MOV10 4691.0 16 64_at Hs.55918 likely ortholog of mouse D11 lp2 LGP2 4717.4 17 03 s-at Hs.1 14191 zinc finger, CCHC domain containing 2 ZCCHC2 4926.5 18 17_at Hs.441975 XIAP associated factor-1 BIRC4BP 4942.0 19 0at --- hypothetical protein FLJ1 1286 FLJ11286 5046.2 20 00_at Hs.528634 2-5'-oligoadenylate synthetase 3, 1OOkDa OAS3 5136.7 21 08_at Hs.526464 promyelocytic leukemia PML 5328.7 22 55 at Hs.514554 KIAA1618 KIAA1618 5344.5 23 86_at Hs.517307 myxovirus (influenza virus) resistance 1, interferon-inducible protein p78 (mouse) MX1 5484.4 24 25_at Hs.17518 radical S-adenosyl methionine domain containing 2 RSAD2 5522.4 25 17 s-at Hs.632258 interferon-induced protein 35 IF135 5529.4 26 39_at Hs.124840 basic leucine zipper transcription factor, ATF-like 2 BATF2 5563.0 27 66 s-at Hs.10784 family with sequence similarity 46, member A FAM46A 5607.1 28 46 s at Hs.130759 phospholipid scramblase 1 PLSCR1 5911.3 29 60_at Hs.118633 2-5'-oligoadenylate synthetase-like OASL 6001.3 30 75 s-at Hs.344812 three prime repair exonuclease 1 TREX1 6062.0 31 9_at Hs.344812 three prime repair exonuclease 1 TREX1 6097.0 32 69_at Hs.524760 2',5'-oligoadenylate synthetase 1, 40/46kDa OAS1 6101.5 33 53 s-at Hs.82316 interferon-induced protein 44 IF144 6210.4 34 491_a at --- hypothetical protein FLJ11286 FLJ11286 6235.7 35 36_at Hs.489118 sterile alpha motif domain containing 9-like SAMD9L 6254.1 36 17 s-at Hs.438723 solute carrier family 27 (fatty acid transporter), member 3 SLC27A3 6257.9 37 41_at Hs.118110 bone marrow stromal cell antigen 2 BST2 6371.4 38 99_at Hs.419259 REC8-like 1 (yeast) REC8L1 6423.3 39 27_at Hs.531314 olutamate-cysteine ligase, modifier subunit GCLM 6500.4 40 91_at Hs.388733 polyribonucleotide nucleotidyltransferase 1 PNPT1 6537.6 41 81xat Hs.374950 metallothionein 1X MT1X 6541.4 42 80_at Hs.520102 KIAA0082 KIAA0082 6547.1 43 47xat Hs.154029 hairy and enhancer of split 4 (Drosophila) HES4 6557.3 44 116 at Hs.257352 apolipoprotein L, 6 APOL6 6571.1 45 69_at Hs.464419 F-box protein 6 FBXO6 6683.0 46 86_at Hs.384598 serpin peptidase inhibitor, clade G (Cl inhibitor), member 1, (angioedema, hereditary) SERPING1 6688.7 47 4_at Hs.459265 interferon stimulated exonuclease gene 20kDa ISG20 6853.8 48 93 s-at Hs.252682 torsin family 1, member B (torsin B) TOR1B 6866.4 49 07 s at Hs.352018 transporter 1, ATP-binding cassette, sub-family B (MDR/TAP) TAP1 6909.0 50 Example 7: The Majority of Lupus Patients Exhibit a Type I IFN-Inducible PD Marker Expression Pattern 5 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 10 that 24/35 of the lupus patients had a statistically significant PD marker signature. See Figure 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 15 Probe ID UniGene ID Gene Title Gene C:\poi\word\SPEC-854193[1].docx 105 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 IFIHI membrane-spanning 4-domains, subfamily A, 1555728_a_at Hs.325960 member 4 MS4A4A 1556643_at Hs.515243 Hypothetical protein BC011840 LOC93343 1557236_at Hs.257352 apolipoprotein L, 6 APOL6 1559585_at Hs.535011 hypothetical protein FLJ31033 FLJ31033 signal transducer and activator of transcription 1, 200887 s at Hs.565365 91kDa STATI lectin, galactoside-binding, soluble, 3 binding 200923_at Hs.514535 protein LGALS3BP serpin peptidase inhibitor, clade G (Cl inhibitor), 200986_at Hs.384598 member 1, (angioedema, hereditary) SERPINGI 201015 s at Hs.514174 junction plakoglobin JUP 201324_at Hs.436298 epithelial membrane protein 1 EMPI 201641_at Hs.1 18110 bone marrow stromal cell antigen 2 BST2 201646_at Hs.349656 scavenger receptor class B, member 2 SCARB2 methylenetetrahydrofolate dehydrogenase (NADP+ dependent) 2, methenyltetrahydrofolate 201761_at Hs.469030 cyclohydrolase MTHFD2 myxovirus (influenza virus) resistance 1, interferon-inducible protein p7 8 (mouse) /// myxovirus (influenza virus) resistance 1, 202086_at Hs.517307 interferon-inducible protein p7 8 (mouse) MX1 202145_at Hs.521903 lymphocyte antigen 6 complex, locus E LY6E guanylate binding protein 1, interferon-inducible, 67kDa /// guanylate binding protein 1, interferon 202270_at Hs.62661 inducible, 67kDa GBP1 202411_at Hs.532634 interferon, alpha-inducible protein 27 IF127 202430 s at Hs.130759 phospholipid scramblase 1 PLSCR1 202446 s at Hs.130759 phospholipid scramblase 1 PLSCR1 AKAP2 /// A kinase (PRKA) anchor protein 2 /// PALM2- PALM2 202759_s at Hs.591908 AKAP2 protein AKAP2 202863_at Hs.369056 SP100 nuclear antigen SP100 202869 at Hs.524760 2',5'-oligoadenylate synthetase 1, 40/46kDa OAS1 interferon-induced protein with tetratricopeptide repeats 1 /// interferon-induced protein with 203153_at Hs.20315 tetratricopeptide repeats 1 IFITI interferon-induced protein with tetratricopeptide 203595sat Hs.252839 repeats 5 IFIT5 interferon-induced protein with tetratricopeptide 203596sat Hs.252839 repeats 5 IFIT5 203771_s at Hs.488143 biliverdin reductase A BLVRA eukaryotic translation initiation factor 2-alpha 204211_x_at Hs.131431 kinase 2 EIF2AK2 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 IF16 204439_at Hs.389724 interferon-induced protein 44-like IFI44L 204533_at Hs.632586 chemokine (C-X-C motif) ligand 10 CXCL1O interferon-induced protein with tetratricopeptide 204747_at Hs.47338 repeats 3 IFIT3 204972_at Hs.414332 2'-5'-oligoadenylate synthetase 2, 69/7lkDa 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 signal transducer and activator of transcription 2, 205170 at Hs.530595 113kDa STAT2 SCO cytochrome oxidase deficient homolog 2 205241_at Hs.567405 (yeast) SCO2 205483_s at Hs.458485 ISG15 ubiquitin-like modifier ISG15 205552 s at Hs.524760 2',5'-oligoadenylate synthetase 1, 40/46kDa OAS1 C:\poi\word\SPEC-8541 93[1].dox 106 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-I BIRC4BP 206332 s at --- interferon, gamma-inducible protein 16 IF116 206513_at Hs.281898 absent in melanoma 2 AIM2 206553_at Hs.414332 2'-5'-oligoadenylate synthetase 2, 69/7lkDa OAS2 carcinoembryonic antigen-related cell adhesion 206576 s at Hs.512682 molecule 1 (biliary glycoprotein) CEACAMI 206715_at Hs.125962 transcription factor EC TFEC Z-DNA binding protein 1 /// Z-DNA binding 208087sat Hs.302123 protein 1 ZBP1 208436_sat 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 IF116 209417 s at Hs.632258 interferon-induced protein 35 IF135 carcinoembryonic antigen-related cell adhesion 209498 at Hs.512682 molecule 1 (biliary glycoprotein) CEACAMI 209593 s at Hs.252682 torsin family 1, member B (torsin B) TORIB 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 apolipoprotein B mRNA editing enzyme, catalytic 210873_x_at Hs.348983 polypeptide-like 3A APOBEC3A 210985 s at Hs.369056 SP100 nuclear antigen SP100 PML /// promyelocytic leukemia /// hypothetical protein LOC161527 LOC161527 /// similar to promyelocytic leukemia /// 211012_s at Hs.498345 protein isoform 9 LOC652671 211456_x_at --- hypothetical protein LOC650610 LOC650610 carcinoembryonic antigen-related cell adhesion 211889 x at Hs.512682 molecule 1 (biliary glycoprotein) CEACAMI 212185_x_at Hs.534330 metallothionein 2A MT2A 212657 s at Hs.81134 interleukin 1 receptor antagonist ILIRN 212659 s at Hs.81134 interleukin 1 receptor antagonist ILIRN 212845_at Hs.98259 sterile alpha motif domain containing 4A SAMD4A 213293 s at Hs.501778 tripartite motif-containing 22 TRIM22 Full-length cDNA clone CSODKO02YF13 of HeLa 213294_at Hs.546523 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 IF144 tumor necrosis factor (ligand) superfamily, member 10 // tumor necrosis factor (ligand) superfamily, 214329 x at Hs.478275 member 10 TNFSF1O 214453_s at Hs.82316 interferon-induced protein 44 IF144 FCGR1A // Fc fragment of IgG, high affinity Ia, receptor LOC440607 (CD64) /// Fc-gamma receptor I B2 /// similar to // 214511_x_at Hs.534956 Fc-gamma receptor I B2 isoform b LOC652758 216243 s at Hs.81134 interleukin 1 receptor antagonist ILIRN 216598 s at Hs.303649 chemokine (C-C motif) ligand 2 CCL2 217165_x_at Hs.513626 metallothionein IF (functional) MT1F interferon-induced protein with tetratricopeptide 217502at Hs.437609 repeats 2 IFIT2 217933 s at Hs.570791 leucine aminopeptidase 3 LAP3 218400 at Hs.528634 2'-5'-oligoadenylate synthetase 3, 1OOkDa 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 C:\poi\word\SPEC-8541 93[1].dox 107 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 IFIHI 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 D111gp2 LGP2 sialic acid binding Ig-like lectin 1, sialoadhesin /// 219519 s at Hs.31869 sialic acid binding Ig-like lectin 1, sialoadhesin SIGLEC1 membrane-spanning 4-domains, subfamily A, 219607 s at Hs.325960 member 4 MS4A4A 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 --- --- -- Mov10, Moloney leukemia virus 10, homolog 223849_sat Hs.514941 (mouse) MOV1O 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 signal transducer and activator of transcription 2, 225636_at Hs.530595 113kDa STAT2 LOC652689 hypothetical protein LOC652689 /// family with /// FAM72A sequence similarity 72, member A /// similar to // family with sequence similarity 72, member A /// LOC653594 similar to family with sequence similarity 72, /// 225834_at Hs.599880 member A LOC653820 225869 s at Hs.502989 unc-93 homolog BI (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 interferon-induced protein with tetratricopeptide 226757_at Hs.437609 repeats 2 IFIT2 227458_at --- --- -- 227609_at Hs.546467 epithelial stromal interaction 1 (breast) EPSTIl 227697 at Hs.527973 suppressor of cytokine signaling 3 SOCS3 228152 s at Hs.535011 hypothetical protein FLJ31033 FLJ31033 peroxisomal proliferator-activated receptor A 228230 at Hs.517180 interacting complex 285 PRIC285 basic leucine zipper transcription factor, ATF-like 228439 at Hs.124840 2 BATF2 228531_at Hs.65641 sterile alpha motif domain containing 9 SAMD9 228607 at Hs.414332 2'-5'-oligoadenylate synthetase 2, 69/7lkDa OAS2 228617_at Hs.441975 XIAP associated factor-I BIRC4BP 229450 at --- --- -- 230036_at Hs.489118 sterile alpha motif domain containing 9-like SAMD9L Transcribed locus, strongly similar to XP_511805.1 230314_at Hs. 112420 PREDICTED: hypothetical protein XP_511805 -- C:\poi\word\SPEC-8541 93[1].dox 108 [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 Signal transducer and activator of transcription 1, 232375_at Hs.565365 91kDa STATI 232666_at Hs.528634 2'-5'-oligoadenylate synthetase 3, l00kDa OAS3 233425_at Hs.631682 zinc finger, CCHC domain containing 2 ZCCHC2 233880 at Hs.195642 chromosome 17 open reading frame 27 Cl7orf27 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 lipase A, lysosomal acid, cholesterol esterase 236156_at Hs.127445 (Wolman disease) LIPA 236692 at --- --- -- 238439 at Hs.217484 ankyrin repeat domain 22 ANKRD22 238581_at Hs.513726 Guanylate binding protein 5 GBP5 Full-length cDNA clone CS0DK002YF13 of HeLa 238743_at Hs.546523 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) EPSTl 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-I 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- signal transducer and activator of transcription 1, HUMISGF3A/M97935_3_at Hs.565365 91kDa STATI AFFX- signal transducer and activator of transcription 1, HUMISGF3A/M97935_5_at Hs.565365 91kDa STATI AFFX- signal transducer and activator of transcription 1, HUMISGF3A/M97935 MB at Hs.565365 91kDa STATI 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 5 a strong/moderate type I IFN inducible signature. See Figure 68a for PCA analysis results and 68b 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 Figure 65 provide further evidence that a high percentage of SLE patients 10 share at least 2-fold overexpression of each individual type I IFN genes. C:\poi\word\SPEC-8541 93[1].dox 109 Table 23: Overexpressed Type-I IFN Genes in Whole Blood of Lupus Patients Number Of Samples Displaying A Fold-Change Average log2 Fold Probe.lD 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 IF16 67 76.14 3.007 217502 at interferon-induced protein with tetratricopeptide repeats 2 IFIT2 65 73.86 1.913 235643 at sterile alpha motif domain containing 9-like SAMD9L 65 73.86 2.020 213797 at radical S-adenosyl methionine domain containing 2 RSAD2 62 70.45 2.978 214059 at Interferon-induced protein 44 IF144 61 69.32 3.050 202411 at interferon, alpha-inducible protein 27 IF127 60 68.18 3.937 204439 at interferon-induced protein 44-like IF144L 60 68.18 2.847 242625 at radical S-adenosyl methionine domain containing 2 RSAD2 59 67.05 2.861 214453 s at interferon-induced protein 44 IF144 59 67.05 2.463 203153_at interferon-induced protein with tetratricopeptide repeats 1 //in IFIT1 59 67.05 2.034 242234 at XIAP associated factor-1 BIRC4BP 59 67.05 2.066 203595_sat interferon-induced protein with tetratricopeptide repeats 5 IFIT5 59 67.05 1.603 202086 at myxovirus (influenza virus) resistance 1, interferon-inducible p MX1 58 65.91 1.777 206133 at XIAP associated factor-1 BIRC4BP 58 65.91 1.803 216243 s at interleukin 1 receptor antagonist ILl RN 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, 40/46kDa 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 tetratricopeptide repeats 3 IFIT3 56 63.64 1.675 1555464 at interferon induced with helicase C domain 1 IFIH1 56 63.64 1.532 218400_at 2-5-oligoadenylate s nthetase 3, 1OOkDa OAS3 55 62.50 1.932 227609_at epithelial stromal interaction 1 (breast) EPST11 55 62.50 1.788 200986 at serpin peptidase inhibitor, clade G (C1 inhibitor), member 1, SERPING1 55 62.50 1.503 202145 at lymphocyte antigen 6 complex, locus E LY6E 54 61.36 2.242 239979 at Epithelial stromal interaction 1 (breast) EPST11 54 61.36 1.895 205552_sat 2,5-oligoadenylate synthetase 1, 40/46kDa OAS1 54 61.36 1.945 225929 s at chromosome 17 open reading frame 27 C1 7orf27 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 210797sat 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 binding protein 1 ZBP1 52 59.09 1.438 243271 at Sterile alpha motif domain containing 9-like SAMD9L 52 59.09 1.126 219519_sat sialic acid binding Ig-like lectin 1, sialoadhesin /// sialic acid bin SIGLEC1 51 57.95 3.019 228617at 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, 1 OOkDa 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) pol merase 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-oligoadenylate synthetase 2, 69/71 kDa OAS2 48 54.55 1.582 219684 at receptor transporter protein 4 RTP4 48 54.55 1.534 230000 at chromosome 17 open reading frame 27 C1 7orf27 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 tetratricopeptide repeats 5 IFIT5 47 53.41 1.327 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 IL1 RN 47 53.41 1.196 228439 at basic leucine zipper transcription factor, ATF-like 2 BATF2 46 52.27 1.180 226757 at interferon-induced protein with tetratricopeptide repeats 2 IFIT2 46 52.27 0.882 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_sat dual adaptor of phosphotyrosine and 3-phosphoinositides DAPP1 46 52.27 1.055 208436 s at interferon reg ulatory 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, 69/71kDa 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-alpha kinase 2 EIF2AK2 44 50.00 1.050 235157 at Poly (ADP-ribose) polymerase family, member 14 PARP14 44 50.00 0.940 209417sat interferon-induced protein 35 IF135 44 50.00 0.957 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 5 as potentially useful. See Table 24. C:\poi\word\SPEC-854193[1].docx 110 Table 24: Twenty one potential overexpressed type I JFN genes useful as PD markers :le IF144 IFI17 IF144L NAPTP LAMP3 LYSE RSAD2 HERC5| IF16 ISGI5 OAS3 SIGLECI OAS2 USP18 RTP4 IFIT1 MI OAS1 EPSTIlPLSCR1 IFRG2S 329 17 3d ~24 7 5 75 ~8~1 812 553 7 482 516 522 714 94 1526 49 7.7' E'~7 ~1 330 .31 4.... 8.. 2..) 42 144 61U4 2;16 _ j':9 344 34U .. 22 2'l3 21 _' 4..'2.71 2.t 2.4 L 6-t- 1 345 - - 1 33 ~5.11 1 16 1 8 373 226 092 303 254 70 ~192 1 4- 106 A . 360 12 13 333 1.3 207 334 246 216 ~'81 217 1379 1 361 3 413 1.'7 731 34 306 46 636 16 1 1 6 1 12 2 11 65 4 - - -. . -. . Il .. .. I l I. l -_ ll) ; : 111 j j - U U - J _j - l _ - 1 2 2 151 161 11I| A~ 7 1~|' 137 15 ~3 1 12 1~1~' 11 6~6 1 107 2~ 6| 22 16 1 -6 - F FF 175 3 08 03 7 E 083 05 527 039 04 070 02 026 05 096 35 A3 I7 063 51 41 148 1 FII I FI J.6 i 0J6 0 J6 0.1 0.36 0 36 032' 0 16 027 042~ 0 12 07~3 (43 (069 (032 (.2 0.2 06 .72B 2 0 271 21 2.82 095 197 070 178 093 045 215 294 A 0' 9 1'76 5 A 1-7 1 7 J 2.2 O' 11 02 6' 0 6 199 026 05 036 1 2 16 34 F2 1.9 136 0 20 3.60 178 )1 3 1 2 14 413 35.1 147 10.03 534 31.9 595 1314 635 15 1 1308 01, 188 0 5 1 7.1 1458 2 135U 0 ~52 076 2~ 1~9 50 ~'317 1~ 6 1 6 71 4 .9 2 .. .l . J I 1 11 12.4 10J 860 181 j32 l 1121 _'lU L 1 J t t 31 )5 113 . 8 631 4 .. 3 6.1 145 la 11.... 146 22.3: 11J63 23.05 11:1) 63'56 110 19-14 174 14.2 E32 66 E1 b 14 1 047 055 02. 073 11. 013 120 070 01~ 031 03 03; 1 03; 3 15- 011 -1? 017 -- 1 4 1 I l 7 0 7 71 10 .17 R7 6,7 11~ 2 -10 l 1425 104 ~- ' '0 7 4 1 2 l2~4 7 29 1| .2 10. 734 1034 183 70 1247 63 1168 1230 7.2 F.14 11 2617 18.) 3.4 6741 24 96 6 35.16 2661~. .I 3 42 23~' 8 27l~1 51.7 2 661 9.1 1663 19 160 1.9 264 12 1-1 131. 5 1 75 1017 7. 819 5~'l 8-1 776 455 101^ 3127 1046 35 83 7 1 1. I 17 3 4 57 913 5 79 4 1313 654 47 667 168 41 1866 69 1037 . IS 1 1 1 41. 1 _ 2 j . 16.75 10:: _'; 18.11 9:4 |. * 1 1 J_' 18.41 449 2.41 16 1 2 I9 - - | '_- llI6-_) : I : ': ' I": 1 IF j Id 'Hl _' UU1 Wb _ -11)| - *l 20 - 1 - -- - 4 4 1 2 1 .21 140 H.' - ' 11'. 46|2 1.-; |4:b 1.|- b . N r21 101 1|5310 1 232I 1 -9 19 19 ~3 ~5'. 1781 8~6 '7 33 645 14'1 58I15 1'60 2'11 1495 2 2 2' 3 41 85 7.0 03 4.1 250 3.01 1.82 26~' 175 061 129" 040 058 55 -~30 156~ 3 198 .7 42 AC4 l.4 314 I. 1393 47.~J32.~1~ 15 24.41~0, 51 60 121 627 13 26l4F 1260 3317 10 1 1 1 RI 4 1363 171 22.06 C 3.24 26.F 135 .73 6.63F 114 12-40 5 23 10.57i 76 853 822 124 535 257 1190 5.8 5.2 5 55 L4 1 3 l6_'2 3.05' 7J47 26.46 2'.. l4 19346 3Y.7 13 1 _' j :l 2396 3326 1J 2 *11 l 1 9 2 1 5311 3 1 21N I 5 1F 115 0~9 | 1-42 17 0~l 11 83 1~1 -. 0 4 -- 2 2t2 2 260 3271 1 75 190 3 ~5~ |143 3'0 ~'~ 45 16 31 ~ 475 7F 4 1 710 415 1 2 1 2.7 mpl laellI22 I i) 40 0:3 M>..O 1?2141 11.37 3; H3 H) 4 IMF3.19~ ~ 2. 15. 1~ 822 U 3I i npriel I1F144 1 107 1IF144L PNAPTP LAP3LYSE IRSAID2 HIERC j FIG ISG15. j AS3 ISIGLECI] OAS2I USP1E RTIP4 IIFITI MXI OA1 EPSTI1 IPISC Ri IFIRG263 Overexpression of these genes, as detected initially using the Affymetrix arrays, was confirmed by Fluidigm dynamic array, validating their overexpression. See Figure 69. 5 C:\po1\word\SPEC-854193[1].docx 111 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 5 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 5 2 1 mpk 2 2 3 mpk 2 1 10 mpk 0 30 mpk 3 2 1 Total 27 14 7 10 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 15 a strong/moderate type I IFN signature or a weak signature in the trial is provided in Figure 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. Figure 29(a) shows that in a group of SLE patients having a type-I IFN gene signature, virtually all of the top 39 genes 20 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 Figure 29(c). The SLE patients who lacked a type I IFN signature and were treated with MEDI-545 displayed an intermediate neutralization pattern, 25 with some type I IFN signature genes neutralized. (See Figure 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 C:\poi\word\SPEC-8541 93[1].docx 112 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. Figure 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 5 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 10 and diagnostic markers, 807 IFN-a/0-inducible probes identified by ex vivo stimulation of healthy donor WB with 10 IFN-a 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 15 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-a mAb, one healthy donor PBMC was stimulated ex vivo with sera from six individual SLE patients. The healthy donor was prescreened to 20 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-a mAb and an anti-IFN-aR mAb, respectively. The intersection between this list of 161 probes and previously determined list of 114 25 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. 30 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 C:\poi\word\SPEC-8541 93[1].docx 113 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 5 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 10 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. 15 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 20 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 25 that from the top 25 upregulated type I IFN-inducible genes. The prevalence and fold change (log2 based) of the 21 IFN a/p-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 a/p-inducible genes in SLE patient whole blood Probe Q value Fold Prevalence Gene name Gene symbol 204415_at qv<le-16 9.38 78.20 interferon, alpha-inducible protein 6 IF16 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 IF144 204439 at 5.85E-12 6.45 69.10 interferon-induced protein 44-like IF144L 202411 at 6.35E-12 14.42 67.30 interferon, alpha-inducible protein 27 IF127 C:\poi\word\SPEC-8541 93[1].docx 114 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 IFITI 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<le-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, lOOkDa OAS3 202869_at 4.95E-11 3.77 61.80 2',5'-oligoadenylate synthetase 1, OAS1 40/46kDa 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<le-16 4.65 60.90 lymphocyte antigen 6 complex, locus E LY6E 204972_at qv<le-16 3.06 58.20 2'-5'-oligoadenylate synthetase 2, OAS2 69/7lkDa 241916_at 6.29E-07 2.46 56.40 Phospholipid scramblase 1 PLSCR1 44673_at qv<le-16 3.91 55.50 sialic acid binding Ig-like lectin 1, SIGLECI 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 Figure 86 and 89. Heatmap (Figure 87a) and PCA calculations (Figure 87b) using these 21 genes showed neutralization of the upregulated IFN a/P gene signature in an SLE patient treated with 30 mg/kg MEDI-545, but not in placebo-treated SLE patients (Figure 88). Thus, 5 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 Figure 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 10 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 figure 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 15 (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 (Figure 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 C:\poi\word\SPEC-8541 93[1].docx 115 using the 21-gene panel of type I IFN-inducible genes was similar to that observed with the larger 114-gene set (Figures 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 5 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 IFNa 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. 10 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 2x TaqMan Universal 15 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). Figure 27 shows the relative overexpression of mRNA of nine IFNa subtypes in the 20 whole blood of lupus patients relative to healthy volunteers. Many of these IFNa subtypes were upregulated at the mRNA level in the whole blood of SLE patients. Figure 66 shows that IFNP, IFNo and IFNAR1 and IFNAR2 genes are also overexpressed in whole blood of lupus patients relative to healthy volunteers. Figure 82 shows that TNF-a, IFN-y, IFN-yR1, and IFN-yR2 transcripts were also 25 upregulated in WB of SLE patients (Figure 82). However, the relative magnitude of overexpression of these transcripts was less than that of the type I IFN family members, especially the IFN-a 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 30 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 IFNa subtypes, as well as IFN3, IFNy, and TNFat. C:\poi\word\SPEC-8541 93[1].docx 116 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 5 were then exposed to a variety of treatments, including: vehicle (lx PBS), a panel of IFNa subtypes (IFNa2a, -4b, -5, -6, -7, -8, -10, -16, -17), IFN, IFNO, IFNX, IFNy, leukocyte IFN, or TNFa. Following exposure, the blood was gently mixed by pipetting and incubated at 37'C, 5% CO 2 for 4 hrs (TNFa treatment was conducted for both 2hrs and 4hrs). Following the incubation period, 2.5 mL of blood was transferred to a PAXgene RNA tube and inverted 10 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 IFNa subtypes and IFN3 up-regulated 900-1200 probe sets by at least 2 15 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 IFNa subtypes and IFN. Using the same approach, 336 probe sets were identified as down-regulated by IFNa/P in the ex vivo stimulated whole blood. Alterations in gene expression in healthy patient whole blood stimulated with TNFa 20 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, IFNy 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 IFNa/P and TNFa (40 probes). By contrast, greater overlap was 25 observed in the probe sets up-regulated by IFNa/P and IFNy. 198 probes were up-regulated by at least 2-fold by both IFNa/P and IFNy. Of the 198 probes up-regulated by at least 2-fold by both IFNa/P and IFNy, the magnitude of up-regulation by IFNa/P was greater for about 2/3 of these probes (p value less than 0.05) than IFNy. Figure 30 provides the hierarchical clustering of 1384 probe sets differentially 30 regulated by either IFNa/p, or IFNy, or TNFa in ex vivo stimulated whole blood. From this hierarchical clustering the similar response of whole blood to challenge with IFNa subtypes and IFN3 can easily be observed, as can the similar but distinctly different effect of IFNy from IFNa/p, and the drastically different effect of TNFat from IFNa/P. C:\poi\word\SPEC-8541 93[1].docx 117 Figure 31a 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 5 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 IFNa2a (15-350 IU/ml, PBL Biomedical Labs), recombinant human TNFa (0.1 ng/ml, R+D Systems) or recombinant human IFNy (3 10 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 IFNa2a and leukocyte IFN. Figure 31b 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 15 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 Figure 3 1a). 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, IF144L, etc. In addition, many of these genes were among those most overexpressed in the lesional 20 skin of psoriasis patients. See discussion in Example 11, below. Example 11: Whole genome array profiling identified IFNa/p 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 25 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 30 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. C:\poi\word\SPEC-8541 93[1].dox 118 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 5 cRNA, from 2 jig 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 10 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 15 Software (GCOS) tool. Stratagene's (La Jolla, CA) 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 20 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. 25 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 30 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. Figure 45 provides a Venn diagram of the probe sets C:\poi\word\SPEC-8541 93[1].docx 119 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 5 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 MetaCoreTM 10 integrated software suite from GeneGo, Inc. (St. Joseph, MI). 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. 15 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 IFNa/P signaling pathway was the most significantly altered in lesional skin with a p value of 3.8 x 10-l. IFNa/P signaling pathway members such as IFNa, IFN3, IFNAR1, IFNAR2, STAT1, IRF1, MPL, ISG15, IF16 were all significantly overexpressed in lesional skin 20 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, IFNy, TNFa and onconstatin 25 M signaling pathways were activated in the lesional skin of psoriatic patients. Of all the signaling pathways altered in lesional and non-lesional skin, IFNa/P signaling pathway topped the list with a p value of 6.6x10-26 (Figure 46). Components of the pathway like IFNa subtypes, IFN3, IFNAR1, IFNAR2, STATI, IRF1, MPL, ISG15, IFI6 were all significantly overexpressed in lesional skin compared to non-lesional skin of psoriatic patients. 30 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 C:\poi\word\SPEC-8541 93[1].docx 120 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 Figure 47a and b for the top 100 upregulated probe 5 sets in lesional skin. These genes included STAT1, a key component in forming the ISGF3 complex; IRF7, a master regulator of the IFNa/p 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 OAS 1, OAS2, OAS3, mediators of resistance to virus infection; ISG15, a ubiquitin-like protein that becomes conjugated to many cellular 10 proteins upon activation by IFNa/p; 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 log2 15 based fold change (log2 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. C:\poi\word\SPEC-8541 93[1].docx 121 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 Probe ID Unigene ID Gene Title Gene S mbol 10.2 fc . value : 102 fc . value 219403 s at Hs.44227 neparanase HPSE 4598 4.46E-22 0.226 0.23589 204972 at Hs.414332 2-5'-oiaoadenv ate svnthetase 2, 69/71kDa OAS2 4.098 8 57E 14 0.096 0.28896 660 at Hs.118633 2-5'-oiaoadenvlate svnthetase-like OASL 4 030 1 34E-12 0.029 0.20341 609 at Hs.546467 epithelial stromal interaction 1 (breast) EPST11 4002 1 14E 14 -0.254 0.10796 227458 at -3859 9.31E-14 -0.591 0.05449 219352 at Hs.529317 nect domain and RLD 6 HERC6 3.842 9.49E6 -0.460 0.04810 216834 at Hs.75256 regulator of G-protein sinallina 1 RGS1 3809 2.47E 17 -5.269 0.00000 204533 at Hs.632586 chemokine (C-X-C motif liaand 10 ;XCL10 3.697 2-97E12 0.338 0.13024 226702 at Hs.7155 ivpothetical protein LOC129607 LOC129607 3.572 237E-6 -0.156 0.26500 242625 at Hs.17518 radical S-adenosvl methionine domain containing 2 RSAD2 3403 1.65E 12 -0.070 0.31309 213797 at Hs.17518 radical S-adenosvl methionine domain containing 2 RSAD2 3.243 336E 10 0.004 0.36209 202086 at Hs.517307 n xovrus (influenza vrus) resistance 1, interferon-inducible protein p78 (mouse MX1 3,235 5 128E-4 0.050 0.33453 205552 s at Hs.524760 2',5'-oliaoadenv ate svnthetase 1, 40/46kDa OAS1 3222 2.41E 14 0.328 0.13669 210797 s at Hs.118633 2-5'-oiaoadenvlate svnthetase-like OASL 3.216 1 63E 0 0.005 0.34940 204439 at Hs.389724 interferon-induced protein 44-like IF144L 3205 4 73E 13 0.120 0.30073 202411 at Hs.532634 interferon, alpha-inducible protein 27 IF127 3 165 4 1E -12 -0.154 0.26878 202869 at Hs.524760 2',5'-oliaoadenv ate svnthetase 1, 40/46kDa OAS1 3.150 2 7E 14 0.248 0.21403 205483 s at Hs.458485 ISG15 ubiauitin-like modifier ISG1 3.088 4 73E13 -0.273 0.11013 1 365 signal transducer and activator of transcription 1, 91kDa STAT1 2.993 7 95E-17 0.199 0.20072 228531 at Hs.65641 sterile alpha motif domain containing 9 SAMD9 2.846 542E -14 -0.033 0.35359 204415 at Hs.523847 interferon, alpha-inducible protein 6 IF16 2769 7 23E 09 -0.045 0.29074 214453 s at Hs.82316 interferon-induced protein 44 IF144 2.679 1 94E+12 0.086 0.32618 222838at Hs.517265 SLAM family member 7 SLAMF7 2659 1 60E- 16 -0.046 0.31222 219684 at Hs.43388 receptor transporter protein 4 RTP4 2649 3 73E11 0.497 0.04912 203127 s at Hs.435661 serine palmitov transferase, lona chain base subunit 2 SPTLC2 2.628 1 04E+20 -1.016 0.00017 205569 at Hs.518448 vsosomal -associated membrane protein 3 LAMP3 2569 2 64E09, 0.293 0.22865 219691 at Hs.65641 sterile alpha motif domain containing 9 SAMD9 2 559 1.30E-3 0.011 0.37349 223220 s at Hs.518200 >olv (ADP-rbose) olvmerase family, member 9 PARP9 2.553 1 08E+15 0.069 0.31416 AFFX-HUMISG Hs.565365 signal transducer and activator of transcription 1, 91kDa STAT1 2525 1 64E10 0.706 0.03338 212268 at Hs.381167 serpin peptidase inhibitor, clade B (ovabumin), member 1 SERPINB1 2.510 3 02E-5 -0.605 0.07749 216202 s at Hs.435661 serine palmitoy transferase, ona chain base subunit 2 SPTLC2 2.507 1-17E+13 -0.682 0.01693 229450 at --- -2492 150E-14 0.224 0.20674 #8436 s at Hs.166120 interferon reaulatorv factor 7 IRF7 2.448 6.90E-15 -0.578 0.01612 FX-H MISG Hs5565 signal transducer and activator of transcription 1, 91kDa STAT1 2.444 3 03E10 0.516 0.05854 204747 at Hs.47338 interferon-induced protein with tetratricopeotide repeats 3 IFIT3 2.424 215E 14 0.365 0.07219 229390 at Hs.381220 nypothetical protein LOC441168 RP1-93H18.5 2.400 2.59E12 -0.369 0.11426 218400 at Hs.528634 2-5'-oigoadenylate synthetase 3, 1OOkDa OAS3 2.397 383E-14 0.179 0.11631 235276 at 2386 361E 15 0.057 0.32771 203153 at Hs.20315 interferon-induced protein with tetratricopeotide repeats 1 IFIT1 2351 1 17E10 0.054 0.34454 210873 x at Hs.348983 aoliporotein B mRNA editing enzyme, catalytic polvoeptide-like 3A APOBEC3A 2348 1 35E 07 -0.048 0.30119 204698 at Hs.459265 interferon stimulated exonuclease aene 20kDa ISG20 2337 1 5OE-12 -0.644 0.05052 232666 at Hs.528634 2-5'-oliaoadenv ate svnthetase 3, 1OOkDa OAS3 2.236 4 5E-10 0.077 0.04816 222881 at Hs.44227 neparanase HPSE 2.230 347E15 0.221 0.17127 205241 at Hs.567405 SCO cvtochrome oxidase deficient homoloa 2 easts) SC02 2 208 1.90E-7 -0.285 0.08517 AFFX-HUMISG Hs.565365 sinal transducer and activator of transcription 1, 91kDa STAT1 2205 5 129E00 0.397 0.10218 206553 at Hs.414332 2-5-oiaoadenvlate svntnetase 2, 69/71kDa OAS2 2.183 134E109 0.043 0.14755 07387 S at Hs.1466 Ivcerol kinase GK 2.160 9 138E-4 0.014 0.37488 716 at Hs!57352 apoliporotein L, 6 APOL6 2123 3 103E-1 -0.126 0.19251 2270 at Hs.626 uanvlate binding protein 1, interferon-inducible, 67kDa GBP1 2.113 4 67E- 14 -0.053 0.31367 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 25 provided. C:\poi\word\SPEC-854193[1].docx 122 Table 27: Top 50 type-I IFN induced genes in lesional relative to non-lesional skin in psoriasis patients Probe.D |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-1 4 96.15 205660 at Hs.1 18633 2-5-oligoadenylate synthetase-like OASL 4.03 1.34E-1 2 96.15 5 227609 at Hs.546467 epithelial stromal interaction 1 (breast) EPST11 4.00 1.1 4E-1 4 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, interferon-inducible protein p78 (mouse) MX1 3.24 5.28E-1 4 92.31 205552_s at Hs.524760 2',5'-oligoadenylate synthetase 1, 40/46kDa OAS1 3.22 2.41 E-1 4 96.15 204439 at Hs.389724 interferon-induced protein 44-like IF144L 3.21 4.73E-1 3 88.46 202411 at Hs.532634 interferon, alpha-inducible protein 27 IF127 3.17 4.81 E-12 92.31 205483_s at Hs.458485 ISG15 ubiquitin-like modifier ISG15 3.09 4.73E-1 3 92.31 209969_s at Hs.565365 signal transducer and activator of transcription 1, 91 kDa STAT1 2.99 7.95E-1 7 96.15 228531 at Hs.65641 sterile alpha motif domain containing 9 SAMD9 2.85 5.42E-1 4 92.31 204415 at Hs.523847 interferon, alpha-inducible protein 6 IF16 2.77 7.23E-09 84.62 214453_s at Hs.82316 interferon-induced protein 44 IF144 2.68 1.94E-1 2 92.31 222838 at Hs.517265 SLAM family member 7 SLAMF7 2.66 1.60E-1 6 92.31 10 219684 at Hs.43388 receptor transporter protein 4 RTP4 2.65 3.73E-1 1 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-1 5 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 factor7 IRF7 2.45 6.90E-15 96.15 204747_at Hs.47338 interferon-induced protein with tetratricopeptide repeats 3 IFIT3 2.42 2.15E-1 4 92.31 218400 at Hs.528634 2-5-oligoadenylate synthetase 3, 1 OOkDa OAS3 2.40 3.83E-1 4 100.00 203153_at Hs.20315 interferon-induced protein with tetratricopeptide repeats 1 IFIT1 2.35 1.1 7E-1 0 84.62 210873_x at Hs.348983 apolipoprotein B mRNA editing enz yme, catalytic polypeptide-like 3A APOBEC3A 2.35 1.35E-07 80.77 204698 at Hs.459265 interferon stimulated exonuclease gene 20kDa ISG20 2.34 1.50E-1 2 92.31 205241 at Hs.567405 SCO cytochrome oxidase deficient homolog 2 (yeast) SC02 2.21 1.90E-1 7 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-1 1 92.31 15 202270 at Hs.62661 guanylate binding protein 1, interferon-inducible, 67kDa GBP1 2.11 4.67E-1 4 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 BlRC4BP 2.05 3.41 E-12 84.62 206513_at Hs.281898 absent in melanoma 2 AIM2 2.04 2.32E-08 76.92 218943_s at Hs.1 90622 DEAD (Asp-Glu-Ala-Asp) box polypeptide 58 DDX58 2.00 1.39E-1 0 88.46 203148 s at Hs.575631 tripartite motif-containing 14 TRIM14 1.94 2.17E-17 96.15 213293s 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 FBX 6 1.86 6.34E-14 88.46 227697_at Hs.527973 suppressor of cytokine signaling 3 SOCS3 1.82 4.55E-10 88.46 206632sat Hs.226307 apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like 3B APOBEC3B 1.81 9.42E-10 92.31 201649_at Hs.425777 ubiquitin-conjugating enzyme E2 Q 6 UBE2L6 1.81 2.15E-13 84.62 204702_sat Hs.404741 nuclear factor (erythroid-derived 2)-like 3 NFE2L3 1.80 1.71 E-1a6 96.15 202531_at Hs.436061 interferon regulatory factor 1 IRF1 1.79 2.13E-1 3 80.77 204994 at Hs.926 myxovirus (influenza virus) resistance 2 (mouse) MX2 1.75 7.99E-09 69.23 20 (215966 x m- gly s cerol kinase pseudogene 3 GKP3 1.73 3.33E-1 1 80.77 207655_s at Hs444049 B-ellliker BLNK 1.71 2.28E-1 4 96.15 216598_s at Hs.303649 Ichemokine (C-C motif) ligand 2 ICCL2 1.71 14.80E-07 65.38 The fold changes (log2 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 25 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 AIM42, were upregulated in at least 84% of the paired lesional/non-lesional skin biopsies (23 of 30 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. C:\poi\word\SPEC-854193[1].docx 123 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 5 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 219463 s at |5s44227 |HPSE 8| 2431 3628 2794 3131 2858 23624 12877 1029 7 12 | 12 25.78 |C 021 2401 5680 10.70 36.26 | 42 86 | 1273 25.78 381 |322 24.58 |460 | 103 204972 at | 414332 OAS2 1260 21 22 1.19 244 4933 4803 3322 4396 1392 71 36 28 17 404 2483 79.4 1584 9699 1027 |328 928 30.11 1638 2427 6043 | 532 132.09 9.7 10 205660 at | 118633 OASL 719 1348 451 903 219 6023 3112 5405 972 994 110 231 24.75 4470 11.91 45.98 1148 14.6 3380 172 47 2422 | 9212 4844 |4.96 3966 227609 at 646467 EPSTI1 11 25 2034 -1 43 138 |5701 32 14 1440 23.42 1063 |5680 3287 886 5954 4771 33.84 7812 1434 2686 3341 1208 | 24 17.8 28.12 2243 |783 1090 227456 at -- -- 1669 1094 1935 11 5431 2330 3076 1069 326 40.43 41 37 670 26.3 23.19 3766 076 76 98 1904 26 19 4950 543 2469 24 13 11.46 2605 967 219352 at | 629317 HERC6 7.86 1570 238 1 46 4925 61 01 11 64 1963 2095 21 72 1564 562 1058 2306 3042 13347 11 03 2694 9.90 1646 19.06 3332 27.96 19.06 2666 .66 216834 at a H75256 RGS1 2792 660 1790 661 5642 1625 497 20.62 1002 2432 1950 991 9441 1463 2300 1564 13 96 31 90 100.03 802 244 1349 163 2264 29.15 1483 204633 at 32566 | C L0 3.92 3.01 672 91 24960 13.12 13.37 15.14 4.76 69.66 56.31 22.30 1275 6.30 1661 28.11 12 96 30.79 66 10 1772 11 69 12.12 41 27 10 90 30.14 566 226702 at 7156 LO12967 3.59 677 3 10 1.27 60 00 12.76 14.72 2200 53 5699 27.56 2 99 599 39.75 2566 22599 19.79 30.96 4.68 4530 14.42 791 3267 14 50 19.65 3.13 242626 at | s17516 | AD2 45 6.19 1 79 1.24 66 13 61 91 1928 23.36 402 32.04 660 1 76 564 1636 1597 9485 947 1468 464 3367 16.26 1067 696 | 2021 4067 599 213797 at , H17516 RAD2 6.33 737 1.16 1 00 7664 3306 11 98 25.13 1 6 21 73 643 273 323 31 91 12.04 4952 6 11 1261 11 92 2402 25.00 1004 7604 17.3E 26.3 6. 2 202066 at 617301 MX1 603 9.7 1 25 1 08 2097 39.06 1463 2364 11.33 1666 11 71 306 693 2003 86 6672 11 04 1960 724 400 1206 1063 2660 11 06 2774 5.6 205562 at 62476 0 1 693 11 05 1.19 276 21 03 29.00 11.76 2737 771 1923 20 14 349 282 3765 21 91 3943 6 13 24.10 666 263 4 16 1346 21 42 930 32.15 1609 210797 a 163 OASL 2.04 690 | 32 1.34 46.94 31.06 16.6 | 6661 9.26 1.69 1 73 1 20 | 19 00| 2373 1 62 43.88 11 71 10.30| 2636 2.27 78.51 15.8 65.7 | 33.47 3632 18.92 204439 at | 3f9724 F144L 452 6.71 | 5 9 -1 06| 1449 68 16 9.26 3221 | 6 |3749 31 82 396 1943 1666 23.1 25356 681 20.34 3 18 1790 2 116 760 1842 462 2693 1.12 202411 at | , H.32634 F127 10.97 1552 I 94 2.66 1202 38.87 14.3 2763 17.02 1722 1769 581 936 26.00| 15.5 38.94 201 30.69 4.59 -473 346 10 69 22 17 7.00 50.18a 737 202869 at H 624760 OAS1 534 799 204 2.09 16.23 3248 1329 |3047 1275 49.00 10 15 552 231 1894 1962 3657 4.58 16.19 481 896 473 11.05 11.6 7 13 1.20 739 205483 s at 58485 | ISG15 564 437 65 | 10 | 1982 4024 830 1389 7.00| 12 18 1449 447 678 1924 1065 | 6701 3.67 12.65 2.96 257 11.30 571 3441 1.06 03.4 5.07 209969 sat | H V56365 STAT1 6.14 6.12 285 2.00 3639 1650 10.35 7.10 12.90 1732 1241 377 1431 749 25.00 18.73 45 963 9.10 1730 7 10 927 11 03 1091 12.19 4.37 226531 at | s.

6

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6 41 | SAMD9 507 5.24 2 2 1.79 12.56 1267 576 15.63 986 1294 2085 1 97 470 24.24 15.22 20.12 10 49 1.39 60 1430 6.6 630 1624 1246 13.49 6.75 5 204415 at | H.52347 IFI6 1 62 6.53 -201 1.00 1390 574 59 16.08 466 | 1165 645 330 543 30.76 |3.29| 38.93 400 20.01 200 1.00 4945 16.05 5843 1795 52.57 6.66 15 214453 s lat|s.62316 F144 2.60 6.23 -289 1.22 1476 |10.5 443 999 267 1232 25.67 366 826 16.22 2.57 61,.6 6.49 20.63 632 1076 493 66 1327 | .2 26.71 2.13 222036 at |s.

5 1 7265 SLAMF7 .26 7.36 1.70 1. 97 iC6 6 97 676 1.62 1591 544 1909 539 14.93 |.86 1010 s69 1542 7.99 469 506 592 5.61 11.22 9.CI 219664 at |Hs.4 33 8 | RTP4 13.11 1302 -307 |-1 1 1395 1 10.09 3.46 325 23.69 63 666 16.47 10.67 16 3.40 17.36 596 1.92 9C 690 4.5 4.92 26.75 3.91 203127 sa ats 435661i SPTLC2 6.06 5.C7 |4.11 |3.50 | i 6. |550 11.49 |6.25 |2.73 |4.53 6.24 | 5.7 |561 |11.38 0 .26 |7.73 10.92 7.32 |4.62 3.64 9.24 5.35 9.32 |13.11 11.C0 12.09 Il.di tol I A ,9 ? 1.I 1 ;311 210 11.9 220 1, 12.23 " IJ .04 2 l. 1 %~ 1D 1".27 12." 1;.24 i 2.t". lI t1 A7 Z I If I th 13 Figure 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 20 patients verified their usefulness as PD markers. Seventeen probe sets were also observed as underexpressed in lesional skin that were also down-regulated by IFNa/p in the ex vivo stimulation studies described in Example 10. These genes include CYP1B1, TGST1, RRAGD, IRS2, MGST1, TGFBR3, and RGS2. 25 C:\poi\word\SPEC-854193[1].dox 124 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 5 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 10 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., RGS 1, SPTLC2, are downregulated in the non-lesional skin compared to normal skin). Figure 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 15 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 20 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 25 samples. Figure 34a 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. Figure 34b provides a PCA plot of 30 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 C:\poi\word\SPEC-8541 93[1].docx 125 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 IFNa/p signaling pathway of non 5 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 Figure 47. Example 13: Validation of type-I IFN-inducible gene up-regulation in psoriatic lesional skin 10 using taqMan-based assays A BioMark m 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. 15 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 20 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. Figure 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. 25 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 Figure 36a. Nineteen of the overexpressed genes had correlation coefficients greater than 0.85, indicating excellent 30 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. Figure 36b 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, C:\poi\word\SPEC-8541 93[1].dox 126 many of the genes had high correlation coefficients, greater than 0.90. These genes include, inter alia, IFI27, CXCL10, ISG15, and MX1. Figures 37a - 37d 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 5 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. Figure 37a and 37b show similar overexpression of ISG15 in each of the 18 paired lesional/non-lesional skin samples as determined by taqMan (37a) and microarray (37b) analysis. Figure 37c and 37d show similar 10 overexpression of MX1 in each of the 18 paired lesional/non-lesional skin samples as determined by taqMan (37c) and microarray (37d) analysis. The correlation coefficient between the taqMan and microarray was 0.9735 for ISG15 and 0.9836 for MX1. Figure 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 15 samples. The correlation coefficient between the taqMan and microarray results for IFI27 and CXCL10 was 0.9456 and 0.9455, respectively. Example 14: IFNa Ab neutralizes type-I IFNa-induced gene expression in ex vivo stimulated keratinocytes of healthy volunteers Keratinocytes of healthy volunteers were isolated and stimulated ex vivo with 20 escalating doses of IFNa2a and leukocyte IFN to induce an escalating type I IFNa-induced gene expression pattern. Anti-IFNa antibody was able to neutralize the type I IFNa-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 25 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 IFNa2a (15-350 IU/ml, PBL Biomedical Labs). In some wells a humanized anti-human IFNa monoclonal antibody (0.01-100 [tg/ml; MEDI-545, MedImmune, Inc) or isotype matched control antibody of irrelevant specificity 30 (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. Expression of a majority of type-I IFN-induced genes was upregulated in the IFNa2a and leukocyte interferon stimulated keratinocytes in a dose-dependent manner. This C:\poi\word\SPEC-8541 93[1].docx 127 upregulation of type-I IFN-induced genes, by either IFNa2a or leukocyte interferon, was likewise inhibited in a dose-dependent manner by IFNa monoclonal antibody (MEDI-545). Control antibody, R347, did not have a significant effect on neutralization of the type-I IFN induced genes. 5 Dose-dependent neutralization of three type-I IFN-induced genes (ISG15, USP18, and IFIT2) by MEDI-545 in IFNa2a or leukocyte IFN stimulated keratinocytes is provided in Figure 39. Figure 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 IFNa2a. Each of these genes was neutralized 100% by MEDI-545. Figure 39 (b), 10 (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 IFNa and IFNp. MEDI-545 neutralizes a majority of IFNa subtypes efficiently, but not IFNp. These neutralization data provide 15 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 20 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) 25 from Applied Biosystems. Expression of 23 genes, including type-I IFNa subtypes 1, 2, 5, 6, 7, 8, 14, 17, and 21; type-I IFNs IFNp, K, and o; IFNy; IFNa receptors IFNAR1 and IFNAR2; IFNy receptors IFNGR1 and IFNGR2; type-I IFNa inducible genes RSAD2, OAS3, IF144, MX1, and CXCL10; and TNFa was monitored and compared in paired lesional and non lesional skin of 18 psoriasis patients. 30 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 C:\poi\word\SPEC-8541 93[1].docx 128 of the diluted pre-amplified cDNA was added to a 50 L volume of 2x 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 5 SDSv2.2.2 software tool (Applied Biosystems). Figure 40a shows the relative overexpression of mRNA of nine IFNa subtypes in the lesional skin compared to either non-lesional skin or normal skin. With the exception of IFNa5 (upregulated by about 4.6 fold; median fold change, p<0.001), none of the IFNa subtypes were significantly altered at the mRNA level in the non-lesional skin compared to 10 that in the normal skin (p<0.05). However, all of these IFNa 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 IFNal, IFNa5, IFNa8, IFNal4, IFNa17, IFNa21 being statistically significant (p<0.05). Figure 40b shows that the overexpression of other members of type I IFN family members, IFN3, -K, and -o mRNA in the lesional skin compared to either non 15 lesional skin or normal skin. The alterations of IFN3 and IFNo 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). IFNK 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 20 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; Figure 40c). While IFNAR2 upregulation was significant in the non-lesional skin, IFNAR1 was not (Figure 40c). Collectively, these data provided strong evidence that mRNA levels of type I IFN family members were comparable between the non 25 lesional skin and healthy normal skin (with the exception of IFNa5 and IFNx), 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 IFNa subtypes 1, 2, 5, 6, 7, 8, 14, 17, and 21; and IFNp, IFNK, and IFNo) mRNAs in lesional skin compared to non-lesional skin of psoriatic patients. Of the 12 type-I 30 IFN family members measured, overexpression of IFNal, 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 IFNa5 which showed the weakest correlation with other type-I IFN family members. C:\poi\word\SPEC-8541 93[1].docx 129 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 1 1 IFNA6 0.45 0.47 -0. 0 1 5 IFNA7 0.77 0.79 0. 0.68 1 IFNA8 0.64 0.99 0 0.49 0.84 1 IFNA14 0.84 0.94 2 0.44 0.72 0.94 1 IFNA17 1.00 0.96 S 5 .7 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 0.33 0.69 0.96 0.80 0.93 0.54 1 IFNK 0.78 0.73 0.59 0127 0.73 0.77 .3 I '22 0.54 1 IFNW1 0.73 0.72 0.44 ,22 0.75 0.70 0.77 0.93 0.90 0.73 1 Example 16: Co-overexpression of type-I IFN, type-II IFN, and TNFa and their gene 10 signatures in lesional skin or psoriasis patients The involvement of IFNy and TNFa 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 IFNy, IFNGR1 and IFNGR2, and TNFa mRNA in lesional and non-lesional skin of psoriasis patients and in 15 normal healthy skin. Unlike the observations for type-I IFN mRNA expression levels, IFNy, IFNGR1, IFNGR2, and TNFa mRNAs were significantly overexpressed in non-lesional skin compared to healthy normal skin (Figure 41; p values of 0.02, <0.001, <0.001 and <0.001 respectively). TNFa mRNA was upregulated by about 5.7 fold, while IFNY, IFNGR1 and IFNGR2 mRNAs 20 were upregulated by about 1.5, 2.2, and 2.8 fold compared to that in the normal skin (median fold change; Figure 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; Figure 41). TNFa, IFNy, IFNGR1 and IFNGR2 mRNAs were upregulated by about 33.5, 116.7, 11.6, and 8.4 fold in 25 the lesional skin compared to that in the normal skin. These observations indicated that the mRNA expression patterns for IFNy and TNFa are different from those of type I IFN family members, which were comparable between healthy skin and non-lesional skin (with the exception of IFNa5 and IFNx), but upregulated in the lesional skin compared to non-lesional skin of psoriasis patients. 30 Example 17: Identification genes induced by type II IFN and TNFa 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 IFNa subtypes, as well as IFN3, IFNy, and TNFa. Stimulating whole blood ex vivo with IFNy or TNFa identified probe sets associated with potential IFNy- or TNFa 35 inducible genes. Three hundred four probe sets were identified as at least 2-fold upregulated C:\poi\word\SPEC-8541 93[1].docx 130 by IFNy four hours post-stimulation. Two hundred thirty four probe sets were identified as at least 2-fold upregulated by TNFa both 2 and 4 hours post-stimulation. The probe sets identified as associated with ex vivo IFNy or TNFa induction were compared with the total 1408 probe sets (Example 11) found to be upregulated in lesional skin 5 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 IFNy or TNFa inducible, respectively (Figure 42). The 106 probe sets identified as IFNy inducible are provided in Figure 49. The 35 probe sets identified as TNFa inducible are provided in Figure 50. The 164 probes sets shown in Figure 42 as identified as type-I IFN inducible are provided 10 in Figure 51. The Fisher's exact test indicated that the p values (one-tailed t-test) of the overexpression of IFNy or TNFa inducible genes in lesional skin were both less than 0.0001. The overexpression of IFNy and TNFa inducible genes was significant. Also using the list of probe sets identified to be type I IFN, IFNy and TNFa inducible from the ex vivo studies, type I IFN, IFNy and TNFa inducible genes upregulated at least 2 15 fold in each of the lesional relative to non-lesional skin sample were identified. Figure 43 shows the number of type I IFN, IFNy and TNFa 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 IFNy and TNFa inducible genes in the same lesional skin biopsy. This 20 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 IFNy, type I IFN and TNFa, and IFNy and TNFa inducible genes in lesional skin compared to non-lesional skin (Figure 43a). Similar analysis was carried out for the downregulated genes in the lesional skin 25 compared to the non-lesional skin of psoriatic patients (Figure 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, IFNy and TNFa inducible. Although IFNy and TNFa mRNAs were found to be upregulated in the non-lesional skin of psoriatic patients when compared to healthy normal skin, IFNy and TNFa inducible 30 genes did not appear to be significantly overexpressed in the non-lesional skin (Figure 42). The absence of type I IFN, IFNy and TNFa inducible gene signatures in the non-lesional skin compared to normal skin, even when IFNy and TNFa mRNAs are overexpressed in the non lesional skin, suggested that either IFNy and TNFa proteins were not made in the non-lesional C:\poi\word\SPEC-8541 93[1].docx 131 skin, or other signaling molecules might have inhibitory effect on the IFNy and TNFa 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 5 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 10 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 1 AM, placed on a "plus" slide, and fixed in cold acetone. The sectioned samples were incubated with 15 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, CA) for 30 minutes and washed with Tris-buffered saline, pH 7.2. Detection was performed with 3,3'-diaminobenzidiine tetrahydrochloride (DAB+; DakoCytomation) as the 20 chromogen. Slides were washed with dH 2 0), 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 25 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 Figure 44 for example immunohistochemistry slides. Example 19: Immunohistochemical and gene expression analysis of biopsies from SLE patient 30 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 10mg/kg MEDI-545 were examined. A heatmap of neutralization of the top 25 type I IFN 35 inducible genes in skin lesions at 0 and 14 days post-treatment is provided in Figure 58(a). All C:\poi\word\SPEC-8541 93[1].docx 132 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 Figure 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 5 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. 10 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., 15 sectioned at 5 [tM, 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, CA) for 30 minutes and washed with Tris-buffered saline, pH 20 7.2. Detection was performed with 3,3'-diaminobenzidiine tetrahydrochloride (DAB+; DakoCytomation) as the chromogen. Slides were washed with dH 2 0), 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 25 days. See Figure 52 which shows an increase in (worsening of) mDC (CD83 staining) and T cell (CD4 staining) infiltration in skin lesions. Figure 52 also shows no change in pDC (BDCA2 staining) infiltration in the placebo-treated SLE patient skin lesions over the 14 days. See also Figure 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 30 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 Figures 54 and 55, which provide immunohistochemical data from a first SLE C:\poi\word\SPEC-8541 93[1].docx 133 patient treated with MEDI-545 and Figures 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 5 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, CA) under the control of an interferon-stimulated response element (ISRE) (TAGTTTCACTTTCCC) 5 ; Biomyx; San Diego, CA) was cloned. HEK293H cells were stably transfected with the construct and these cells were used for the IFN detection 10 assays. 25,000 of the stably transfected HEK293H cells were seeded per assay well in 50uL of cell culture medium overnight in a CO 2 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 15 adding 50uL 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 50uL of supernatant from the wells to a B&W Isoplate, adding 50uL of chemiluminescent substrate, and detecting 20 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 Figure 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. 25 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 pre-incubated 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 30 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. C:\poi\word\SPEC-8541 93[1].docx 134 Figure 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 (Figure 60(b)). Figures 61 63 show that IFNy, IFNo, and IFNp, respectively, are neutralized by antibodies specific for IFNy, IFNo, and IFNp, as expected. 5 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 10 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 15 of a panel of normal human serum (n=17) and significance was determined using a paired t test. Figure 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. 20 Example 22: Alternative Assay, Panomics QuantiGenePlex 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 IFNa2b. The 22 IFN inducible transcripts detected by this initial QuantiGenePlex assay were selected based on 25 their consistent up-regulation in SLE patients and are shown on the x-axis of the graphs shown in Figures 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 IFNa2b for 4 hours. Following this incubation, 2.5 mL of the stimulated whole blood was added to PAXgene tubes, mixed, and 30 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. C:\poi\word\SPEC-8541 93[1].docx 135 PAXgene blood was analyzed for expression levels of the IFN-inducible transcripts. PAXgene blood (500 pL) was pelleted and then lysed in 139 PL 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 5 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. Figure 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 10 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 IFNa2b to determine whether upregulation of the IFN-inducible genes by IFNa2b was dose-dependent and could be detected by the QuantiGenePlex assay. For each of the 22 transcripts, a dose-dependent induction was observed. See Figure 76, which provides the fold 15 change in expression for each of the 22 transcripts at each IFNa2b 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 IF127 transcripts were poorly induced 20 by IFNa2b 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 IFNa subtype, IFNa2b. 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 25 in whole blood of SLE patients. Twenty of the 22 probes from the original QuantiGenePlex kit, probes identified in Figures 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 IF16. 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 30 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 C:\poi\word\SPEC-8541 93[1].docx 136 Example 20. Figure 77a shows a comparison of the gene signature of an SLE patient (red bars) having no detectable serum IFNa 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. Figure 5 77b shows a comparison of the gene signature of an SLE patient with high levels of serum IFNa 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 IF127. The data obtained from the QuantiGenePlex assay was next evaluated for its 10 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 IFNa) relative to a composite median gene score from 10 healthy donors. Fluidigm analyses were carried out using a mixture of TaqMan Gene 15 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, 20 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. Figure 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 25 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 30 collected d irectly into PAXgene tubes on Day 0 (pre-dose) and multiple subsequent time points following administration of a single dose of an anti-IFNa 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. Figure 79a shows the changes in gene signature for placebo- or antibody-treated SLE patients using Fluidigm technology. C:\poi\word\SPEC-8541 93[1].docx 137 Figure 79b 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 5 administration were also highly similar between QuantiGenePlex and Fluidigm technologies. C:\poi\word\SPEC-8541 93[1].docx

Claims (16)

1. A method of treating a patient having a type I IFN or an IFNa-mediated disease or disorder comprising: 5 administering an agent that binds to and modulates type I IFN or IFNa activity; wherein the patient comprises a type I IFN or IFNa-inducible PD marker expression profile comprising up-regulated expression or activity of genes radical S-adenosyl methionine domain containing 2 (RSAD2), interferon-induced protein 44 (IFI44), interferon induced protein 44-like (IFI44L), and interferon-induced protein 27 (IFI27); 10 and wherein the agent neutralizes the type I IFN or IFNa-inducible PD marker expression profile of the patient.

2. A method of treating patient having an autoimmune disease comprising: identifying an autoimmune disease patient as a candidate for an agent that binds to and modulates type I IFN or IFNa activity, wherein the autoimmune disease patient is identified 15 by having a type I IFN or an IFNa-inducible PD marker expression profile comprising up regulated expression or activity of genes radical S-adenosyl methionine domain containing 2 (RSAD2), interferon-induced protein 44 (IFI44), interferon-induced protein 44-like (IFI44L), and interferon-induced protein 27 (IFI27); administering to the identified autoimmune disease patient the agent that binds to and 20 modulates type I IFN or IFNa activity; wherein the agent neutralizes the type I IFN or IFNa-inducible PD marker expression profile of the patient.

3. The method of claim 1 or 2 further comprising detecting neutralization of the type I IFN or IFNa-inducible PD marker expression profile of the patient. 25

4. The method of any one of claims 1 to 3 wherein the agent is a biologic agent.

5. The method of claim 4 wherein the agent is an antibody.

6. The method of claim 5 wherein the antibody is MEDI-545.

7. The method of claim 5 wherein the antibody is specific for one or more type I IFN or IFNa subtype but is not MEDI-545. 30

8. The method of any one of claims 1 to 7 wherein the administering the agent alleviates one or more symptoms of the disease or disorder. C:\poi\word\SPEC-8541 93[1].dox 139

9. The method of any one of claims 1 to 8 wherein the type I IFN or an IFNa-mediated disease or disorder or autoimmune disease is one of lupus, psoriasis, vasculitis, sarcoidosis, Sjogren's syndrome, or idiopathic inflammatory myositis.

10. A method of monitoring disease progression of a patient receiving treatment with a 5 therapeutic agent that binds to and modulates IFNa activity comprising: obtaining a first IFNa-inducible PD marker expression profile comprising levels of expression or activity of genes radical S-adenosyl methionine domain containing 2 (RSAD2), interferon-induced protein 44 (IF144), interferon-induced protein 44-like (IF144L), and interferon-induced protein 27 (IF127) in a first sample from the patient; 10 administering a therapeutic agent that binds to and modulates IFNa activity; obtaining a second IFNa-inducible PD marker expression profile in a second sample from the patient; and comparing the first and the second IFNa-inducible PD marker expression profiles, wherein a variance in the first and the second IFNa-inducible PD marker 15 expression profiles indicates a level of efficacy of the therapeutic agent that binds to and modulates IFNa activity.

11. The method of claim 10 wherein the variance is a decrease in the levels of expression or activity of the genes.

12. A method of identifying a patient as a candidate for a therapeutic agent that binds to and 20 modulates IFNa activity comprising: detecting presence or absence of an IFNa-inducible PD marker expression profile comprising up-regulated expression or activity of genes radical S-adenosyl methionine domain containing 2 (RSAD2), interferon-induced protein 44 (IF144), interferon-induced protein 44 like (IF144L), and interferon-induced protein 27 (IF127) in a sample from the patient, 25 wherein detecting presence of the IFNa-induced PD marker expression profile identifies the patient as a candidate for the therapeutic agent that binds to and modulates IFNa activity.

13. A set of probes comprising: polynucleotides that specifically detect expression of the genes RSAD2, IF144, IF144L, and 30 IF127.

14. A kit comprising the set of probes recited in claim 13, when used for a method according to any one of claims 1-12. C:\poi\word\SPEC-8541 93[1].docx 140

15. A method according to any one of claims 1, 2, 10 or 12 substantially as hereinbefore described with reference to the Examples and/or Figures.

16. A set of probes according to claim 13 substantially as hereinbefore described with reference to the Examples and/or Figures. 5 C:\poi\word\SPEC-8541 93[1].docx