INTERFERON ALPHA-INDUCED PHARMACODYNAMIC MARKERS AND USES THEREOF

SEQUENCE LISTING

The instant application contains a Sequence Listing which has been submitted electronically in ASCII format and is hereby incorporated by reference in its entirety. Said ASCII copy, created on Jan. 19, 2014, is named MDI-0400-CT SL.txt and is 5,393 bytes in size.

FIELD OF THE INVENTION

The present invention relates to pharmacodynamic (PD) markers inducible by interferon (IFN) alpha, probes and kits that detect the PD markers, and methods employing the same.

BACKGROUND OF THE INVENTION

The present invention encompasses PD markers that are induced by IFNα. The PD markers can be used in methods of treating patients with a therapeutic agent that binds to and modulates IFNα activity, methods that identify patients as candidates for a therapeutic agent that binds to and modulates IFNα activity, methods of diagnosing a patient as having a disorder associated with increased IFNα levels, methods of monitoring disease progression of a patient receiving treatment with a therapeutic agent that binds to and modulates IFNα activity, and methods of identifying a candidate therapeutic for treating IFNα-mediated disorders

SUMMARY OF THE INVENTION

One embodiment of the invention encompasses a method of identifying a patient as a candidate for a therapeutic agent that binds to and modulates IFNα activity. Presence or absence of an IFNα-inducible PD marker expression profile is detected in a sample from the patient.

Another embodiment of the invention encompasses a method of treating a patient having a type I IFN or IFNα-mediated disease or disorder. An agent that binds to and modulates type I IFN or IFNα activity is administered to the patient. The agent neutralizes a type I IFN or IFNα-inducible PD marker expression profile of the patient.

Yet another embodiment of the invention encompasses a method of treating an autoimmune disease patient comprising a moderate or strong type I IFN or an IFNα PD marker profile. An agent that binds to and modulates type I IFN or IFNα activity is administered to the patient. The agent neutralizes the type I IFN or IFNα-inducible PD marker expression profile of the patient.

A further embodiment of the invention encompasses a method of neutralizing a type I IFN or IFNα-inducible PD marker expression profile in a patient in need thereof. An agent that binds to and modulates type I IFN or IFNα activity is administered to the patient. The agent neutralizes the type I IFN or IFNα-inducible PD marker expression profile of the patient.

Another embodiment of the invention encompasses a method of diagnosing a patient as having a disorder associated with increased IFNα levels. Presence or absence of an IFNα-inducible PD marker expression profile is detected in a sample from the patient.

A further embodiment of the invention encompasses a method of monitoring disease progression of a patient receiving treatment with a therapeutic agent that binds to and modulates IFNα activity. A first IFNα-inducible PD marker expression profile is obtained in a first sample from the patient. A therapeutic agent that binds to and modulates IFNα activity is administered to the patient. A second IFNα-inducible PD marker expression profile is obtained from a second sample from the patient. The first and the second IFNα-inducible PD marker expression profiles are compared.

Yet another embodiment of the invention encompasses a method of identifying a candidate therapeutic for treating IFNα-mediated disorders. Cells comprising an IFNα-inducible PD marker expression profile are contacted with an agent. Presence or absence of a change in the IFNα-induced PD marker expression profile of the cells is detected.

A further embodiment of the invention encompasses a set of probes.

Yet a further embodiment of the invention encompasses kits that comprise the probes.

Another embodiment of the invention encompasses a method of detecting IFN activity in a sample. Cells comprising a polynucleotide sequence comprising a reporter gene under the control of an IFN-stimulated response element are incubated with a sample. Expression of the reporter gene is detected.

BRIEF DESCRIPTION OF THE FIGURES

FIG. 1: TAQMAN qPCR IFI44 gene expression analysis of IFNα-stimulated whole blood of healthy donors.

FIG. 2: TAQMAN qPCR IRF2 gene expression analysis of IFNα-stimulated whole blood of healthy donors.

FIG. 3: TAQMAN qPCR RSAD2 gene expression analysis of IFNα-stimulated whole blood of healthy donors.

FIG. 4: TAQMAN qPCR G1P3 gene expression analysis of IFNα-stimulated whole blood of healthy donors.

FIG. 5: TAQMAN qPCR HERC5 gene expression analysis of IFNα-stimulated whole blood of healthy donors.

FIG. 6: MEDI-545 neutralization of RAB8B gene expression induced by IFN-α in whole blood of healthy donors.

FIG. 7: MEDI-545 neutralization of IRF7 gene expression induced by IFN-α in whole blood of healthy donors.

FIG. 8: MEDI-545 neutralization of MARCKS gene expression induced by IFN-α in whole blood of healthy donors.

FIG. 9: MEDI-545 neutralization of IL6ST gene expression induced by IFN-α in whole blood of healthy donors.

FIG. 10: MEDI-545 neutralization of Ly6E gene expression induced by IFN-α in whole blood of healthy donors.

FIG. 11: MEDI-545 neutralization of IFIT3 gene expression induced by IFN-α in whole blood of healthy donors.

FIG. 12: MEDI-545 neutralization of IFIT1 gene expression induced by IFN-α in whole blood of healthy donors.

FIG. 13: MEDI-545 neutralization of HERC5 gene expression induced by IFN-α in whole blood of healthy donors.

FIG. 14: MEDI-545 neutralization of OAS1 gene expression induced by IFN-α in whole blood of healthy donors.

FIG. 15: MEDI-545 neutralization of OAS3 gene expression induced by IFN-α in whole blood of healthy donors.

FIG. 16: MEDI-545 neutralization of RSAD2 gene expression induced by IFN-α in whole blood of healthy donors.

FIG. 17: Ex vivo stimulation in whole blood identifies genes inducible by type I IFN.

FIG. 18: MEDI-545 neutralization of top 25 type I IFN inducible genes in individual lupus patients' whole blood.

FIG. 19: Heatmap of target modulation and PCA plot using top 25 up-regulated type I IFN inducible probe sets in whole blood of patient 1541 before and after MEDI-545 treatment.

FIG. 20: Heatmap of target modulation and PCA plot based on 25 most up-regulated type I IFN inducible genes in whole blood of patient 1449 before and after MEDI-545 treatment.

FIG. 21: Heatmap of target modulation calculated based on 165 type I IFN inducible genes up-regulated in whole blood of one patient treated with 0.3 mg/kg MEDI-545.

FIG. 22: PCA using 169 probe sets that are type I IFN inducible—24/35 SLE patients have statistically significant type I IFN signature in whole blood.

FIG. 23: MEDI-545 neutralizes the top 25 most upregulated type I IFN inducible probe sets of lupus patients. Target neutralization of the top 25 most upregulated type I IFN inducible genes was measured at days 1, 4, 7, 14, 28, and 84 for each patient. Dose range was from 1 (placebo) to 3 mg/kg MedI 545.

FIG. 24: MEDI-545 neutralizes the top 25 most upregulated type I IFN inducible probe sets of lupus patients. Target neutralization of the top 25 most upregulated type I IFN inducible genes was measured at days 1, 4, 7, 14, and 28 for each patient. Dose range was from 0 (placebo) to 30 mg/kg MEDI-545.

FIGS. 25
a and 25b: Heatmap (a) and PCA (b) showing neutralization of the top 25 type I IFN inducible probe sets in whole blood of a SLE patient treated with 30 mg/kg MEDI-545 at 0, 1, 4, 7, and 14 days post-dosing.

FIGS. 26
a and 26b: PCA plots of lupus patient before (a) and after (b) dosing with placebo control show no trend in the change of type I IFN inducible gene signature. The 25 most upregulated type I IFN inducible probe sets were used to perform the PCA analysis.

FIG. 27: Type-I IFNα subtypes are upregulated in the whole blood of individual lupus patients.

FIG. 28: Distribution of average fold-change of top 25 type I IFN inducible probe sets in whole blood of individual lupus patients.

FIG. 29
a-29c: Pair-wise fold change ranking test proves MEDI-545 neutralizes type I IFN genes in a clinical trial. Top genes neutralized are shown for (a) SLE patients having a type I IFN gene signature at 14 days following MEDI-545 treatment; (FIG. 29a discloses “DEAD (Asp-Glu-Ala-Asp)” as SEQ ID NO: 1) (b) SLE patients not having a type I IFN gene signature at 14 days following MEDI-545 treatment; and (c) SLE patients 14 days following treatment with placebo. Genes highlighted in yellow are genes identified as having a type-I IFN signature.

FIG. 30: Hierarchical clustering of 1384 probe sets differentially regulated by IFNα subtypes, IFNβ, IFNγ, and TNFα in ex vivo stimulated whole blood. Each row corresponds to a single probe set, while each column corresponds to a single sample. The branch lengths indicate the correlation with which probe sets/samples are joined, with a longer branch indicating a weaker correlation. Color represents relative expression level of individual probe sets as compared to the average expression of the no treatment controls. Red indicates up-regulation versus control; green indicates down-regulation versus control; black indicates no change.

FIG. 31
a-31b: a. Hierarchical clustering of the relative expression of the top 25 most overexpressed type-I IFN inducible probe sets in whole blood ex vivo challenged with a variety of IFNα subtypes, IFNβ, IFNγ, and TNFα. b. Heatmap of the relative expression of the same 25 probe sets compared to no-treatment control in keratinocyte ex vivo challenged with IFNα2a, IFNβ, IFNγ, and TNFα. Red indicates upregulated gene expression relative to no treatment control, green indicates downregulated gene expression relative to no treatment control, black indicates no significant change in gene expression of challenged samples relative to control.

FIG. 32
a-32c: The distribution of the average (a) and median (b) fold change of the top 25 most overexpressed type-I IFN inducible probe sets in 26 pairs of lesional skin compared to non-lesional skin. (c) the average of the average and median fold change of the top 25 most overexpressed type-I IFN inducible probe sets in 26 pairs of lesional and non-lesional skin.

FIG. 33
a-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 (LS) compared to non-lesional skin (NS), and non-lesional skin compared to normal skin (NN) in psoriatic patients based on microarray data. The fold change of these genes in LS is compared to its paired NS, while NS is compared to the average of 21 normal skin controls. The p value for HPSE, OASL, HERC6, and SERPINB4 is a comparison between NS and NN, between LS and NS are (listed in pairs): 0.468, <0.00001; 0.376, <0.00001; 0.03, <0.00001; 0.0002, <0.00001.

FIG. 34
a-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 patients, and 3 lesional skin (red bars) from 3 psoriatic patients whose paired non lesional skin either did not yield sufficient cRNA for hybridization or scanned arrays had scaling factors that were more than 3 times the average) using the 164 upregulated type-I IFN inducible probe sets in lesional skin compared to those in mostly paired non-lesional skin. Each row corresponds to a single probe set, while each column corresponds to a single sample. The branch lengths indicate the degree of correlation with which samples are joined, with a longer branch indicating a weaker correlation. Color represents relative expression level of individual probe set as compared to the average expression of the 21 normals. Red represents upregulation vs. control and green represents downregulation vs. control. (b) PCA of all psoriasis samples profiled using the 164 upregulated type-I IFN inducible probe sets in lesional skin compared to those in mostly paired non-lesional skin. (PCA is calculated and data is visualized in Spotfire). Each circle represents one sample (blue circles=normal skin; black circles=non-lesional skin; red circles=lesional skin).

FIG. 35: Overexpression of selected type-I IFN inducible genes in 18 pairs of lesional and non-lesional skin from 18 psoriatic patients based on TAQMAN QRT-PCR assays using FLUIDIGM's BIOMARK™ 48.48 dynamic array.

FIG. 36
a-36b: Correlation coefficient distribution of overexpressed genes in lesional skin of psoriatic patients between TAQMAN QRT-PCR and array results. The genes are grouped based on correlation coefficient between TAQMAN QRT-PCR and microarray measurement. (a) correlation coefficient distribution of all 40 upregulated genes in lesional skin that are validated by TAQMAN QRT-PCR; (b) correlation coefficient distribution of 29 type-IFN inducible genes.

FIG. 37
a-37d: Comparison of TAQMAN QRT-PCR based assay using BIOMARK™ 48.48 dynamic array and AFFYMETRIX® GENECHIP microarray results for selected type-I IFN inducible genes ISG15 and MX1.

FIG. 38: TAQMAN QRT-PCR validation of AFFYMETRIX® GENECHIP microarray results of overexpression of type-I IFN inducible genes IFI27 and CXCL10.

FIG. 39
a-39f: Ex vivo stimulation of normal keratinocytes with leukocyte IFN and IFNα2a and dose-dependent neutralization of type-I IFN induced genes by IFNα antibody. (a) neutralization of ISG15 overexpression in response to 350 I.U./mL IFNα2a, (b) neutralization of ISG15 overexpression in response to 150 I.U./mL leukocyte IFN, (c) neutralization of USP18 overexpression in response to 350 I.U./mL IFNα2a, (d) neutralization of USP18 overexpression in response to 150 I.U./mL leukocyte IFN, (e) neutralization of IFIT2 overexpression in response to 350 I.U./mL IFNα2a, and (f) neutralization of IFIT2 overexpression in response to 150 I.U./mL leukocyte IFN. Each dose titration curve is generated on three technical replicates. The overexpression of individual genes with no IFNα antibody is normalized to 1.

FIG. 40
a-40c: Relative expression of mRNA and median fold changes of type-I IFNα subtypes (FIG. 40a), other members of the type-I IFNs (FIG. 40b), and IFNα receptors (FIG. 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 and their receptors in the normal skin of two healthy donors were scaled to be 1 based on TAQMAN QRT-PCR assays using TLDA from Applied Biosciences. Black: the relative fold change of mRNA in the non-lesional skin compared to normal skin (NS/NN); Red: the relative fold change of mRNA in the lesional skin compared to normal skin (LS/NS). The p values for the overexpression of these individual genes in the non-lesional skin or lesional skin compared to healthy normal skin (listed in pairs) are as follows: IFNα1, 0.303, <0.001; IFNα2, 0.389, 0.072; IFNα5, <0.001, 0.002; IFNα6, 0.664, 0.093; IFNα7, 0.586, 0.077; IFNα8, 0.430, 0.049; IFNα14, 0.224, 0.049; IFNα17, 0.552, 0.0203; IFNα21, 0.113, 0.003; IFNβ, 0.255, 0.022; IFNκ, 0.03, <0.001; IFNω, 0.516, 0.049; IFNAR1, 0.192, <0.001; IFNAR2, <0.001, <0.001, respectively.

FIG. 41: Relative expression of mRNA and median fold changes of IFNγ, TNFα, and IFNγ receptors in the lesional skin (LS), or the non-lesional skin (NS) compared to skin from healthy normal controls (NN). The averages of the relative mRNA levels of these cytokines and their receptors in the normal skin of two healthy donors were scaled to be 1 based on TAQMAN QRT-PCR assays using TLDA from Applied Biosciences. Black: the relative fold change of mRNA in the non-lesional skin compared to normal skin; Red: the relative fold change of mRNA in the lesional skin compared to normal skin. The p values for the overexpression of these individual genes in the non-lesional skin or lesional skin compared to healthy normal skin (listed in pairs) are as follows: IFNγ, 0.02, <0.001; IFNGR1, <0.001, <0.001; IFNGR2, <0.001, <0.001; TNFα, <0.001, <0.001, respectively.

FIG. 42: A Venn diagram illustrating both the number of probe sets that are altered by type I IFN, IFNγ, and TNFα during ex vivo stimulation, and probe sets that are altered in the lesional skin compared to non-lesional skin. Red numbers: probe sets that show increased expression with cytokine treatment or compared to non-lesional skin baseline; Green numbers: probe sets that show decreased expression with cytokine treatment or compared to non-lesional skin baseline. The intersecting regions represent the probe sets that are common to both comparisons.

FIGS. 43
a and 43b: Co-overexpression type-I IFN, type-II IFN, and TNF-inducible genes in lesional/non-lesional skin of psoriatic patients based on Affymetrix GENECHIP® microarray results. The type-I IFN, type-II IFN, and TNFα inducible genes were selected based on ex vivo stimulation experiments (Examples 10 and 16). A probe set with an at least 2-fold change from non-lesional to lesion skin was considered overexpressed. (a) the number of up-regulated type I IFN, IFNγ, and TNFα inducible genes in the lesional skin shows strong correlation. (b) the number of type I IFN, IFNγ, and TNFα inducible genes in the lesional skin were significantly different amongst pairwise comparisons.

FIG. 44: Immunohistochemical analysis of biopsies from psoriatic skin, non-lesional skin and skin from normal donors. BDCA2 is a specific marker for pDCs which are present at greater numbers in lesional skin compared to non-lesional skin, and not at all in normal skin. CD83 is a marker for mDCs, CD4 is present on T cells and dendritic cells. STAT1 protein staining was observed in the epidermis of lesional skin (both nuclear and cytoplasmic) and dermal mononuclear inflammatory cells, but not in non-lesional or normal skin. ISG15 protein increase was observed in psoriatic skin and to a lesser extent in non-lesional skin, but was not detected in normal skin.

FIG. 45: A Venn diagram illustrating the number of probe sets that show altered expression at mRNA level in the lesional skin compared to non-lesional skin, or in the non-lesional skin compared to normal skin of psoriatic patients. Values shaded in red indicate the number of probe sets significantly upregulated while those values shaded in green indicate the number of probe sets significantly downregulated. The intersecting region represents probe sets that are common to both comparisons.

FIG. 46: Graphic representation of type-IFN signaling pathway that is activated in the lesional skin of psoriatic patients. Pathway image was generated with GENEGO's METACORE integrated software suite. Individual symbols within the image represent well characterized proteins or protein complexes. Arrows linking the proteins represent the stimulatory, inhibitory, or interactive effect of the protein on the target protein. Thermometers adjacent to the individual symbols represent relative expression levels (red indicates overexpression, while green indicates underexpression) of transcripts that comprise the protein (or protein complex) within the particular pathway.

FIGS. 47
a and 47b: Table providing fold change (fc; log 2 transformed) and q value (calculated by FDR) of the top 100 probe sets upregulated in the lesional skin compared to non-lesional skin in psoriasis. Also listed are the log 2 transformed fold change and q values of these genes when comparing non-lesional skin with healthy normal skin controls. Type I IFN inducible genes are listed in bold font.

FIG. 48: Distinctive separation of the lesional skin from non-lesional skin and normal skin—hierarchical clustering of all samples using transcript profiles of all genes on a whole genome (Affymetrix whole genome U133 plus v2.0 array) array.

FIG. 49
a-49d: Probe sets identified as IFNγ inducible by overlap in FIG. 42. FIG. 49b discloses “DEAD (Asp-Glu-Ala-Asp)” as SEQ ID NO: 1.

FIG. 50
a-50b: Probe sets identified as TNFα inducible by overlap in FIG. 42.

FIG. 51
a-51g: Probe sets identified as type I IFN inducible by overlap in FIG. 42. FIG. 51c discloses “DEAD (Asp-Glu-Ala-Asp)” as SEQ ID NO: 1.

FIG. 52: Immunohistochemical analysis of biopsies from skin lesions of a placebo-treated SLE patient to detect pDC, mDC, and T cell infiltrates.

FIG. 53: Immunohistochemical analysis of biopsies from skin lesions of a placebo-treated SLE patient to detect HERC5, ISG15, and IP10 proteins, proteins expressed from type I IFN-induced genes.

FIG. 54: Immunohistochemical analysis of biopsies from skin lesions of an SLE patient treated with 10 mg/kg MEDI-545 to detect pDC, mDC, and T cell infiltrates.

FIG. 55: Immunohistochemical analysis of biopsies from skin lesions of an SLE patient treated with 10 mg/kg MEDI-545 to detect HERC5, ISG15, and IP10 proteins, proteins expressed from type I IFN-induced genes.

FIG. 56: Immunohistochemical analysis of biopsies from skin lesions of an SLE patient treated with 10 mg/kg MEDI-545 to detect pDC, mDC, and T cell infiltrates.

FIG. 57: Immunohistochemical analysis of biopsies from skin lesions of an SLE patient treated with 10 mg/kg MEDI-545 to detect HERC5, ISG15, and IP10 proteins, proteins expressed from type I IFN-induced genes.

FIGS. 58
a and 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.

FIG. 59
a-d: Detection of type I and type II IFN activity in an IFN bioassay.

FIGS. 60
a and 60b: Detection of MEDI-545 (a) and MEDI-546 (b)-mediated neutralization of IFNα activity in the IFN bioassay.

FIG. 61: Detection of anti-IFNγ-mediated neutralization of IFNγ activity in the IFN bioassay.

FIG. 62: Detection of anti-IFNω-mediated neutralization of IFNω activity in the IFN bioassay.

FIG. 63: Detection of anti-IFNβ-mediated neutralization of IFNβ activity in the IFN bioassay.

FIG. 64: Heat map showing modulation of gene expression in whole blood from healthy donors ex vivo stimulated with IFNγ, TNFα, or IFNα/β. Negative control (NT).

FIG. 65: Type I IFN-inducible genes were among the most upregulated genes in whole blood of SLE patients.

FIG. 66: IFNγ, IFNω, IFNAR1 and IFNAR2 mRNAs are upregulated in whole blood of lupus patients.

FIG. 67: Heat map showing modulation of gene expression in healthy donor PBMCs ex vivo stimulated with lupus patient serum.

FIGS. 68
a and 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.

FIG. 69: Confirmation of overexpression of selected type-I IFN inducible genes in lupus patients based on TAQMAN QRT-PCR assays using FLUIDIGM's BIOMARK™ 48.48 dynamic array.

FIGS. 70
a and 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 hour co-incubation.

FIGS. 71
a and 71b: The majority of genes neutralized by an anti-IFNα Ab 4 hours post co-incubation of SLE patient serum and healthy human PBMCs are type I IFN genes, while the majority of genes neutralized by the anti-IFNα Ab 18 hours post co-incubation of SLE patient serum and healthy human PBMCs are non-type I IFN genes as shown by (a) heatmap analysis and represented (b) in bar graphs.

FIGS. 72
a and 72b: Provides the (a) type I IFN genes and (b) non-type I IFN genes that were upregulated and neutralized by an anti-IFNα Ab 18 hours post co-incubation of SLE patient serum and healthy human PBMCs, but that were not upregulated 4 hours post co-incubation of SLE patient serum and healthy human PBMCs.

FIG. 73: Provides pathways and cell processes neutralized by an anti-IFNα Ab 18 hours following co-incubation of SLE patient serum and healthy human PBMCs.

FIGS. 74
a and 74b: Detection of (a) increased and (b) decreased levels of specific proteins in serum of lupus patients.

FIG. 75: QUANTIGENEPLEX 1.0 analysis of IFN-inducible gene signatures from whole blood of 5 healthy donors stimulated with 20 IU/mL IFNα2b.

FIG. 76: Dose-dependent changes in gene expression in blood from a single healthy donor treated with multiple concentrations of IFNα2b.

FIG. 77: Detection of IFN-inducible transcripts in PAXgene-preserved whole blood samples from SLE subjects with and without detectable serum IFNα activity.

FIGS. 78
a and 78b: Correlation between QUANTIGENEPLEX and FLUIDIGM technologies in SLE PAXgene-preserved whole blood samples.

FIGS. 79
a and 79b: Longitudinal testing of SLE samples following administration of an anti-IFNα monoclonal antibody: comparison of QUANTIGENEPLEX 2.0 and FLUIDIGM technologies.

FIG. 80: Representative heat map visualizing the (in descending order) overexpression of type I IFN gene signature; overexpression of granulocyte signature; underexpression of T-cell signature, underexpression of NK-cell signature, and underexpression of B-cell signature, in whole blood from 46 SLE patients (indicated by red bar under the heat map) compared with whole blood from 24 healthy donors (indicated by blue bar under the heat map) IFN=interferon; SLE=systemic lupus erythematosus.

FIG. 81
a-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 using the 114 upregulated type I IFN-inducible probe set confirmed the overexpression of type I IFN gene signatures in SLE patients. (c) PCA plot of whole blood from 100 SLE samples in both discovery and prospective study using 21 upregulated type I IFN-inducible gene panel in SLE patients compared with 24 healthy donors. Each point represents one sample (blue dots, healthy normals; red dots, SLE patients). IFN=interferon; PCA=principal components analysis; SLE=systemic lupus erythematosus.

FIG. 82: Relative expression of mRNAs and median fold changes (horizontal bars) of TNF-α, IFN-γ, and IFN-γ receptors in whole blood of SLE patients compared with healthy controls (P<0.05 for all). Averages of relative mRNA levels of these cytokines and their receptors in whole blood from 24 healthy donors were scaled to 1 based on TAQMAN QRT-PCR assays. IFN=interferon; QRT-PCR=quantitative real-time reverse transcriptase polymerase chain reaction; SLE=systemic lupus erythematosus; TNF=tumor necrosis factor.

FIG. 83
a-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 genes (generically labeled 1-15) in SLE patients were compared with healthy donors (p<0.05 for all). Averages of relative mRNA levels of genes in the pooled RNA from 24 healthy donors were scaled to 1 based on TAQMAN QRT-PCR assays. Horizontal bars represent average fold change. (b and c) TAQMAN QRT-PCR validation of overexpression of the 21-gene panel of type I IFN-inducible genes in whole blood of SLE patients as determined by whole genome array. The relative overexpression of 21 type I IFN-inducible genes in 2 SLE patients is shown via microarray (left) and TAQMAN QRT-PCR (right) assays. Correlation coefficients between TAQMAN QRT-PCR and microarray were 0.9861 and 0.9888 for patient X and Y, respectively. IFN=interferon; QRT-PCR=quantitative real-time reverse transcriptase polymerase chain reaction; SLE=systemic lupus erythematosus.

FIG. 84: Magnitude of overexpression of type I IFN gene signature in whole blood of SLE patients as measured by the median fold change of the 25 most overexpressed type I IFN-inducible genes or type I IFN gene signature score in individual SLE patients. The horizontal bars represent the median values. Patients whose type I IFN gene signature score was ≧10 were considered to have strong type I IFN gene signatures; those with scores between 4 and 10 were considered to have moderate type I IFN gene signatures, whereas those with scores ≦4 were considered to have weak type I IFN gene signatures. IFN=interferon; SLE=systemic lupus erythematosus.

FIG. 85
a-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 log₂scale 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 log₂scale), 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 log₂scale). IFN=interferon; SLE=systemic lupus erythematosus.

FIG. 86: Dose-dependent neutralization of 21 upregulated IFN-α/β-inducible genes in SLE patients by MEDI-545.

FIGS. 87
a and 87b: Heatmap (a) and PCA (b) showing neutralization of 21 upregulated IFN-α/β-inducible genes in whole blood of an SLE patient treated with 30 mg/kg MEDI-545 (0, 1, 4, 7, and 14 days post-dose).

FIGS. 88
a and 88b: PCA plots prepared using the 21 upregulated IFN-α/β-inducible probe sets do not show IFN signature neutralization in placebo-treated patients.

FIG. 89: Neutralization of the 21 upregulated IFN-α/β-inducible probe sets in patients treated with 0.3, 1.0, 3.0, 10.0, and 30.0 mg/kg MEDI-545.

FIG. 90: Methodology for calculating target neutralization for FIG. 89.

FIG. 91 shows the nucleotide sequence (SEQ ID NO: 11) and amino acid sequence (SEQ ID NO: 9) of the heavy chain variable region of the 9D4 human monoclonal antibody. The CDR1 (SEQ ID NO: 3), CDR2 (SEQ ID NO: 4) and CDR3 (SEQ ID NO: 5) regions are delineated.

FIG. 92 shows the nucleotide sequence (SEQ ID NO: 12) and amino acid sequence (SEQ ID NO: 10) of the light chain variable region of the 9D4 human monoclonal antibody. The CDR1 (SEQ ID NO: 6), CDR2 (SEQ ID NO: 7) and CDR3 (SEQ ID NO: 8) regions are delineated.

DETAILED DESCRIPTION

The invention encompasses methods of identifying, diagnosing, treating, and monitoring disease progression in patients. Patients include any animal having a type I IFN or an IFNα-inducible disease, disorder, or condition. The patient may have the disease, disorder, or condition as a result of experimental research, e.g., it may be an experimental model developed for the disease, disorder, or condition. Alternatively, the patient may have the disease, disorder, or condition in the absence of experimental manipulation. Patients include humans, mice, rats, horses, pigs, cats, dogs, and any animal used for research.

The patient may comprise a type I IFN or IFNα-inducible PD marker expression profile. The type I IFN or IFNα-inducible PD marker expression profile may be a strong profile, a moderate profile, or a weak profile. The type I IFN or IFNα-inducible PD marker expression profile can readily be designated as strong, moderate, or weak by determining the fold dysregulation of the type I IFN or IFNα-inducible PD marker expression profile of the patient, (e.g., the fold increase in expression of upregulated type I IFN or IFNα-inducible PD markers in the patient), relative to a control sample(s) or control patient(s) and comparing the patient's fold dysregulation to that of other patients having a type I IFN or IFNα-inducible PD marker expression profile. Fold dysregulation can be calculated by well known methods in the art as can the comparing. See, e.g., Example 8.

The type I IFN or IFNα-inducible PD marker expression profile may comprise upregulation of any group of genes or group of genes detected by the probes identified in Tables 19, 20, 21, 22, 23, 24, 26, 28, or 30. The group of genes or group of genes detected by the probes identified in Tables 19, 20, 21, 22, 23, 24, 26, 28 or 30 may include any at least 2, any at least 3, any at least 4, any at least 5, any at least 6, any at least 7, any at least 8, any at least 9, any at least 10, any at least 11, any at least 12, any at least 13, any at least 14, any at least 15, any at least 16, any at least 17, any at least 18, any at least 19, any at least 20, any at least 21, any at least 22, any at least 23, any at least 24, any at least 25, any at least 26, any at least 27, any at least 28, any at least 29, any at least 30, any at least 40, or any at least 50 of the genes or genes detected by the probes identified in the Tables.

The group of genes that may be included in the type I IFN or IFNα-inducible PD marker expression profile of the patient may be MX1, LY6E, IFI27, OAS1, IFIT1, IFI6, IFI44L, ISG15, LAMP3, OASL, RASD2, and IFI44. The genes or genes detected by the probes may include IFI44, IFI27, IFI44L, DNAPTP6, LAMP3, LY6E, RSAD2, HERC5, IFI6, ISG15, OAS3, SIGLEC1, OAS2, USP18, RTP4, IFIT1, MX1, OAS1, EPSTI1, PLSCR1, and IFRG28.

The genes may include any at least 2, any at least 3, any at least 4, any at least 5, any at least 6, any at least 7, any at least 8, any at least 9, any at least 10, or any at least 11, or any at least 12, or any at least 13, or any at least 14, or any at least 15, or any at least 16, or any at least 17, or any at least 18, or any at least 19, or at least 20, or any at least 21, or any at least 22, or any at least 23, or any at least 24, or any least 25, or any at least 26, or any at least 27, or any at least 28, or any at least 29, or any at least 30 of LAMP3, DNAPTP6, FLJ31033, HERC6, SERPING1, EPST11, RTP4, OASL, FBXO6, IFIT2, IFI44, OAS3, BATF2, ISG15, IRF7, RSAD2, IF135, OAS1, LAP3, IFIT1, IFIT5, PLSCR1, IFI44L, MS4A4A, GALM, UBE2L6, TOR1B, SAMD9L, HERC5, TDRD7, TREX1, PARP12, and AXUD1.

The type I IFN or IFNα-inducible PD marker expression profile may contain upregulation of the entire group of genes or group of genes detected by the probes identified in one of Table 19, or Table 20, or Table 21, or Table 22, or Table 23, or Table 24, or Table 26, or Table 28, or Table 30 or may be any one or more of the genes identified in FIG. 72. The type I IFN or IFNα-inducible PD marker expression profile may include upregulation of all the genes identified in Table 24. The type I IFN or IFNα-inducible PD marker expression profile may include upregulation of the genes identified in FIG. 72 A or FIG. 72b, or FIG. 72a and FIG. 72b.

The patient comprising the type I IFN or IFNα-inducible PD marker expression profile may further comprise downregulated type I IFN or IFNα PD marker(s). The downregulated PD markers may include any one, any two, any three, any four, any five, any six, any seven, any eight, any nine, any ten, any 15, any 20, any 25, any 30, any 35, any 40, any 45, or any 50 of the genes in Table 31 or any of CYP1B1, TGST1, RRAGD, IRS2, MGST1, TGFBR3, and RGS2.

The patient comprising the type I IFN or IFNα-inducible PD marker expression profile may further comprise upregulation of expression of any number of IFNα or type-I IFN subtypes. The IFNα or type-I IFN subtypes may include any more than one, more than two, more than three, more than four, more than five, more than six, more than seven, more than eight, more than nine, or more than ten IFNα or type-I IFN subtypes. These subtypes may include IFNα1, IFNα2, IFNα4, IFNα5, IFNα6, IFNα7, IFNα8, IFNα10, IFNα14, IFNα17, IFNα21, IFNβ, or IFNω. The patient may comprise upregulation of expression of IFN subtypes IFNα1, IFNα2, IFNα8, and IFNα14.

Alternatively, a patient treated in the methods encompassed by the invention may simply be one identified as comprising a gene expression profile with upregulation of expression of any number of IFNα or type-I IFN subtypes. The IFNα or type-I IFN subtypes may include any more than one, more than two, more than three, more than four, more than five, more than six, more than seven, more than eight, more than nine, or more than ten IFNα or type-I IFN subtypes. These subtypes may include IFNα1, IFNα2, IFNα4, IFNα5, IFNα6, IFNα7, IFNα8, IFNα10, IFNα14, IFNα17, IFNα21, IFNβ, or IFNω. These subtypes may include IFNα1, IFNα2, IFNα8, and IFNα14.

The patient comprising the type I IFN or IFNα-inducible PD marker expression profile may further comprise upregulation of expression of IFNα receptors, either IFNAR1 or IFNAR2, or both, or TNFα, or IFNγ, or IFNγ receptors (either IFNGR1, IFNGR2, or both IFNGR1 and IFNGR2). The patient may simply be identified as one who comprises upregulation of expression of IFNα receptors, either IFNAR1 or IFNAR2, or both, or TNFα, or IFNγ, or IFNγ receptors (either IFNGR1, IFNGR2, or both IFNGR1 and IFNGR2).

The upregulation or downregulation of the type I IFN or IFNα-inducible PD markers in the patient's expression profile may be by any degree relative to that of a sample from a control (which may be from a sample that is not disease tissue of the patient (e.g., non-lesional skin of a psoriasis patient) or from a healthy person not afflicted with the disease or disorder). The degree upregulation or downregulation may be at least 10%, at least 15%, at least 20%, at least 25%, at least 30%, at least 40%, at least 50%, at least 60%, at least 70%, at least 75%, at least 80%, at least 90%, at least 100%, at least 125%, at least 150%, or at least 200%, or at least 300%, or at least 400%, or at least 500% that of the control or control sample.

Furthermore, the patient may overexpress or have a tissue that overexpresses a type I IFN subtype at least 10%, at least 15%, at least 20%, at least 25%, at least 30%, at least 40%, at least 50%, at least 60%, at least 70%, at least 75%, at least 80%, at least 90%, at least 100%, at least 125%, at least 150%, or at least 200%, or at least 300%, or at least 400%, or at least 500% that of the control. The type I IFN subtype may be any one of IFNα1, IFNα2, IFNα4, IFNα5, IFNα6, IFNα7, IFNα8, IFNα10, IFNα14, IFNα17, IFNα21, IFNβ, or IFNω. The type I IFN subtypes may include all of IFNα1, IFNα2, IFNα8, and IFNα14.

The patient may further comprise or alternatively comprise alterations in levels of proteins in serum. The patient may have increased serum levels of proteins such as adiponectin, alpha-fetoprotein, apolipoprotein CIII, beta-2 microglobulin, cancer antigen 125, cancer antigen 19-9, eotaxin, FABP, factor VII, ferritin, IL-10, IL-12p70, IL-16, IL-18, IL-1ra, IL-3, MCP-1, MMP-3, myoglobin, SGOT, tissue factor, TIMP-1, TNF RII, TNF-alpha, VCAM-1, or vWF. The patient may have increased serum levels of any 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13 14, 15, 16, 17, 18, 19, 20, 21, o22, 23, 24, 25, or 26 of these proteins in serum. The increased level may be at least 10%, at least 15%, at least 20%, at least 25%, at least 30%, at least 40%, at least 50%, at least 60%, at least 70%, at least 75%, at least 80%, at least 90%, at least 100%, at least 125%, at least 150%, or at least 200%, or at least 300%, or at least 400%, or at least 500% that of a control, e.g., a healthy subject. The alteration may be a decrease in serum levels of proteins such as BDNK, complement 3, CD40 ligand, EGF, ENA-78, EN-RAGE, IGF-1, MDC, myeloperoxidase, RANTES, or thrombopoietin, The patient may have decreased serum levels of any 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or 11 or these proteins. The decreased level may be at least 10%, at least 15%, at least 20%, at least 25%, at least 30%, at least 40%, at least 50%, at least 60%, at least 70%, at least 75%, at least 80%, at least 90%, or at least 100% that of a control, e.g., a healthy subject. The PD marker profile may comprise one or more of these increased or decreased serum levels of proteins.

The patient may further comprise auto-antibodies that bind to any one of the following auto-antigens: (a) Myxovirus (influenza virus) resistance 1, interferon-inducible protein p78; (b) surfeit 5, transcript variant c; (c) proteasome (posome, macropain) activator subunit 3 (PA28 gamma; Ki) transc; (d) retinoic acid receptor, alpha; (e) Heat shock 10 kDa protein 1 (chaperonin 10); (f) tropomyosin 3; (g) pleckstrin homology-like domain, family A, member 1; (h) cytoskeleton-associated protein 1; (i) Sjogren syndrome antigen A2 (60 kDa, ribonucleoprotein auto-antigen SS-A/Ro); (j) NADH dehydrogenase (ubiquinone) 1, alpha/beta subcomplex 1, 8 kDa; (k) NudE nuclear distribution gene E homolog 1 (A. nidulans); (l) MutL homolog 1, colon cancer, nonpolyposis type 2 (E. coli); (m) leucine rich repeat (in FLIT) interacting protein 2; (n) tropomyosin 1 (alpha); (o) spastic paraplegia 20, spartin (Troyer syndrome); (p) preimplantation protein, transcript variant 1; (r) mitochondrial ribosomal protein L45; (s) Lin-28 homolog (C. elegans); (t) heat shock 90 kDa protein 1, alpha; (u) dom-3 homolog Z (C. elegans); (v) dynein, cytoplasmic, light intermediate polypeptide 2; (w) Ras-related C3 botulinum toxin substrate 1 (rho family, small GTP binding protein); (x) synovial sarcoma, X breakpoint 2, transcript variant 2; (y) moesin; (z) homer homolog (Drosophila), transcript variant 1; (aa) GCN5 general control of amino-acid synthesis 5-like 2 (yeast); (bb) eukaryotic translation elongation factor 1 gamma; (cc) eukaryotic translation elongation factor 1, delta; (dd) DNA-damage-inducible transcript 3; (ee) CCAAT/enhancer binding protein (C/EBP) gamma; and any other auto-antigen described in provisional application entitled “Auto-antibody markers of autoimmune disease” filed May 3, 2007 or in provisional application entitled entitled “Auto-antibody markers of autoimmune disease” to be filed Nov. 6, 2007 (for example, but not limited to, those described on Tables 2, 4, 5, and 9). The patient may comprise auto-antibodies that bind to any number of these auto-antigens, e.g., any at least 2, at least 3, at least 4, at least 5, at least 6, at least 7, at least 8, at least 9 at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 20, at least 25.

A type I IFN or an IFNα-inducible disease, disorder, or condition is any that exhibits a type I IFN or an IFNα PD marker expression profile or gene signature. A PD marker expression profile and a gene signature will be understood to be equivalent. These diseases, disorders, or conditions include those with an autoimmune component such as systemic lupus erythematosus, insulin dependent diabetes mellitus, inflammatory bowel disease (including Crohn's disease, ulcerative colitis, and Celiac's disease), multiple sclerosis, psoriasis, autoimmune thyroiditis, rheumatoid arthritis, glomerulonephritis, idiopathic inflammatory myositis, Sjogren's syndrome, vasculitis, dermatomyositis, polymyositis, and sarcoidosis. Other diseases, disorders, or conditions include graft versus host disease and transplant rejection.

The patients may also exhibit any of a number of symptoms as discussed in, e.g., provisional patent application Methods of Treating Systemic Lupus Erythematosis filed Apr. 16, 2007, or may have a clinical SLEDAI score or BILAG score as discussed in the same. These symptoms may include fatigue, organ damage, malar rash, and alopecia. The patient may be scored using a known clinical scoring system, e.g., SLEDAI which is an index of SLE disease activity as measured and evaluated within the last 10 days (Bombardier C, Gladman D D, Urowitz M B, Caron D, Chang C H and the Committee on Prognosis Studies in SLE: Derivation of the SLEDAI for Lupus Patients. Arthritis Rheum 35:630-640, 1992.). Disease activity under the SLEDAI scoring system can range from 0 to 105. The following categories of SLEDAI activity have been defined: no activity (SLEDAI=0); mild activity (SLEDAI=1-5); moderate activity (SLEDAI=6-10); high activity (SLEDAI=11-19); very high activity (SLEDAI=20 or higher). (Griffiths, et al., Assessment of Patients with Systemic Lupus Erythematosus and the use of Lupus Disease Activity Indices). Another disease scoring index is the BILAG index which is an activity index of SLE that is based on specific clinical manifestations in eight organ systems: general, mucocutaneous, neurological, musculoskeletal, cardiovascular, respiratory, renal, and hematology results. Scoring is based on a letter system, but weighted numerical scores can also be assigned to each letter, making it possible to calculate a BILAG score in the range of 0-72. (Griffiths, et al., Assessment of Patients with Systemic Lupus Erythematosus and the use of Lupus Disease Activity Indices). Other scoring indices include the PGA score, the composite responder index (CRI), and the ANAM4™ test. The methods described herein, e.g., of treating an autoimmune disorder, may be used for any subject identified as having any activity level of disease activity as measured by any classification methodology known in the art, e.g., mild, moderate, high, or very high. The methods described herein, e.g., of treating an autoimmune disorder, may result in a decrease in a patient's symptoms or may result in an improvement in a score of disease for the patient's type I IFN or an IFNα-inducible disease, disorder, or condition.

A therapeutic agent may be administered to a patient or a patient may be identified as a candidate for administration of an agent or a therapeutic agent. A therapeutic agent is any molecule that binds to and modulates type I IFN or IFNα activity. The therapeutic agent may be a small molecule or a biological agent. If the therapeutic agent is a small molecule it may be synthesized or identified and isolated from a natural source.

If the therapeutic agent is a biological agent, it may be an antibody specific for any subtype(s) of type I IFN or IFNα. For instance, the antibody may be specific for any one of IFNα1, IFNα2, IFNα4, IFNα5, IFNα6, IFNα7, IFNα8, IFNα10, IFNα14, IFNα17, IFNα21, IFNβ, or IFNω. Alternatively, the antibody may be specific for any two, any three, any four, any five, any six, any seven, any eight, any nine, any ten, any eleven, any twelve type I IFN of IFNα subtypes. If the antibody is specific for more than one type I IFN subtype, the antibody may be specific for IFNα1, IFNα2, IFNα4, IFNα5, IFNα8, IFNα10, and IFNα21; or it may be specific for IFNα1, IFNα2, IFNα4, IFNα5, IFNα8, and IFNα10; or it may be specific for IFNα1, IFNα2, IFNα4, IFNα5, IFNα8, and IFNα21; or it may be specific for IFNα1, IFNα2, IFNα4, IFNα5, IFNα10, and IFNα21. Antibodies specific for type I IFN or IFNα include MEDI-545, any biologic or antibody other than MEDI-545, antibodies described in U.S. patent application Ser. No. 11/009,410 filed Dec. 10, 2004 which published as U.S. Patent Application Publication No. US20070014724 on Jan. 18, 2007 and issued as U.S. Pat. No. 7,741,449; and Ser. No. 11/157,494 filed Jun. 20, 2005 which published as U.S. Patent Application Publication No. US20060029601 on Feb. 9, 2006 and issued as U.S. Pat. No. 7,662,381, 9F3 and other antibodies described in U.S. Pat. No. 7,087,726 (Example 1 and Example 2, those disclosed in Table 3 and Table 4, and/or those disclosed in the table entitled “Deposit of Material” on lines 25-54, column 56), NK-2 and YOK5/19 (WO 84/03105), LO-22 (U.S. Pat. No. 4,902,618), 144 BS (U.S. Pat. No. 4,885,166), and EBI-1, EBI-2, and EBI-3 (EP 119476). A therapeutic agent that modulates IFNα activity may neutralize IFNα activity. One of skill in the art is well aware of preparation and formulation of such biological agents and methods of their administration.

In an embodiment, an antibody, or antigen binding portion thereof, comprises: (a) a heavy chain variable region CDR1 comprising SEQ ID NO: 3; (b) a heavy chain variable region CDR2 comprising SEQ ID NO: 4; (c) a heavy chain variable region CDR3 comprising SEQ ID NO: 5; (d) a light chain variable region CDR1 comprising SEQ ID NO: 6; (e) a light chain variable region CDR2 comprising SEQ ID NO: 7; and (f) a light chain variable region CDR3 comprising SEQ ID NO: 8. In an embodiment, an antibody, or antigen binding portion thereof, comprises (a) a heavy chain variable region comprising the amino acid sequence of SEQ ID NO: 9; and (b) a light chain variable region comprising the amino acid sequence of SEQ ID NO: 10. An antibody, or antigen binding portion thereof, specifically binds to IFN alpha receptor 1 (IFNAR-1) in certain embodiments. In certain embodiments, an antibody, or antigen binding portion thereof, exhibits one or more of the following properties: (a) binds to IFNAR-1 with a K_Dof 1×10⁷M or greater affinity; (b) inhibits the biological activity of multiple Type I interferons; (c) inhibits the activity of IFN α 2b in a Daudi cell proliferation assay; (d) inhibits the activity of IFN omega in a Daudi cell proliferation assay; (e) inhibits IP-10 secretion by peripheral blood mononuclear cells induced by IFN α 2b; (f) inhibits IP-10 secretion by peripheral blood mononuclear cells induced by IFN omega; (g) inhibits dendritic cell development mediated by Systemic Lupus Erythematosus plasma; and (h) binds to a different epitope than murine monoclonal antibody 64G12 (ECACC Deposit No. 92022605).

The antibody may be a synthetic antibody, a monoclonal antibody, polyclonal antibodies, a recombinantly produced antibody, an intrabody, a multispecific antibody (including bi-specific antibodies), a human antibody, a humanized antibody, a chimeric antibody, a single-chain Fv (scFv) (including bi-specific scFv), a BiTE molecule, a single chain antibody, a Fab fragments, a F(ab′) fragment, a disulfide-linked Fv (sdFv), or an epitope-binding fragment of any of the above. The antibody may be any of an immunoglobulin molecule or immunologically active portion of an immunoglobulin molecule. Furthermore, the antibody may be of any isotype. For example, it may be any of isotypes IgG1, IgG2, IgG3 or IgG4. The antibody may be a full-length antibody comprising variable and constant regions, or an antigen-binding fragment thereof, such as a single chain antibody, or a Fab or Fab′2 fragment. The antibody may also be conjugated or linked to a therapeutic agent, such as a cytotoxin or a radioactive isotope.

In the methods of treatment a second agent other than the agent that binds to modulates IFNα activity may be administered to the patient. Second agents include, but are not limited to non-steroidal anti-inflammatory drugs such as ibuprofen, naproxen, sulindac, diclofenac, piroxicam, ketoprofen, diflunisal, nabumetone, etodolac, and oxaprozin, indomethacin; anti-malarial drugs such as hydroxychloroquine; corticosteroid hormones, such as prednisone, hydrocortisone, methylprednisolone, and dexamethasone; methotrexate; immunosuppressive agents, such as azathioprine and cyclophosphamide; and biologic agents that, e.g., target T cells such as Alefacept and Efalizumab, or target TNFα, such as, Enbrel, Remicade, and Humira.

Treatment with the agent may result in neutralization of the type I IFN or IFNα-inducible profile. Treatment with the agent may result in a decrease in one or more symptoms of the type I IFN or an IFNα-mediated disease or disorder. Treatment with the agent may result in fewer flare-ups related to the type I IFN or an IFNα-mediated disease or disorder. Treatment with the agent may result in improved prognosis for the patient having the type I IFN or an IFNα-mediated disease or disorder. Treatment with the agent may result in a higher quality of life for the patient. Treatment with the agent may alleviate the need to co-administer second agents or may lessen the dosage of administration of the second agent to the patient. Treatment with the agent may reduce the number of hospitalizations of the patient that are related to the type I IFN or an IFNα-mediated disease or disorder.

The agent that binds to and modulates type I IFN or IFNα activity may neutralize a type I IFN or IFNα-inducible profile. Neutralization of the type I IFN or IFNα-inducible profile may be a reduction in at least one, at least two, at least three, at least five, at least seven, at least eight, at least ten, at least twelve, at least fifteen, at least twenty, at least twenty five, at least thirty, at least thirty five, at least forty, at least forty five, or at least fifty genes up-regulated by type I IFN or IFNα. The genes upregulated by type I IFN or IFNα may be any group of genes in Tables 19, 20, 21, 22, 23, 24, 26, 28, or 30 as discussed above. Neutralization of the type I IFN or IFNα-inducible profile is a reduction of at least 2%, at least 3%, at least 4%, at least 5%, at least 7%, at least 8%, at least 10%, at least 15%, at least 25%, at least 30%, at least 35%, at least 40%, at least 45%, at least 50%, at least 60%, at least 70%, at least 75%, at least 80%, or at least 90% of any of the at least one, at least two, at least three, at least five, at least seven, at least eight, at least ten, at least twelve, at least fifteen, at least twenty, at least twenty five, at least thirty, at least thirty five, at least forty, at least forty five, or at least fifty genes up-regulated in any type I IFN or IFNα-inducible profile. Alternatively, neutralization of the type I IFN or IFNα-inducible profile refers to a reduction of expression of up-regulated type I IFN or IFNα-inducible genes that is within at most 50%, at most 45%, at most 40%, at most 35%, at most 30%, at most 25%, at most 20%, at most 15%, at most 10%, at most 5%, at most 4%, at most 3%, at most 2%, or at most 1% of expression levels of those type I IFN or IFNα-inducible genes in a control sample. If the agent that binds to and modulates type I IFN or IFNα activity is a biologic agent, such as an antibody, the agent may neutralize the type I IFN or IFNα profile at doses of 0.3 to 30 mg/kg, 0.3 to 10 mg/kg, 0.3 to 3 mg/kg, 0.3 to 1 mg/kg, 1 to 30 mg/kg, 3 to 30 mg/kg, 5 to 30 mg/kg, 10 to 30 mg/kg, 1 to 10 mg/kg, 3 to 10 mg/kg, or 1 to 5 mg/kg.

Neutralization of the type I IFN or IFNα-inducible profile may be increased expression of at least one, at least two, at least three, at least five, at least seven, at least eight, at least ten, at least twelve, at least fifteen, at least twenty, at least twenty five, at least thirty, at least thirty five, at least forty, at least forty five, or at least fifty genes whose expression is reduced by type I IFN or IFNα. The genes whose expression is reduced by type I IFN or IFNα may be any group of genes in Table 30. Neutralization of down-regulated genes in a type I IFN or IFNα-inducible profile is an increase of at least 2%, at least 3%, at least 4%, at least 5%, at least 7%, at least 8%, at least 10%, at least 15%, at least 25%, at least 30%, at least 35%, at least 40%, at least 45%, at least 50%, at least 60%, at least 70%, at least 75%, at least 80%, or at least 90%, or at least 100%, or at least 125%, or at least 130%, or at least 140%, or at least 150%, or at least 175%, or at least 200%, or at least 250%, or at least 300%, or at least 500% of any of the at least one, at least two, at least three, at least five, at least seven, at least eight, at least ten, at least twelve, at least fifteen, at least twenty, or at least twenty five genes whose expression is downregulated in any type I IFN or IFNα-inducible profile. Alternatively, neutralization of the type I IFN or IFNα-inducible profile refers to an increase in expression of type I IFN or IFNα-inducible genes to within at most 50%, at most 45%, at most 40%, at most 35%, at most 30%, at most 25%, at most 20%, at most 15%, at most 10%, at most 5%, at most 4%, at most 3%, at most 2%, or at most 1% of expression levels of those type I IFN or IFNα-inducible (downregulated) genes in a control sample. If the agent that binds to and modulates type I IFN or IFNα activity is a biologic agent, such as an antibody, the agent may neutralize the type I IFN or IFNα profile at doses of 0.3 to 30 mg/kg, 0.3 to 10 mg/kg, 0.3 to 3 mg/kg, 0.3 to 1 mg/kg, 1 to 30 mg/kg, 3 to 30 mg/kg, 5 to 30 mg/kg, 10 to 30 mg/kg, 1 to 10 mg/kg, 3 to 10 mg/kg, or 1 to 5 mg/kg.

The agent that binds to and modulates type I IFN or IFNα activity may further or alternatively neutralize expression of one or more type I IFN or IFNα subtypes. The IFNα or type-I IFN subtypes may include any more than one, more than two, more than three, more than four, more than five, more than six, more than seven, more than eight, more than nine, or more than ten IFNα or type-I IFN subtypes. These subtypes may include IFNα1, IFNα2, IFNα4, IFNα5, IFNα6, IFNα7, IFNα8, IFNα10, IFNα14, IFNα17, IFNα21, IFNβ, or IFNω. These subtypes may include all of IFNα1, IFNα2, IFNα8, and IFNα14. Alternatively, these subtypes may include IFNα1, IFNα2, IFNα4, IFNα5, IFNα8, IFNα10, IFNα21. Neutralization of the IFNα or type-I IFN subtypes may be a reduction of at least 2%, at least 3%, at least 4%, at least 5%, at least 7%, at least 8%, at least 10%, at least 15%, at least 25%, at least 30%, at least 35%, at least 40%, at least 45%, at least 50%, at least 60%, at least 70%, at least 75%, at least 80%, or at least 90% of any of the at least one, at least two, at least three, at least five, at least seven, at least eight, or at least ten of the subtypes. Neutralization of the IFNα or type-I IFN subtypes may be a reduction in expression of IFNα or type-I IFN subtype genes that is within at most 50%, at most 45%, at most 40%, at most 35%, at most 30%, at most 25%, at most 20%, at most 15%, at most 10%, at most 5%, at most 4%, at most 3%, at most 2%, or at most 1% of expression levels of those IFNα or type I IFN subtypes in a control sample. If the agent that binds to and modulates IFNα activity or type I IFN activity is a biologic agent, such as an antibody, the agent may neutralize the IFNα or type I IFN subtypes at doses of 0.3 to 30 mg/kg, 0.3 to 10 mg/kg, 0.3 to 3 mg/kg, 0.3 to 1 mg/kg, 1 to 30 mg/kg, 3 to 30 mg/kg, 5 to 30 mg/kg, 10 to 30 mg/kg, 1 to 10 mg/kg, 3 to 10 mg/kg, or 1 to 5 mg/kg.

The agent that binds to and modulates type I IFN or IFNα activity may further or alternatively neutralize expression of IFNα receptors, either IFNAR1 or IFNAR2, or both, or TNFα, or IFNγ, or IFNγ receptors (either IFNGR1, IFNGR2, or both IFNGR1 and IFNGR2). Neutralization of expression of IFNα receptors, either IFNAR1 or IFNAR2, or both, or TNFα, or IFNγ, or IFNγ receptors (either IFNGR1, IFNGR2, or both IFNGR1 and IFNGR2) may be a reduction of at least 2%, at least 3%, at least 4%, at least 5%, at least 7%, at least 8%, at least 10%, at least 15%, at least 25%, at least 30%, at least 35%, at least 40%, at least 45%, at least 50%, at least 60%, at least 70%, at least 75%, at least 80%, or at least 90% of any of the at least one, at least two, at least three, at least five, or at least six of these genes. Neutralization of expression of IFNα receptors, either IFNAR1 or IFNAR2, or TNFα, or IFNγ, or IFNγ receptors (either IFNGR1, IFNGR2, or both IFNGR1 and IFNGR2) is a reduction of expression of at most 50%, at most 45%, at most 40%, at most 35%, at most 30%, at most 25%, at most 20%, at most 15%, at most 10%, at most 5%, at most 4%, at most 3%, at most 2%, or at most 1% of expression levels of these genes in a control sample. If the agent that binds to and modulates type I IFN or IFNα activity is a biologic agent, such as an antibody, the agent may neutralize expression of IFNα receptors IFNAR1 or IFNAR2, or TNFα, or IFNγ, or IFNγ receptors IFNGR1 or IFNGR2 at doses of 0.3 to 30 mg/kg, 0.3 to 10 mg/kg, 0.3 to 3 mg/kg, 0.3 to 1 mg/kg, 1 to 30 mg/kg, 3 to 30 mg/kg, 5 to 30 mg/kg, 10 to 30 mg/kg, 1 to 10 mg/kg, 3 to 10 mg/kg, or 1 to 5 mg/kg.

The agent that binds to and modulates type I IFN or IFNα activity may further or alternatively neutralize alterations of levels of proteins in serum, e.g., increase levels of those proteins whose serum levels are downregulated or decrease levels of those proteins whose serum levels are upregulated to levels closer to those of control subjects. Neutralization of expression of proteins in serum, such as adiponectin, alpha-fetoprotein, apolipoprotein CIII, beta-2 microglobulin, cancer antigen 125, cancer antigen 19-9, eotaxin, FABP, factor VII, ferritin, IL-10, IL-12p70, IL-16, IL-18, IL-1ra, IL-3, MCP-1, MMP-3, myoglobin, SGOT, tissue factor, TIMP-1, TNF RII, TNF-alpha, VCAM-1, vWF, BDNK, complement 3, CD40 ligand, EGF, ENA-78, EN-RAGE, IGF-1, MDC, myeloperoxidase, RANTES, or thrombopoietin may be by bringing the level of at least one, at least two, at least three, at least five, at least six, at least seven, at least eight, at least nine, at least ten, at least twelve, at least fifteen, at least twenty, or at least 25 of these proteins to within at least 2%, at least 3%, at least 4%, at least 5%, at least 7%, at least 8%, at least 10%, at least 15%, at least 25%, at least 30%, at least 35%, at least 40%, at least 45%, at least 50%, at least 60%, at least 70%, at least 75%, at least 80%, or at least 90% levels of the protein in serum of a healthy subject. If the agent that binds to and modulates type I IFN or IFNα activity is a biologic agent, such as an antibody, the agent may neutralize levels of the serum proteins, e.g., adiponectin, alpha-fetoprotein, apolipoprotein CIII, beta-2 microglobulin, cancer antigen 125, cancer antigen 19-9, eotaxin, FABP, factor VII, ferritin, IL-10, IL-12p70, IL-16, IL-18, IL-1ra, IL-3, MCP-1, MMP-3, myoglobin, SGOT, tissue factor, TIMP-1, TNF RII, TNF-alpha, VCAM-1, vWF, BDNK, complement 3, CD40 ligand, EGF, ENA-78, EN-RAGE, IGF-1, MDC, myeloperoxidase, RANTES, or thrombopoietin, at doses of 0.3 to 30 mg/kg, 0.3 to 10 mg/kg, 0.3 to 3 mg/kg, 0.3 to 1 mg/kg, 1 to 30 mg/kg, 3 to 30 mg/kg, 5 to 30 mg/kg, 10 to 30 mg/kg, 1 to 10 mg/kg, 3 to 10 mg/kg, or 1 to 5 mg/kg.

The agent that binds to and modulates type I IFN or IFNα activity may further or alternatively reduce number or level of auto-antibodies that bind to any one, any at least 2, any at least 3, any at least 4, any at least 5, any at least 6, any at least 7, any at least 8, any at least 9, any at least 10, any at least 15, or any at least 20 of the following auto-antigens: (a) Myxovirus (influenza virus) resistance 1, interferon-inducible protein p′78; (b) surfeit 5, transcript variant c; (c) proteasome (posome, macropain) activator subunit 3 (PA28 gamma; Ki) transc; (d) retinoic acid receptor, alpha; (e) Heat shock 10 kDa protein 1 (chaperonin 10); (f) tropomyosin 3; (g) pleckstrin homology-like domain, family A, member 1; (h) cytoskeleton-associated protein 1; (i) Sjogren syndrome antigen A2 (60 kDa, ribonucleoprotein auto-antigen SS-A/Ro); (j) NADH dehydrogenase (ubiquinone) 1, alpha/beta subcomplex 1, 8 kDa; (k) NudE nuclear distribution gene E homolog 1 (A. nidulans); (l) MutL homolog 1, colon cancer, nonpolyposis type 2 (E. coli); (m) leucine rich repeat (in FLII) interacting protein 2; (n) tropomyosin 1 (alpha); (o) spastic paraplegia 20, spartin (Troyer syndrome); (p) preimplantation protein, transcript variant 1; (r) mitochondrial ribosomal protein L45; (s) Lin-28 homolog (C. elegans); (t) heat shock 90 kDa protein 1, alpha; (u) dom-3 homolog Z (C. elegans); (v) dynein, cytoplasmic, light intermediate polypeptide 2; (w) Ras-related C3 botulinum toxin substrate 1 (rho family, small GTP binding protein); (x) synovial sarcoma, X breakpoint 2, transcript variant 2; (y) moesin; (z) homer homolog (Drosophila), transcript variant 1; (aa) GCN5 general control of amino-acid synthesis 5-like 2 (yeast); (bb) eukaryotic translation elongation factor 1 gamma; (cc) eukaryotic translation elongation factor 1, delta; (dd) DNA-damage-inducible transcript 3; (ee) CCAAT/enhancer binding protein (C/EBP) gamma; and any other auto-antigen described in provisional application entitled “Auto-antibody markers of autoimmune disease” filed May 3, 2007; and any other auto-antigen described in provisional application entitled “Auto-antibody markers of autoimmune disease” filed Nov. 6, 2007 (for example, but not limited to, those described on Tables 2, 4, 5, and 9). Reduction in level of auto-antibody may be a reduction of at least 2%, at least 3%, at least 4%, at least 5%, at least 7%, at least 8%, at least 10%, at least 15%, at least 25%, at least 30%, at least 35%, at least 40%, at least 45%, at least 50%, at least 60%, at least 70%, at least 75%, at least 80%, or at least 90% in presence of any of the auto-antibodies. If the agent that binds to and modulates type I IFN or IFNα activity is a biologic agent, such as an antibody, the agent may reduce number or level or auto-antibodies at doses of 0.3 to 30 mg/kg, 0.3 to 10 mg/kg, 0.3 to 3 mg/kg, 0.3 to 1 mg/kg, 1 to 30 mg/kg, 3 to 30 mg/kg, 5 to 30 mg/kg, 10 to 30 mg/kg, 1 to 10 mg/kg, 3 to 10 mg/kg, or 1 to 5 mg/kg.

The agent that binds to and modulates type I IFN or IFNα activity may not neutralize expression of genes that are not included in an interferon-inducible signature or PD marker profile.

Samples may also be obtained from patients in the methods of the invention. Samples include any biological fluid or tissue, such as whole blood, saliva, urine, synovial fluid, bone marrow, cerebrospinal fluid, nasal secretions, sputum, amniotic fluid, bronchioalveolar lavage fluid, peripheral blood mononuclear cells, total white blood cells, lymph node cells, spleen cells, tonsil cells, or skin. The samples may be obtained by any means known in the art.

IFNα-inducible PD marker expression profiles may include up-regulated expression or activity of genes in cells exposed to elevated IFNα levels relative to baseline. Up-regulated expression or activity of genes includes an increase in expression of mRNA from a gene, an increase in expression of a protein encoded by a gene, or an increase in activity of a protein encoded by a gene. The expression or activity of the genes may be up-regulated as a direct or indirect response to IFNα.

The up-regulated expression or activity of any gene detected in a sample, by probes, or by probes in kits in an IFNα-inducible PD marker expression profile may be at least 1.2-fold, at least 1.25-fold, at least 1.3-fold, at least 1.4-fold, at least 1.5-fold, at least 2.0-fold, at least 2.25-fold, at least 2.5-fold, at least 2.75-fold, at least 3.0-fold, at least 3.5-fold, at least 4.0-fold, at least 4.5-fold, at least 5.0-fold, at least 6.0-fold, at least 7.0-fold, at least 8.0-fold, at least 9.0-fold, at least 10.0-fold, at least 15.0-fold, at least 20.0-fold, at least 25.0-fold, or at least 50.0-fold relative to baseline levels of control cells, e.g., cells of healthy volunteers or cells of control animals or cells not exposed to IFNα in culture. All of the genes in the IFNα-inducible PD marker expression profile may have up-regulated expression or activity at the same fold increase. Alternatively, the genes in the PD marker expression profile may have varying levels of up-regulated expression or activity.

The down-regulated expression or activity of any gene detected in a sample, by probes, or by probes in kits in an IFNα-inducible PD marker expression profile may be at least 5%, at least 10%, at least 15%, at least 20%, at least 25%, at least 30%, at least 35%, at least 40%, at least 45%, at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% relative to baseline levels of control cells, e.g., cells of healthy volunteers or cells of control animals or cells not exposed to IFNα in culture. All of the genes in the IFNα-inducible PD marker expression profile may have down-regulated expression or activity at the same fold decrease. Alternatively, the genes in the PD marker expression profile may have varying levels of down-regulated expression or activity.

The number of genes included in IFNα-inducible PD marker expression profile may be at least 2, at least 3, at least 4, at least 5, at least 10, at least 20, at least 25 at least 30, at least 50, at least 75, at least 100, at least 150, at least 200, at least 250, at least 300, at least 400, at least 500, at least 750, at least 1000, at least 1500, at least 2000, at least 2500, at least 5000, at least 10000, or at least 15000 genes. These genes may include those listed in Tables 19 and/or 20 and/or 21 and/or 22 and/or 23 and/or 24 and/or 26 and/or 28 and/or 30 and/or 31 and/or any of the genes identified in FIG. 72, 74, 75, or 77. The genes included in IFNα-inducible PD marker expression profile may be up-regulated genes, down-regulated genes, or a combination of up- and down-regulated genes.

The genes included in the IFNα-inducible PD marker expression profile may be the genes provided in Tables 19 and/or 20 and/or 21 and/or 22 and/or 23 and/or 24 and/or 26 and/or 28 and/or 30 and/or 31 and/or any of the genes identified in FIG. 72, 74, 75, or 77. The genes included in the IFNα-inducible PD marker expression profile may consist of or comprise at least 10%, at least 20%, at least 25%, at least 30%, at least 40%, at least 50%, at least 60%, at least 75%, at least 80%, at least 85% at least 90%, at least 95%, or at least 100% of the genes provided in Tables 19 and/or 20 and/or 21 and/or 22 and/or 23 and/or 24 and/or 26 and/or 28 and/or 30 and/or 31 and/or any of the genes identified in FIG. 72, 74, 75, or 77.

The IFNα-inducible PD markers in an expression profile may include any at least 5 genes such as, for example: MX1, LLY6E, IFI27, OAS1, IFIT1; or MX1, LLY6E, IFI27, OAS1, IFI6; or MX1, LLY6E, IFI27, OAS1, IFI44L; or MX1, LLY6E, IFI27, OAS1, ISG15; or MX1, LLY6E, IFI27, OAS1, LAMP3; or MX1, LLY6E, IFI27, OAS1, OASL; or MX1, LLY6E, IFI27, OAS1, RSAD2; or MX1, LLY6E, IFI27, OAS1, IFI44; or MX1, LLY6E, IFI27, OAS1, IFIT2; or MX1, LLY6E, IFI27, OAS1, OAS3; or MX1, LLY6E, IFI27, OAS1, USP18; or MX1, LLY6E, IFI27, OAS1, SIGLEC1; or MX1, LLY6E, IFI27, OAS1, HERC5; or MX1, LLY6E, IFI27, OAS1, DNAPTP6; or MX1, LLY6E, IFI27, OAS1, LOC129607; or MX1, LLY6E, IFI27, OAS1, EPSTI1; or MX1, LLY6E, IFI27, OAS1, BIRC4BP; or MX1, LLY6E, IFI27, OAS1, SIGLEC1; or MX1, LLY6E, IFI27, OAS1, gene detected by probe 229450_at; or MX1, LLY6E, IFI27, OAS1, gene detected by probe 235276_at; or LLY6E, IFI27, OAS1, IFIT1, IFI6; or LLY6E, IFI27, OAS1, IFIT1, IFI44L; or LLY6E, IFI27, OAS1, IFIT1, ISG15; or LLY6E, IFI27, OAS1, IFIT1, LAMP3; or LLY6E, IFI27, OAS1, IFIT1, OASL; or LLY6E, IFI27, OAS1, IFIT1, RSAD2; or LLY6E, IFI27, OAS1, IFIT1, IFI44; or LLY6E, IFI27, OAS1, IFIT1, IFIT2; or LLY6E, IFI27, OAS1, IFIT1, OAS3; or LLY6E, IFI27, OAS1, IFIT1, USP18; or LLY6E, IFI27, OAS1, IFIT1, SIGLEC1; or LLY6E, IFI27, OAS1, IFIT1, HERC5; or LLY6E, IFI27, OAS1, IFIT1, DNAPTP6; or LLY6E, IFI27, OAS1, IFIT1, LOC129607; or LLY6E, IFI27, OAS1, IFIT1, EPSTI1; or LLY6E, IFI27, OAS1, IFIT1, BIRC4BP; or LLY6E, IFI27, OAS1, IFIT1, SIGLEC1; or LLY6E, IFI27, OAS1, IFIT1, gene detected by probe 229450_at; or LLY6E, IFI27, OAS1, IFIT1, gene detected by probe 235276_at; or IFI27, OAS1, IFIT1, IFI6, IFI44L, ISG15; or IFI27, OAS1, IFIT1, IFI6, LAMP3; or IFI27, OAS1, IFIT1, IFI6, OASL; or IFI27, OAS1, IFIT1, IFI6, RSAD2; or IFI27, OAS1, IFIT1, IFI6, IFI44; or IFI27, OAS1, IFIT1, IFI6, IFIT2; or IFI27, OAS1, IFIT1, IFI6, OAS3; or IFI27, OAS1, IFIT1, IFI6, USP18; or IFI27, OAS1, IFIT1, IFI6, SIGLEC1; or IFI27, OAS1, IFIT1, IFI6, HERC5; or IFI27, OAS1, IFIT1, IFI6, DNAPTP6; or IFI27, OAS1, IFIT1, IFI6, LOC129607; or IFI27, OAS1, IFIT1, IFI6, EPSTI1; or IFI27, OAS1, IFIT1, IFI6, BIRC4BP; or IFI27, OAS1, IFIT1, IFI6, SIGLEC1; or IFI27, OAS1, IFIT1, IFI6, gene detected by probe 229450_at; or IFI27, OAS1, IFIT1, IFI6, gene detected by probe 235276_at; or OAS1, IFIT1, IFI6, IFI44L, ISG15; or OAS1, IFIT1, IFI6, IFI44L, LAMP3; or OAS1, IFIT1, IFI6, IFI44L, OASL; or OAS1, IFIT1, IFI6, IFI44L, RSAD2; or OAS1, IFIT1, IFI6, IFI44L, IFI44; or OAS1, IFIT1, IFI6, IFI44L, IFIT2; or OAS1, IFIT1, IFI6, IFI44L, OAS3; or OAS1, IFIT1, IFI6, IFI44L, USP18; or OAS1, IFIT1, IFI6, IFI44L, SIGLEC1; or OAS1, IFIT1, IFI6, IFI44L, HERC5; or OAS1, IFIT1, IFI6, IFI44L, DNAPTP6; or OAS1, IFIT1, IFI6, IFI44L, LOC129607; or OAS1, IFIT1, IFI6, IFI44L, EPSTI1; or OAS1, IFIT1, IFI6, IFI44L, BIRC4BP; or OAS1, IFIT1, IFI6, IFI44L, SIGLEC1; or OAS1, IFIT1, IFI6, IFI44L, gene detected by probe 229450_at; or OAS1, IFIT1, IFI6, IFI44L, gene detected by probe 235276_at; or IFIT1, IFI6, IFI44L, ISG15, LAMP3; or IFIT1, IFI6, IFI44L, ISG15, OASL; or IFIT1, IFI6, IFI44L, ISG15, RSAD2; or IFIT1, IFI6, IFI44L, ISG15, IFI44; or IFIT1, IFI6, IFI44L, ISG15, IFIT2 or IFIT1, IFI6, IFI44L, ISG15, OAS3; or IFIT1, IFI6, IFI44L, ISG15, USP18; or IFIT1, IFI6, IFI44L, ISG15, SIGLEC1; or IFIT1, IFI6, IFI44L, ISG15, HERC5; or IFIT1, IFI6, IFI44L, ISG15, DNAPTP6; or IFIT1, IFI6, IFI44L, ISG15, LOC129607; or IFIT1, IFI6, IFI44L, ISG15, EPSTI1; or IFIT1, IFI6, IFI44L, ISG15, BIRC4BP; or IFIT1, IFI6, IFI44L, ISG15, gene detected by probe 229450_at; or IFIT1, IFI6, IFI44L, ISG15, gene detected by probe 235276_at; or IFI6, IFI44L, ISG15, LAMP3, HERC5; or IFI6, IFI44L, ISG15, LAMP3, DNAPTP6; or IFI6, IFI44L, ISG15, LAMP3, LOC129607; or IFI6, IFI44L, ISG15, LAMP3, EPSTI1; or IFI6, IFI44L, ISG15, LAMP3, BIRC4BP; or IFI6, IFI44L, ISG15, LAMP3, gene detected by probe 229450_at; or IFI6, IFI44L, ISG15, LAMP3, gene detected by probe 235276_at; or IFI6, IFI44L, ISG15, LAMP3, SIGLEC1; or IFI6, IFI44L, ISG15, LAMP3, USP18; or IFI6, IFI44L, ISG15, LAMP3, OAS3; or IFI6, IFI44L, ISG15, LAMP3, IFIT2; or IFI6, IFI44L, ISG15, LAMP3, IFI44; or IFI6, IFI44L, ISG15, LAMP3, RSAD2; or IFI6, IFI44L, ISG15, LAMP3, OASL; or IFI44L, ISG15, LAMP3, OASL, RSAD2; or IFI44L, ISG15, LAMP3, OASL, IFI44; or IFI44L, ISG15, LAMP3, OASL, IFIT2; or IFI44L, ISG15, LAMP3, OASL, OAS3; or IFI44L, ISG15, LAMP3, OASL, USP18; or IFI44L, ISG15, LAMP3, OASL, SIGLEC1; or IFI44L, ISG15, LAMP3, OASL, HERC5; or IFI44L, ISG15, LAMP3, OASL, DNAPTP6; or IFI44L, ISG15, LAMP3, OASL, LOC129607; or IFI44L, ISG15, LAMP3, OASL, EPSTI1; or IFI44L, ISG15, LAMP3, OASL, BIRC4BP; or IFI44L, ISG15, LAMP3, OASL, gene detected by probe 229450_at; or IFI44L, ISG15, LAMP3, OASL, gene detected by probe 235276_at; or ISG15, LAMP3, OASL, RSAD2, IFI44; or ISG15, LAMP3, OASL, RSAD2, IFIT2; or ISG15, LAMP3, OASL, RSAD2, OAS3; or ISG15, LAMP3, OASL, RSAD2, USP18; or ISG15, LAMP3, OASL, RSAD2, SIGLEC1; or ISG15, LAMP3, OASL, RSAD2, HERC5; or ISG15, LAMP3, OASL, RSAD2, DNAPTP6; or ISG15, LAMP3, OASL, RSAD2, LOC129607; or ISG15, LAMP3, OASL, RSAD2, EPSTI1; or ISG15, LAMP3, OASL, RSAD2, BIRC4BP; or ISG15, LAMP3, OASL, RSAD2, gene detected by probe 229450_at; or ISG15, LAMP3, OASL, RSAD2, gene detected by probe 235276_at; or LAMP3, OASL, RSAD2, IFI44, IFIT2; or LAMP3, OASL, RSAD2, IFI44, OAS3; or LAMP3, OASL, RSAD2, IFI44, USP18; or LAMP3, OASL, RSAD2, IFI44, SIGLEC1; or LAMP3, OASL, RSAD2, IFI44, HERC5; or LAMP3, OASL, RSAD2, IFI44, DNAPTP6; or LAMP3, OASL, RSAD2, IFI44, LOC129607; or LAMP3, OASL, RSAD2, IFI44, EPSTI1; or LAMP3, OASL, RSAD2, IFI44, BIRC4BP; or LAMP3, OASL, RSAD2, IFI44, gene detected by probe 229450_at; or LAMP3, OASL, RSAD2, IFI44, gene detected by probe 235276_at; or OASL, RSAD2, IFI44, IFIT2, OAS3; or OASL, RSAD2, IFI44, IFIT2, USP18; or OASL, RSAD2, IFI44, IFIT2, SIGLEC1; or OASL, RSAD2, IFI44, IFIT2, HERC5; or OASL, RSAD2, IFI44, IFIT2, DNAPTP6; or OASL, RSAD2, IFI44, IFIT2, LOC129607; or OASL, RSAD2, IFI44, IFIT2, EPSTI1; or OASL, RSAD2, IFI44, IFIT2, BIRC4BP; or OASL, RSAD2, IFI44, IFIT2, gene detected by probe 229450_at; or OASL, RSAD2, IFI44, IFIT2, gene detected by probe 235276_at; or RSAD2, IFI44, IFIT2, OAS3, USP18; or RSAD2, IFI44, IFIT2, OAS3, SIGLEC1; or RSAD2, IFI44, IFIT2, OAS3, HERC5; or RSAD2, IFI44, IFIT2, OAS3, DNAPTP6; or RSAD2, IFI44, IFIT2, OAS3, LOC129607; or RSAD2, IFI44, IFIT2, OAS3, EPSTI1; or RSAD2, IFI44, IFIT2, OAS3, BIRC4BP; or RSAD2, IFI44, IFIT2, OAS3, gene detected by probe 229450_at; or RSAD2, IFI44, IFIT2, OAS3, gene detected by probe 235276_at; or IFI44, IFIT2, OAS3, USP18, SIGLEC1; or IFI44, IFIT2, OAS3, USP18, HERC5; or IFI44, IFIT2, OAS3, USP18, DNAPTP6; or IFI44, IFIT2, OAS3, USP18, LOC129607; or IFI44, IFIT2, OAS3, USP18, EPSTI1; or IFI44, IFIT2, OAS3, USP18, BIRC4BP; or IFI44, IFIT2, OAS3, USP18, gene detected by probe 229450_at; or IFI44, 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, SIGLEC1, LOC129607; or IFIT2, OAS3, USP18, SIGLEC1, EPSTI1; or IFIT2, OAS3, USP18, SIGLEC1, BIRC4BP; or IFIT2, OAS3, USP18, SIGLEC1, gene detected by probe 229450_at; 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, EPSTI1; or OAS3, USP18, SIGLEC1, HERC5, 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, EPSTI1; or USP18, SIGLEC1, HERC5, DNAPTP6, BIRC4BP; or USP18, SIGLEC1, HERC5, DNAPTP6, gene detected by probe 229450_at; or USP18, SIGLEC1, HERC5, DNAPTP6, gene detected by probe 235276_at; or SIGLEC1, HERC5, DNAPTP6, LOC129607, EPSTI1; 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, LOC129607, EPSTI1, BIRC4BP; or HERC5, DNAPTP6, LOC129607, 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 detected by probe 235276_at. The IFNα-inducible PD markers in such an expression profile may further include at least one or more gene listed in Tables 19 and/or 20 and/or 21 and/or 22 and/or 23 and/or 24 and/or 26 and/or 28 and/or 30.

The IFNα-inducible PD markers in an expression profile may include any at least 6 genes such as, for example: MX1, LLY6E, IFI27, OAS1, IFIT1, IFI6; or MX1, LLY6E, IFI27, OAS1, IFIT1, IFI44L; or MX1, LLY6E, IFI27, OAS1, IFIT1, ISG15; or MX1, LLY6E, IFI27, OAS1, IFIT1, LAMP3; or MX1, LLY6E, IFI27, OAS1, IFIT1, OASL; or MX1, LLY6E, IFI27, OAS1, IFIT1, RSAD2; or MX1, LLY6E, IFI27, OAS1, IFIT1, IFI44; or MX1, LLY6E, IFI27, OAS1, IFIT1, IFIT2; or MX1, LLY6E, IFI27, OAS1, IFIT1, OAS3; or MX1, LLY6E, IFI27, OAS1, IFIT1, USP18; or MX1, LLY6E, IFI27, OAS1, IFIT1, SIGLEC1; or MX1, LLY6E, IFI27, OAS1, IFIT1, HERC5; or MX1, LLY6E, IFI27, OAS1, IFIT1, DNAPTP6; or MX1, LLY6E, IFI27, OAS1, IFIT1, LOC129607; or MX1, LLY6E, IFI27, OAS1, IFIT1, EPSTI1; or MX1, LLY6E, IFI27, OAS1, IFIT1, BIRC4BP; or MX1, LLY6E, IFI27, OAS1, IFIT1, gene detected by probe 229450_at; or MX1, LLY6E, IFI27, OAS1, IFIT1, gene detected by probe 235276_at; or LLY6E, IFI27, OAS1, IFIT1, IFI6, IFI44L; or LLY6E, IFI27, OAS1, IFIT1, IFI6, ISG15; or LLY6E, IFI27, OAS1, IFIT1, IFI6, LAMP3; or LLY6E, IFI27, OAS1, IFIT1, IFI6, OASL; or LLY6E, IFI27, OAS1, IFIT1, IFI6, RSAD2; or LLY6E, IFI27, OAS1, IFIT1, IFI6, IFI44; or LLY6E, IFI27, OAS1, IFIT1, IFI6, IFIT2; or LLY6E, IFI27, OAS1, IFIT1, IFI6, OAS3; or LLY6E, IFI27, OAS1, IFIT1, IFI6, USP18; or LLY6E, IFI27, OAS1, IFIT1, IFI6, SIGLEC1; or LLY6E, IFI27, OAS1, IFIT1, IFI6, HERC5; or LLY6E, IFI27, OAS1, IFIT1, IFI6, DNAPTP6; or LLY6E, IFI27, OAS1, IFIT1, IFI6, LOC129607; or LLY6E, IFI27, OAS1, IFIT1, IFI6, EPSTI1; or LLY6E, IFI27, OAS1, IFIT1, IFI6, BIRC4BP; or LLY6E, IFI27, OAS1, IFIT1, IFI6, gene detected by probe 229450_at; or LLY6E, IFI27, OAS1, IFIT1, IFI6, gene detected by probe 235276_at; or IFI27, OAS1, IFIT1, IFI6, IFI44L, ISG15; or IFI27, OAS1, IFIT1, IFI6, IFI44L, LAMP3; or IFI27, OAS1, IFIT1, IFI6, IFI44L, OASL; or IFI27, OAS1, IFIT1, IFI6, IFI44L, RSAD2; or IFI27, OAS1, IFIT1, IFI6, IFI44L, IFI44; or IFI27, OAS1, IFIT1, IFI6, IFI44L, IFIT2; or IFI27, OAS1, IFIT1, IFI6, IFI44L, OAS3; or IFI27, OAS1, IFIT1, IFI6, IFI44L, USP18; or IFI27, OAS1, IFIT1, IFI6, IFI44L, SIGLEC1; or IFI27, OAS1, IFIT1, IFI6, IFI44L, HERC5; or IFI27, OAS1, IFIT1, IFI6, IFI44L, DNAPTP6; or IFI27, OAS1, IFIT1, IFI6, IFI44L, LOC129607; or IFI27, OAS1, IFIT1, IFI6, IFI44L, EPSTI1; or IFI27, OAS1, IFIT1, IFI6, IFI44L, BIRC4BP; or IFI27, OAS1, IFIT1, IFI6, IFI44L, gene detected by probe 229450_at; or IFI27, OAS1, IFIT1, IFI6, IFI44L, gene detected by probe 235276_at; or OAS1, IFIT1, IFI6, IFI44L, ISG15, LAMP3; or OAS1, IFIT1, IFI6, IFI44L, ISG15, OASL; or OAS1, IFIT1, IFI6, IFI44L, ISG15, RSAD2; or OAS1, IFIT1, IFI6, IFI44L, ISG15, IFI44; or OAS1, IFIT1, IFI6, IFI44L, ISG15, IFIT2; or OAS1, IFIT1, IFI6, IFI44L, ISG15, OAS3; or OAS1, IFIT1, IFI6, IFI44L, ISG15, USP18; or OAS1, IFIT1, IFI6, IFI44L, ISG15, SIGLEC1; or OAS1, IFIT1, IFI6, IFI44L, ISG15, HERC5; or OAS1, IFIT1, IFI6, IFI44L, ISG15, DNAPTP6; or OAS1, IFIT1, IFI6, IFI44L, ISG15, LOC129607; or OAS1, IFIT1, IFI6, IFI44L, ISG15, EPSTI1; or OAS1, IFIT1, IFI6, IFI44L, ISG15, BIRC4BP; or OAS1, IFIT1, IFI6, IFI44L, ISG15, gene detected by probe 229450_at; or OAS1, IFIT1, IFI6, IFI44L, ISG15, gene detected by probe 235276_at; or IFIT1, IFI6, IFI44L, ISG15, LAMP3, OASL; or IFIT1, IFI6, IFI44L, ISG15, LAMP3, RSAD2; or IFIT1, IFI6, IFI44L, ISG15, LAMP3, IFI44; or IFIT1, IFI6, IFI44L, ISG15, LAMP3, IFIT2; or IFIT1, IFI6, IFI44L, ISG15, LAMP3, OAS3; or IFIT1, IFI6, IFI44L, ISG15, LAMP3, USP18; or IFIT1, IFI6, IFI44L, ISG15, LAMP3, SIGLEC1; or IFIT1, IFI6, IFI44L, ISG15, LAMP3, HERC5; or IFIT1, IFI6, IFI44L, ISG15, LAMP3, DNAPTP6; or IFIT1, IFI6, IFI44L, ISG15, LAMP3, LOC129607; or IFIT1, IFI6, IFI44L, ISG15, LAMP3, EPSTI1; or IFIT1, IFI6, IFI44L, ISG15, LAMP3, BIRC4BP; or IFIT1, IFI6, IFI44L, ISG15, LAMP3, gene detected by probe 229450_at; or IFIT1, IFI6, IFI44L, ISG15, LAMP3, gene detected by probe 235276_at; or IFI6, IFI44L, ISG15, LAMP3, OASL, RSAD2; or IFI6, IFI44L, ISG15, LAMP3, OASL, IFI44; or IFI6, IFI44L, ISG15, LAMP3, OASL, IFIT2; or IFI6, IFI44L, ISG15, LAMP3, OASL, OAS3; or IFI6, IFI44L, ISG15, LAMP3, OASL, USP18; or IFI6, IFI44L, ISG15, LAMP3, OASL, SIGLEC1; or IFI6, IFI44L, ISG15, LAMP3, OASL, HERC5; or IFI6, IFI44L, ISG15, LAMP3, OASL, DNAPTP6; or IFI6, IFI44L, ISG15, LAMP3, OASL, LOC129607; or IFI6, IFI44L, ISG15, LAMP3, OASL, EPSTI1; or IFI6, IFI44L, ISG15, LAMP3, OASL, BIRC4BP; or IFI6, IFI44L, ISG15, LAMP3, OASL, gene detected by probe 229450_at; or IFI6, IFI44L, ISG15, LAMP3, OASL, gene detected by probe 235276_at; or IFI44L, ISG15, LAMP3, OASL, RSAD2, IFI44; or IFI44L, ISG15, LAMP3, OASL, RSAD2, IFIT2; or IFI44L, ISG15, LAMP3, OASL, RSAD2, OAS3; or IFI44L, ISG15, LAMP3, OASL, RSAD2, USP18; or IFI44L, ISG15, LAMP3, OASL, RSAD2, SIGLEC1; or IFI44L, ISG15, LAMP3, OASL, RSAD2, HERC5; or IFI44L, ISG15, LAMP3, OASL, RSAD2, DNAPTP6; or IFI44L, ISG15, LAMP3, OASL, RSAD2, LOC129607; or IFI44L, ISG15, LAMP3, OASL, RSAD2, EPSTI1; or IFI44L, ISG15, LAMP3, OASL, RSAD2, BIRC4BP; or IFI44L, ISG15, LAMP3, OASL, RSAD2, gene detected by probe 229450_at; or IFI44L, ISG15, LAMP3, OASL, RSAD2, gene detected by probe 235276_at; or ISG15, LAMP3, OASL, RSAD2, IFI44, IFIT2; or ISG15, LAMP3, OASL, RSAD2, IFI44, OAS3; or ISG15, LAMP3, OASL, RSAD2, IFI44, USP18; or ISG15, LAMP3, OASL, RSAD2, IFI44, SIGLEC1; or ISG15, LAMP3, OASL, RSAD2, IFI44, HERC5; or ISG15, LAMP3, OASL, RSAD2, IFI44, DNAPTP6; or ISG15, LAMP3, OASL, RSAD2, IFI44, LOC129607; or ISG15, LAMP3, OASL, RSAD2, IFI44, EPSTI1; or ISG15, LAMP3, OASL, RSAD2, IFI44, BIRC4BP; or ISG15, LAMP3, OASL, RSAD2, IFI44, gene detected by probe 229450_at; or ISG15, LAMP3, OASL, RSAD2, IFI44, gene detected by probe 235276_at; or LAMP3, OASL, RSAD2, IFI44, IFIT2, OAS3; or LAMP3, OASL, RSAD2, IFI44, IFIT2, USP18; or LAMP3, OASL, RSAD2, IFI44, IFIT2, SIGLEC1; or LAMP3, OASL, RSAD2, IFI44, IFIT2, HERC5; or LAMP3, OASL, RSAD2, IFI44, IFIT2, DNAPTP6; or LAMP3, OASL, RSAD2, IFI44, IFIT2, LOC129607; or LAMP3, OASL, RSAD2, IFI44, IFIT2, EPSTI1; or LAMP3, OASL, RSAD2, IFI44, IFIT2, BIRC4BP; or LAMP3, OASL, RSAD2, IFI44, IFIT2, gene detected by probe 229450_at; or LAMP3, OASL, RSAD2, IFI44, IFIT2, gene detected by probe 235276_at; or OASL, RSAD2, IFI44, IFIT2, OAS3, USP18; or OASL, RSAD2, IFI44, IFIT2, OAS3, SIGLEC1; or OASL, RSAD2, IFI44, IFIT2, OAS3, HERC5; or OASL, RSAD2, IFI44, IFIT2, OAS3, DNAPTP6; or OASL, RSAD2, IFI44, IFIT2, OAS3, LOC129607; or OASL, RSAD2, IFI44, IFIT2, OAS3, EPSTI1; or OASL, RSAD2, IFI44, IFIT2, OAS3, BIRC4BP; or OASL, RSAD2, IFI44, IFIT2, OAS3, gene detected by probe 229450_at; or OASL, RSAD2, IFI44, IFIT2, OAS3, gene detected by probe 235276_at; or RSAD2, IFI44, IFIT2, OAS3, USP18, SIGLEC1; or RSAD2, IFI44, IFIT2, OAS3, USP18, HERC5; or RSAD2, IFI44, IFIT2, OAS3, USP18, DNAPTP6; or RSAD2, IFI44, IFIT2, OAS3, USP18, LOC129607; or RSAD2, IFI44, IFIT2, OAS3, USP18, EPSTI1; or RSAD2, IFI44, IFIT2, OAS3, USP18, BIRC4BP; or RSAD2, IFI44, IFIT2, OAS3, USP18, gene detected by probe 229450_at; or RSAD2, IFI44, IFIT2, OAS3, USP18, gene detected by probe 235276_at; or IFI44, IFIT2, OAS3, USP18, SIGLEC1, HERC5; or IFI44, IFIT2, OAS3, USP18, SIGLEC1, DNAPTP6; or IFI44, IFIT2, OAS3, USP18, SIGLEC1, LOC129607; or IFI44, IFIT2, OAS3, USP18, SIGLEC1, EPSTI1; or IFI44, IFIT2, OAS3, USP18, SIGLEC1, BIRC4BP; or IFI44, IFIT2, OAS3, USP18, SIGLEC1, gene detected by probe 229450_at; or IFI44, 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, EPSTI1; or IFIT2, OAS3, USP18, SIGLEC1, HERC5, BIRC4BP; or IFIT2, OAS3, USP18, SIGLEC1, HERC5, gene detected by 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, EPSTI1; 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 235276_at; or USP18, SIGLEC1, HERC5, DNAPTP6, LOC129607, EPSTI1; or USP18, SIGLEC1, HERC5, DNAPTP6, LOC129607, BIRC4BP; or USP18, SIGLEC1, HERC5, DNAPTP6, LOC129607, gene detected by probe 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, 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 IFNα-inducible PD markers in such an expression profile may further include at least one or more gene listed in Tables 19 and/or 20 and/or 21 and/or 22 and/or 23 and/or 24 and/or 26 and/or 28 and/or 30.

The IFNα-inducible PD markers in an expression profile may include any at least 7 genes such as, for example: MX1, LLY6E, IFI27, OAS1, IFIT1, IFI6, IFI44L; or MX1, LLY6E, IFI27, OAS1, IFIT1, IFI6, ISG15; or MX1, LLY6E, IFI27, OAS1, IFIT1, IFI6, LAMP3; or MX1, LLY6E, IFI27, OAS1, IFIT1, IFI6, OASL; or MX1, LLY6E, IFI27, OAS1, IFIT1, IFI6, RSAD2; or MX1, LLY6E, IFI27, OAS1, IFIT1, IFI6, IFI44; or MX1, LLY6E, IFI27, OAS1, IFIT1, IFI6, IFIT2; or MX1, LLY6E, IFI27, OAS1, IFIT1, IFI6, OAS3; or MX1, LLY6E, IFI27, OAS1, IFIT1, IFI6, USP18; or MX1, LLY6E, IFI27, OAS1, IFIT1, IFI6, SIGLEC1; or MX1, LLY6E, IFI27, OAS1, IFIT1, IFI6, HERC5; or MX1, LLY6E, IFI27, OAS1, IFIT1, IFI6, DNAPTP6; or MX1, LLY6E, IFI27, OAS1, IFIT1, IFI6, LOC129607; or MX1, LLY6E, IFI27, OAS1, IFIT1, IFI6, EPSTI1; or MX1, LLY6E, IFI27, OAS1, IFIT1, IFI6, BIRC4BP; or MX1, LLY6E, IFI27, OAS1, IFIT1, IFI6, gene detected by probe 229450_at; or MX1, LLY6E, IFI27, OAS1, IFIT1, IFI6, gene detected by probe 235276_at; or LLY6E, IFI27, OAS1, IFIT1, IFI6, IFI44L, ISG15; or LLY6E, IFI27, OAS1, IFIT1, IFI6, IFI44L, LAMP3; or LLY6E, IFI27, OAS1, IFIT1, IFI6, IFI44L, OASL; or LLY6E, IFI27, OAS1, IFIT1, IFI6, IFI44L, RSAD2; or LLY6E, IFI27, OAS1, IFIT1, IFI6, IFI44L, IFI44; or LLY6E, IFI27, OAS1, IFIT1, IFI6, IFI44L, IFIT2; or LLY6E, IFI27, OAS1, IFIT1, IFI6, IFI44L, OAS3; or LLY6E, IFI27, OAS1, IFIT1, IFI6, IFI44L, USP18; or LLY6E, IFI27, OAS1, IFIT1, IFI6, IFI44L, SIGLEC1; or LLY6E, IFI27, OAS1, IFIT1, IFI6, IFI44L, HERC5; or LLY6E, IFI27, OAS1, IFIT1, IFI6, IFI44L, DNAPTP6; or LLY6E, IFI27, OAS1, IFIT1, IFI6, IFI44L, LOC129607; or LLY6E, IFI27, OAS1, IFIT1, IFI6, IFI44L, EPSTI1; or LLY6E, IFI27, OAS1, IFIT1, IFI6, IFI44L, BIRC4BP; or LLY6E, IFI27, OAS1, IFIT1, IFI6, IFI44L, gene detected by probe 229450_at; or LLY6E, IFI27, OAS1, IFIT1, IFI6, IFI44L, gene detected by probe 235276_at; or IFI27, OAS1, IFIT1, IFI6, IFI44L, ISG15, LAMP3; or IFI27, OAS1, IFIT1, IFI6, IFI44L, ISG15, OASL; or IFI27, OAS1, IFIT1, IFI6, IFI44L, ISG15, RSAD2; or IFI27, OAS1, IFIT1, IFI6, IFI44L, ISG15, IFI44; or IFI27, OAS1, IFIT1, IFI6, IFI44L, ISG15, IFIT2; or IFI27, OAS1, IFIT1, IFI6, IFI44L, ISG15, OAS3; or IFI27, OAS1, IFIT1, IFI6, IFI44L, ISG15, USP18; or IFI27, OAS1, IFIT1, IFI6, IFI44L, ISG15, SIGLEC1; or IFI27, OAS1, IFIT1, IFI6, IFI44L, ISG15, HERC5; or IFI27, OAS1, IFIT1, IFI6, IFI44L, ISG15, DNAPTP6; or IFI27, OAS1, IFIT1, IFI6, IFI44L, ISG15, LOC129607; or IFI27, OAS1, IFIT1, IFI6, IFI44L, ISG15, EPSTI1; or IFI27, OAS1, IFIT1, IFI6, IFI44L, ISG15, BIRC4BP; or IFI27, OAS1, IFIT1, IFI6, IFI44L, ISG15, gene detected by probe 229450_at; or IFI27, OAS1, IFIT1, IFI6, IFI44L, ISG15, gene detected by probe 235276_at; or OAS1, IFIT1, IFI6, IFI44L, ISG15, LAMP3, OASL; or OAS1, IFIT1, IFI6, IFI44L, ISG15, LAMP3, RSAD2; or OAS1, IFIT1, IFI6, IFI44L, ISG15, LAMP3, IFI44; or OAS1, IFIT1, IFI6, IFI44L, ISG15, LAMP3, IFIT2; or OAS1, IFIT1, IFI6, IFI44L, ISG15, LAMP3, OAS3; or OAS1, IFIT1, IFI6, IFI44L, ISG15, LAMP3, USP18; or OAS1, IFIT1, IFI6, IFI44L, ISG15, LAMP3, SIGLEC1; or OAS1, IFIT1, IFI6, IFI44L, ISG15, LAMP3, HERC5; or OAS1, IFIT1, IFI6, IFI44L, ISG15, LAMP3, DNAPTP6; or OAS1, IFIT1, IFI6, IFI44L, ISG15, LAMP3, LOC129607; or OAS1, IFIT1, IFI6, IFI44L, ISG15, LAMP3, EPSTI1; or OAS1, IFIT1, IFI6, IFI44L, ISG15, LAMP3, BIRC4BP; or OAS1, IFIT1, IFI6, IFI44L, ISG15, LAMP3, gene detected by probe 229450_at; or OAS1, IFIT1, IFI6, IFI44L, ISG15, LAMP3, gene detected by probe 235276_at; or IFIT1, IFI6, IFI44L, ISG15, LAMP3, OASL, RSAD2; or IFIT1, IFI6, IFI44L, ISG15, LAMP3, OASL, IFI44; or IFIT1, IFI6, IFI44L, ISG15, LAMP3, OASL, IFIT2; or IFIT1, IFI6, IFI44L, ISG15, LAMP3, OASL, OAS3; or IFIT1, IFI6, IFI44L, ISG15, LAMP3, OASL, USP18; or IFIT1, IFI6, IFI44L, ISG15, LAMP3, OASL, SIGLEC1; or IFIT1, IFI6, IFI44L, ISG15, LAMP3, OASL, HERC5; or IFIT1, IFI6, IFI44L, ISG15, LAMP3, OASL, DNAPTP6; or IFIT1, IFI6, IFI44L, ISG15, LAMP3, OASL, LOC129607; or IFIT1, IFI6, IFI44L, ISG15, LAMP3, OASL, EPSTI1; or IFIT1, IFI6, IFI44L, ISG15, LAMP3, OASL, BIRC4BP; or IFIT1, IFI6, IFI44L, ISG15, LAMP3, OASL, gene detected by probe 229450_at; or IFIT1, IFI6, IFI44L, ISG15, LAMP3, OASL, gene detected by probe 235276_at; or IFI6, IFI44L, ISG15, LAMP3, OASL, RSAD2, IFI44; or IFI6, IFI44L, ISG15, LAMP3, OASL, RSAD2, IFIT2; or IFI6, IFI44L, ISG15, LAMP3, OASL, RSAD2, OAS3; or IFI6, IFI44L, ISG15, LAMP3, OASL, RSAD2, USP18; or IFI6, IFI44L, ISG15, LAMP3, OASL, RSAD2, SIGLEC1; or IFI6, IFI44L, ISG15, LAMP3, OASL, RSAD2, HERC5; or IFI6, IFI44L, ISG15, LAMP3, OASL, RSAD2, DNAPTP6; or IFI6, IFI44L, ISG15, LAMP3, OASL, RSAD2, LOC129607; or IFI6, IFI44L, ISG15, LAMP3, OASL, RSAD2, EPSTI1; or IFI6, IFI44L, ISG15, LAMP3, OASL, RSAD2, BIRC4BP; or IFI6, IFI44L, ISG15, LAMP3, OASL, RSAD2, gene detected by probe 229450_at; or IFI6, IFI44L, ISG15, LAMP3, OASL, RSAD2, gene detected by probe 235276_at; or IFI44L, ISG15, LAMP3, OASL, RSAD2, IFI44, IFIT2; or IFI44L, ISG15, LAMP3, OASL, RSAD2, IFI44, OAS3; or IFI44L, ISG15, LAMP3, OASL, RSAD2, IFI44, USP18; or IFI44L, ISG15, LAMP3, OASL, RSAD2, IFI44, SIGLEC1; or IFI44L, ISG15, LAMP3, OASL, RSAD2, IFI44, HERC5; or IFI44L, ISG15, LAMP3, OASL, RSAD2, IFI44, DNAPTP6; or IFI44L, ISG15, LAMP3, OASL, RSAD2, IFI44, LOC129607; or IFI44L, ISG15, LAMP3, OASL, RSAD2, IFI44, EPSTI1; or IFI44L, ISG15, LAMP3, OASL, RSAD2, IFI44, BIRC4BP; or IFI44L, ISG15, LAMP3, OASL, RSAD2, IFI44, gene detected by probe 229450_at; or IFI44L, ISG15, LAMP3, OASL, RSAD2, IFI44, gene detected by probe 235276_at; or ISG15, LAMP3, OASL, RSAD2, IFI44, IFIT2, OAS3; or ISG15, LAMP3, OASL, RSAD2, IFI44, IFIT2, USP18; or ISG15, LAMP3, OASL, RSAD2, IFI44, IFIT2, SIGLEC1; or ISG15, LAMP3, OASL, RSAD2, IFI44, IFIT2, HERC5; or ISG15, LAMP3, OASL, RSAD2, IFI44, IFIT2, DNAPTP6; or ISG15, LAMP3, OASL, RSAD2, IFI44, IFIT2, LOC129607; or ISG15, LAMP3, OASL, RSAD2, IFI44, IFIT2, EPSTI1; or ISG15, LAMP3, OASL, RSAD2, IFI44, IFIT2, BIRC4BP; or ISG15, LAMP3, OASL, RSAD2, IFI44, IFIT2, gene detected by probe 229450_at; or ISG15, LAMP3, OASL, RSAD2, IFI44, IFIT2, gene detected by probe 235276_at; or LAMP3, OASL, RSAD2, IFI44, IFIT2, OAS3, USP18; or LAMP3, OASL, RSAD2, IFI44, IFIT2, OAS3, SIGLEC1; or LAMP3, OASL, RSAD2, IFI44, IFIT2, OAS3, HERC5; or LAMP3, OASL, RSAD2, IFI44, IFIT2, OAS3, DNAPTP6; or LAMP3, OASL, RSAD2, IFI44, IFIT2, OAS3, LOC129607; or LAMP3, OASL, RSAD2, IFI44, IFIT2, OAS3, EPSTI1; or LAMP3, OASL, RSAD2, IFI44, IFIT2, OAS3, BIRC4BP; or LAMP3, OASL, RSAD2, IFI44, IFIT2, OAS3, gene detected by probe 229450_at; or LAMP3, OASL, RSAD2, IFI44, IFIT2, OAS3, gene detected by probe 235276_at; or OASL, RSAD2, IFI44, IFIT2, OAS3, USP18, SIGLEC1; or OASL, RSAD2, IFI44, IFIT2, OAS3, USP18, HERC5; or OASL, RSAD2, IFI44, IFIT2, OAS3, USP18, DNAPTP6; or OASL, RSAD2, IFI44, IFIT2, OAS3, USP18, LOC129607; or OASL, RSAD2, IFI44, IFIT2, OAS3, USP18, EPSTI1; or OASL, RSAD2, IFI44, IFIT2, OAS3, USP18, BIRC4BP; or OASL, RSAD2, IFI44, IFIT2, OAS3, USP18, gene detected by probe 229450_at; or OASL, RSAD2, IFI44, IFIT2, OAS3, USP18, gene detected by probe 235276_at; or RSAD2, IFI44, IFIT2, OAS3, USP18, SIGLEC1, HERC5; or RSAD2, IFI44, IFIT2, OAS3, USP18, SIGLEC1, DNAPTP6; or RSAD2, IFI44, IFIT2, OAS3, USP18, SIGLEC1, LOC129607; or RSAD2, IFI44, IFIT2, OAS3, USP18, SIGLEC1, EPSTI1; or RSAD2, IFI44, IFIT2, OAS3, USP18, SIGLEC1, BIRC4BP; or RSAD2, IFI44, IFIT2, OAS3, USP18, SIGLEC1, gene detected by probe 229450_at; or RSAD2, IFI44, IFIT2, OAS3, USP18, SIGLEC1, gene detected by probe 235276_at; or IFI44, IFIT2, OAS3, USP18, SIGLEC1, HERC5, DNAPTP6; or IFI44, IFIT2, OAS3, USP18, SIGLEC1, HERC5, LOC129607; or IFI44, IFIT2, OAS3, USP18, SIGLEC1, HERC5, EPSTI1; or IFI44, IFIT2, OAS3, USP18, SIGLEC1, HERC5, BIRC4BP; or IFI44, IFIT2, OAS3, USP18, SIGLEC1, HERC5, gene detected by probe 229450_at; or IFI44, 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, EPSTI1; or IFIT2, OAS3, USP18, SIGLEC1, HERC5, DNAPTP6, BIRC4BP; or IFIT2, OAS3, USP18, SIGLEC1, HERC5, DNAPTP6, gene detected by probe 229450_at; or IFIT2, OAS3, USP18, SIGLEC1, HERC5, DNAPTP6, gene detected by probe 235276_at; or OAS3, USP18, SIGLEC1, HERC5, DNAPTP6, LOC129607, EPSTI1; or OAS3, USP18, SIGLEC1, HERC5, DNAPTP6, LOC129607, BIRC4BP; or OAS3, USP18, SIGLEC1, HERC5, DNAPTP6, LOC129607, gene detected by probe 229450_at; or OAS3, 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 235276_at; or SIGLEC1, HERC5, DNAPTP6, LOC129607, EPSTI1, BIRC4BP, gene detected by probe 229450_at; or SIGLEC1, HERC5, DNAPTP6, LOC129607, EPSTI1, BIRC4BP, gene detected by probe 235276_at; or HERC5, DNAPTP6, LOC129607, EPSTI1, BIRC4BP, gene detected by probe 229450_at, gene detected by probe 235276_at. The IFNα-inducible PD markers in such an expression profile may further include at least one or more gene listed in Tables 19 and/or 20 and/or 21 and/or 22 and/or 23 and/or 24 and/or 26 and/or 28 and/or 30.

The IFNα-inducible PD markers in an expression profile may include any at least 8 genes such as, for example: MX1, LLY6E, IFI27, OAS1, IFIT1, IFI6, IFI44L, ISG15; or MX1, LLY6E, IFI27, OAS1, IFIT1, IFI6, IFI44L, LAMP3; or MX1, LLY6E, IFI27, OAS1, IFIT1, IFI6, IFI44L, OASL; or MX1, LLY6E, IFI27, OAS1, IFIT1, IFI6, IFI44L, RSAD2; or MX1, LLY6E, IFI27, OAS1, IFIT1, IFI6, IFI44L, IFI44; or MX1, LLY6E, IFI27, OAS1, IFIT1, IFI6, IFI44L, IFIT2; or MX1, LLY6E, IFI27, OAS1, IFIT1, IFI6, IFI44L, OAS3; or MX1, LLY6E, IFI27, OAS1, IFIT1, IFI6, IFI44L, USP18; or MX1, LLY6E, IFI27, OAS1, IFIT1, IFI6, IFI44L, SIGLEC1; or MX1, LLY6E, IFI27, OAS1, IFIT1, IFI6, IFI44L, HERC5; or MX1, LLY6E, IFI27, OAS1, IFIT1, IFI6, IFI44L, DNAPTP6; or MX1, LLY6E, IFI27, OAS1, IFIT1, IFI6, IFI44L, LOC129607; or MX1, LLY6E, IFI27, OAS1, IFIT1, IFI6, IFI44L, EPSTI1; or MX1, LLY6E, IFI27, OAS1, IFIT1, IFI6, IFI44L, BIRC4BP; or MX1, LLY6E, IFI27, OAS1, IFIT1, IFI6, IFI44L, gene detected by probe 229450_at; or MX1, LLY6E, IFI27, OAS1, IFIT1, IFI6, IFI44L, gene detected by probe 235276_at; or LLY6E, IFI27, OAS1, IFIT1, IFI6, IFI44L, ISG15, LAMP3; or LLY6E, IFI27, OAS1, IFIT1, IFI6, IFI44L, ISG15, OASL; or LLY6E, IFI27, OAS1, IFIT1, IFI6, IFI44L, ISG15, RSAD2; or LLY6E, IFI27, OAS1, IFIT1, IFI6, IFI44L, ISG15, IFI44; or LLY6E, IFI27, OAS1, IFIT1, IFI6, IFI44L, ISG15, IFIT2; or LLY6E, IFI27, OAS1, IFIT1, IFI6, IFI44L, ISG15, OAS3; or LLY6E, IFI27, OAS1, IFIT1, IFI6, IFI44L, ISG15, USP18; or LLY6E, IFI27, OAS1, IFIT1, IFI6, IFI44L, ISG15, SIGLEC1; or LLY6E, IFI27, OAS1, IFIT1, IFI6, IFI44L, ISG15, HERC5; or LLY6E, IFI27, OAS1, IFIT1, IFI6, IFI44L, ISG15, DNAPTP6; or LLY6E, IFI27, OAS1, IFIT1, IFI6, IFI44L, ISG15, LOC129607; or LLY6E, IFI27, OAS1, IFIT1, IFI6, IFI44L, ISG15, EPSTI1; or LLY6E, IFI27, OAS1, IFIT1, IFI6, IFI44L, ISG15, BIRC4BP; or LLY6E, IFI27, OAS1, IFIT1, IFI6, IFI44L, ISG15, gene detected by probe 229450_at; or LLY6E, IFI27, OAS1, IFIT1, IFI6, IFI44L, ISG15, gene detected by probe 235276_at; orIFI27, OAS1, IFIT1, IFI6, IFI44L, ISG15, LAMP3, OASL; or IFI27, OAS1, IFIT1, IFI6, IFI44L, ISG15, LAMP3, RSAD2; or IFI27, OAS1, IFIT1, IFI6, IFI44L, ISG15, LAMP3, IFI44; or IFI27, OAS1, IFIT1, IFI6, IFI44L, ISG15, LAMP3, IFIT2; or IFI27, OAS1, IFIT1, IFI6, IFI44L, ISG15, LAMP3, OAS3; or IFI27, OAS1, IFIT1, IFI6, IFI44L, ISG15, LAMP3, USP18; or IFI27, OAS1, IFIT1, IFI6, IFI44L, ISG15, LAMP3, SIGLEC1; or IFI27, OAS1, IFIT1, IFI6, IFI44L, ISG15, LAMP3, HERC5; or IFI27, OAS1, IFIT1, IFI6, IFI44L, ISG15, LAMP3, DNAPTP6; or IFI27, OAS1, IFIT1, IFI6, IFI44L, ISG15, LAMP3, LOC129607; or IFI27, OAS1, IFIT1, IFI6, IFI44L, ISG15, LAMP3, EPSTI1; or IFI27, OAS1, IFIT1, IFI6, IFI44L, ISG15, LAMP3, gene detected by probe 229450_at; or IFI27, OAS1, IFIT1, IFI6, IFI44L, ISG15, LAMP3, BIRC4BP; or IFI27, OAS1, IFIT1, IFI6, IFI44L, ISG15, LAMP3, gene detected by probe 235276_at; or OAS1, IFIT1, IFI6, IFI44L, ISG15, LAMP3, OASL, RSAD2; or OAS1, IFIT1, IFI6, IFI44L, ISG15, LAMP3, OASL, IFI44; or OAS1, IFIT1, IFI6, IFI44L, ISG15, LAMP3, OASL, IFIT2; or OAS1, IFIT1, IFI6, IFI44L, ISG15, LAMP3, OASL, OAS3; or OAS1, IFIT1, IFI6, IFI44L, ISG15, LAMP3, OASL, USP18; or OAS1, IFIT1, IFI6, IFI44L, ISG15, LAMP3, OASL, SIGLEC1; or OAS1, IFIT1, IFI6, IFI44L, ISG15, LAMP3, OASL, HERC5; or OAS1, IFIT1, IFI6, IFI44L, ISG15, LAMP3, OASL, DNAPTP6; or OAS1, IFIT1, IFI6, IFI44L, ISG15, LAMP3, OASL, LOC129607; or OAS1, IFIT1, IFI6, IFI44L, ISG15, LAMP3, OASL, EPSTI1; or OAS1, IFIT1, IFI6, IFI44L, ISG15, LAMP3, OASL, BIRC4BP; or OAS1, IFIT1, IFI6, IFI44L, ISG15, LAMP3, OASL, gene detected by probe 229450_at; or OAS1, IFIT1, IFI6, IFI44L, ISG15, LAMP3, OASL, gene detected by probe 235276_at; or IFIT1, IFI6, IFI44L, ISG15, LAMP3, OASL, RSAD2, IFI44; or IFIT1, IFI6, IFI44L, ISG15, LAMP3, OASL, RSAD2, IFIT2; or IFIT1, IFI6, IFI44L, ISG15, LAMP3, OASL, RSAD2, OAS3; or IFIT1, IFI6, IFI44L, ISG15, LAMP3, OASL, RSAD2, USP18; or IFIT1, IFI6, IFI44L, ISG15, LAMP3, OASL, RSAD2, SIGLEC1; or IFIT1, IFI6, IFI44L, ISG15, LAMP3, OASL, RSAD2, HERC5; or IFIT1, IFI6, IFI44L, ISG15, LAMP3, OASL, RSAD2, DNAPTP6; or IFIT1, IFI6, IFI44L, ISG15, LAMP3, OASL, RSAD2, LOC129607; or IFIT1, IFI6, IFI44L, ISG15, LAMP3, OASL, RSAD2, EPSTI1; or IFIT1, IFI6, IFI44L, ISG15, LAMP3, OASL, RSAD2, BIRC4BP; or IFIT1, IFI6, IFI44L, ISG15, LAMP3, OASL, RSAD2, gene detected by probe 229450_at; or IFIT1, IFI6, IFI44L, ISG15, LAMP3, OASL, RSAD2, gene detected by probe 235276_at; or IFI6, IFI44L, ISG15, LAMP3, OASL, RSAD2, IFI44, IFIT2; or IFI6, IFI44L, ISG15, LAMP3, OASL, RSAD2, IFI44, OAS3; or IFI6, IFI44L, ISG15, LAMP3, OASL, RSAD2, IFI44, USP18; or IFI6, IFI44L, ISG15, LAMP3, OASL, RSAD2, IFI44, SIGLEC1; or IFI6, IFI44L, ISG15, LAMP3, OASL, RSAD2, IFI44, HERC5; or IFI6, IFI44L, ISG15, LAMP3, OASL, RSAD2, IFI44, DNAPTP6; or IFI6, IFI44L, ISG15, LAMP3, OASL, RSAD2, IFI44, LOC129607; or IFI6, IFI44L, ISG15, LAMP3, OASL, RSAD2, IFI44, EPSTI1; or IFI6, IFI44L, ISG15, LAMP3, OASL, RSAD2, IFI44, BIRC4BP; or IFI6, IFI44L, ISG15, LAMP3, OASL, RSAD2, IFI44, gene detected by probe 229450_at; or IFI6, IFI44L, ISG15, LAMP3, OASL, RSAD2, IFI44, gene detected by probe 235276_at; or IFI44L, ISG15, LAMP3, OASL, RSAD2, IFI44, IFIT2, OAS3; or IFI44L, ISG15, LAMP3, OASL, RSAD2, IFI44, IFIT2, USP18; or IFI44L, ISG15, LAMP3, OASL, RSAD2, IFI44, IFIT2, SIGLEC1; or IFI44L, ISG15, LAMP3, OASL, RSAD2, IFI44, IFIT2, HERC5; or IFI44L, ISG15, LAMP3, OASL, RSAD2, IFI44, IFIT2, DNAPTP6; or IFI44L, ISG15, LAMP3, OASL, RSAD2, IFI44, IFIT2, LOC129607; or IFI44L, ISG15, LAMP3, OASL, RSAD2, IFI44, IFIT2, EPSTI1; or IFI44L, ISG15, LAMP3, OASL, RSAD2, IFI44, IFIT2, BIRC4BP; or IFI44L, ISG15, LAMP3, OASL, RSAD2, IFI44, IFIT2, gene detected by probe 229450_at; or IFI44L, ISG15, LAMP3, OASL, RSAD2, IFI44, IFIT2, gene detected by probe 235276_at; or ISG15, LAMP3, OASL, RSAD2, IFI44, IFIT2, OAS3, USP18; or ISG15, LAMP3, OASL, RSAD2, IFI44, IFIT2, OAS3, SIGLEC1; or ISG15, LAMP3, OASL, RSAD2, IFI44, IFIT2, OAS3, HERC5; or ISG15, LAMP3, OASL, RSAD2, IFI44, IFIT2, OAS3, DNAPTP6; or ISG15, LAMP3, OASL, RSAD2, IFI44, IFIT2, OAS3, LOC129607; or ISG15, LAMP3, OASL, RSAD2, IFI44, IFIT2, OAS3, EPSTI1; or ISG15, LAMP3, OASL, RSAD2, IFI44, IFIT2, OAS3, BIRC4BP; or ISG15, LAMP3, OASL, RSAD2, IFI44, IFIT2, OAS3, gene detected by probe 229450_at; or ISG15, LAMP3, OASL, RSAD2, IFI44, IFIT2, OAS3, gene detected by probe 235276_at; or LAMP3, OASL, RSAD2, IFI44, IFIT2, OAS3, USP18, SIGLEC1; or LAMP3, OASL, RSAD2, IFI44, IFIT2, OAS3, USP18, HERC5; or LAMP3, OASL, RSAD2, IFI44, IFIT2, OAS3, USP18, DNAPTP6; or LAMP3, OASL, RSAD2, IFI44, IFIT2, OAS3, USP18, LOC129607; or LAMP3, OASL, RSAD2, IFI44, IFIT2, OAS3, USP18, EPSTI1; or LAMP3, OASL, RSAD2, IFI44, IFIT2, OAS3, USP18, BIRC4BP; or LAMP3, OASL, RSAD2, IFI44, IFIT2, OAS3, USP18, gene detected by probe 229450_at; or LAMP3, OASL, RSAD2, IFI44, IFIT2, OAS3, USP18, gene detected by probe 235276_at; or OASL, RSAD2, IFI44, IFIT2, OAS3, USP18, SIGLEC1, HERC5; or OASL, RSAD2, IFI44, IFIT2, OAS3, USP18, SIGLEC1, DNAPTP6; or OASL, RSAD2, IFI44, IFIT2, OAS3, USP18, SIGLEC1, LOC129607; or OASL, RSAD2, IFI44, IFIT2, OAS3, USP18, SIGLEC1, EPSTI1; or OASL, RSAD2, IFI44, IFIT2, OAS3, USP18, SIGLEC1, BIRC4BP; or OASL, RSAD2, IFI44, IFIT2, OAS3, USP18, SIGLEC1, gene detected by probe 229450_at; or OASL, RSAD2, IFI44, IFIT2, OAS3, USP18, SIGLEC1, gene detected by probe 235276_at; or RSAD2, IFI44, IFIT2, OAS3, USP18, SIGLEC1, HERC5, DNAPTP6; or RSAD2, IFI44, IFIT2, OAS3, USP18, SIGLEC1, HERC5, LOC129607; or RSAD2, IFI44, IFIT2, OAS3, USP18, SIGLEC1, HERC5, EPSTI1; or RSAD2, IFI44, IFIT2, OAS3, USP18, SIGLEC1, HERC5, gene detected by probe 229450_at; or RSAD2, IFI44, IFIT2, OAS3, USP18, SIGLEC1, HERC5, BIRC4BP; or RSAD2, IFI44, IFIT2, OAS3, USP18, SIGLEC1, HERC5, gene detected by probe 235276_at; or IFI44, IFIT2, OAS3, USP18, SIGLEC1, HERC5, DNAPTP6, LOC129607; or IFI44, IFIT2, OAS3, USP18, SIGLEC1, HERC5, DNAPTP6, EPSTI1; or IFI44, IFIT2, OAS3, USP18, SIGLEC1, HERC5, DNAPTP6, BIRC4BP; or IFI44, IFIT2, OAS3, USP18, SIGLEC1, HERC5, DNAPTP6, gene detected by probe 229450_at; or IFI44, IFIT2, OAS3, USP18, SIGLEC1, HERC5, DNAPTP6, gene detected by probe 235276_at; or IFIT2, OAS3, USP18, SIGLEC1, HERC5, DNAPTP6, LOC129607, EPSTI1; or IFIT2, OAS3, USP18, SIGLEC1, HERC5, DNAPTP6, LOC129607, BIRC4BP; or IFIT2, OAS3, USP18, SIGLEC1, HERC5, DNAPTP6, LOC129607, gene detected by probe 229450_at; or IFIT2, OAS3, USP18, SIGLEC1, HERC5, DNAPTP6, LOC129607, gene detected by probe 235276_at; or OAS3, USP18, SIGLEC1, HERC5, 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, 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 IFNα-inducible PD markers in such an expression profile may further include at least one or more gene listed in Tables 19 and/or 20 and/or 21 and/or 22 and/or 23 and/or 24 and/or 26 and/or 28 and/or 30.

The IFNα-inducible PD markers in an expression profile may include any at least 12 genes such as, for example: MX1, LLY6E, IFI27, OAS1, IFIT1, IFI6, IFI44L, ISG15, LAMP3, OASL, RSAD2, IFI44; or MX1, LLY6E, IFI27, OAS1, IFIT1, IFI6, IFI44L, ISG15, LAMP3, OASL, RSAD2, IFIT2; or MX1, LLY6E, IFI27, OAS1, IFIT1, IFI6, IFI44L, ISG15, LAMP3, OASL, RSAD2, OAS3; or MX1, LLY6E, IFI27, OAS1, IFIT1, IFI6, IFI44L, ISG15, LAMP3, OASL, RSAD2, USP18; or MX1, LLY6E, IFI27, OAS1, IFIT1, IFI6, IFI44L, ISG15, LAMP3, OASL, RSAD2, SIGLEC1; or MX1, LLY6E, IFI27, OAS1, IFIT1, IFI6, IFI44L, ISG15, LAMP3, OASL, RSAD2, HERC5; or MX1, LLY6E, IFI27, OAS1, IFIT1, IFI6, IFI44L, ISG15, LAMP3, OASL, RSAD2, DNAPTP6; or MX1, LLY6E, IFI27, OAS1, IFIT1, IFI6, IFI44L, ISG15, LAMP3, OASL, RSAD2, LOC129607; or MX1, LLY6E, IFI27, OAS1, IFIT1, IFI6, IFI44L, ISG15, LAMP3, OASL, RSAD2, EPSTI1; or MX1, LLY6E, IFI27, OAS1, IFIT1, IFI6, IFI44L, ISG15, LAMP3, OASL, RSAD2, BIRC4BP; or MX1, LLY6E, IFI27, OAS1, IFIT1, IFI6, IFI44L, ISG15, LAMP3, OASL, RSAD2, gene detected by probe 229450_at; or MX1, LLY6E, IFI27, OAS1, IFIT1, IFI6, IFI44L, ISG15, LAMP3, OASL, RSAD2, gene detected by probe 235276_at; or LLY6E, IFI27, OAS1, IFIT1, IFI6, IFI44L, ISG15, LAMP3, OASL, RSAD2, IFI44, IFIT2; or LLY6E, IFI27, OAS1, IFIT1, IFI6, IFI44L, ISG15, LAMP3, OASL, RSAD2, IFI44, OAS3; or LLY6E, IFI27, OAS1, IFIT1, IFI6, IFI44L, ISG15, LAMP3, OASL, RSAD2, IFI44, USP18; or LLY6E, IFI27, OAS1, IFIT1, IFI6, IFI44L, ISG15, LAMP3, OASL, RSAD2, IFI44, SIGLEC1; or LLY6E, IFI27, OAS1, IFIT1, IFI6, IFI44L, ISG15, LAMP3, OASL, RSAD2, IFI44, HERC5; or LLY6E, IFI27, OAS1, IFIT1, IFI6, IFI44L, ISG15, LAMP3, OASL, RSAD2, IFI44, DNAPTP6; or LLY6E, IFI27, OAS1, IFIT1, IFI6, IFI44L, ISG15, LAMP3, OASL, RSAD2, IFI44, LOC129607; or LLY6E, IFI27, OAS1, IFIT1, IFI6, IFI44L, ISG15, LAMP3, OASL, RSAD2, IFI44, EPSTI1; or LLY6E, IFI27, OAS1, IFIT1, IFI6, IFI44L, ISG15, LAMP3, OASL, RSAD2, IFI44, BIRC4BP; or LLY6E, IFI27, OAS1, IFIT1, IFI6, IFI44L, ISG15, LAMP3, OASL, RSAD2, IFI44, gene detected by probe 229450_at; or LLY6E, IFI27, OAS1, IFIT1, IFI6, IFI44L, ISG15, LAMP3, OASL, RSAD2, IFI44, gene detected by probe 235276_at; or IFI27, OAS1, IFIT1, IFI6, IFI44L, ISG15, LAMP3, OASL, RSAD2, IFI44, IFIT2, OAS; or IFI27, OAS1, IFIT1, IFI6, IFI44L, ISG15, LAMP3, OASL, RSAD2, IFI44, IFIT2, USP18; or IFI27, OAS1, IFIT1, IFI6, IFI44L, ISG15, LAMP3, OASL, RSAD2, IFI44, IFIT2, SIGLEC1; or IFI27, OAS1, IFIT1, IFI6, IFI44L, ISG15, LAMP3, OASL, RSAD2, IFI44, IFIT2, HERC5; or IFI27, OAS1, IFIT1, IFI6, IFI44L, ISG15, LAMP3, OASL, RSAD2, IFI44, IFIT2, DNAPTP6; or IFI27, OAS1, IFIT1, IFI6, IFI44L, ISG15, LAMP3, OASL, RSAD2, IFI44, IFIT2, LOC129607; or IFI27, OAS1, IFIT1, IFI6, IFI44L, ISG15, LAMP3, OASL, RSAD2, IFI44, IFIT2, EPSTI1; or IFI27, OAS1, IFIT1, IFI6, IFI44L, ISG15, LAMP3, OASL, RSAD2, IFI44, IFIT2, BIRC4BP; or IFI27, OAS1, IFIT1, IFI6, IFI44L, ISG15, LAMP3, OASL, RSAD2, IFI44, IFIT2, gene detected by probe 229450_at; or IFI27, OAS1, IFIT1, IFI6, IFI44L, ISG15, LAMP3, OASL, RSAD2, IFI44, IFIT2, gene detected by probe 235276_at; or OAS1, IFIT1, IFI6, IFI44L, ISG15, LAMP3, OASL, RSAD2, IFI44, IFIT2, OAS3, USP18; or OAS1, IFIT1, IFI6, IFI44L, ISG15, LAMP3, OASL, RSAD2, IFI44, IFIT2, OAS3, SIGLEC1; or OAS1, IFIT1, IFI6, IFI44L, ISG15, LAMP3, OASL, RSAD2, IFI44, IFIT2, OAS3, HERC5; or OAS1, IFIT1, IFI6, IFI44L, ISG15, LAMP3, OASL, RSAD2, IFI44, IFIT2, OAS3, DNAPTP6; or OAS1, IFIT1, IFI6, IFI44L, ISG15, LAMP3, OASL, RSAD2, IFI44, IFIT2, OAS3, LOC129607; or OAS1, IFIT1, IFI6, IFI44L, ISG15, LAMP3, OASL, RSAD2, IFI44, IFIT2, OAS3, EPSTI1; or OAS1, IFIT1, IFI6, IFI44L, ISG15, LAMP3, OASL, RSAD2, IFI44, IFIT2, OAS3, BIRC4BP; or OAS1, IFIT1, IFI6, IFI44L, ISG15, LAMP3, OASL, RSAD2, IFI44, IFIT2, OAS3, gene detected by probe 229450_at; or OAS1, IFIT1, IFI6, IFI44L, ISG15, LAMP3, OASL, RSAD2, IFI44, IFIT2, OAS3, gene detected by probe 235276_at; or IFIT1, IFI6, IFI44L, ISG15, LAMP3, OASL, RSAD2, IFI44, IFIT2, OAS3, USP18, SIGLEC1; or IFIT1, IFI6, IFI44L, ISG15, LAMP3, OASL, RSAD2, IFI44, IFIT2, OAS3, USP18, HERC5; or IFIT1, IFI6, IFI44L, ISG15, LAMP3, OASL, RSAD2, IFI44, IFIT2, OAS3, USP18, DNAPTP6; or IFIT1, IFI6, IFI44L, ISG15, LAMP3, OASL, RSAD2, IFI44, IFIT2, OAS3, USP18, LOC129607; or IFIT1, IFI6, IFI44L, ISG15, LAMP3, OASL, RSAD2, IFI44, IFIT2, OAS3, USP18, EPSTI1; or IFIT1, IFI6, IFI44L, ISG15, LAMP3, OASL, RSAD2, IFI44, IFIT2, OAS3, USP18, BIRC4BP; or IFIT1, IFI6, IFI44L, ISG15, LAMP3, OASL, RSAD2, IFI44, IFIT2, OAS3, USP18, gene detected by probe 229450_at; or IFIT1, IFI6, IFI44L, ISG15, LAMP3, OASL, RSAD2, IFI44, IFIT2, OAS3, USP18, gene detected by probe 235276_at; or IFI6, IFI44L, ISG15, LAMP3, OASL, RSAD2, IFI44, IFIT2, OAS3, USP18, SIGLEC1, HERC5; or IFI6, IFI44L, ISG15, LAMP3, OASL, RSAD2, IFI44, IFIT2, OAS3, USP18, SIGLEC1, DNAPTP6; or IFI6, IFI44L, ISG15, LAMP3, OASL, RSAD2, IFI44, IFIT2, OAS3, USP18, SIGLEC1, LOC129607; or IFI6, IFI44L, ISG15, LAMP3, OASL, RSAD2, IFI44, IFIT2, OAS3, USP18, SIGLEC1, EPSTI1; or IFI6, IFI44L, ISG15, LAMP3, OASL, RSAD2, IFI44, IFIT2, OAS3, USP18, SIGLEC1, BIRC4BP; or IFI6, IFI44L, ISG15, LAMP3, OASL, RSAD2, IFI44, IFIT2, OAS3, USP18, SIGLEC1, gene detected by probe 229450_at; or IFI6, IFI44L, ISG15, LAMP3, OASL, RSAD2, IFI44, IFIT2, OAS3, USP18, SIGLEC1, gene detected by probe 235276_at; or IFI44L, ISG15, LAMP3, OASL, RSAD2, IFI44, IFIT2, OAS3, USP18, SIGLEC1, HERC5, DNAPTP6; or IFI44L, ISG15, LAMP3, OASL, RSAD2, IFI44, IFIT2, OAS3, USP18, SIGLEC1, HERC5, LOC129607; or IFI44L, ISG15, LAMP3, OASL, RSAD2, IFI44, IFIT2, OAS3, USP18, SIGLEC1, HERC5, EPSTI1; or IFI44L, ISG15, LAMP3, OASL, RSAD2, IFI44, IFIT2, OAS3, USP18, SIGLEC1, HERC5, BIRC4BP; or IFI44L, ISG15, LAMP3, OASL, RSAD2, IFI44, IFIT2, OAS3, USP18, SIGLEC1, HERC5, gene detected by probe 229450_at; or IFI44L, ISG15, LAMP3, OASL, RSAD2, IFI44, IFIT2, OAS3, USP18, SIGLEC1, HERC5, gene detected by probe 235276_at; or ISG15, LAMP3, OASL, RSAD2, IFI44, IFIT2, OAS3, USP18, SIGLEC1, HERC5, DNAPTP6, LOC129607; or ISG15, LAMP3, OASL, RSAD2, IFI44, IFIT2, OAS3, USP18, SIGLEC1, HERC5, DNAPTP6, EPSTI1; or ISG15, LAMP3, OASL, RSAD2, IFI44, IFIT2, OAS3, USP18, SIGLEC1, HERC5, DNAPTP6, BIRC4BP; or ISG15, LAMP3, OASL, RSAD2, IFI44, IFIT2, OAS3, USP18, SIGLEC1, HERC5, DNAPTP6, gene detected by probe 229450_at; or ISG15, LAMP3, OASL, RSAD2, IFI44, IFIT2, OAS3, USP18, SIGLEC1, HERC5, DNAPTP6, gene detected by probe 235276_at; or LAMP3, OASL, RSAD2, IFI44, IFIT2, OAS3, USP18, SIGLEC1, HERC5, DNAPTP6, LOC129607, EPSTI1; or LAMP3, OASL, RSAD2, IFI44, IFIT2, OAS3, USP18, SIGLEC1, HERC5, DNAPTP6, LOC129607, BIRC4BP; or LAMP3, OASL, RSAD2, IFI44, IFIT2, OAS3, USP18, SIGLEC1, HERC5, DNAPTP6, LOC129607, gene detected by probe 229450_at; or LAMP3, OASL, RSAD2, IFI44, IFIT2, OAS3, USP18, SIGLEC1, HERC5, DNAPTP6, LOC129607, gene detected by probe 235276_at; or OASL, RSAD2, IFI44, IFIT2, OAS3, USP18, SIGLEC1, HERC5, DNAPTP6, LOC129607, EPSTI1, BIRC4BP; or OASL, RSAD2, IFI44, IFIT2, OAS3, USP18, SIGLEC1, HERC5, DNAPTP6, LOC129607, EPSTI1, gene detected by probe 229450_at; or OASL, RSAD2, IFI44, IFIT2, OAS3, USP18, SIGLEC1, HERC5, DNAPTP6, LOC129607, EPSTI1, gene detected by probe 235276_at; or RSAD2, IFI44, IFIT2, OAS3, USP18, SIGLEC1, HERC5, DNAPTP6, LOC129607, EPSTI1, BIRC4BP, gene detected by probe 229450_at; or RSAD2, IFI44, IFIT2, OAS3, USP18, SIGLEC1, HERC5, DNAPTP6, LOC129607, EPSTI1, BIRC4BP, gene detected by probe 229450_at; or IFI44, IFIT2, OAS3, USP18, SIGLEC1, HERC5, DNAPTP6, LOC129607, EPSTI1, BIRC4BP, gene detected by probe 229450_at gene detected by probe 235276_at. The IFNα-inducible PD markers in such an expression profile may further include at least one or more gene listed in Table 19 and/or 20 and/or 21, and/or 22, and/or 23, and/or 24, and/or 26, and/or 28 and/or 30.

The IFNα-inducible PD markers in an expression profile may include at least genes IFI27, SIGLEC1, RSAD2, IFI6, IFI44L, IFI44, USP18, IFIT2, SAMD9L, BIRC4BP, DNAPTP6, OAS3, LY6E, IFIT1, LIPA, LOC129607, ISG15, PARP14, MX1, OAS2, OASL, CCL2, HERC5, OAS1. The IFNα-inducible PD markers in such an expression profile may further include at least one or more gene listed in Table 19 and/or 20 and/or 21, and/or 22, and/or 23, and/or 24, and/or 26, and/or 28, and/or 30.

The IFNα-inducible PD markers in an expression profile may include at least genes IFIT1, IFIT3, IRF7, IFI6, IL6ST, IRF2, LY6E, MARCKS, MX1, MX2, OAS1, EIF2AK2, ISG15, STAT2, OAS3, IFI44, IFI44L, HERC5, RAB8B, LILRA5, RSAD2, and FCHO2. The IFNα-inducible PD markers in such an expression profile may further include at least one or more gene listed in Table 19 and/or 20 and/or 21, and/or 22, and/or 23, and/or 24, and/or 26, and/or 28 and/or 30.

The IFNα-inducible PD markers in an expression profile may include at least genes SERPING1, IFIT2, IFIT3, IFI6, LY6E, MX1, OAS1, ISG15, IFI27, OAS3, IFI44, LAMP3, DNAPTP6, ETV7, HERC5, OAS2, USP18, XAF1, RTP4, SIGLEC1, and EPSTI1. The IFNα-inducible PD markers in such an expression profile may further include at least one or more gene listed in Table 19 and/or 20 and/or 21, and/or 22, and/or 23, and/or 24, and/or 26, and/or 28 and/or 30.

The IFNα-inducible PD markers in an expression profile may include at least genes SERPING1, IFIT2, IFIT3, IFI6, LY6E, MX1, OAS1, ISG15, IFI27, OAS3, IFI44, LAMP3, DNAPTP6, ETV7, HERC5, OAS2, USP18, XAF1, RTP4, SIGLEC1, EPSTI1, and RSAD2. The IFNα-inducible PD markers in such an expression profile may further include at least one or more gene listed in Table 19 and/or 20 and/or 21, and/or 22, and/or 23, and/or 24, and/or 26, and/or 28 and/or 30.

The IFNα-inducible PD markers in an expression profile may include at least genes BCL2, BAK1, BAD, BAX, and BCL2L1. The IFNα-inducible PD markers in such an expression profile may further include at least one or more gene listed in Table 19 and/or 20 and/or 21, and/or 22, and/or 23, and/or 24, and/or 26, and/or 28 and/or 30.

The IFNα-inducible PD markers in an expression profile may include at least genes RTP4, RSAD2, HERC5, SIGLEC1, USP18, LY6E, ETV7, SERPING1, IFIT3, OAS1, HSXIAPAF1, G1P3, MX1, OAS3, IFI27, DNAPTP6, LAMP3, EPSTI1, IFI44, OAS2, IFIT2, and ISG15. The IFNα-inducible PD markers in such an expression profile may further include at least one or more gene listed in Table 19 and/or 20 and/or 21, and/or 22, and/or 23, and/or 24, and/or 26, and/or 28 and/or 30.

The IFNα-inducible PD markers in an expression profile may include at least genes LAMP3, SIGLEC1, DNAPTP6, IFIT2, ETV7, RTP4, SERPING1, HERC5, XAF1, MX1, EPSTI1, OAS2, OAS1, OAS3, IFIT3, IFI6, USP18, RSAD2, IFI44, LY6E, ISG15, and IFI27. The IFNα-inducible PD markers in such an expression profile may further include at least one or more gene listed in Table 19 and/or 20 and/or 21, and/or 22, and/or 23, and/or 24, and/or 26, and/or 28 and/or 30.

The IFNα-inducible PD markers in an expression profile may include at least genes DNAPTP6, EPSTI1, HERC5, IFI27, IFI44, IFI44L, IFI6, IFIT1, IFIT3, ISG15, LAMP3, LY6E, MX1, OAS1, OAS2, OAS3, PLSCR1, RSAD2, RTP4, SIGLEC1, and USP18. The IFNα-inducible PD markers in such an expression profile may further include at least one or more gene listed in Table 19 and/or 20 and/or 21, and/or 22, and/or 23, and/or 24, and/or 26, and/or 28 and/or 30.

The IFNα-inducible PD markers in an expression profile may include at least genes SAMD9L, IFI6, IFI44, IFIT2, ZC3HAV1, ETV6, DAPP1, IL1RN, CEACAM1, OAS1, IFI27, OAS3, IFI44L, HERC5, IFIT1, EPSTI1, ISG15, SERPING1, OASL, GBP1, and MX1. The IFNα-inducible PD markers in such an expression profile may further include at least one or more gene listed in Table 19 and/or 20 and/or 21, and/or 22, and/or 23, and/or 24, and/or 26, and/or 28 and/or 30.

The IFNα-inducible PD markers in an expression profile may include at least genes IFI6, RSAD2, IFI44, IFI44L, IFI27, MX1, IFIT1, ISG15, LAMP3, OAS3, OAS1, EPSTI1, IFIT3, OAS2, SIGLEC1, and USP18. The IFNα-inducible PD markers in such an expression profile may further include at least one or more gene listed in Table 19 and/or 20 and/or 21, and/or 22, and/or 23, and/or 24, and/or 26, and/or 28 and/or 30.

The IFNα-inducible PD markers in an expression profile may include at least genes IFI6, RSAD2, IFI44, IFI44L, IFI27, MX1, IFIT1, HERC5, ISG15, LAMP3, OAS3, OAS1, EPSTI1, IFIT3, OAS2, LY6E, SIGLEC1, and USP18. The IFNα-inducible PD markers in such an expression profile may further include at least one or more gene listed in Table 19 and/or 20 and/or 21, and/or 22, and/or 23, and/or 24, and/or 26, and/or 28 and/or 30.

The IFNα-inducible PD markers in an expression profile may include at least genes IFI6, RSAD2, IFI44, IFI44L, IFI27, MX1, and IFIT1. The IFNα-inducible PD markers in such an expression profile may further include at least one or more gene listed in Table 19 and/or 20 and/or 21, and/or 22, and/or 23, and/or 24, and/or 26, and/or 28 and/or 30.

The IFNα-inducible PD markers in an expression profile may include at least genes IFI6, RSAD2, IFI44, IFI44L, and IFI27. The IFNα-inducible PD markers in such an expression profile may further include at least one or more gene listed in Table 19 and/or 20 and/or 21, and/or 22, and/or 23, and/or 24, and/or 26, and/or 28 and/or 30.

The IFNα-inducible PD markers in an expression profile may include at least genes SAMD9L, IFI6, IFI44, IFIT2, OAS1, IFI27, OAS3, IFI44L, HERC5, IFIT1, EPSTI1, ISG15, SERPING1, OASL, GBP1, and MX1. The IFNα-inducible PD markers in such an expression profile may further include at least one or more gene listed in Table 19 and/or 20 and/or 21, and/or 22, and/or 23, and/or 24, and/or 26, and/or 28 and/or 30.

The IFNα-inducible PD markers in an expression profile may include at least genes IFI27, IL-121R beta2, IL-15R alpha, IL-15, suppressor of cytokine signaling 1 (SOCS1), janus kinase 2, CXCL11 (T-TAC), TNFSF13B (BAFF), TRAF-type domain 1 (TRAFD1), SERPING1, CD274 (PD1-L), indoleamine 2,3 dioxygenase (INDO), lymphocyte-activation gene 3 (LAG3), and caspase 5. The IFNα-inducible PD markers in such an expression profile may further include at least one or more gene listed in Table 19 and/or 20 and/or 21, and/or 22, and/or 23, and/or 24, and/or 26, and/or 28 and/or 30.

The IFNα-inducible PD markers in an expression profile may include at least genes complement factor B, insulin-like growth factor (IGF2BP3), cyclin A1, neuropilin 2, complement 1qB, complement 1qC, CD80, CD47, MMP14, toll-like receptor 3 (TLR3), TLR adaptor molecule 2 (TICAM2), macrophage scavenger receptor-1 (MSR1), desmoplakin, PDGR receptor, CCL13 (MCP-4), CXCL13 (BCA-1), CCL19 (CCR7), IL-1 family 5, purinergic receptor P2X7, IRS1, caspase 3, and cyclin-dependent kinase-like 1 (CDKL1). The IFNα-inducible PD markers in such an expression profile may further include at least one or more gene listed in Table 19 and/or 20 and/or 21, and/or 22, and/or 23, and/or 24, and/or 26, and/or 28 and/or 30.

The IFNα-inducible PD markers in an expression profile may include alterations in any one or more of serum protein levels of adiponectin, alpha-fetoprotein, apolipoprotein CIII, beta-2 microglobulin, cancer antigen 125, cancer antigen 19-9, eotaxin, FABP, factor VII, ferritin, IL-10, IL-12p70, IL-16, IL-18, IL-1ra, IL-3, MCP-1, MMP-3, myoglobin, SGOT, tissue factor, TIMP-1, TNF RII, TNF-alpha, VCAM-1, vWF, BDNK, complement 3, CD40 ligand, EGF, ENA-78, EN-RAGE, IGF-1, MDC, myeloperoxidase, RANTES, or thrombopoietin.

The IFNα-inducible PD markers in an expression profile may include alterations in any one or more of serum protein levels of adiponectin, alpha-fetoprotein, apolipoprotein CIII, beta-2 microglobulin, cancer antigen 125, cancer antigen 19-9, eotaxin, FABP, factor VII, ferritin, IL-10, IL-12p70, IL-16, IL-18, IL-1ra, IL-3, MCP-1, MMP-3, myoglobin, SGOT, tissue factor, TIMP-1, TNF RII, TNF-alpha, VCAM-1, or vWF. The IFNα-inducible PD markers in such an expression profile may further include at least one or more gene listed in Table 19 and/or 20 and/or 21, and/or 22, and/or 23, and/or 24, and/or 26, and/or 28 and/or 30.

The IFNα-inducible PD markers in an expression profile may include alterations in any one or more of serum protein levels of BDNK, complement 3, CD40 ligand, EGF, ENA-78, EN-RAGE, IGF-1, MDC, myeloperoxidase, RANTES, or thrombopoietin. The IFNα-inducible PD markers in such an expression profile may further include at least one or more gene listed in Table 19 and/or 20 and/or 21, and/or 22, and/or 23, and/or 24, and/or 26, and/or 28 and/or 30.

An IFNα-inducible PD marker expression profile may further include genes whose expression or activity is down-regulated in cells exposed to non-baseline IFNα levels. The genes whose expression or activity is down-regulated may be any of the genes that are identified in Table 31. The genes may include any one or more of SLC4A1, PRSS33, FCER1A, BACH2, KLRB1, D4S234E, T cell receptor alpha locus/T cell receptor delta locus, FEZ1, AFF3, CD160, ABCB1, PTCH1, OR2W3, IGHD, NOG, NR3C2, TNS1, PDZK1IP1, SH2D1B, STRBP, ZMYND11, TMOD1, FCRLA, DKFZp761P0423, EPB42, NR6A1, LOC341333, MS4A1, IGHM, SIGLECP3, KIR2DS2, PKIA, BLR1, C5orf4, MYLK, LOC283663, MAD1L1, CXCL5, D4S234E, FCRLA, KRT1, c16orf74, ABCB4, or GPRASP1. Any number of these genes may serve as PD markers in an IFNα-inducible PD marker expression profile. For example, at least 2, at least 3, at least 4, at least 5, at least 6, at least 7, at least 8, at least 9, at least 10, at least 11, at least 12 at least 15, at least 20, at least 25, at least 30, at least 35, at least 40, at least 45, or at least 50 down-regulated genes may be included in the IFNα-inducible PD marker expression profile. The IFNα-inducible PD marker expression profile may further include genes listed in Tables 19 and/or 20 and/or 21 and/or 22 and/or 23 and/or 24 and/or 26 and/or 28.

The IFNα-inducible PD marker expression profile may include gene FEZ1, or may include genes FEZ1 and NOG, or may include gene NOG, or may include genes FEZ1, NOG, and SLC4A1, or may include gene SLC4A1, or may include genes NOG and SLC4A1, or may include genes FEZ1, NOG, SLC4A1, and D4S234E, or may include genes FEZ1, NOG, SLC4A1, D4S234E, and PRSS33. The IFNα-inducible PD marker expression profile may further include genes listed in Tables 19 and/or 20 and/or 21 and/or 22 and/or 23 and/or 24 and/or 26 and/or 28 and/or 30, and/or 31.

Down-regulated genes may have down-regulated expression or activity of at least 5%, at least 10%, at least 15%, at least 20%, at least 25%, at least 30%, at least 35%, at least 40%, at least 45%, at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% that of control cells, e.g., cells of healthy volunteers or cells of control animals or cells not exposed to IFNα in culture.

Up- or down-regulation of gene expression or activity of IFNα-inducible PD markers may be determined by any means known in the art. For example, up- or down-regulation of gene expression may be detected by determining mRNA levels. mRNA expression may be determined by northern blotting, slot blotting, quantitative reverse transcriptase polymerase chain reaction, or gene chip hybridization techniques. See U.S. Pat. Nos. 5,744,305 and 5,143,854 for examples of making nucleic acid arrays for gene chip hybridization techniques.

Up- or down-regulation of gene expression or activity of IFNα-inducible PD markers may be determined by detecting protein levels. The up- or down-regulated gene whose protein levels are detected may be any one, any two, any three, any four, any five, any six, any seven, any eight, any nine, any ten, any twelve, any fifteen, any twenty, any twenty five, any thirty, any thirty five, or more of adiponectin, alpha-fetoprotein, apolipoprotein CIII, beta-2 microglobulin, cancer antigen 125, cancer antigen 19-9, eotaxin, FABP, factor VII, ferritin, IL-10, IL-12p70, IL-16, IL-18, IL-1ra, IL-3, MCP-1, MMP-3, myoglobin, SGOT, tissue factor, TIMP-1, TNF RII, TNF-alpha, VCAM-1, vWF, BDNK, complement 3, CD40 ligand, EGF, ENA-78, EN-RAGE, IGF-1, MDC, myeloperoxidase, RANTES, or thrombopoietin. Methods for detecting protein expression levels include immuno-based assays such as enzyme-linked immunosorbant assays, western blotting, protein arrays, and silver staining.

An IFNα-inducible PD marker expression profile may comprise a profile of protein activity. Up- or down-regulation of gene expression or activity of IFNα-inducible PD markers may be determined by detecting activity of proteins including, but not limited to, detectable phosphorylation activity, de-phosphorylation activity, or cleavage activity. Furthermore, up- or down-regulation of gene expression or activity of IFNα-inducible PD markers may be determined by detecting any combination of these gene expression levels or activities.

A candidate therapeutic for treating IFNα-mediated disorders may be identified by the methods encompassed by the invention. Candidate therapeutics may be any type of molecule including a small molecule or a biological agent. A candidate therapeutic identified by the methods encompassed by the invention may immediately be identified as useful as a therapeutic for a disease, disorder, or condition. Alternatively, a candidate therapeutic identified by the methods encompassed by the invention may need to be further tested and/or modified before selection for treating patients. Alternatively, a candidate therapeutic identified by the methods encompassed by the invention may, after further testing, be de-selected as a molecule for treating patients.

In methods that identify candidate therapeutics, cells comprising an IFNα-inducible PD marker expression profile are contacted with an agent. The cells may be any type of cells, such as commercially available immortalized cell lines that comprise an IFNα-inducible PD marker expression profile, commercially available immortalized cell lines that have been treated with IFNα to induce an IFNα-inducible PD marker expression profile, cells isolated from a patient having an IFNα-inducible PD marker expression profile, or cells isolated from a healthy patient and treated with IFNα to induce an IFNα-inducible PD marker expression profile.

Presence or absence of a change in the IFNα-inducible PD marker expression profile of the cells is detected following contacting the cells with the agent. Presence of change may be any change in IFNα-inducible PD marker expression profile including at least a 10% decrease in up-regulated expression or activity of at least 1 gene in the IFNα-inducible PD marker expression profile, at least a 20% decrease of the at least 1 up-regulated gene, at least a 30% decrease of the at least up-regulated 1 gene, at least a 40% decrease of the at least 1 up-regulated gene, at least a 50% decrease of the at least 1 up-regulated gene, at least a 60% decrease of the at least 1 up-regulated gene, at least a 70% decrease of the at least 1 up-regulated gene, at least a 75% decrease of the at least 1 up-regulated gene, at least an 80% decrease of the at least 1 up-regulated gene, at least an 85% decrease of the at least 1 up-regulated gene, at least a 90% decrease of the at least 1 up-regulated gene, at least a 95% decrease of the at least 1 up-regulated gene, at least a 96% decrease of the at least 1 up-regulated gene, at least a 97% decrease of the at least 1 up-regulated gene, at least a 98% decrease of the at least 1 up-regulated gene, at least a 99% decrease of the at least 1 up-regulated gene, or a 100% decrease of the at least 1 up-regulated gene. Alternatively, or in addition, presence of change may be any change in IFNα-inducible PD marker expression profile including at least a 10% increase in expression or activity of at least 1 down-regulated gene in the IFNα-inducible PD marker expression profile, at least a 20% increase of the at least 1 down-regulated gene, at least a 30% increase of the at least 1 down-regulated gene, at least a 40% increase of the at least 1 down-regulated gene, at least a 50% increase of the at least 1 down-regulated gene, at least a 60% increase of the at least 1 down-regulated gene, at least a 70% increase of the at least 1 down-regulated gene, at least a 75% increase of the at least 1 down-regulated gene, at least an 80% increase of the at least 1 down-regulated gene, at least an 85% increase of the at least 1 down-regulated gene, at least a 90% increase of the at least 1 down-regulated gene, at least a 95% increase of the at least 1 down-regulated gene, at least a 96% increase of the at least 1 down-regulated gene, at least a 97% increase of the at least 1 down-regulated gene, at least a 98% increase of the at least 1 down-regulated gene, at least a 99% increase of the at least 1 down-regulated gene, or a 100% increase of the at least 1 down-regulated gene.

In methods of monitoring disease progression of a patient samples from the patient may be obtained before and after administration of an agent, e.g., an agent that binds to and modulates type I IFN or IFNα activity, or an agent that binds to and does not modulate type I IFN or IFNα activity, or a combination of agents that may or may not include an agent that binds to and modulates type I IFN or IFNα activity. Type I IFN or IFNα inducible PD marker expression profiles are obtained in the (before and after agent administration) samples. The type I IFN or IFNα inducible PD marker expression profiles in the samples are compared. Comparison may be of the number of type I IFN or IFNα inducible PD markers present in the samples or may be of the quantity of type I IFN or IFNα inducible PD markers present in the samples, or any combination thereof. Variance indicating efficacy of the therapeutic agent may be indicated if the number or level (or any combination thereof) of up-regulated type I IFN or IFNα inducible PD markers decreases in the sample obtained after administration of the therapeutic agent relative to the sample obtained before administration of the therapeutic agent. The number of up-regulated type I IFN or IFNα inducible PD markers may decrease by at least 1, at least 2, at least 3, at least 4, at least 5, at least 6, at least 7, at least 8, at least 9, or at least 10. The level of any given up-regulated type I IFN or IFNα inducible PD marker may decrease by at least 10%, at least 20%, at least 25%, at least 30%, at least 35%, at least 40%, at least 50%, at least 60%, at least 70%, at least 80%, at least 90%, or at least 95%. The number of up-regulated type I IFN or IFNα inducible PD markers with decreased levels may be at least 1, at least 2, at least 3, at least 4, at least 5, at least 6, at least 7, at least 8, at least 9, at least 10, at least 15, at least 20, at least 25, at least 30, or at least 35. Any combination of decreased number and decreased level of up-regulated type I IFN or IFNα inducible PD markers may indicate efficacy. Variance indicating efficacy of the therapeutic agent may be indicated if the number or level (or any combination thereof) of down-regulated type I IFN or IFNα inducible PD markers decreases in the sample obtained after administration of the therapeutic agent relative to the sample obtained before administration of the therapeutic agent. The number of down-regulated type I IFN or IFNα inducible PD markers may decrease by at least 1, at least 2, at least 3, at least 4, at least 5, at least 6, at least 7, at least 8, at least 9, or at least 10. The level of any given down-regulated type I IFN or IFNα inducible PD marker may increase by at least 10%, at least 20%, at least 25%, at least 30%, at least 35%, at least 40%, at least 50%, at least 60%, at least 70%, at least 80%, at least 90%, or at least 95%. The number of down-regulated type I IFN or IFNα inducible PD markers with increased levels may be at least 1, at least 2, at least 3, at least 4, at least 5, at least 6, at least 7, at least 8, at least 9, at least 10, at least 15, at least 20, at least 25, at least 30, or at least 35. Any combination of decreased number and increased level of down-regulated type I IFN or IFNα inducible PD markers may indicate efficacy.

The sample obtained from the patient may be obtained prior to a first administration of the agent, i.e., the patient is naïve to the agent. Alternatively, the sample obtained from the patient may occur after administration of the agent in the course of treatment. For example, the agent may have been administered prior to the initiation of the monitoring protocol. Following administration of the agent an additional samples may be obtained from the patient and type I IFN or IFNα inducible PD markers in the samples are compared. The samples may be of the same or different type, e.g., each sample obtained may be a blood sample, or each sample obtained may be a serum sample. The type I IFN or IFNα inducible PD markers detected in each sample may be the same, may overlap substantially, or may be similar.

The samples may be obtained at any time before and after the administration of the therapeutic agent. The sample obtained after administration of the therapeutic agent may be obtained at least 2, at least 3, at least 4, at least 5, at least 6, at least 7, at least 8, at least 9, at least 10, at least 12, or at least 14 days after administration of the therapeutic agent. The sample obtained after administration of the therapeutic agent may be obtained at least 2, at least 3, at least 4, at least 5, at least 6, at least 7, or at least 8 weeks after administration of the therapeutic agent. The sample obtained after administration of the therapeutic agent may be obtained at least 2, at least 3, at least 4, at least 5, or at least 6 months following administration of the therapeutic agent.

Additional samples may be obtained from the patient following administration of the therapeutic agent. At least 2, at least 3, at least 4, at least 5, at least 6, at least 7, at least 8, at least 9, at least 10, at least 12, at least 15, at least 20, at least 25 samples may be obtained from the patient to monitor progression or regression of the disease or disorder over time. Disease progression may be monitored over a time period of at least 1 week, at least 2 weeks, at least 3 weeks, at least 4 weeks, at least 5 weeks, at least 6 weeks, at least 7 weeks, at least 2 months, at least 3 months, at least 4 months, at least 5 months, at least 6 months, at least 1 year, at least 2 years, at least 3 years, at least 4 years, at least 5 years, at least 10 years, or over the lifetime of the patient. Additional samples may be obtained from the patient at regular intervals such as at monthly, bi-monthly, once a quarter year, twice a year, or yearly intervals. The samples may be obtained from the patient following administration of the agent at regular intervals. For instance, the samples may be obtained from the patient at one week following each administration of the agent, or at two weeks following each administration of the agent, or at three weeks following each administration of the agent, or at one month following each administration of the agent, or at two months following each administration of the agent. Alternatively, multiple samples may be obtained from the patient following an or each administration of the agent.

Disease progression in a patient may similarly be monitored in the absence of administration of an agent. Samples may periodically be obtained from the patient having the disease or disorder. Disease progression may be identified if the number of type I IFN or IFNα inducible PD markers increases in a later-obtained sample relative to an earlier obtained sample. The number of type I IFN or IFNα inducible PD markers may increase by at least 1, at least 2, at least 3, at least 4, at least 5, at least 6, at least 7, at least 8, at least 9, or at least 10. Disease progression may be identified if level of any given up-regulated type I IFN or IFNα inducible PD marker increases by at least 10%, at least 20%, at least 25%, at least 30%, at least 35%, at least 40%, at least 50%, at least 60%, at least 70%, at least 80%, at least 90%, or at least 95%. Disease progression may be identified if level of any given down-regulated type I IFN or IFNα inducible PD marker decreases by at least 10%, at least 20%, at least 25%, at least 30%, at least 35%, at least 40%, at least 50%, at least 60%, at least 70%, at least 80%, at least 90%, or at least 95%. The number of up-regulated type I IFN or IFNα inducible PD markers with increased levels may be at least 1, at least 2, at least 3, at least 4, at least 5, at least 6, at least 7, at least 8, at least 9, at least 10, at least 15, at least 20, at least 25, at least 30, or at least 35. The number of down-regulated type I IFN or IFNα inducible PD markers with decreased levels may be at least 1, at least 2, at least 3, at least 4, at least 5, at least 6, at least 7, at least 8, at least 9, at least 10, at least 15, at least 20, at least 25, at least 30, or at least 35. Any combination of increased number and increased level of up-regulated type I IFN or IFNα inducible PD marker may indicate disease progression. Alternatively, or in combination, any combination of decreased number and decreased level of down-regulated type I IFN or IFNα inducible PD marker may indicate disease progression. Disease regression may also be identified in a patient having a disease or disorder, not treated by an agent. In this instance, regression may be identified if the number of type I IFN or IFNα inducible PD markers decreases in a later-obtained sample relative to an earlier obtained sample. The number of type I IFN or IFNα inducible PD markers may decrease by at least 1, at least 2, at least 3, at least 4, at least 5, at least 6, at least 7, at least 8, at least 9, or at least 10. Disease regression may be identified if level of any given up-regulated type I IFN or IFNα inducible PD marker decreases by at least 10%, at least 20%, at least 25%, at least 30%, at least 35%, at least 40%, at least 50%, at least 60%, at least 70%, at least 80%, at least 90%, or at least 95%. Disease regression may be identified if level of any given down-regulated type I IFN or IFNα inducible PD marker increases by at least 10%, at least 20%, at least 25%, at least 30%, at least 35%, at least 40%, at least 50%, at least 60%, at least 70%, at least 80%, at least 90%, or at least 95%. The number of up-regulated type I IFN or IFNα inducible PD markers with decreased levels may be at least 1, at least 2, at least 3, at least 4, at least 5, at least 6, at least 7, at least 8, at least 9, at least 10, at least 15, at least 20, at least 25, at least 30, or at least 35. The number of down-regulated type I IFN or IFNα inducible PD markers with increased levels may be at least 1, at least 2, at least 3, at least 4, at least 5, at least 6, at least 7, at least 8, at least 9, at least 10, at least 15, at least 20, at least 25, at least 30, or at least 35. Disease progression or disease regression may be monitored by obtaining samples over any period of time and at any interval. Disease progression or disease regression may be monitored by obtaining samples over the course of at least 1 week, at least 2 weeks, at least 3 weeks, at least 4 weeks, at least 5 weeks, at least 6 weeks, at least 7 weeks, at least 2 months, at least 3 months, at least 4 months, at least 5 months, at least 6 months, at least 1 year, at least 2 years, at least 3 years, at least 4 years, at least 5 years, at least 10 years, or over the lifetime of the patient. Disease progression or disease regression may be monitored by obtaining samples at least monthly, bi-monthly, once a quarter year, twice a year, or yearly. The samples need not be obtained at strict intervals.

The invention also encompasses kits and probes. The probes may be any molecule that detects any expression or activity of any gene that may be included in an IFNα-inducible PD marker expression profile.

The invention also encompasses methods of detecting IFN activity. These methods may employ cells comprising a polynucleotide sequence comprising a reporter gene under the control of an interferon-stimulated response element. The cells comprising the polynucleotide sequence may be any cells amenable to transfection or transformation with a polynucleotide sequence and that can be maintained in culture. These cells include animal cells, bacterial cells, yeast cells, insect cells, or plant cells. These cells may be adherent or may grow in suspension. If the cells are animal cells, they may be from a known cell line such as HeLa, COS, NIH3T3, AGS, 293, CHO, Huh-7, HUVEC, MCF-7, C6, BHK-21, BNL CL 2, C2C12, HepG2, and ATDC5. Countless other cell lines are known and can be obtained by those of skill in the art. The cells may alternatively be primary cells that have or have not been immortalized.

The cells may comprise a polynucleotide sequence comprising a reporter gene under the control of an interferon-stimulated response element. The polynucleotide sequence may be stably integrated in the DNA of the cell or may be an extrachromosomal element that is stably or transiently in the cell. The polynucleotide may have been introduced to the cell as a naked polynucleotide molecule, a polynucleotide molecule complexed with lipids or other molecules, or a polynucleotide in a virus particle.

If the polynucleotide was introduced as a naked polynucleotide molecule, the polynucleotide may have been a linear or a circular molecule. Non-limiting examples of circular polynucleotide molecules include plasmids, and artificial chromosomes. These vectors may be cleaved with enzymes, for example, to generate linear polynucleotide molecules.

Furthermore, if the polynucleotide was introduced as a naked polynucleotide it may have been introduced into the cells by any of many well known techniques in the art. These techniques include, but are not limited to, electroporation, microinjection, and biolistic particle delivery. See, also, e.g., Loeffler and Behr, 1993, Meth. Enzymol. 217:599-618; Cohen et al., 1993, Meth. Enzymol. 217:618-644; Clin. Pharma. Ther. 29:69-92 (1985), Sambrook, et al. Molecular Cloning: A Laboratory Manual. 2nd, ed., Cold Spring Harbor Laboratory, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y., 1989 and Ausubel et al., ed. Current Protocols in Molecular Biology, John Wiley & Sons, Inc., N.Y., N.Y. (1987-2001).

If the polynucleotide was introduced as a complex with lipids or liposomes, it too may have been introduced by one of many known techniques to the skilled artisan. Lipids or liposomes comprise a mixture of fat particles or lipids which bind to DNA or RNA to provide a hydrophobic coated delivery vehicle. Suitable liposomes may comprise any of the conventional synthetic or natural phospholipid liposome materials including phospholipids from natural sources such as egg, plant or animal sources such as phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol, sphingomyelin, phosphatidylserine or phosphatidylinositol. Synthetic phospholipids also may be used, e.g., dimyristoylphosphatidylcholine, dioleoylphosphatidylcholine, dioleoylphosphatidycholine and corresponding synthetic phosphatidylethanolamines and phosphatidylglycerols. Lipids or liposomes that may be conjugated with the vector are also commercially available to the skilled artisan. Examples of commercially available lipid or liposome transfection reagents known to those of skill in the art include LIPOFECTAMINE™ (Invitrogen), GENEJUICE® (Novagen), GENEJAMMER® (Stratagene), FUGENE® HD (Roche), MEGAFECTIN™ (Qbiogene), SUPERFECT® (Qiagen), and EFFECTENE® (Qiagen).

If the polynucleotide was introduced as a complex with other molecules it may have been compacted or in a nanosphere. Compacted polynucleotide complexes are described in U.S. Pat. Nos. 5,972,901, 6,008,336, and 6,077,835. Nanospheres are described in U.S. Pat. Nos. 5,718,905 and 6,207,195. These compacted polynucleotide complexes and nanospheres that complex nucleic acids utilize polymeric cations. Typical polymeric cations include gelatin, poly-L-lysine, and chitosan. Alternatively, the polynucleotide may have been complexed with DEAE-dextran, or transfected using techniques such as calcium phosphate coprecipitation, or calcium chloride coprecipitation.

If the polynucleotide was introduced associated with a virus, the virus may have been any well known suitable virus for polynucleotide delivery. Example viruses that may be used as vectors include adenovirus, adeno-associated virus, lentivirus, retrovirus, herpes virus (e.g. herpes simplex virus), vaccina virus, papovirus, Sendai virus, SV40 virus, respiratory syncytial virus, etc.

The polynucleotide sequence may include a reporter gene and an interferon-stimulated response element. The reporter gene may be any one of luciferase, chloramphenicol acetyl transferase, β-galactosidase, green fluorescent protein, β-glucuronidase, or secreted placental alkaline phosphatase. Variations of many of these reporter genes, e.g., green fluorescent protein and luceriferase, are known and can be readily identified and/or produced by those of skill in the art. Other reporter genes in addition to those listed will also be known to those of skill in the art and are readily available. Interferon-stimulated response elements are also known to those of skill in the art. They may be obtained from commercial vendors such as Stratagene, Clonetech, and Biomyx. They have also been reported in, for instance, Alcantara et al. (Nuc. Acid. Res. 30 (2002):2068-2075 and Kirchhoff et al. (Oncogene 18 (1999):3725-3736).

The cells employed in the assay may be incubated with a sample. The sample may be obtained from a patient, from a vendor with patient samples, or a control sample used for calibration or as a control. If the sample is obtained from a patient it may be any biological fluid or tissue, such as whole blood, saliva, urine, synovial fluid, bone marrow, cerebrospinal fluid, nasal secretions, sputum, amniotic fluid, bronchioalveolar lavage fluid, peripheral blood mononuclear cells, total white blood cells, lymph node cells, spleen cells, tonsil cells, or skin.

Expression of the reporter gene is detected by any well known means in the art. The expression, even if “0” indicates IFN activity in the sample. One of skill in the art may further quantitate any level of expression of the reporter gene which may then correlate to level of IFN activity in the sample.

Applicants provide a set of non-limiting embodiments to describe some of the aspects of the invention.

EMBODIMENTS
Embodiment 1

A method of treating a patient having a type I IFN or an IFNα-mediated disease or disorder comprising:

administering an agent that binds to and modulates type I IFN or IFNα activity;

- wherein the patient comprises a type I IFN or IFNα-inducible PD marker expression profile;
- and wherein the agent neutralizes the type I IFN or IFNα-inducible PD marker expression profile of the patient.

Embodiment 2

The method of 1 further comprising detecting neutralization of the type I IFN or IFNα-inducible PD marker expression profile of the patient.

Embodiment 3

The method of embodiment 1 wherein the type I IFN or IFNα-inducible PD marker expression profile comprises up-regulated expression or activity of genes MX1, LY6E, IFI27, OAS1 IFIT1, IFI6, IFI44L, ISG15, LAMP3, OASL, RSAD2, and IFI44.

Embodiment 4

The method of embodiment 1 wherein the agent is a biologic agent.

Embodiment 5

The method of embodiment 4 wherein the agent is an antibody.

Embodiment 6

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

Embodiment 7

The method of embodiment 5 wherein the antibody is specific for one or more type I IFN or IFNα subtype but is not MEDI-545.

Embodiment 8

The method of embodiment 1 wherein the administering the agent alleviates one or more symptoms of the disease or disorder.

Embodiment 9

The method of embodiment 5 wherein the antibody is administered at a dose between approximately 0.03 and 30 mg/kg.

Embodiment 10

The method of embodiment 9 wherein the antibody is administered at a dose between 0.3 and 3 mg/kg.

Embodiment 11

The method of embodiment 10 wherein the antibody is administered at a dose between 0.03 and 1 mg/kg.

Embodiment 12

The method of any one of embodiments 9-11 wherein the agent neutralizes the type I IFN or IFNα-inducible PD marker expression profile of the patient by at least 10%.

Embodiment 13

The method of embodiment 12 wherein the agent neutralizes the type I IFN or IFNα-inducible PD marker expression profile of the patient by at least 20%.

Embodiment 14

The method of embodiment 13 wherein the agent neutralizes the type I IFN or IFNα-inducible PD marker expression profile of the patient by at least 30%.

Embodiment 15

The method of embodiment 14 wherein the agent neutralizes the type I IFN or IFNα-inducible PD marker expression profile of the patient by at least 40%.

Embodiment 16

The method of embodiment 15 wherein the agent neutralizes the type I IFN or IFNα-inducible PD marker expression profile of the patient by at least 50%.

Embodiment 17

The method of embodiment 1 wherein the type I IFN or an IFNα-mediated disease or disorder is one of lupus, psoriasis, vasculitis, sarcoidosis, Sjogren's syndrome, or idiopathic inflammatory myositis.

Embodiment 18

The method of embodiment 17 wherein the type I IFN or an IFNα-mediated disease or disorder is lupus.

Embodiment 19

The method of embodiment 17 wherein the type I IFN or an IFNα-mediated disease or disorder is psoriasis.

Embodiment 20

The method of embodiment 1 wherein the type I IFN or IFNα-inducible PD marker expression profile comprises up-regulated expression or activity of at least IFNα subtypes 1, 2, 8, and 14.

Embodiment 21

The method of embodiment 1 wherein the type I IFN or IFNα-inducible PD marker expression profile comprises transcripts of PD marker genes.

Embodiment 22

The method of embodiment 1 wherein the type I IFN or IFNα-inducible PD marker expression profile comprises polypeptides expressed from PD marker genes.

Embodiment 23

The method of embodiment 1 wherein the type I IFN or IFNα-inducible PD marker expression profile comprises up-regulated expression or activity of genes IFI27, SIGLEC1, RSAD2, IFI6, IFI44L, IFI44, USP18, IFIT2, SAMD9L, BIRC4BP, DNAPTP6, OAS3, LY6E, IFIT1, LIPA, LOC129607, ISG15, PARP14, MX1, OAS2, OASL, CCL2, HERC5, OAS1

Embodiment 24

The method of embodiment 1 wherein the type I IFN or IFNα-inducible PD marker expression profile comprises up-regulated expression or activity of genes IFIT1, IFIT3, IRF7, IFI6, IL6ST, IRF2, LY6E, MARCKS, MX1, MX2, OAS1, EIF2AK2, ISG15, STAT2, OAS3, IFI44, IFI44L, HERC5, RAB8B, LILRA5, RSAD2, and FCHO2

Embodiment 25

The method of embodiment 1 wherein the type I IFN or IFNα-inducible PD marker expression profile comprises up-regulated expression or activity of genes SERPING1, IFIT2, IFIT3, IFI6, LY6E, MX1, OAS1, ISG15, IFI27, OAS3, IFI44, LAMP3, DNAPTP6, ETV7, HERC5, OAS2, USP18, XAF1, RTP4, SIGLEC1, and EPSTI1.

Embodiment 26

The method of embodiment 1 wherein the type I IFN or IFNα-inducible PD marker expression profile comprises up-regulated expression or activity of genes RTP4, RSAD2, HERC5, SIGLEC1, USP18, LY6E, ETV7, SERPING1, IFIT3, OAS1, HSXIAPAF1, G1P3, MX1, OAS3, IFI27, DNAPTP6, LAMP3, EPSTI1, IFI44, OAS2, IFIT2, and ISG15.

Embodiment 27

The method of embodiment 1 wherein the type I IFN or IFNα-inducible PD marker expression profile comprises up-regulated expression or activity of genes LAMP3, SIGLEC1, DNAPTP6, IFIT2, ETV7, RTP4, SERPING1, HERC5, XAF1, MX1, EPSTI1, OAS2, OAS1, OAS3, IFIT3, IFI6, USP18, RSAD2, IFI44, LY6E, ISG15, and IFI27.

Embodiment 28

The method of embodiment 1 wherein the type I IFN or IFNα-inducible PD marker expression profile comprises up-regulated expression or activity of genes DNAPTP6, EPSTI1, HERC5, IFI27, IFI44, IFI44L, IFI6, IFIT1, IFIT3, ISG15, LAMP3, LY6E, MX1, OAS1, OAS2, OAS3, PLSCR1, RSAD2, RTP4, SIGLEC1, and USP18.

Embodiment 29

The method of embodiment 1 wherein the type I IFN or IFNα-inducible PD marker expression profile comprises up-regulated expression or activity of genes SAMD9L, IFI6, IFI44, IFIT2, ZC3HAV1, ETV6, DAPP1, IL1RN, CEACAM1, OAS1, IFI27, OAS3, IFI44L, HERC5, IFIT1, EPSTI1, ISG15, SERPING1, OASL, GBP1, and MX1.

Embodiment 30

The method of embodiment 1 wherein the type I IFN or IFNα-inducible PD marker expression profile comprises up-regulated expression or activity of genes SAMD9L, IFI6, IFI44, IFIT2, OAS1, IFI27, OAS3, IFI44L, HERC5, IFIT1, EPSTI1, ISG15, SERPING1, OASL, GBP1, and MX1.

Embodiment 31

The method of embodiment 1 wherein the type I IFN or IFNα-inducible PD marker expression profile comprises up-regulated expression or activity of genes IFI6, RSAD2, IFI44, IFI44L, IFI27, MX1, IFIT1, ISG15, LAMP3, OAS3, OAS1, EPSTI1, IFIT3, OAS2, SIGLEC1, and USP18.

Embodiment 32

The method of embodiment 1 wherein the type I IFN or IFNα-inducible PD marker expression profile comprises up-regulated expression or activity of genes IFI6, RSAD2, IFI44, IFI44L, and IFI27.

Embodiment 33

The method of embodiment 32 wherein the type I IFN or IFNα-inducible PD marker expression profile further comprises up-regulated expression or activity of genes MX1 and IFIT1.

Embodiment 34

The method of embodiment 33 wherein the type I IFN or IFNα-inducible PD marker expression profile further comprises up-regulated expression or activity of genes OAS2 and OAS1.

Embodiment 35

The method of any one of embodiments 3 or 23-33 wherein the type I IFN or IFNα-inducible PD marker expression profile further comprises down-regulated expression or activity of genes NOG, SLC4A1, PRSS33, and FEZ1.

Embodiment 36

The method of embodiment 1 wherein the type I IFN or IFNα-inducible PD marker expression profile comprises down-regulated expression or activity of genes NOG, SLC4A1, PRSS33, and FEZ1.

Embodiment 37

The method of embodiment 22 wherein the polypeptides are detected at increased levels in serum.

Embodiment 38

The method of embodiment 37 wherein polypeptides include cancer antigen 125, ferritin, tissue factor, and MMP-3.

Embodiment 39

The method of embodiment 22 wherein the polypeptides are detected at decreased levels in serum.

Embodiment 40

The method of embodiment 39 wherein the polypeptides include EGF, thrombopoietin, and CD40 ligand.

Embodiment 41

A method of treating an autoimmune disease patient comprising a moderate or strong type I IFN or an IFNα PD marker profile comprising:

administering an agent that binds to and modulates type I IFN or IFNα activity;

- wherein the agent neutralizes the type I IFN or IFNα-inducible PD marker expression profile of the patient.

Embodiment 42

The method of 41 further comprising detecting neutralization of the type I IFN or IFNα-inducible PD marker expression profile of the patient.

Embodiment 43

The method of embodiment 41 wherein the type I IFN or IFNα-inducible PD marker expression profile comprises up-regulated expression or activity of genes MX1, LY6E, IFI27, OAS1 IFIT1, IFI6, IFI44L, ISG15, LAMP3, OASL, RSAD2, and IFI44.

Embodiment 44

The method of embodiment 41 wherein the type I IFN or IFNα-inducible PD marker expression profile comprises up-regulated expression or activity of genes IFI27, SIGLEC1, RSAD2, IFI6, IFI44L, IFI44, USP18, IFIT2, SAMD9L, BIRC4BP, DNAPTP6, OAS3, LY6E, IFIT1, LIPA, LOC129607, ISG15, PARP14, MX1, OAS2, OASL, CCL2, HERC5, OAS1

Embodiment 45

The method of embodiment 41 wherein the type I IFN or IFNα-inducible PD marker expression profile comprises up-regulated expression or activity of genes IFIT1, IFIT3, IRF7, IFI6, IL6ST, IRF2, LY6E, MARCKS, MX1, MX2, OAS1, EIF2AK2, ISG15, STAT2, OAS3, IFI44, IFI44L, HERC5, RAB8B, LILRA5, RSAD2, and FCHO2

Embodiment 46

The method of embodiment 41 wherein the type I IFN or IFNα-inducible PD marker expression profile comprises up-regulated expression or activity of genes SERPING1, IFIT2, IFIT3, IFI6, LY6E, MX1, OAS1, ISG15, IFI27, OAS3, IFI44, LAMP3, DNAPTP6, ETV7, HERC5, OAS2, USP18, XAF1, RTP4, SIGLEC1, and EPSTI1.

Embodiment 47

The method of embodiment 41 wherein the type I IFN or IFNα-inducible PD marker expression profile comprises up-regulated expression or activity of genes RTP4, RSAD2, HERC5, SIGLEC1, USP18, LY6E, ETV7, SERPING1, IFIT3, OAS1, HSXIAPAF1, G1P3, MX1, OAS3, IFI27, DNAPTP6, LAMP3, EPSTI1, IFI44, OAS2, IFIT2, and ISG15.

Embodiment 48

The method of embodiment 41 wherein the type I IFN or IFNα-inducible PD marker expression profile comprises up-regulated expression or activity of genes LAMP3, SIGLEC1, DNAPTP6, IFIT2, ETV7, RTP4, SERPING1, HERC5, XAF1, MX1, EPSTI1, OAS2, OAS1, OAS3, IFIT3, IFI6, USP18, RSAD2, IFI44, LY6E, ISG15, and IFI27.

Embodiment 49

The method of embodiment 41 wherein the type I IFN or IFNα-inducible PD marker expression profile comprises up-regulated expression or activity of genes DNAPTP6, EPSTI1, HERC5, IFI27, IFI44, IFI44L, IFI6, IFIT1, IFIT3, ISG15, LAMP3, LY6E, MX1, OAS1, OAS2, OAS3, PLSCR1, RSAD2, RTP4, SIGLEC1, and USP18.

Embodiment 50

The method of embodiment 41 wherein the type I IFN or IFNα-inducible PD marker expression profile comprises up-regulated expression or activity of genes SAMD9L, IFI6, IFI44, IFIT2, ZC3HAV1, ETV6, DAPP1, IL1RN, CEACAM1, OAS1, IFI27, OAS3, IFI44L, HERC5, IFIT1, EPSTI1, ISG15, SERPING1, OASL, GBP1, and MX1.

Embodiment 51

The method of embodiment 41 wherein the type I IFN or IFNα-inducible PD marker expression profile comprises up-regulated expression or activity of genes SAMD9L, IFI6, IFI44, IFIT2, OAS1, IFI27, OAS3, IFI44L, HERC5, IFIT1, EPSTI1, ISG15, SERPING1, OASL, GBP1, and MX1.

Embodiment 52

The method of embodiment 41 wherein the type I IFN or IFNα-inducible PD marker expression profile comprises up-regulated expression or activity of genes IFI6, RSAD2, IFI44, IFI44L, IFI27, MX1, IFIT1, ISG15, LAMP3, OAS3, OAS1, EPSTI1, IFIT3, OAS2, SIGLEC1, and USP18.

Embodiment 53

The method of embodiment 41 wherein the type I IFN or IFNα-inducible PD marker expression profile comprises up-regulated expression or activity of genes IFI6, RSAD2, IFI44, and IFI27.

Embodiment 54

The method of embodiment 53 wherein the type I IFN or IFNα-inducible PD marker expression profile further comprises up-regulated expression or activity of genes MX1 and IFIT1.

Embodiment 55

The method of embodiment 41 wherein the type I IFN or IFNα-inducible PD marker expression profile comprises up-regulated expression or activity of at least IFNα subtypes 1, 2, 8, and 14.

Embodiment 56

The method of embodiment 41 wherein the agent is a biologic agent.

Embodiment 57

The method of embodiment 41 wherein the agent is an antibody.

Embodiment 58

The method of embodiment 57 wherein the antibody is MEDI-545.

Embodiment 59

The method of embodiment 57 wherein the antibody is specific for one or more type I IFN or IFNα subtype but is not MEDI-545.

Embodiment 60

The method of embodiment 41 wherein the administering the agent alleviates one or more symptoms of the disease or disorder.

Embodiment 61

The method of embodiment 57 wherein the antibody is administered at a dose between approximately 0.03 and 30 mg/kg.

Embodiment 62

The method of embodiment 57 wherein the antibody is administered at a dose between 0.3 and 3 mg/kg.

Embodiment 63

The method of embodiment 57 wherein the antibody is administered at a dose between 0.03 and 1 mg/kg.

Embodiment 64

The method of embodiment 41 wherein the wherein the agent neutralizes the type I IFN or IFNα-inducible PD marker expression profile by at least 10%.

Embodiment 65

The method of embodiment 64 wherein the wherein the agent neutralizes the type I IFN or IFNα-inducible PD marker expression profile by at least 20%.

Embodiment 66

The method of embodiment 65 wherein the agent neutralizes the type I IFN or IFNα-inducible PD marker expression profile by at least 30%.

Embodiment 67

The method of embodiment 66 wherein the wherein the agent neutralizes the type I IFN or IFNα-inducible PD marker expression profile by at least 40%.

Embodiment 68

The method of embodiment 67 wherein the wherein the agent neutralizes the type I IFN or IFNα-inducible PD marker expression profile by at least 50%.

Embodiment 69

The method of embodiment 41 wherein the autoimmune disease patient is a lupus, psoriasis, vasculitis, sarcoidosis, Sjogren's syndrome, or idiopathic inflammatory myositis patient.

Embodiment 70

The method of embodiment 69 wherein the patient is a lupus patient.

Embodiment 71

The method of embodiment 69 wherein the patient is a psoriasis patient.

Embodiment 72

A method of neutralizing a type I IFN or IFNα-inducible PD marker expression profile in a patient in need thereof, comprising:

administering an agent that binds to and modulates type I IFN or IFNα activity to the patient;

- wherein the agent neutralizes the type I IFN or IFNα-inducible PD marker expression profile of the patient.

Embodiment 73

The method of 72 further comprising detecting neutralization of the type I IFN or IFNα-inducible PD marker expression profile of the patient.

Embodiment 74

The method of embodiment 72 wherein the type I IFN or IFNα-inducible PD marker expression profile comprises up-regulated expression or activity of genes MX1, LY6E, IFI27, OAS1 IFIT1, IFI6, IFI44L, ISG15, LAMP3, OASL, RSAD2, and IFI44.

Embodiment 75

The method of embodiment 72 wherein the agent is a biologic agent.

Embodiment 76

The method of embodiment 75 wherein the agent is an antibody.

Embodiment 77

The method of embodiment 76 wherein the antibody is MEDI-545.

Embodiment 78

The method of embodiment 76 wherein the antibody is specific for one or more type I IFN or IFNα subtype but is not MEDI-545.

Embodiment 79

The method of embodiment 72 wherein the administering the agent alleviates one or more symptoms of the disease or disorder.

Embodiment 80

The method of embodiment 76 wherein the antibody is administered at a dose between approximately 0.03 and 30 mg/kg.

Embodiment 81

The method of embodiment 80 wherein the antibody is administered at a dose between 0.3 and 3 mg/kg.

Embodiment 82

The method of embodiment 81 wherein the antibody is administered at a dose between 0.03 and 1 mg/kg.

Embodiment 83

The method of any one of embodiments 80-82 wherein the agent neutralizes the type I IFN or IFNα-inducible PD marker expression profile of the patient by at least 10%.

Embodiment 84

The method of embodiment 83 wherein the agent neutralizes the type I IFN or IFNα-inducible PD marker expression profile of the patient by at least 20%.

Embodiment 85

The method of embodiment 84 wherein the agent neutralizes the type I IFN or IFNα-inducible PD marker expression profile of the patient at least 30%.

Embodiment 86

The method of embodiment 85 wherein the agent neutralizes the type I IFN or IFNα-inducible PD marker expression profile of the patient at least 40%.

Embodiment 87

The method of embodiment 86 wherein the agent neutralizes the type I IFN or IFNα-inducible PD marker expression profile of the patient at least 50%.

Embodiment 88

The method of embodiment 72 wherein the patient is a lupus, psoriasis, vasculitis, sarcoidosis, Sjogren's syndrome, or idiopathic inflammatory myositis patient.

Embodiment 89

The method of embodiment 88 wherein the patient is a lupus patient.

Embodiment 90

The method of embodiment 88 wherein the patient is a psoriasis patient.

Embodiment 91

The method of embodiment 72 wherein the type I IFN or IFNα-inducible PD marker expression profile comprises up-regulated expression or activity of at least IFNα subtypes 1, 2, 8, and 14.

Embodiment 92

The method of embodiment 72 wherein the type I IFN or IFNα-inducible PD marker expression profile comprises transcripts of PD marker genes.

Embodiment 93

The method of embodiment 72 wherein the type I IFN or IFNα-inducible PD marker expression profile comprises polypeptides expressed from PD marker genes.

Embodiment 94

The method of embodiment 72 wherein the type I IFN or IFNα-inducible PD marker expression profile comprises up-regulated expression or activity of genes IFI27, SIGLEC1, RSAD2, IFI6, IFI44L, IFI44, USP18, IFIT2, SAMD9L, BIRC4BP, DNAPTP6, OAS3, LY6E, IFIT1, LIPA, LOC129607, ISG15, PARP14, MX1, OAS2, OASL, CCL2, HERC5, OAS1.

Embodiment 95

The method of embodiment 72 wherein the type I IFN or IFNα-inducible PD marker expression profile comprises up-regulated expression or activity of genes IFIT1, IFIT3, IRF7, IFI6, IL6ST, IRF2, LY6E, MARCKS, MX1, MX2, OAS1, EIF2AK2, ISG15, STAT2, OAS3, IFI44, IFI44L, HERC5, RAB8B, LILRA5, RSAD2, and FCHO2.

Embodiment 96

The method of embodiment 72 wherein the type I IFN or IFNα-inducible PD marker expression profile comprises up-regulated expression or activity of genes SERPING1, IFIT2, IFIT3, IFI6, LY6E, MX1, OAS1, ISG15, IFI27, OAS3, IFI44, LAMP3, DNAPTP6, ETV7, HERC5, OAS2, USP18, XAF1, RTP4, SIGLEC1, and EPSTI1.

Embodiment 97

The method of embodiment 72 wherein the type I IFN or IFNα-inducible PD marker expression profile comprises up-regulated expression or activity of genes RTP4, RSAD2, HERC5, SIGLEC1, USP18, LY6E, ETV7, SERPING1, IFIT3, OAS1, HSXIAPAF1, G1P3, MX1, OAS3, IFI27, DNAPTP6, LAMP3, EPSTI1, IFI44, OAS2, IFIT2, and ISG15.

Embodiment 98

The method of embodiment 72 wherein the type I IFN or IFNα-inducible PD marker expression profile comprises up-regulated expression or activity of genes LAMP3, SIGLEC1, DNAPTP6, IFIT2, ETV7, RTP4, SERPING1, HERC5, XAF1, MX1, EPSTI1, OAS2, OAS1, OAS3, IFIT3, IFI6, USP18, RSAD2, IFI44, LY6E, ISG15, and IFI27.

Embodiment 99

The method of embodiment 72 wherein the type I IFN or IFNα-inducible PD marker expression profile comprises up-regulated expression or activity of genes DNAPTP6, EPSTI1, HERC5, IFI27, IFI44, IFI44L, IFI6, IFIT1, IFIT3, ISG15, LAMP3, LY6E, MX1, OAS1, OAS2, OAS3, PLSCR1, RSAD2, RTP4, SIGLEC1, and USP18.

Embodiment 100

The method of embodiment 72 wherein the type I IFN or IFNα-inducible PD marker expression profile comprises up-regulated expression or activity of genes SAMD9L, IFI6, IFI44, IFIT2, ZC3HAV1, ETV6, DAPP1, IL1RN, CEACAM1, OAS1, IFI27, OAS3, IFI44L, HERC5, IFIT1, EPSTI1, ISG15, SERPING1, OASL, GBP1, and MX1.

Embodiment 101

The method of embodiment 72 wherein the type I IFN or IFNα-inducible PD marker expression profile comprises up-regulated expression or activity of genes SAMD9L, IFI6, IFI44, IFIT2, OAS1, IFI27, OAS3, IFI44L, HERC5, IFIT1, EPSTI1, ISG15, SERPING1, OASL, GBP1, and MX1.

Embodiment 102

The method of embodiment 72 wherein the type I IFN or IFNα-inducible PD marker expression profile comprises up-regulated expression or activity of genes IFI6, RSAD2, IFI44, IFI44L, IFI27, MX1, IFIT1, ISG15, LAMP3, OAS3, OAS1, EPSTI1, IFIT3, OAS2, SIGLEC1, and USP18.

Embodiment 103

The method of embodiment 72 wherein the type I IFN or IFNα-inducible PD marker expression profile comprises up-regulated expression or activity of genes IFI6, RSAD2, IFI44, IFI44L, and IFI27.

Embodiment 104

The method of embodiment 103 wherein the type I IFN or IFNα-inducible PD marker expression profile further comprises up-regulated expression or activity of genes MX1 and IFIT1.

Embodiment 105

The method of any one of embodiments 74 or 94-104 wherein the type I IFN or IFNα-inducible PD marker expression profile further comprises down-regulated expression or activity of genes NOG, SLC4A1, PRSS33, and FEZ1.

Embodiment 106

The method of embodiment 72 wherein the type I IFN or IFNα-inducible PD marker expression profile comprises down-regulated expression or activity of genes NOG, SLC4A1, PRSS33, and FEZ1.

Embodiment 107

The method of embodiment 93 wherein the polypeptides are detected at increased levels in serum.

Embodiment 108

The method of embodiment 107 wherein polypeptides include cancer antigen 125, ferritin, tissue factor, and MMP-3.

Embodiment 109

The method of embodiment 93 wherein the polypeptides are detected at decreased levels in serum.

Embodiment 110

The method of embodiment 109 wherein the polypeptides include EGF, thrombopoietin, and CD40 ligand.

Embodiment 111

A method of monitoring or prognosing autoimmune disease progression of a patient comprising:

obtaining a first IFNα-inducible PD marker expression profile in a first sample from a patient.

Embodiment 112

The method of embodiment 111 wherein the first IFNα-inducible PD marker expression profile is a strong profile and the patient prognosis is disease progression.

Embodiment 113

The method of embodiment 112 wherein the autoimmune disease is SLE and the progression is an SLE flare.

Embodiment 114

The method of embodiment 111 wherein the first IFNα-inducible PD marker expression profile is a weak profile and the patient prognosis is disease regression.

Embodiment 115

The method of embodiment 111 further comprising:

obtaining a second IFNα-inducible PD marker expression profile in a second sample from a patient;

wherein an increase in number or level of type I IFN or IFNα inducible PD markers in the second relative to the first expression profile prognoses disease progression; or

wherein a decrease in number or level of type I IFN or IFNα inducible PD markers in the second relative to the first expression profile prognoses disease regression.

Embodiment 116

A method of monitoring disease progression of a patient receiving treatment with a therapeutic agent that binds to and modulates IFNα activity comprising:

obtaining a first IFNα-inducible PD marker expression profile in a first sample from the patient;

administering a therapeutic agent that binds to and modulates IFNα activity;

obtaining a second IFNα-inducible PD marker expression profile in a second sample from the patient; and

comparing the first and the second IFNα-inducible PD marker expression profiles,

- wherein a variance in the first and the second IFNα-inducible PD marker expression profiles indicates a level of efficacy of the therapeutic agent that binds to and modulates IFNα activity.

Embodiment 117

The method of embodiment 116 wherein the first IFNα-inducible PD marker expression profile comprises up-regulated expression or activity of genes MX1, LY6E, IFI27, OAS1, IFIT1, IFI6, IFI44L, ISG15, LAMP3, OASL, RSAD2, and IFI44

Embodiment 118

The method of embodiment 116 wherein the first type I IFN or IFNα-inducible PD marker expression profile comprises up-regulated expression or activity of genes IFI27, SIGLEC1, RSAD2, IFI6, IFI44L, IFI44, USP18, IFIT2, SAMD9L, BIRC4BP, DNAPTP6, OAS3, LY6E, IFIT1, LIPA, LOC129607, ISG15, PARP14, MX1, OAS2, OASL, CCL2, HERC5, OAS1.

Embodiment 119

The method of embodiment 116 wherein the first type I IFN or IFNα-inducible PD marker expression profile comprises up-regulated expression or activity of genes IFIT1, IFIT3, IRF7, IFI6, IL6ST, IRF2, LY6E, MARCKS, MX1, MX2, OAS1, EIF2AK2, ISG15, STAT2, OAS3, IFI44, IFI44L, HERC5, RAB8B, LILRA5, RSAD2, and FCHO2.

Embodiment 120

The method of embodiment 116 wherein the first type I IFN or IFNα-inducible PD marker expression profile comprises up-regulated expression or activity of genes SERPING1, IFIT2, IFIT3, IFI6, LY6E, MX1, OAS1, ISG15, IFI27, OAS3, IFI44, LAMP3, DNAPTP6, ETV7, HERC5, OAS2, USP18, XAF1, RTP4, SIGLEC1, and EPSTI1.

Embodiment 121

The method of embodiment 116 wherein the first type I IFN or IFNα-inducible PD marker expression profile comprises up-regulated expression or activity of genes RTP4, RSAD2, HERC5, SIGLEC1, USP18, LY6E, ETV7, SERPING1, IFIT3, OAS1, HSXIAPAF1, G1P3, MX1, OAS3, IFI27, DNAPTP6, LAMP3, EPSTI1, IFI44, OAS2, IFIT2, and ISG15.

Embodiment 122

The method of embodiment 116 wherein the first type I IFN or IFNα-inducible PD marker expression profile comprises up-regulated expression or activity of genes LAMP3, SIGLEC1, DNAPTP6, IFIT2, ETV7, RTP4, SERPING1, HERC5, XAF1, MX1, EPSTI1, OAS2, OAS1, OAS3, IFIT3, IFI6, USP18, RSAD2, IFI44, LY6E, ISG15, and IFI27.

Embodiment 123

The method of embodiment 116 wherein the first type I IFN or IFNα-inducible PD marker expression profile comprises up-regulated expression or activity of genes DNAPTP6, EPSTI1, HERC5, IFI27, IFI44, IFI44L, IFI6, IFIT1, IFIT3, ISG15, LAMP3, LY6E, MX1, OAS1, OAS2, OAS3, PLSCR1, RSAD2, RTP4, SIGLEC1, and USP18.

Embodiment 124

The method of embodiment 116 wherein the first type I IFN or IFNα-inducible PD marker expression profile comprises up-regulated expression or activity of genes SAMD9L, IFI6, IFI44, IFIT2, ZC3HAV1, ETV6, DAPP1, IL1RN, CEACAM1, OAS1, IFI27, OAS3, IFI44L, HERC5, IFIT1, EPSTI1, ISG15, SERPING1, OASL, GBP1, and MX1.

Embodiment 125

The method of embodiment 116 wherein the first type I IFN or IFNα-inducible PD marker expression profile comprises up-regulated expression or activity of genes SAMD9L, IFI6, IFI44, IFIT2, OAS1, IFI27, OAS3, IFI44L, HERC5, IFIT1, EPSTI1, ISG15, SERPING1, OASL, GBP1, and MX1.

Embodiment 126

The method of embodiment 116 wherein the first type I IFN or IFNα-inducible PD marker expression profile comprises up-regulated expression or activity of genes IFI6, RSAD2, IFI44, IFI44L, IFI27, MX1, IFIT1, ISG15, LAMP3, OAS3, OAS1, EPSTI1, IFIT3, OAS2, SIGLEC1, and USP18.

Embodiment 127

The method of embodiment 116 wherein the first type I IFN or IFNα-inducible PD marker expression profile comprises up-regulated expression or activity of genes IFI6, RSAD2, IFI44, IFI44L, and IFI27.

Embodiment 128

The method of embodiment 116 wherein the variance is a decrease in up-regulated expression of activity levels of the genes.

Embodiment 129

The method of embodiment 116 wherein the disease is lupus, idiopathic inflammatory myositis, Sjogren's syndrome, vasculitis, sarcoidosis, and psoriasis.

Embodiment 130

The method of embodiment 131 wherein the disease is lupus.

Embodiment 131

The method of embodiment 116 wherein the therapeutic agent is a small molecule or a biologic agent.

Embodiment 132

The method of embodiment 131 wherein the biologic agent is an antibody.

Embodiment 133

The method of embodiment 132 wherein the antibody is MEDI-545.

Embodiment 134

The method of embodiment 116 wherein the first IFNα-inducible PD marker expression profile is obtained prior to administration of the therapeutic agent.

Embodiment 135

The method of embodiment 116 wherein the first IFNα-inducible PD marker expression profile is obtained at the time of administration of the therapeutic agent.

Embodiment 136

The method of embodiment 116 wherein the first and the second sample are whole blood or serum.

Embodiment 137

The method of embodiment 116 further comprising obtaining a third IFNα-inducible PD marker expression profile in a third sample from the patient.

Embodiment 138

The method of 137 further comprising obtaining a fourth IFNα-inducible PD marker expression profile in a fourth sample from the patient.

Embodiment 139

The method of 138 further comprising obtaining a fifth IFNα-inducible PD marker expression profile in a fifth sample from the patient.

Embodiment 140

The method of 139 further comprising obtaining a sixth IFNα-inducible PD marker expression profile in a sixth sample from the patient.

Embodiment 141

The method of 116 wherein the second sample is obtained at least one week, at least 2 weeks, at least three weeks, at least one month or at least two months following administration of the therapeutic agent.

Embodiment 142

The method of 137 wherein the third sample is obtained at least 2 days, at least 5 days, at least one week, at least 2 weeks, at least three weeks, at least one month or at least two months following obtaining the second sample.

Embodiment 143

The method of 138 wherein the fourth sample is obtained at least 2 days, at least 5 days, at least one week, at least 2 weeks, at least three weeks, at least one month or at least two months following obtaining the third sample.

Embodiment 144

The method of 139 wherein the fifth sample is obtained at least 2 days, at least 5 days, at least one week, at least 2 weeks, at least three weeks, at least one month or at least two months following obtaining the fourth sample.

Embodiment 145

The method of embodiment 116 wherein variance is a decrease in up-regulated expression or activity of the gene.

Embodiment 146

The method of embodiment 145 wherein the decrease is at least 10%, at least 20%, at least 25%, at least 30%, at least 40%, at least 45%, at least 50%, at least 60%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or 100%.

Embodiment 147

A method of identifying a patient as a candidate for a therapeutic agent that binds to and modulates IFNα activity comprising:

detecting presence or absence of an IFNα-inducible PD marker expression profile in a sample from the patient,

- wherein detecting presence of the IFNα-induced PD marker expression profile identifies the patient as a candidate for the therapeutic agent that binds to and modulates IFNα activity.

Embodiment 148

The method of embodiment 147 wherein the IFNα-inducible PD marker expression profile comprises up-regulated expression or activity of genes MX1, LY6E, IFI27, OAS1, IFIT1, IFI6, IFI44L, ISG15, LAMP3, OASL, RSAD2, and IFI44.

Embodiment 149

The method of embodiment 147 wherein type I IFN or IFNα-inducible PD marker expression profile comprises up-regulated expression or activity of genes IFI27, SIGLEC1, RSAD2, IFI6, IFI44L, IFI44, USP18, IFIT2, SAMD9L, BIRC4BP, DNAPTP6, OAS3, LY6E, IFIT1, LIPA, LOC129607, ISG15, PARP14, MX1, OAS2, OASL, CCL2, HERC5, OAS1.

Embodiment 150

The method of embodiment 147 wherein the type I IFN or IFNα-inducible PD marker expression profile comprises up-regulated expression or activity of genes IFIT1, IFIT3, IRF7, IFI6, IL6ST, IRF2, LY6E, MARCKS, MX1, MX2, OAS1, EIF2AK2, ISG15, STAT2, OAS3, IFI44, IFI44L, HERC5, RAB8B, LILRA5, RSAD2, and FCHO2.

Embodiment 151

The method of embodiment 147 wherein the type I IFN or IFNα-inducible PD marker expression profile comprises up-regulated expression or activity of genes SERPING1, IFIT2, IFIT3, IFI6, LY6E, MX1, OAS1, ISG15, IFI27, OAS3, IFI44, LAMP3, DNAPTP6, ETV7, HERC5, OAS2, USP18, XAF1, RTP4, SIGLEC1, and EPSTI1.

Embodiment 152

The method of embodiment 147 wherein the type I IFN or IFNα-inducible PD marker expression profile comprises up-regulated expression or activity of genes RTP4, RSAD2, HERC5, SIGLEC1, USP18, LY6E, ETV7, SERPING1, IFIT3, OAS1, HSXIAPAF1, G1P3, MX1, OAS3, IFI27, DNAPTP6, LAMP3, EPSTI1, IFI44, OAS2, IFIT2, and ISG15.

Embodiment 153

The method of embodiment 147 wherein the type I IFN or IFNα-inducible PD marker expression profile comprises up-regulated expression or activity of genes LAMP3, SIGLEC1, DNAPTP6, IFIT2, ETV7, RTP4, SERPING1, HERC5, XAF1, MX1, EPSTI1, OAS2, OAS1, OAS3, IFIT3, IFI6, USP18, RSAD2, IFI44, LY6E, ISG15, and IFI27.

Embodiment 154

The method of embodiment 147 wherein the type I IFN or IFNα-inducible PD marker expression profile comprises up-regulated expression or activity of genes DNAPTP6, EPSTI1, HERC5, IFI27, IFI44, IFI44L, IFI6, IFIT1, IFIT3, ISG15, LAMP3, LY6E, MX1, OAS1, OAS2, OAS3, PLSCR1, RSAD2, RTP4, SIGLEC1, and USP18.

Embodiment 155

The method of embodiment 147 wherein the type I IFN or IFNα-inducible PD marker expression profile comprises up-regulated expression or activity of genes SAMD9L, IFI6, IFI44, IFIT2, ZC3HAV1, ETV6, DAPP1, IL1RN, CEACAM1, OAS1, IFI27, OAS3, IFI44L, HERC5, IFIT1, EPSTI1, ISG15, SERPING1, OASL, GBP1, and MX1.

Embodiment 156

The method of embodiment 147 wherein the type I IFN or IFNα-inducible PD marker expression profile comprises up-regulated expression or activity of genes SAMD9L, IFI6, IFI44, IFIT2, OAS1, IFI27, OAS3, IFI44L, HERC5, IFIT1, EPSTI1, ISG15, SERPING1, OASL, GBP1, and MX1.

Embodiment 157

The method of embodiment 147 wherein the type I IFN or IFNα-inducible PD marker expression profile comprises up-regulated expression or activity of genes IFI6, RSAD2, IFI44, IFI44L, IFI27, MX1, IFIT1, ISG15, LAMP3, OAS3, OAS1, EPSTI1, IFIT3, OAS2, SIGLEC1, and USP18.

Embodiment 158

The method of embodiment 147 wherein the type I IFN or IFNα-inducible PD marker expression profile comprises up-regulated expression or activity of genes IFI6, RSAD2, IFI44, IFI44L, and IFI27.

Embodiment 159

The method of embodiment 147 wherein the patient has been diagnosed as having a disorder selected from the group consisting of lupus, idiopathic inflammatory myositis, Sjogren's syndrome, vasculitis, sarcoidosis, and psoriasis.

Embodiment 160

The method of embodiment 159 wherein the disorder is lupus.

Embodiment 161

The method of embodiment 147 wherein the therapeutic agent is a small molecule or a biologic agent.

Embodiment 162

The method of embodiment 161 wherein the biologic agent is an antibody.

Embodiment 163

The method of embodiment 162 wherein the antibody is MEDI-545.

Embodiment 164

The method of any one of embodiments 148-158 wherein the up-regulated expression or activity comprises at least a 2-fold increase in expression of one or more of the genes.

Embodiment 165

The method of any one of embodiments 148-158 wherein the up-regulated expression or activity comprises at least a 3-fold increase in expression of one or more of the genes.

Embodiment 166

The method of any one of embodiments 148-158 wherein the up-regulated expression or activity comprises an increase in mRNA levels of one or more of the genes.

Embodiment 167

The method of any one of embodiments 148-158 wherein the up-regulated expression or activity comprises an increase in protein levels of one or more of the genes.

Embodiment 168

The method of any one of embodiments 148-158 wherein the up-regulated expression or activity comprises an increase in enzymatic activity of a protein expressed from one or more of the genes.

Embodiment 169

The method of embodiment 147 wherein the sample is whole blood.

Embodiment 170

The method of embodiment 147 wherein the type I IFN or IFNα-inducible PD marker expression profile comprises down-regulated expression or activity of genes NOG, SLC4A1, PRSS33, and FEZ1.

Embodiment 171

The method of embodiment 147 wherein the type I IFN or IFNα-inducible PD marker expression profile comprises increased serum levels of polypeptides cancer antigen 125, ferritin, tissue factor, and MMP-3.

Embodiment 172

The method of embodiment 147 wherein the type I IFN or IFNα-inducible PD marker expression profile comprises decreased serum levels of polypeptides EGF, thrombopoietin, and CD40 ligand.

Embodiment 173

A method of diagnosing a patient as a having a disorder associated with increased IFNα levels comprising:

detecting presence or absence of an IFNα-inducible PD marker expression profile in a sample from the patient,

- wherein detecting presence of the IFNα-induced PD marker expression profile identifies the patient as having a disorder associated with increased IFNα levels.

Embodiment 174

The method of embodiment 173 wherein the IFNα-inducible PD marker expression profile comprises up-regulated expression or activity of genes MX1, LY6E, IFI27, OAS1, IFIT1, IFI6, IFI44L, ISG15, LAMP3, OASL, RSAD2, and IFI44.

Embodiment 175

The method of embodiment 173 wherein the IFNα-inducible PD marker expression profile comprises up-regulated expression or activity of genes IFI27, SIGLEC1, RSAD2, IFI6, IFI44L, IFI44, USP18, IFIT2, SAMD9L, BIRC4BP, DNAPTP6, OAS3, LY6E, IFIT1, LIPA, LOC129607, ISG15, PARP14, MX1, OAS2, OASL, CCL2, HERC5, OAS1.

Embodiment 176

The method of embodiment 173 wherein the IFNα-inducible PD marker expression profile comprises up-regulated expression or activity of genes IFIT1, IFIT3, IRF7, IFI6, IL6ST, IRF2, LY6E, MARCKS, MX1, MX2, OAS1, EIF2AK2, ISG15, STAT2, OAS3, IFI44, IFI44L, HERC5, RAB8B, LILRA5, RSAD2, and FCHO2.

Embodiment 177

The method of embodiment 173 wherein the IFNα-inducible PD marker expression profile comprises up-regulated expression or activity of genes SERPING1, IFIT2, IFIT3, IFI6, LY6E, MX1, OAS1, ISG15, IFI27, OAS3, IFI44, LAMP3, DNAPTP6, ETV7, HERC5, OAS2, USP18, XAF1, RTP4, SIGLEC1, and EPSTI1.

Embodiment 178

The method of embodiment 173 wherein the IFNα-inducible PD marker expression profile comprises up-regulated expression or activity of genes RTP4, RSAD2, HERC5, SIGLEC1, USP18, LY6E, ETV7, SERPING1, IFIT3, OAS1, HSXIAPAF1, G1P3, MX1, OAS3, IFI27, DNAPTP6, LAMP3, EPSTI1, IFI44, OAS2, IFIT2, and ISG15.

Embodiment 179

The method of embodiment 173 wherein the IFNα-inducible PD marker expression profile comprises up-regulated expression or activity of genes LAMP3, SIGLEC1, DNAPTP6, IFIT2, ETV7, RTP4, SERPING1, HERC5, XAF1, MX1, EPSTI1, OAS2, OAS1, OAS3, IFIT3, IFI6, USP18, RSAD2, IFI44, LY6E, ISG15, and IFI27.

Embodiment 180

The method of embodiment 173 wherein the IFNα-inducible PD marker expression profile comprises up-regulated expression or activity of genes DNAPTP6, EPSTI1, HERC5, IFI27, IFI44, IFI44L, IFI6, IFIT1, IFIT3, ISG15, LAMP3, LY6E, MX1, OAS1, OAS2, OAS3, PLSCR1, RSAD2, RTP4, SIGLEC1, and USP18.

Embodiment 181

The method of embodiment 173 wherein the IFNα-inducible PD marker expression profile comprises up-regulated expression or activity of genes SAMD9L, IFI6, IFI44, IFIT2, ZC3HAV1, ETV6, DAPP1, IL1RN, CEACAM1, OAS1, IFI27, OAS3, IFI44L, HERC5, IFIT1, EPSTI1, ISG15, SERPING1, OASL, GBP1, and MX1.

Embodiment 182

The method of embodiment 173 wherein the IFNα-inducible PD marker expression profile comprises up-regulated expression or activity of genes SAMD9L, IFI6, IFI44, IFIT2, OAS1, IFI27, OAS3, IFI44L, HERC5, IFIT1, EPSTI1, ISG15, SERPING1, OASL, GBP1, and MX1.

Embodiment 183

The method of embodiment 173 wherein the IFNα-inducible PD marker expression profile comprises up-regulated expression or activity of genes IFI6, RSAD2, IFI44, IFI44L, IFI27, MX1, IFIT1, ISG15, LAMP3, OAS3, OAS1, EPSTI1, IFIT3, OAS2, SIGLEC1, and USP18.

Embodiment 184

The method of embodiment 173 wherein the IFNα-inducible PD marker expression profile comprises up-regulated expression or activity of genes IFI6, RSAD2, IFI44, IFI44L, and IFI27.

Embodiment 185

The method of embodiment 173 wherein the disorder is lupus, idiopathic inflammatory myositis, Sjogren's syndrome, vasculitis, sarcoidosis, or psoriasis.

Embodiment 186

The method of embodiment 185 wherein the disorder is lupus.

Embodiment 187

The method of any one of embodiments 174-184 wherein the up-regulated expression or activity comprises at least a 2-fold increase in expression or activity of one or more of the genes.

Embodiment 188

The method of embodiment 187 wherein the up-regulated expression or activity comprises at least a 3-fold increase in expression or activity of one or more of the genes.

Embodiment 189

The method of any one of embodiments 174-184 wherein the up-regulated expression or activity comprises an increase in mRNA levels of one or more of the genes.

Embodiment 190

The method of any one of embodiments 174-184 wherein the up-regulated expression or activity comprises an increase in protein levels of one or more of the genes.

Embodiment 191

The method of any one of embodiments 174-184 wherein the up-regulated expression or activity comprises an increase in enzymatic activity of a protein expressed from one or more of the genes.

Embodiment 192

The method of any one of embodiments 174-184 wherein the type I IFN or IFNα-inducible PD marker expression profile further comprises down-regulated expression or activity of genes NOGSLC4A1, PRSS33, and FEZ1.

Embodiment 193

The method any one of embodiments 174-184 wherein the type I IFN or IFNα-inducible PD marker expression profile further comprises increased serum levels of polypeptides cancer antigen 125, ferritin, tissue factor, and MMP-3.

Embodiment 194

The method of any one of embodiments 174-184 wherein the type I IFN or IFNα-inducible PD marker expression profile further comprises decreased serum levels of polypeptides EGF, thrombopoietin, and CD40 ligand.

Embodiment 195

A method of identifying a candidate therapeutic for treating IFNα-mediated disorders comprising:

contacting cells comprising an IFNα-inducible PD marker expression profile with an agent; and

detecting presence or absence of a change in the IFNα-induced PD marker expression profile of the cells,

- wherein the presence of a change comprising a reduction in the up-regulation of the genes of the IFNα-inducible PD marker expression profile indicates the agent is a candidate therapeutic agent.

Embodiment 196

The method of embodiment 195 wherein the IFNα-inducible PD marker expression profile comprises up-regulated expression or activity of genes MX1, LY6E, IFI27, OAS1, IFIT1, IFI6, IFI44L, ISG15, LAMP3, OASL, RSAD2, and IFI44.

Embodiment 197

The method of embodiment 195 wherein the IFNα-inducible PD marker expression profile comprises up-regulated expression or activity of genes IFI27, SIGLEC1, RSAD2, IFI6, IFI44L, IFI44, USP18, IFIT2, SAMD9L, BIRC4BP, DNAPTP6, OAS3, LY6E, IFIT1, LIPA, LOC129607, ISG15, PARP14, MX1, OAS2, OASL, CCL2, HERC5, and OAS1.

Embodiment 198

The method of embodiment 195 wherein the IFNα-inducible PD marker expression profile comprises up-regulated expression or activity of genes IFIT1, IFIT3, IRF7, IFI6, IL6ST, IRF2, LY6E, MARCKS, MX1, MX2, OAS1, EIF2AK2, ISG15, STAT2, OAS3, IFI44, IFI44L, HERC5, RAB8B, LILRA5, RSAD2, and FCHO2.

Embodiment 199

The method of embodiment 195 wherein the IFNα-inducible PD marker expression profile comprises up-regulated expression or activity of genes SERPING1, IFIT2, IFIT3, IFI6, LY6E, MX1, OAS1, ISG15, IFI27, OAS3, IFI44, LAMP3, DNAPTP6, ETV7, HERC5, OAS2, USP18, XAF1, RTP4, SIGLEC1, and EPSTI1.

Embodiment 200

The method of embodiment 195 wherein the IFNα-inducible PD marker expression profile comprises up-regulated expression or activity of genes RTP4, RSAD2, HERC5, SIGLEC1, USP18, LY6E, ETV7, SERPING1, IFIT3, OAS1, HSXIAPAF1, G1P3, MX1, OAS3, IFI27, DNAPTP6, LAMP3, EPSTI1, IFI44, OAS2, IFIT2, and ISG15.

Embodiment 201

The method of embodiment 195 wherein the IFNα-inducible PD marker expression profile comprises up-regulated expression or activity of genes LAMP3, SIGLEC1, DNAPTP6, IFIT2, ETV7, RTP4, SERPING1, HERC5, XAF1, MX1, EPSTI1, OAS2, OAS1, OAS3, IFIT3, IFI6, USP18, RSAD2, IFI44, LY6E, ISG15, and IFI27.

Embodiment 202

The method of embodiment 195 wherein the IFNα-inducible PD marker expression profile comprises up-regulated expression or activity of genes DNAPTP6, EPSTI1, HERC5, IFI27, IFI44, IFI44L, IFI6, IFIT1, IFIT3, ISG15, LAMP3, LY6E, MX1, OAS1, OAS2, OAS3, PLSCR1, RSAD2, RTP4, SIGLEC1, and USP18.

Embodiment 203

The method of embodiment 195 wherein the IFNα-inducible PD marker expression profile comprises up-regulated expression or activity of genes SAMD9L, IFI6, IFI44, IFIT2, ZC3HAV1, ETV6, DAPP1, IL1RN, CEACAM1, OAS1, IFI27, OAS3, IFI44L, HERC5, IFIT1, EPSTI1, ISG15, SERPING1, OASL, GBP1, and MX1.

Embodiment 204

The method of embodiment 195 wherein the IFNα-inducible PD marker expression profile comprises up-regulated expression or activity of genes SAMD9L, IFI6, IFI44, IFIT2, OAS1, IFI27, OAS3, IFI44L, HERC5, IFIT1, EPSTI1, ISG15, SERPING1, OASL, GBP1, and MX1.

Embodiment 205

The method of embodiment 195 wherein the IFNα-inducible PD marker expression profile comprises up-regulated expression or activity of genes IFI6, RSAD2, IFI44, IFI44L, IFI27, MX1, IFIT1, ISG15, LAMP3, OAS3, OAS1, EPSTI1, IFIT3, OAS2, SIGLEC1, and USP18.

Embodiment 206

The method of embodiment 195 wherein the IFNα-inducible PD marker expression profile comprises up-regulated expression or activity of genes IFI6, RSAD2, IFI44, IFI44L, and IFI27.

Embodiment 207

The method of embodiment 195 wherein the cells obtained from a patient comprising a disorder associated with increased IFNα levels.

Embodiment 208

The method of embodiment 195 wherein the cells are cells treated with IFNα to induce the IFNα-inducible PD marker expression profile.

Embodiment 209

The method of embodiment 195 wherein the up-regulation of the genes of the IFNα-inducible PD marker expression profile is at least a 2-fold increase in expression of one or more of the genes of the profile.

Embodiment 210

The method of embodiment 195 wherein the up-regulation of the genes of the IFNα-inducible PD marker expression profile is at least a 3-fold increase in expression of one or more of the genes of the IFNα-inducible PD marker expression profile.

Embodiment 211

The method of embodiment 195 wherein the up-regulation of the genes of the IFNα-inducible PD marker expression profile comprises an increase in mRNA levels of one or more of the genes of the IFNα-inducible PD marker expression profile.

Embodiment 212

The method of embodiment 195 wherein the up-regulation of the genes of the IFNα-inducible PD marker expression profile comprises an increase in protein levels of one or more of the genes of the IFNα-inducible PD marker expression profile.

Embodiment 213

The method of embodiment 195 wherein the up-regulation of the genes of the IFNα-inducible PD marker expression profile comprises an increase in enzymatic activity of a protein expressed from one or more of the genes of the IFNα-inducible PD marker expression profile.

Embodiment 214

The method of any one of embodiments 196-206 wherein the type I IFN or IFNα-inducible PD marker expression profile further comprises down-regulated expression or activity of genes NOGSLC4A1, PRSS33, and FEZ1; and wherein the presence of a change comprising an increase in expression or activity of the down-regulated genes indicates the agent is a candidate therapeutic agent.

Embodiment 215

The method of any one of embodiments 196-206 wherein the type I IFN or IFNα-inducible PD marker expression profile further comprises increased serum levels of polypeptides cancer antigen 125, ferritin, tissue factor, and MMP-3; and wherein the presence of a change comprising a decrease in serum levels of the polypeptide indicates the agent is a candidate therapeutic agent.

Embodiment 216

The method of any one of embodiments 196-206 wherein the type I IFN or IFNα-inducible PD marker expression profile further comprises decreased serum levels of polypeptides EGF, thrombopoietin, and CD40 ligand wherein the presence of a change comprising an increase in serum levels of the polypeptide indicates the agent is a candidate therapeutic agent.

Embodiment 217

A set of probes comprising:

polynucleotides that specifically detect expression of any one of the sets of genes:

- (a) MX1, LY6E, IFI27, OAS1, IFIT1, IFI6, IFI44L, ISG15, LAMP3, OASL, RSAD2, and IFI44; or
- (b) IFI27, SIGLEC1, RSAD2, IFI6, IFI44L, IFI44, USP18, IFIT2, SAMD9L, BIRC4BP, DNAPTP6, OAS3, LY6E, IFIT1, LIPA, LOC129607, ISG15, PARP14, MX1, OAS2, OASL, CCL2, HERC5, OAS1; or
- (c) IFIT1, IFIT3, IRF7, IFI6, IL6ST, IRF2, LY6E, MARCKS, MX1, MX2, OAS1, EIF2AK2, ISG15, STAT2, OAS3, IFI44, IFI44L, HERC5, RAB8B, LILRA5, RSAD2, and FCHO2; or
- (d) SERPING1, IFIT2, IFIT3, IFI6, LY6E, MX1, OAS1, ISG15, IFI27, OAS3, IFI44, LAMP3, DNAPTP6, ETV7, HERC5, OAS2, USP18, XAF1, RTP4, SIGLEC1, and EPSTI1; or
- (e) RTP4, RSAD2, HERC5, SIGLEC1, USP18, LY6E, ETV7, SERPING1, IFIT3, OAS1, HSXIAPAF1, G1P3, MX1, OAS3, IFI27, DNAPTP6, LAMP3, EPSTI1, IFI44, OAS2, IFIT2, and ISG15; or
- (f) LAMP3, SIGLEC1, DNAPTP6, IFIT2, ETV7, RTP4, SERPING1, HERC5, XAF1, MX1, EPSTI1, OAS2, OAS1, OAS3, IFIT3, IFI6, USP18, RSAD2, IFI44, LY6E, ISG15, and IFI27; or
- (g) DNAPTP6, EPSTI1, HERC5, IFI27, IFI44, IFI44L, IFI6, IFIT1, IFIT3, ISG15, LAMP3, LY6E, MX1, OAS1, OAS2, OAS3, PLSCR1, RSAD2, RTP4, SIGLEC1, and USP18; or
- (h) SAMD9L, IFI6, IFI44, IFIT2, ZC3HAV1, ETV6, DAPP1, IL1RN, CEACAM1, OAS1, IFI27, OAS3, IFI44L, HERC5, IFIT1, EPSTI1, ISG15, SERPING1, OASL, GBP1, and MX1; or
- (i) SAMD9L, IFI6, IFI44, IFIT2, OAS1, IFI27, OAS3, IFI44L, HERC5, IFIT1, EPSTI1, ISG15, SERPING1, OASL, GBP1, and MX1; or
- (j) IFI6, RSAD2, IFI44, IFI44L, IFI27, MX1, IFIT1, ISG15, LAMP3, OAS3, OAS1, EPSTI1, IFIT3, OAS2, SIGLEC1, and USP18; or
- (k) IFI6, RSAD2, IFI44, IFI44L, and IFI27; or
- (l) NOGSLC4A1, PRSS33, and FEZ1.

Embodiment 218

A kit comprising any of the set of probes recited in embodiment 217.

Embodiment 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

detecting expression of the reporter gene,

- wherein expression of the reporter gene indicates IFN activity in the sample.

Embodiment 220

The method of embodiment 219 wherein cells are HEK293H cells.

Embodiment 221

The method of embodiment 219 wherein the reporter gene is luciferase, chloramphenicol acetyl transferase, β-galactosidase, green fluorescent protein, β-glucuronidase, or secreted placental alkaline phosphatase.

Embodiment 222

The method of embodiment 221 wherein the reporter gene is luciferase.

Embodiment 223

The method of embodiment 222 wherein the luciferase is Gaussia princeps luciferase.

Embodiment 224

The method of embodiment 219 further comprising quantitating level of expression of the reporter gene.

Embodiment 225

The method of embodiment 224 further comprising correlating the level of expression of the reporter gene to level of IFN activity in the sample.

All publications, patents and patent applications mentioned in this specification are herein incorporated by reference into the specification to the same extent as if each individual publication, patent or patent application was specifically and individually indicated to be incorporated herein by reference.

This application claims the benefit of priority of U.S. Provisional Application Ser. No. 60/873,008 filed Dec. 6, 2006, U.S. Provisional Application Ser. No. 60/907,762 filed Apr. 16, 2007, U.S. Provisional Application Ser. No. 60/924,219 filed May 3, 2007, U.S. Provisional Application Ser. No. 60/924,584 filed May 21, 2007, U.S. Provisional Application Ser. No. 60/960,187 filed Sep. 19, 2007, and U.S. Provisional Application Ser. No. 60/996,176 filed Nov. 5, 2007, herein incorporated by reference for all purposes. This application also claims the benefit of priority of U.S. Provisional Application Ser. No. 60/924,220 filed May 3, 2007, U.S. Provisional application entitled “Auto-Antibody Markers of Autoimmune Disease” filed Nov. 6, 2007 (Attorney docket no. IA201P2), and U.S. Provisional application entitled “Auto-Antibody Markers of Autoimmune Disease” filed Dec. 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 Ser. No. 60/907,767 filed Apr. 16, 2007, U.S. Provisional Application Ser. No. 60/996,174 filed Nov. 5, 2007, and PCT application entitled “Methods of Treating Systemic Lupus Erythematosus”, filed Dec. 6, 2007 (Attorney docket no. IA210PCT), herein incorporated by reference for all purposes.

The set of examples that follow are provided for the purpose of illustration only and the invention should in no way be construed as being limited to these examples.

EXAMPLES
Example 1a
Initial Identification of Up-Regulated Genes in Lupus Patients

Gene expression in whole blood of 5 (2 cutaneous and 3 severe) lupus patients and 5 healthy volunteers was profiled using Affymetrix whole genome array technology and qPCR validation. Gene expression fold-change values were determined by calculating the log₂signal intensity difference between individual lupus patient samples and the mean log₂signal intensity for the 5 healthy donor samples. 118 genes were identified as up-regulated by at least 2-fold in whole blood of all 5 lupus patients relative to the healthy volunteers.

Table 1 provides a summary for 71 of the 118 annotated genes identified as up-regulated by at least 2-fold in all 5 lupus patients. Table 2 provides the fold-up-regulation in gene expression for a subset of the 118 genes for each of the five lupus patients relative to the healthy volunteers. Table 2 also provides a comparison between fold-change values determined on two unique platforms (Affy GENECHIP microarray and TAQMAN (i.e. qPCR)).

TABLE 1

Genes Identified as Up-Regulated at Least 2-Fold in Whole Blood of Lupus Patients

(Table 1 discloses “DEAD (Asp-Glu-Ala-Asp)” as SEQ ID NO: 1)

Gene

Probe_ID
UniGene ID
Gene Title
Gene Sym
Ontology text missing or illegible when filed

Gene

Pathway
Avg. text missing or illegible when filed

Avg.

p-value

223674_s_

Hs.22065
CDC42 small effector 1
CDC42SE
7165//signal text missing or illegible when filed

5886//

5095//

—
2.355
6.012
3.657
1.20E−05
2.787
4.166
4.429
3.165
3.737

204415_at
Hs.523847
Interferon alpha-inducible
G1P3
6955//immune text missing or illegible when filed

16021//

—
—
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
FCHO2
—
—
—
—
4.381
7.361
2.980
0.023153
4.085
2.810
1.084
2.995
3.928

226312_at
Hs.407926
TORC2-specific protien A
AVO3
—
—
5488// text missing or illegible when filed

—
7.034
9.818
2.784
0.025167
3.163
2.487
1.045
3.274
3..953

215245_at
Hs.103183

text missing or illegible when filed

FMR1
6397//mRNA text missing or illegible when filed

5625//

3723//

—
6.070
6.826
2.758
0.032436
3.156
2.225
1.234
3.377
3.767

202194_x_ text missing or illegible when filed

Hs.482873
transmembrane emp24 text missing or illegible when filed

TMED5
6886// text missing or illegible when filed

5783//

8320//

—
6.365
9.064
2.699
0.085615
3.433
2.392

text missing or illegible when filed

2.553
4.064

226641_at
Hs.432706
Ankyrun repeat domain 44
LOC91526
—
—
—
—
7.476
10.170
2.694
0.030007
3.184
2.337
1.070
2.878
4.001

212585_at
Hs.430849
oxysterol binding
OSBPL8
6869// lipid text missing or illegible when filed

—
—
—
8.182
10.818
2.636
0.28512
3.093
2.358
1.163
2.445
4.120

protein- text missing or illegible when filed

201237_at
Hs.446123
capping protein (actin text missing or illegible when filed

CAPZA2
6461// protein text missing or illegible when filed

8290//F-

3779//

—
6.438
9.060
2.622
0.026777
3.338
2.289
1.004
2.64
3.836

226934_at
Hs.369606
Cleavage and text missing or illegible when filed

CPSF6
6397//mRNA text missing or illegible when filed

5634//

166//

—
5.619
8.241
2.622
0.007781
2.441
2.553
1.672
2.505
3.940

203983_at
Hs.96247
translin-associated text missing or illegible when filed

TSNAX
—
5634// text missing or illegible when filed

3677//

—
5.522
8.141
2.619
0.018885
2.958
2.306
1.051
2.878
3.900

221428_s_ text missing or illegible when filed

Hs.438970
transducin (beta)-like text missing or illegible when filed

TBL1XR1
6350// text missing or illegible when filed

5634//

—
—
5.859
8.472
2.568
0.017844
3.004
2.258
1.524
2.398
3.654

245838_at
Hs.512233
leukocyte text missing or illegible when filed

LILRA5
—
—
—
—
6.647
9.190
2.543
0.000349
2.071
2.399
2.263
2.840
3.144

209884_s_
Hs.250072
solute carrier family 4, text missing or illegible when filed

SLC4A7
6820//anion text missing or illegible when filed

16020//

5452//

—
5.525
7.068
2.543
0.006683
2.579
2.292
1.432
2.495
3.918

222605_at
Hs.356399
REST corepress or 3
RCOR3
45449// text missing or illegible when filed

5634//

3677//

—
5.249
7.775
2.526
0.032918
2.965
1.850
1.330
2.689
3.796

202304_at
Hs.508010
fibronectin type III text missing or illegible when filed

FNDC3A
—
—
—
—
4.793
7.268
2.475
0.014487
3.070
2.013
1.088
2.686
3.510

212579_at
Hs.8118
structural maintenence text missing or illegible when filed

SMCHD1
51276// text missing or illegible when filed

5694//

5515//

—
8.996
11.436
2.440
0.014165
2.930
2.037
1.088
3.002
3.143

208783_s_
Hs.510402
membrane text missing or illegible when filed

MCP
6955//immune text missing or illegible when filed

5886//

4872//

—
8.995
11.431
2.435
0.033522
3.101
2.327
1.100
2.518
3.068

155643_s
Hs.512233
leukocyte text missing or illegible when filed

LILRA5
—
—
—
—
6.942
9.367
2.426
0.001163
2.004
2.163
1.967
2.854
3.140

226617_at
Hs.470233
ADP-ribosylation factor- text missing or illegible when filed

ARL5
6886// text missing or illegible when filed

—
166// text missing or illegible when filed

—
4.385
6.781
2.385
0.07287
2.903
1.994
1.025
2.486
3.570

229584_at
Hs.187636
leucine-rich repeat
LRRK2
6468//protein text missing or illegible when filed

—
4672// text missing or illegible when filed

—
8.541
10.926
2.385
0.008927
2.872
1.812
1.216
2.938
3.087

kinase text missing or illegible when filed

211967_at
Hs.503709
pro-oncosis receptor text missing or illegible when filed

PORIMIN
—
16021// text missing or illegible when filed

4872//

—
8.352
10.735
2.383
0.032836
2.049
1.805
1.025
3.397
3.640

212192_at
Hs.109438
potassium channel text missing or illegible when filed

KCTD12
6813// text missing or illegible when filed

8076//

5249//

—
8.386
10.763
2.377
0.040801
2.993
1.615
1.076
2.365
3.838

208719_s_
Hs.5283305
DEAD (Asp-Glu-Ala-Asp)
DDX17
6396//RNA text missing or illegible when filed

5634//

166//

—
4.196
6.546
2.349
0.009291
1.614
4.874
1.826
2.018
1.416

201669_s_ text missing or illegible when filed

Hs.519909
myristoylayed alanine- text missing or illegible when filed

MARCKS
6928//cell text missing or illegible when filed

5886//

5516//

—
8.355
10.688
2.333
0.007803
2.738
2.177
1.128
3.141
2.479

222572_at
Hs.22256
protein phosphatase 2C, text missing or illegible when filed

PPM2C
6470//protein text missing or illegible when filed

5739//

287//

Krebs-TCA
5.335
7.664
2.329
0.069262
2.681
1.957
1.016
2.279
3.712

212195_at
Hs.532082
Interkeukin 6 signal text missing or illegible when filed

IL6ST
6955//immune text missing or illegible when filed

5886//

4872//

Ribosomal
8.733
11.015
2.282
0.006803
2.104
2.242
1.440
2.020
3.605

226711_at
Hs.468478
human T-cell leukimia text missing or illegible when filed

HTLF
6350// text missing or illegible when filed

5634//

3700//

—
7.581
9.859
2.278
0.016463
2.791
1.734
1.043
2.440
3.384

222846_at
Hs.389733
RAB8B, member RAS text missing or illegible when filed

RAB8B
6886// text missing or illegible when filed

—
166/ text missing or illegible when filed

—
5.584
7.857
2.273
0.044318
2.897
1.665
1.193
2.829
2.779

203566_s_ text missing or illegible when filed

Hs.904
amylo-1, 6-glucosidase, text missing or illegible when filed

AGL
5975// text missing or illegible when filed

43033//

4132//

Glycogen_
4.862
7.131
2.269
0.041967
2.283
1.758
1.057
2.579
3.668

text missing or illegible when filed

207564_x_

Hs.405410
O-linked N- text missing or illegible when filed

OGT
6493// protein text missing or illegible when filed

5634//

5515//

—
6.919
9.156
2.236
0.004017
2.212
2.086
1.479
2.355
3.048

219237_s_
Hs.512743
DnaJ (Hsp40) homolog, text missing or illegible when filed

DNAJB14
6457// protein text missing or illegible when filed

—
31072// text missing or illegible when filed

—
6.022
8.229
2.207
0.004813
2.454
1.832
1.172
2.322
3.253

214093_s_
Hs.567255
far upstream element text missing or illegible when filed

FUBP1
6350// text missing or illegible when filed

5634//

3697//

—
5.205
7.403
2.198
0.007941
1.994
1.644
1.199
2.491
3.661

218589_at
Hs.123464
purinergic receptior
P2RY5
7165// text missing or illegible when filed

16021//

1584//

GPCRDB_
6.422
8.576
2.154
0.011493
2.263
1.396
1.174
1.868
4.067

P2Y, text missing or illegible when filed

217941_s_
Hs.519346
erbb2 interacting protein
ERBB2IP
7049//cell
5634// text missing or illegible when filed

5176//

—
7.497
9.637
2.140
0.20564
2.313
2.026
1.112
2.354
2.895

cycle text missing or illegible when filed

203603_s_
Hs.34871
zinc finger homeobox 1b
ZFHX1B
6355//
5634// text missing or illegible when filed

3700//

TGF_Beta
4.781
6.915
2.134
0.021477
2.750
1.278
1.039
2.257
3.346

regulation text missing or illegible when filed

213111_at
Hs.173939
phosphatidy linositol-3- text missing or illegible when filed

PIP5K3
7242// text missing or illegible when filed

45121//

5515//

—
5.914
8.033
2.119
0.013802
2.394
1.869
1.048
2.315
2.968

213070_at
Hs.175343
Phosphoinositide-3- text missing or illegible when filed

PIK3C2A
6661// text missing or illegible when filed

5634//

4428//

Inositol

4.886
6.996
2.111
0.043279
2.405
1.654
1.103
1.921
3.472

218041_x_ text missing or illegible when filed

Hs.221847
solute carrier family 38, text missing or illegible when filed

SLC38A2
6865//amino text missing or illegible when filed

16020//

5279//

—
7.527
9.629
2.102
0.023894
2.417
1.890
1.140
1.927
3.136

202033_s_ text missing or illegible when filed

Hs.196102
RB1-inducible coiled- text missing or illegible when filed

RB1CC1
6350// text missing or illegible when filed

5634//

16301//

—
7.096
9.178
2.082
0.018164
2.798
1.406
1.272
2.225
2.709

200603_at
Hs.280342
protein kinase, cAMP- text missing or illegible when filed

PRKAR1A
6357//
5952// text missing or illegible when filed

166//

G_Protein_
9.293
11.373
2.080
0.030496
2.654
2.062
1.004
2.031
2.653

regulation text missing or illegible when filed

228996_at
Hs.495097
ring finger and CCCH- text missing or illegible when filed

RC3H1
16567// protein text missing or illegible when filed

151//

3723//

—
4.366
6.436
2.070
0.004022
3.253
1.738
1.435
1.897
2.026

1554479_ text missing or illegible when filed

Hs.446146
capase recruitment text missing or illegible when filed

CARD8
42981// text missing or illegible when filed

5634//

5515//

—
7.947
10.012
2.065
0.23092
2.558
1.733
1.054
2.133
2.848

203011_at
Hs.492120
inositol(myo)-1 (or 4)- text missing or illegible when filed

IMPA1
5975// text missing or illegible when filed

—
287// text missing or illegible when filed

5.383
7.442
2.059
0.043964
2.487
1.447
1.001
2.187
3.173

223940_x_ text missing or illegible when filed

Hs.187199
metastasis associated text missing or illegible when filed

MALAT1
—
—
—
—
4.166
6.212
2.046
0.003564
2.139
1.026
1.120
2.671
3.273

222317_at
Hs.445711
Phosphodiesterase 3B, text missing or illegible when filed

PDE3B
7165//signal text missing or illegible when filed

16020//

4119//

—
4.840
6.865
2.025
0.021022
2.593
1.664
1.155
1.901
2.812

228157_at
Hs.500775
zinc finger protein 207
ZNF207
6355//
5634// text missing or illegible when filed

3700//

—
6.352
8.371
2.019
0.043641
2.300
1.363
1.074
2.263
3.094

regulation text missing or illegible when filed

221505_at
Hs.385913
acidic (leucine-rich) text missing or illegible when filed

ANP32E
—
5634// text missing or illegible when filed

19212//

—
7.489
9.501
2.012
0.057164
2.070
1.656
1.053
2.051
3.028

1554472_ text missing or illegible when filed

Hs.304362
PHD finger protein 20-
PHF20L1
6355//
—
5515// text missing or illegible when filed

—
4.062
6.074
2.012
0.000292
2.270
1.460
1.355
2.254
2.718

like text missing or illegible when filed

regulation text missing or illegible when filed

226345_at
Hs.25362
ADP-ribosylation factor- text missing or illegible when filed

ARL8
6886// text missing or illegible when filed

—
166// text missing or illegible when filed

—
5.050
7.057
2.007
0.03497
2.308
1.707
1.169
1.898
2.953

224862_at
Hs.169782
Guanine nucleotide text missing or illegible when filed

GNAQ
6471//protein text missing or illegible when filed

5737//

166//

G_Protein_
6.663
8.665
2.002
0.046272
2.679
1.850
1.197
1.605
2.682

text missing or illegible when filed

207387_s_

Hs.1466
glycerol kinase
GK
5975// text missing or illegible when filed

5737//

166//

6.577
8.656
1.987
0.00655
2.663
1.071
1.146
2.292
2.765

222633_at
Hs.438970
transducin (beta)-like text missing or illegible when filed

TBL1XR1
6350// text missing or illegible when filed

5634//

—
—
5.358
7.324
1.966
3.89E−05
2.171
1.460
1.799
1.689
2.711

236244_at
Hs.491234
Ras-like without CAAX 1
RIT1
6886// text missing or illegible when filed

5886//

166//

—
5.105
7.064
1.960
0.018708
2.825
2.017
1.110
2.178
1.669

203080_s_ text missing or illegible when filed

Hs.470369
bromodomain adjacent text missing or illegible when filed

BAZ2B
6350// text missing or illegible when filed

5634//

3677//

—
7.254
9.212
1.959
0.008344
2.597
1.166
1.051
2.058
2.921

222587_s_ text missing or illegible when filed

Hs.127407
UDP-N-acetyl-alpha-D text missing or illegible when filed

GALNT7
5975// text missing or illegible when filed

5795//

4653//

O-Glycan
4.095
6.038
1.944
0.006624
2.585
1.283
1.121
2.393
2.336

text missing or illegible when filed

235057_at
Hs.472509
itchy homolog E3 text missing or illegible when filed

ITCH
1558//
5634// text missing or illegible when filed

3677//

—
3.238
5.161
1.923
0.001003
1.885
1.781
1.343
1.272
3.337

regulation text missing or illegible when filed

1554154_

Hs.310809
ganglioside induced text missing or illegible when filed

GDAP2
—
—
—
—
4.572
6.494
1.922
0.001031
2.092
1.729
1.615
1.761
2.413

226444_at
Hs.413434
solute carrier family 39 text missing or illegible when filed

SLC39A10
30001//metal text missing or illegible when filed

5634//

3676//

—
5.668
7.583
1.915
0.24435
1.542
1.861
1.070
1.880
3.221

204646_at
Hs.335034
dihydropyrimidine text missing or illegible when filed

DPYD
6118//electron text missing or illegible when filed

5737//

4152//

Pyrimidine
7.632
9.545
1.913
0.049899
2.288
1.489
1.263
1.806
2.719

text missing or illegible when filed

205321_at
Hs.539684
eukaryotic translation text missing or illegible when filed

EIF2S3
6412//protein text missing or illegible when filed

5843//

166//

Translation
6.682
8.563
1.881
0.030696
2.094
2.213
1.758
1.309
2.030

text missing or illegible when filed

202165_at
Hs.535731
protein phosphatase 1, text missing or illegible when filed

PPP1R2
5975// text missing or illegible when filed

—
4865// text missing or illegible when filed

— //

5.590
7.464
1.874
0.064575
2.078
1.532
1.055
1.763
2.943

201668_x_ text missing or illegible when filed

Hs.519909
myristoylated alaine- text missing or illegible when filed

MARCKS
6928//cell text missing or illegible when filed

5886//

5516//

—
4.137
5.987
1.850
0.001437
2.370
1.760
1.413
2.538
1.170

213701_at
Hs.494204
hypotheical protein DK text missing or illegible when filed

DKFZp434
—
—
—
—
3.954
5.802
1.848
0.044061
1.833
1.388
1.137
1.485
3.345

201110_s_ text missing or illegible when filed

Hs.164226
thrombospondin 1
THBS1
6928//cell text missing or illegible when filed

5576//

4866//

TGF_Beta
4.265
6.106
1.841
0.000653
1.953
1.964
1.018
2.122
2.149

text missing or illegible when filed

224800_at
Hs.368359
WD repeat and FYVE text missing or illegible when filed

WDFY1
—
5634// text missing or illegible when filed

5545//

—
6.372
8.193
1.820
0.027641
2.080
1.251
1.067
2.247
2.457

218396_at
Hs.511668
vacuolar protein sorting text missing or illegible when filed

VPS13C
80104//protein text missing or illegible when filed

—
—
—
7.271
9.069
1.798
0.020416
1.839
1.550
1.168
1.532
2.902

213737_x_ text missing or illegible when filed

Hs.146211
hypotheical text missing or illegible when filed

LOC28376
—
—
—
—
7.771
9.551
1.780
0.02147
1.892
1.274
1.120
1.602
3.013

202973_x_ text missing or illegible when filed

Hs.97270
family with sequence text missing or illegible when filed

FAM13A1
—
—
—
—
5.718
7.492
1.774
0.010098
1.538
2.187
1.599
1.388
2.157

205198_s_ text missing or illegible when filed

Hs.496414
ATPase, Cu++ text missing or illegible when filed

ATP7A
6825//copper text missing or illegible when filed

5783//

166//

Oxidative
4.069
5.842
1.773
0.008607
2.038
1.332
1.003
1.660
2.833

text missing or illegible when filed

208867_s_

Hs.529862
casein kinase 1, alpha 1
CSNK1A1
6468// protein text missing or illegible when filed

—
166// text missing or illegible when filed

—
5.746
7.514
1.786
0.007708
2.015
1.473
1.260
1.787
2.304

text missing or illegible when filed

indicates data missing or illegible when filed

TABLE 2

Up-Regulation in Gene Expression for a Set of Genes for each of Five Lupus Patients

I29KHR.SLE
I29KHR.S
RH33XR.SLE
RH33XR.S

Probe_ID
Gene Symbol
(TaqMan)
LE (Affy)
(TaqMan)
LE (Affy)

text missing or illegible when filed

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
7.44
4.86
6.49

205170_at
STAT2
11.55
8.67
9.74
2.25
8.08
2.16
6.37
2.92
4.12
2.62

text missing or illegible when filed

indicates data missing or illegible when filed

Example 1a
Validation of Genes Identified as Up-Regulated Genes in Lupus Patients

To further identify candidate PD markers for anti-IFN-α mAb clinical trials in SLE, the Affymetrix Human Genome U133 Plus 2.0 GENECHIP® array platform was used to profile WB from 46 SLE patients and WB from 24 age- and sex-matched healthy donors. It was observed that 245 and 77 probe sets were upregulated and downregulated, respectively, in WB of SLE patients compared with that from healthy control donors.

Of the 245 probe sets upregulated in WB of SLE patients, 114 were type I IFN inducible. Table 30 lists the 50 most upregulated probe sets in WB of these SLE patients; 76% of them are type I IFN inducible. Table 30 also lists the prevalence of the overexpression of these genes in WB of SLE patients. The majority of these genes are overexpressed by at least 2-fold in 65% to 80% of the patients profiled. The robust and prevalent overexpression of a large number of type I IFN-inducible genes in SLE patients suggests that they might be suitable PD markers for clinical trials that investigate an anti-IFN-α mAb therapy for SLE.

TABLE 30

50 most upregulated probe sets in whole blood of SLE patients

Gene

q Value

Probe ID
Gene Title
Symbol
log₂fc
(FDR)
Prevalence

202411_at
interferon, alpha-inducible protein 27
IEI27
4.60
8.41E−07
73.91

219519_s_at
sialic acid binding Ig-like lectin 1,
SIGLEC1
3.52
7.28E−07
65.22

sialoadhesin

214059_at
Interferon-induced protein 44
IEI44
3.51
8.04E−07
73.91

213797_at
radical S-adenosyl methionine domain
RSAD2
3.29
9.86E−06
71.74

containing 2

204415_at
interferon, alpha-inducible protein 6
IEI6
3.21
2.25E−09
82.61

242625_at
radical S-adenosyl methionine domain
RSAD2
3.19
1.55E−06
69.57

containing 2

204439_at
interferon-induced protein 44-like
IFI44L
3.14
4.99E−06
71.74

219211_at
ubiquitin specific peptidase 18
USP18
2.84
2.23E−06
67.39

214453_s_at
interferon-induced protein 44
IEI44
2.72
1.07E−05
71.74

202145_at
lymphocyte antigen 6 complex, locus E
LY6E
2.53
7.28E−07
63.04

207329_at
matrix metallopeptidase 8 (neutrophil
MMP8
2.51
0.00111
60.87

collagenase)

202869_at
2′-5′-oligoadenylate synthetase 1, 40/46 kDa
OAS1
2.33
1.66E−06
69.57

222154_s_at
DNA polymerase-transactivated protein 6
DNAPTP6
2.32
1.14E−05
65.22

44673_at
sialic acid binding Ig-like lectin 1,
SIGLEC1
2.31
2.23E−06
58.70

sialoadhesin

242234_at
XIAP associated factor-1
BIRC4BP
2.31
8.41E−07
65.22

203153_at
interferon-induced protein with
IFIT1
2.25
9.53E−05
67.39

tetratricopeptide repeats 1

218400_at
2′-5′-oligoadenylate synthetase 3, 100 kDa
OAS3
2.24
1.23E−05
67.39

212768_s_at
olfactomedin 4
OLFM4
2.23
0.00608
60.87

241869_at
apolipoprotein L, 6
APOL6
2.22
0.00045
80.43

235643_at
sterile alpha motif domain containing 9-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, 40/46 kDa
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

1555643_s_at
leukocyte immunoglobulin-like receptor,
LILRAS
2.14
8.41E−07
76.09

subfamily A

222816_s_at
zinc finger, CCHC domain containing 2
ZCCHC2
2.09
5.43E−05
80.43

205569_at
lysosomal-associated membrane protein 3
LAMP3
2.08
2.74E−06
65.22

226702_at
hypothetical protein LOC129607
LOC12960
2.07
5.96E−05
67.39

7

215838_at
leukocyte immunoglobulin-like receptor,
LILRAS
2.07
1.87E−05
71.74

subfamily A

219863_at
hect domain and RLD 5
HERCS
2.03
1.53E−05
67.39

204747_at
interferon-induced protein with
IFIT3
2.01
1.55E−06
67.39

tetratricopeptide repeats 3

200986_at
serpin peptidase inhibitor, Glade G (C1
SERPING
1.98
0.00013
67.39

inhibitor), member 1
1

224225_s_at
ets variant gene 7 (TEL2 oncogene)
ETV7
1.98
2.48E−05
58.70

219684_at
receptor (chemosensory) transporter protein
RTP4
1.96
2.74E−06
63.04

4

206133_at
XIAP associated factor-1
BIRC4BP
1.96
7.28E−07
65.22

206871_at
elastase 2, neutrophil
ELA2
1.95
0.00316
54.35

217502_at
interferon-induced protein with
IFIT2
1.95
4.86E−06
71.74

tetratricopeptide repeats 2

237340_at
solute carrier family 26, member 8
SLC26A8
1.93
6.68E−06
60.87

235276_at
—
—
1.93
6.44E−06
65.22

203757_s_at
carcinoembryonic antigen-related cell adhesion
CEACAM6
1.91
0.00124
47.83

molecule 6

202086_at
myxovirus (influenza virus) resistance 1,
MX1
1.90
2.66E−05
67.39

interferon-inducible protein p78 (mouse) ///

myxovirus (influenza virus) resistance 1,

interferon-inducible protein p78 (mouse)

241916_at
Phospholipid scramblase 1
PLSCR1
1.89
4.86E−06
73.91

203595_s_at
interferon-induced protein with
IFITS
1.89
2.81E−08
69.57

tetratricopeptide repeats 5

205660_at
2′-5′-oligoadenylate synthetase-like
OASL
1.89
1.94E−05
65.22

219352_at
hect domain and RLD 6
HERC6
1.87
9.79E−06
63.04

211657_at
carcinoembryonic antigen-related cell adhesion
CEACAM6
1.86
0.00667
60.87

molecule 6

228439_at
basic leucine zipper transcription factor,
BATF2
1.86
2.63E−05
63.04

ATF-like 2

Data were generated from 46 SLE patients and 24 healthy controls using SAM and FDR in R (see Methods).

Type I IFN-inducible genes are highlighted in bold.

FDR = false discovery rate;

SAM = significance analysis of microarrays;

SLE = systemic lupus erythematosus;

WB = whole blood.

FIG. 80 (top panel) shows a heat map of the expression of the 114 upregulated type I IFN-inducible probe sets in SLE patients and healthy controls. A total of 32/46 of the SLE patients profiled showed significant overexpression of the type I IFN gene signature. To confirm the observation that type I IFN-inducible genes are overexpressed in WB of SLE patients, WB was procured from 54 SLE patients in a prospective study. FIG. 81A shows the PCA plot of the 46 SLE patients in the first study using the 114 overexpressed type I IFN-inducible probes. A clear difference was observed between SLE patients that had distinct overexpression of type I IFN gene signature from healthy donors and SLE patients that had weak or nondetectable type I IFN gene signature in WB. FIG. 81B shows the PCA plot from the 54 SLE patients in the prospective study using the same 114 type I IFN-inducible probe sets identified. A similar separation of SLE patients was observed based on type I IFN gene signature as in FIG. 81A. The distribution of the type I IFN gene signature scores in the prospective study was also similar to that of the first study (data not shown). The ability to use the overexpressed type I IFN-inducible genes identified to segregate SLE patients into 2 distinct groups—patients with or without type I IFN gene signature—validated the accurate identification of overexpression in the type I IFN gene signature in WB of SLE patients.

In addition to the overexpression of a type I IFN gene signature, the overexpression of a gene signature that is indicative of granulocyte activation in WB of SLE patients was observed. The granulocyte gene signature included (but was not limited to) the following genes: AZU, DEFA1, DEFA4, ELA2, MMP8, MMP9, RNAS2, MPO, CAMP, FCAR, and CYBB (FIG. 80, second panel). The granulocyte gene signature was present in about 50% of the SLE patients profiled.

The 50 most downregulated probe sets observed in WB of SLE patients are shown in Table 31. The downregulation of T, NK, and B cell gene signatures was observed in WB of SLE patients (FIG. 80, panels three, four, and five, respectively); this is in agreement with the observation of lymphopenia in SLE patients previously reported in the literature (Bennett L, Palucka A K, Arce E et al.: Interferon and granulopoiesis signatures in systemic lupus erythematosus blood. J Exp Med. 197(6), 711-723 (2003), Rivero S J, Diaz-Jouanen E and Alarcon-Segovia D: Lymphopenia in systemic lupus erythematosus. Clinical, diagnostic, and prognostic significance. Arthritis Rheum. 21(3), 295-305 (1978).

TABLE 31

Top 50 most downregulated transcripts in whole blood of SLE patients

q Value

Probe ID
Gene Title
Gene Symbol
log₂fc
(FDR)
Prevalence

1552713_a_at
solute carrier family 4, anion
SLC4A1
−1.82
0.00021
69.57

exchanger, member 1 (erythrocyte

membrane protein band 3, Diego

blood group)

1552348_at
protease, serine, 33
PRSS33
−1.71
0.00046
63.04

211734_s_at
Fc fragment of IgE, high affinity I,
FCER1A
−1.59
0.00083
54.35

receptor for; alpha polypeptide /// Fc

fragment of IgE, high affinity I,

receptor for; alpha polypeptide

236307_at
BTB and CNC homology 1, basic
BACH2
−1.51
0.00012
54.35

leucine zipper transcription factor 2

214470_at
killer cell lectin-like receptor
KLRB1
−1.50
0.00000
58.70

subfamily B, member 1 /// killer cell

lectin-like receptor subfamily B,

member 1

209570_s_at
DNA segment on chromosome 4
D4S234E
−1.46
0.00000
65.22

(unique) 234 expressed sequence

217143_s_at
T cell receptor alpha locus /// T cell
TRA@///
−1.38
0.00001
58.70

receptor delta locus
TRD@

203562_at
fasciculation and elongation protein
FEZ1
−1.36
0.00028
89.13

zeta 1 (zygin I)

227198_at
AF4/FMR2 family, member 3
AFF3
−1.35
0.00046
45.65

207840_at
CD160 molecule
CD160
−1.34
0.00079
47.83

232286_at
AF4/FMR2 family, member 3
AFF3
−1.34
0.00003
56.52

209993_at
ATP-binding cassette, sub-family B
ABCB1
−1.32
0.00002
63.04

(MDR/TAP), member 1

209815_at
patched homolog 1 (Drosophila)
PTCH1
−1.29
0.00003
54.35

241881_at
olfactory receptor, family 2,
OR2W3
−1.29
0.01736
50.00

subfamily W, member 3

213674_x_at
immunoglobulin heavy constant delta
IGHD
−1.29
0.01801
50.00

231798_at
Noggin
NOG
−1.28
0.00234
73.91

239673_at
Nuclear receptor subfamily 3, group
NR3C2
−1.27
0.00004
56.52

C, member 2

221748_s_at
tensin 1 /// tensin 1
TNS1
−1.23
0.00953
50.00

218864_at
tensin 1
TNS1
−1.22
0.00718
50.00

219630_at
PDZK1 interacting protein 1
PDZK1IP1
−1.20
0.00528
56.52

1553177_at
SH2 domain containing 1B
SH2D1B
−1.20
0.00187
47.83

229513_at
Spermatid perinuclear RNA binding
STRBP
−1.20
0.00017
58.70

protein

243054_at
Zinc finger, MYND domain
ZMYND11
−1.20
0.00101
60.87

containing 11

236796_at
BTB and CNC homology 1, basic
BACH2
−1.20
0.00004
56.52

leucine zipper transcription factor 2

203661_s_at
tropomodulin 1
TMOD1
−1.19
0.00675
50.00

239278_at
CDNA clone IMAGE:5301129

−1.17
0.00002
65.22

235400_at
Fc receptor-like A
FCRLA
−1.17
0.00099
52.17

240690_at
Homolog of rat pragma of Rnd2
DKFZp761P0
−1.17
0.00012
52.17

423

210746_s_at
erythrocyte membrane protein band
EPB42
−1.16
0.00552
45.65

4.2 /// erythrocyte membrane protein

band 4.2

232478_at
Nuclear receptor subfamily 6, group
NR6A1
−1.15
0.00004
47.83

A, member 1

243810_at
Similar to Heterogeneous nuclear
LOC341333
−1.15
0.00014
47.83

ribonucleoprotein Al (Helix-

destabilizing protein) (Single-strand

RNA-binding protein) (hnRNP core

protein Al)

228599_at
membrane-spanning 4-domains,
MS4A1
−1.14
0.00454
45.65

subfamily A, member 1

212827_at
immunoglobulin heavy constant mu
IGHM
−1.14
0.00324
45.65

/// immunoglobulin heavy constant

mu

1552349_a_at
protease, serine, 33
PRSS33
−1.13
0.02357
47.83

216191_s_at
T cell receptor alpha locus /// T cell
TRA@///
−1.12
0.01073
50.00

receptor delta locus /// B-cell
TRD @///

CLL/lymphoma 11B (zinc finger
BCL11B

protein)

232686_at
sialic acid binding Ig-like lectin,
SIGLECP3
−1.12
0.00003
58.70

pseudogene 3

211532_x_at
killer cell immunoglobulin-like
KIR2DS2
−1.10
0.04011
54.35

receptor, two domains, short

cytoplasmic tail, 2

1563217_at
Protein kinase (cAMP-dependent,
PKIA
−1.10
0.00024
58.70

catalytic) inhibitor alpha

243798_at
Burkitt lymphoma receptor 1, GTP
BLR1
−1.10
0.00044
54.35

binding protein (chemokine (C-X-C

motif) receptor 5)

220751_s_at
chromosome 5 open reading frame 4
C5orf4
−1.09
0.00531
50.00

202555_s_at
myosin, light chain kinase /// myosin,
MYLK
−1.09
0.00149
52.17

light chain kinase

230245_s_at
hypothetical protein LOC283663
LOC283663
−1.09
0.00977
47.83

233921_s_at
MAD1 mitotic arrest deficient-like 1
MAD1L1
−1.08
0.00001
41.30

(yeast)

214974_x_at
chemokine (C-X-C motif) ligand 5
CXCLS
−1.08
0.00717
54.35

209569_x_at
DNA segment on chromosome 4
D4S234E
−1.08
0.00005
58.70

(unique) 234 expressed sequence

235401_s_at
Fc receptor-like A
FCRLA
−1.08
0.00173
50.00

205900_at
keratin 1 (epidermolytic
KRT1
−1.08
0.04518
43.48

hyperkeratosis)

242509_at
Chromosome 16 open reading frame
C16orf74
−1.08
0.00016
47.83

74

209994_s_at
ATP-binding cassette, sub-family B
ABCB1 ///
−1.08
0.00000
56.52

(MDR/TAP), member 1 /// ATP-
ABCB4

binding cassette, sub-family B

(MDR/TAP), member 4

204793_at
G protein-coupled receptor associated
GPRASP1
−1.08
0.00026
45.65

sorting protein 1

Data were generated from 46 SLE patients and 24 healthy controls using SAM and FDR in R (see Methods).

FDR = false discovery rate;

SLE = systemic lupus erythematosus;

SAM = significance analysis of microarrays;

WB = whole blood.

To further confirm the observation of overexpression of the type I IFN and granulocyte signatures and to identify other signaling pathways that may be altered in SLE, a pathway and network analysis was carried out with GENEGO software (see Methods). Overall, for SLE, this pathway analysis confirmed the activation of the type I IFN pathway, along with the activation of a granulocyte signature, and the underexpression of the T-cell signaling pathway. Additionally, in the patients profiled, the activation of the IL-10 signaling pathway was among the other notable pathways found to be altered. This may suggest B cell activation and be indicative of the abnormal apoptosis of T-cell subsets observed in SLE patients. (Diaz-Alderete A, Crispin J C, Vargas-Rojas M I and Alcocer-Varela J: IL-10 production in B cells is confined to CD154+ cells in patients with systemic lupus erythematosus. J Autoimmun. 23(4), 379-383 (2004), Wang H, Xu J, Ji X et al.: The abnormal apoptosis of T cell subsets and possible involvement of IL-10 in systemic lupus erythematosus. Cell Immunol. 235(2), 117-121 (2005)).

Confirmation of Overexpression of Type I IFN-Inducible Genes:

To confirm the overexpression of type I IFN-inducible genes in SLE that were observed in the microarray analyses, a BIOMARK™ 48.48 dynamic array was used to perform high throughput (HTP) TAQMAN QRT-PCR on 40 of the type I IFN-inducible genes (selected based on their magnitude and prevalence of overexpression in whole blood of SLE patients). TAQMAN QRT-PCR assays confirmed the overexpression of all 40 genes in whole blood of 35 of the originally profiled 46 SLE patients. The overexpression of 15 of the 40 type I IFN-inducible genes using TAQMAN QRT-PCR assays is shown in FIG. 83A. These genes were upregulated by an average of 8- to 92-fold, and all were significantly overexpressed (P<0.05). These observations provide evidence that type I IFN-inducible genes are significantly overexpressed in SLE patients. The consistency of the results among microarray and TAQMAN assays and the strong correlation (correlation coefficient >0.98) between microarray and TAQMAN assays for 21 IFN-inducible genes in 2 example SLE patients (FIGS. 83B and 4C) argues for their potential as PD and diagnostic markers in clinical trials that investigate anti-IFN-α approaches in the treatment of SLE.

Example 2
Potential PD Markers Selected from Genes Up-Regulated in Lupus Patients

Using the whole genome profiling data described in Example 1a, a group of candidate PD markers were selected. These candidate markers are provided in Table 3.

TABLE 3

Candidate PD markers

Probe_ID
Gene Symbol
Group

204415_at
HERC5
1

202411_at
IFI27
1

214453_s_at
IFI44
1

229450_at
IFIT3
1

1555643_s_at
LILRA5
1

205483_s_at
G1P2
1

204439_at
IFI44L
1

203153_at
IFIT1
1

202145_at
LY6E
1

202869_at
OAS1
1

218400_at
OAS3
1

242625_at
RSAD2
1

228220_at
FCHO2
2

205483_s_at
G1P3
2

212195_at
IL6ST
2

203275_at
IRF2
2

1555643_s_at
LILRA5
2

205170_at
STAT2
2

208436_s_at
IRF7
3

211967_at
PORIMIN
3

226312_at
AVO3
3

201669_s_at
MARCKS
3

222846_at
RAB8B
3

Example 3
Candidate PD Markers Exhibit Minimal Variation in Healthy Donors

qPCR was conducted for a selected group of candidate PD markers to determine whether they exhibited variation at baseline in the whole blood of healthy volunteers. qPCR indicated that baseline variation was minimal. See Table 4, which provides the baseline qPCR data (healthy volunteers shown in shaded columns).

TABLE 4

Baseline Variation of Candidate PD Markers

embedded image

Example 4
IFNα Stimulates Up-Regulation in Expression of Candidate PD Markers in Whole Blood of Healthy Volunteers

A study was performed to determine whether IFNα could stimulate expression of candidate PD markers in whole blood of healthy volunteers. Whole blood of healthy volunteers was collected in heparinized tubes, transferred to the appropriate wells of 6-well culture plates, and incubated with leukocyte IFN doses of 3, 30, 100, and 300 I.U. and then incubated for 4 hours at 37° C., 5% CO₂. Fold-induction of expression of candidate PD markers for genes IFI44, IRF2, RSAD2, G1P3, and HERC5 was determined using RNA isolated from PBMCs (Peripheral Blood Mononuclear Cells) with Qiagen's RNAeasy kit. As shown in Table 5 (IFI44 and IRF2), Table 6 (RSAD2), and Table 7 (G1P3 and HERC5) leukocyte IFN causes up-regulation in expression of each of these candidate PD markers. See also FIG. 1 (IFI44), FIG. 2 (IRF2), FIG. 3 (RSAD2), FIG. 4 (G1P3), and FIG. 5 (HERC5) for a graphical analysis of these candidate PD marker expression results.

A summary hierarchical clustering of all samples using 1384 genes differentially regulated by IFN type 1, IFN type 2, or TNFα obtained from a separate experiment is shown in FIG. 17. A heat map with a summary hierarchical clustering is also provided for 689 type I IFN inducible probe sets used on whole blood samples from healthy donors ex vivo stimulated with IFN type 1, IFN type 2, or TNFα. See FIG. 64.

TABLE 5

Induced IFI44 and IRF2 Expression Following Leukocyte IFN

Stimulation of Healthy Volunteer's Whole Blood

Sample
Gene
Average FC
StDev

63A Media
IFI44
1.00

63A IFN3
IFI44
8.58
0.16

63A IFN30
IFI44
8.27
0.07

63A IFN100
IFI44
15.12
0.50

63A IFN300
IFI44
12.42
0.04

63A Media
IRF2
1.00

63A IFN3
IRF2
2.25
0.08

63A IFN30
IRF2
1.96
0.06

63A IFN100
IRF2
2.19
0.06

63A IFN300
IRF2
3.75
0.10

TABLE 6

Induced RSAD2 Expression Following Leukocyte IFN

Stimulation of Healthy Volunteer's Whole Blood

Sample
Gene
Average FC
StDev

63A Media
RSAD2
1.00

63A IFN3
RSAD2
10.88
0.11

63A IFN30
RSAD2
11.14
0.21

63A IFN100
RSAD2
14.96
0.12

63A IFN300
RSAD2
25.50
0.50

TABLE 7

Induced G1P3 and HERC5 Expression Following Leukocyte

IFN Stimulation of Healthy Volunteer's Whole Blood

Sample
Gene
Average FC
StDev

63A Media
G1P3
1.00

63A IFN3
G1P3
42.88
1.03

63A IFN30
G1P3
25.76
0.10

63A IFN100
G1P3
21.72
0.48

63A IFN300
G1P3
16.02
0.06

63A Media
HERC5
1.00

63A IFN3
HERC5
14.17
0.12

63A IFN30
HERC5
13.74
0.12

63A IFN100
HERC5
18.51
0.58

63A IFN300
HERC5
23.55
0.54

Example 5
IFNα Ab Neutralizes IFNα-Induced Candidate PD Marker Expression in Healthy Volunteers' Whole Blood
Source of Interferon=IFNα2a

Because IFNα treatment of healthy volunteers' whole blood induced expression of candidate PD markers, it was determined whether IFNα Ab, MEDI-545, could neutralize the induction of expression of these markers.

Blood was drawn from each of three donors into heparin tubes. Aliquots of 2.5 ml of drawn blood were added to each of 4 wells of 6- or 24-well treatment plates. The 4 wells were designated for treatment as follows: (a) blood+vehicle, (b) blood+100 IU IFNα2a, (c) blood+100 IU IFNα2a+MEDI-545 (IFNα Ab), and (d) blood+100 IU IFNα2a+R347 (control Ab).

Wells containing blood to be treated with Ab were first incubated with either MEDI-545 (IFNα Ab; well (c)) or R347 (control Ab; well (d)) for 30 minutes. Following Ab treatment, vehicle (well (a)) or IFN α2a (wells (b), (c), and (d)) was added to the appropriate wells and was then incubated for an additional 4 hours at 37° C., 5% CO₂. The samples were then transferred to PAXgene tubes and incubated at room temperature for 2 hr. Following the 2 hr incubation the tubes were transferred to −80° C. for storage.

Following, at least, an overnight incubation at −80° C. the total RNA of the cells was prepared according to the PAXgene protocol. First and second strand cDNA was prepared via Affy GRP methods and TAQMAN was conducted on the cDNA samples.

Expression of at least 11 candidate PD markers, previously identified as up-regulated in lupus patients, could be neutralized by MEDI-545 in the IFNα2a-stimulated whole blood. See Table 8 (RAB8B), Table 9 (IRF7), Table 10 (MARCKS), Table 11 (IL6ST), Table 12 (LY6E), Table 13 (IFIT3), Table 14 (IFIT1), Table 15 (HERC5), Table 16 (OAS1), Table 17 (OAS3), and Table 18 (RSAD2), which provide quantitative gene expression analysis for each of these 11 genes in the whole blood of each of the 3 healthy volunteers.

TABLE 8

IFN α2a-Induced RAB8B Gene Expression is Neutralized by MEDI-545

Sample
Gene
Average
StDev

107 VEH
RAB8B
1.0

107 IFN
RAB8B
3.45
0.31

107 IFN + 545
RAB8B
1.30
0.04

107 IFN + R347
RAB8B
3.15
0.03

163 VEH
RAB8B
0.70
0.01

163 IFN
RAB8B
2.20
0.04

163 IFN + 545
RAB8B
1.18
0.01

163 IFN + R3437
RAB8B
3.71
0.02

175 VEH
RAB8B
0.64
0.01

175 IFN
RAB8B
2.63
0.04

175 IFN + 545
RAB8B
1.15
0.02

175 IFN + R347
RAB8B
2.51
0.05

TABLE 9

IFN α2a-Induced IRF7 Gene Expression is Neutralized by MEDI-545

Sample
Gene
Average
StDev

107 VEH
IRF7
1.00

107 IFN
IRF7
18.53
3.32

107 IFN + 545
IRF7
3.42
0.33

107 IFN + R347
IRF7
19.48
1.67

163 VEH
IRF7
0.91
0.02

163 IFN
IRF7
17.16
1.39

163 IFN + 545
IRF7
2.92
0.22

163 IFN + R3437
IRF7
23.28
1.46

175 VEH
IRF7
1.25
0.10

175 IFN
IRF7
24.65
0.80

175 IFN + 545
IRF7
2.43
0.08

175 IFN + R347
IRF7
26.34
8.61

TABLE 10

IFN α2a-Induced MARCKS Gene Expression is Neutralized by MEDI-545

Sample
Gene
Average
StDev

107 VEH
MARCKS
1.00

107 FN
MARCKS
3.97
0.09

107 IFN + 545
MARCKS
1.30
0.08

107 IFN + R347
MARCKS
2.99
0.10

163 VEH
MARCKS
0.56
0.01

163 IFN
MARCKS
2.59
0.12

163 IFN + 545
MARCKS
1.55
0.05

163 IFN + R3437
MARCKS
4.42
0.07

175 VEH
MARCKS
0.41
0.01

175 IFN
MARCKS
2.59
0.06

175 IFN + 545
MARCKS
0.55
0.02

175 IFN + R347
MARCKS
3.38
0.05

TABLE 11

IFN α2a-Induced IL6ST Gene Expression is Neutralized by MEDI-545

Sample
Gene
Average
StDev

107 VEH
IL6ST
1.00

107 IFN
IL6ST
3.54
0.60

107 IFN + 545
IL6ST
2.62
0.16

107 IFN + R347
IL6ST
8.19
0.54

163 VEH
IL6ST
2.50
0.58

163 IFN
IL6ST
7.69
0.47

163 IFN + 545
IL6ST
4.18
0.44

163 IFN + R3437
IL6ST
13.24
0.12

175 VEH
IL6ST
1.37
0.09

175 IFN
IL6ST
7.62
0.56

175 IFN + 545
IL6ST
2.95
0.38

175 IFN + R347
IL6ST
23.91
2.77

TABLE 12

IFN α2a-Induced LY6E Gene Expression is Neutralized by MEDI-545

Sample
Gene
Average
StDev

107 VEH
LY6E
1.00

107 IFN
LY6E
19.09
0.03

107 IFN + 545
LY6E
3.50
0.15

107 IFN + R347
LY6E
12.54
0.20

163 VEH
LY6E
1.02
0.04

163 IFN
LY6E
13.52
0.35

163 IFN + 545
LY6E
4.80
0.18

163 IFN + R3437
LY6E
22.56
0.35

175 VEH
LY6E
1.61
0.15

175 IFN
LY6E
19.32
0.68

175 IFN + 545
LY6E
3.74
0.00

175 IFN + R347
LY6E
15.57
0.44

TABLE 13

IFN α2a-Induced IFIT3 Gene Expression is Neutralized by MEDI-545

Sample
Gene
Average
StDev

107 VEH
IFIT3
1.00

107 IFN
IFIT3
38.43
0.78

107 IFN + 545
IFIT3
6.78
0.14

107 IFN + R347
IFIT3
42.59
0.75

163 VEH
IFIT3
0.62
0.01

163 IFN
IFIT3
25.94
0.57

163 IFN + 545
IFIT3
4.58
0.08

163 IFN + R3437
IFIT3
44.83
0.44

175 VEH
IFIT3
1.32
0.02

175 IFN
IFIT3
35.02
0.48

175 IFN + 545
IFIT3
5.28
0.05

175 IFN + R347
IFIT3
29.71
0.79

TABLE 14

IFN α2a-Induced IFIT1 Gene Expression is Neutralized by MEDI-545

Sample
Gene
Average
StDev

107 VEH
IFIT1
1.00

107 IFN
IFIT1
80.21
3.44

107 IFN + 545
IFIT1
13.14
0.02

107 IFN + R347
IFIT1
86.44
0.57

163 VEH
IFIT1
0.92
0.03

163 IFN
IFIT1
51.65
1.21

163 IFN + 545
IFIT1
7.60
0.05

163 IFN + R3437
IFIT1
86.63
2.67

175 VEH
IFIT1
1.47
0.17

175 IFN
IFIT1
82.98
2.94

175 IFN + 545
IFIT1
8.40
0.24

175 IFN + R347
IFIT1
58.50
1.47

TABLE 15

IFN α2a-Induced HERC5 Gene Expression is Neutralized by MEDI-545

Sample
Gene
Average
StDev

107 VEH
HERC5
1.00

107 IFN
HERC5
41.12
2.87

107 IFN + 545
HERC5
6.29
0.49

107 IFN + R347
HERC5
55.04
0.69

163 VEH
HERC5
1.05
0.07

163 IFN
HERC5
75.81
0.50

163 IFN + 545
HERC5
7.83
0.00

163 IFN + R3437
HERC5
95.44
7.79

175 VEH
HERC5
1.19
0.06

175 IFN
HERC5
74.58
5.79

175 IFN + 545
HERC5
6.89
0.13

175 IFN + R347
HERC5
98.15
19.40

TABLE 16

IFN α2a-Induced OAS1 Gene Expression is Neutralized by MEDI-545

Sample
Gene
Average
StDev

107 VEH
OAS1
1.00

107 IFN
OAS1
15.11
4.27

107 IFN + 545
OAS1
3.45
1.03

107 IFN + R347
OAS1
17.82
3.93

163 VEH
OAS1
0.77
0.22

163 IFN
OAS1
14.19
3.14

163 IFN + 545
OAS1
3.05
0.75

163 IFN + R3437
OAS1
22.44
3.49

175 VEH
OAS1
1.62
0.38

175 IFN
OAS1
22.09
0.97

175 IFN + 545
OAS1
4.04
0.45

175 IFN + R347
OAS1
15.22
4.48

TABLE 17

IFN α2a-Induced OAS3 Gene Expression is Neutralized by MEDI-545

Sample
Gene
Average
StDev

107 VEH
OAS3
1.00

107 IFN
OAS3
49.04
13.74

107 IFN + 545
OAS3
7.03
0.84

107 IFN + R347
OAS3
76.88
13.69

163 VEH
OAS3
0.49
0.06

163 IFN
OAS3
42.01
10.01

163 IFN + 545
OAS3
14.60
4.53

163 IFN + R3437
OAS3
52.60
7.04

175 VEH
OAS3
1.27
0.14

175 IFN
OAS3
37.87
3.57

175 IFN + 545
OAS3
3.92
0.06

175 IFN + R347
OAS3
34.91
2.07

TABLE 18

IFN α2a-Induced RSAD2 Gene Expression is Neutralized by MEDI-545

Sample
Gene
Average
StDev

107 VEH
RSAD2
1.00

107 IFN
RSAD2
109.64
36.65

107 IFN + 545
RSAD2
9.88
0.32

107 IFN + R347
RSAD2
107.32
35.38

163 VEH
RSAD2
0.56
0.11

163 IFN
RSAD2
71.47
21.17

163 IFN + 545
RSAD2
4.39
0.60

163 IFN + R3437
RSAD2
114.51
28.63

175 VEH
RSAD2
1.88
0.43

175 IFN
RSAD2
126.27
22.95

175 IFN + 545
RSAD2
8.43
0.36

175 IFN + R347
RSAD2
90.97
7.42

See also FIG. 6 (RAB8B), FIG. 7 (IRF7), FIG. 8 (MARCKS), FIG. 9 (IL6ST), FIG. 10 (LY6E), FIG. 11 (IFIT3), FIG. 12 (IFIT1), FIG. 13, (HERC5), FIG. 14 (OAS1), FIG. 15 (OAS3), and FIG. 16 (RSAD2) for graphical representations of the gene expression data for each of the 11 genes.

Source of Interferon=SLE Patient Serum

(a) Neutralization of type I IFN-induced genes by MEDI-545 could also be observed in whole blood of healthy volunteers that had been stimulated with serum obtained from lupus patients. Serum samples were obtained from SLE patients that had been tested in an IFN bioassay. Whole blood was collected from healthy donors in heparinized vacutainer tubes and PBMC were isolated using Ficoll gradient centrifugation method. PBMC were resuspended at 1×10⁷cells/mL in RPMI media with 10% fetal bovine serum (FBS) and 125 μL of cells were aliquoted into each well of a 24 well flat bottom plate (1.25×10⁶cells/well). Serum from SLE patients was preincubated for one hour with MEDI-545 (0.1, 1, 10 μg/mL), anti-IFN-γ antibody (1 μg/mL) or control antibody (10 μg/mL). SLE serum was added to the PBMC at a final concentration 25% (62.5 μL per well). Additional volume of RPMI+10% FBS was added to the wells to obtain a final volume of 250 μL per well. Plates were incubated at 37° C. for either 4 or 18 hours. Following the incubation, RNA was harvested by adding 750 μL of Trizol LS to each well. Samples were frozen at −70° C. until the time of RNA isolation. Table 21 provides the MEDI-545 blockade of 74 type I IFN genes in healthy volunteers' whole blood stimulated ex vivo with SLE patient serum.

TABLE 21

MEDI-545 blocks overexpression of type I IFN genes in whole blood of

healthy volunteers stimulated ex vivo with lupus patient serum

Probe ID
D1_002_545.10
D1_004_545.10
D1_17021_545.10
UniGene.ID
Gene.Symbol

219211_at
−3.1949

text missing or illegible when filed

−4.0543
Hs.38260
USP18

217502_at

text missing or illegible when filed

−3.0247
Hs.437609
IFIT2

218400_at
−3.1235
−4.3204

text missing or illegible when filed

Hs.528634
OAS3

213797_at
−3.0752
−3.3250
−2.5795
Hs.17518
RSAD2

203153_at

text missing or illegible when filed

Hs.20315
IFIT1

242625_at
−2.8104
−2.9508
−2.2214
Hs.17518
RSAD2

204747_at

text missing or illegible when filed

−3.6590

Hs.47338
IFIT3

205483_s_at
−2.5237

text missing or illegible when filed

−3.1558
Hs.458485
ISG15

204439_at
−2.5133

text missing or illegible when filed

Hs.389724
IFI44L

202145_at
−2.4809

text missing or illegible when filed

Hs.521903
LY6E

202869_at
−2.4582
−3.5402
−3.2304
Hs.524760
OAS1

235643_at
−2.4535

text missing or illegible when filed

−2.9115
Hs.489118
SAMD9L

219352_at
−2.4496
−3.5983

text missing or illegible when filed

Hs.529317
HERC6

204415_at
−2.4417
−2.5228
−2.3149
Hs.523847
IFI6

219684_at

text missing or illegible when filed

−2.1421
Hs.43388
RTP4

236156_at

text missing or illegible when filed

−2.5440
−2.8885
Hs.127445
LIPA

205552_s_at

text missing or illegible when filed

−3.3879
−2.7561
Hs.524760
OAS1

206133_at
−2.3139
−3.0772
−2.4737
Hs.441975
BIRC4BP

214453_s_at
−2.2905
−3.1707
−3.3204
Hs.82316
IFI44

1556643_at

text missing or illegible when filed

−2.0429
−1.7120
Hs.515243
LOC93343

228607_at
−2.2597

text missing or illegible when filed

−2.3234
Hs.414332
OAS2

218943_s_at
−2.2563
−2.4118
−2.6600
Hs.190622
DDX58

242020_s_at
−2.2542
−2.6438
−1.7975
Hs.302123
ZBP1

204959_at
−2.2501
−1.3731
−1.5559
Hs.153837
MNDA

226757_at
−2.2481

text missing or illegible when filed

Hs.437609
IFIT2

219863_at

text missing or illegible when filed

Hs.26663
HERC5

229450_at
−2.2281
−3.2200
−2.2151
—
—

214059_at

−3.2929
−3.5281
Hs.82316
IFI44

232517_s_at
−2.1925
−2.2750

text missing or illegible when filed

Hs.51780
PRIC285

232666_at
−2.1925
−1.9208
−1.4908
Hs.528634
OAS3

230036_at
−2.1854
−3.0258
−2.4379
Hs.489118
SAMD9L

227609_at
−2.1548
−2.5808
−1.1577
Hs.546467
EPSTI1

226702_at
−2.1420
−3.0150
−3.0155
Hs.7155
LOC129607

226603_at
−2.1183
−2.8872
−2.4103
Hs.489118
SAMD9L

210397_at
−2.1095
−0.5687
−2.0322
Hs.32949
DEFB1

204994_at
−2.0685
−3.2727
−3.6132
Hs.926
MX2

202086_at
−2.0861
−3.2741
−3.6408
Hs.517307
MX1

228617_at

text missing or illegible when filed

−2.3139
Hs.441975
BIRC4BP

219364_at

text missing or illegible when filed

−2.3774
−2.4651
Hs.55918
LGP2

209417_s_at
−2.0364
−2.5262
−2.4132
Hs.632258
IFI35

222154_s_at
−2.0330
−2.4582

text missing or illegible when filed

Hs.120323
DNAPTP6

228230_at
−2.0323
−2.9821
−3.0255
Hs.517180
PRIC285

242234_at

text missing or illegible when filed

−3.0047

Hs.441975
BIRC4BP

219519_s_at
−2.0077
−0.2596

text missing or illegible when filed

Hs.31869
SIGLEC1

207713_s_at
−1.9940
−1.0134
−1.6345
Hs.247280
C20orf18

218974_at
−1.8904
−2.5122
−2.5244
Hs.445244
FLJ10159

1552309_a_at
−1.8820
−2.4284

text missing or illegible when filed

Hs.632387
NEXIN

210873_x_at

text missing or illegible when filed

−1.2891
−1.2710
Hs.348983
APOBEC3A

243271_at

text missing or illegible when filed

−2.2857
−2.0595
Hs.489118
SAMD9L

202411_at
−1.8385
−0.1345
−2.4757
Hs.532634
IFI27

222793_at
−1.8137
−2.4540
−2.6578
Hs.190622
DDX58

235276_at
−1.8007
−2.6121
−1.4780
—
—

203236_s_at

text missing or illegible when filed

Hs.81337
LGALS9

225291_at
−1.7801
−2.0157
−2.4613
Hs.388733
PNPT1

44673_at
−1.7547
−0.1337

text missing or illegible when filed

Hs.31869
SIGLEC1

213294_at
−1.7361
−2.4393
−2.5907
Hs.546523
—

211122_s_at
−1.7296

text missing or illegible when filed

−1.5743
Hs.632592
CXCL11

224701_at

text missing or illegible when filed

−1.7880

Hs.583792
PARP14

230314_at

text missing or illegible when filed

−2.2159
−2.3478
Hs.112420
—

218986_s_at

text missing or illegible when filed

−2.1915
−2.0204
Hs.591710
FLJ20035

205569_at
−1.8847
−2.5741

text missing or illegible when filed

Hs.518448
LAMP3

219691_at
−1.8420
−1.8434
−1.8310
Hs.65641
SAMD9

204211_x_at
−1.5244
−2.0812
−2.3379
Hs.131431
EIF2AK2

220146_at
−1.5033
−2.7419
−1.7471
Hs.443036
TLR7

241916_at

text missing or illegible when filed

−1.3802
Hs.130759
PLSCR1

229350_x_at
−1.5906

text missing or illegible when filed

−1.3577
Hs.348609
PARP10

1555464_at

text missing or illegible when filed

−1.7337
−1.3101
Hs.163173
IFIH1

204972_at
−1.5822

text missing or illegible when filed

−2.8355
Hs.414332
OAS2

204698_at
−1.5277
−1.5978
−1.6553
Hs.459265
ISG20

203595_s_at
−1.4853
−1.8724
−1.5442
Hs.252839
IFIT5

220576_at
−1.4834
−1.7834
−1.0040
Hs.229988
PGAP1

1555491_a_at
−1.4739

text missing or illegible when filed

−1.4991
—
FLJ11286

1565752_at
−1.4418
−0.0040
−1.0835
Hs.509564
FGD2

203596_s_at
−1.4383
−2.0358
−1.9284
Hs.252839
IFIT5

text missing or illegible when filed

indicates data missing or illegible when filed

Analysis of the genes uniquely activated at the 18 hour time point revealed upregulation of genes involved in the innate immune response (TLR, NFκB), adaptive immune response (NFAT, IL-1/IL-6), complement activation as well as leukocyte chemotaxis and adhesion. It is possible that neutralization of the type IFN pathway has the potential to modify downstream pathways that may significantly impact the pathogenesis of SLE.

Heatmap analysis was also performed to examine induction of a type I IFN signature in PBMCs of a healthy donor by serum of an SLE patient and neutralization of the type I IFN signature by MEDI-545. See FIG. 67. The anti-IFN-α mAb treatment (lanes 4-6) demonstrated strong neutralization of a large number of genes stimulated with the serum of an SLE patient. Furthermore, neutralization by the anti-IFN-α mAb was dose-dependent, which suggests that these genes could be good candidates for PD. The reference mAb itself inhibited the overexpression of some of the genes upregulated when challenged with SLE patient sera; some of these were identified as type I IFN-inducible genes. However, the effect of anti-IFN-α mAb was much broader, with strong neutralization observed in a large number of genes of which neither the reference mAb nor anti-IFN-γ mAb had any significant effect (lane 2; lanes 4-6). It should be noted that treatment with anti-IFN-αR mAb (lane 7) induced more neutralization than anti-IFN-α mAb, which suggests the presence of other type I IFN family members in the serum of the SLE patients, in addition to IFN-α.

(b) Further investigation was conducted to identify early and late transcriptional responses in healthy donor PBMCs stimulated with SLE patient serum. In this study, four SLE patient serum samples, with varying levels of IFNα activity, were used to stimulate PBMCs isolated from a healthy donor. The varying levels of IFNα activity in the four SLE serum samples were determined in a luciferase reporter gene assay as described in Example 20. Briefly, HEK293H cells were stably transfected with a luciferase construct (Gaussia princeps) under the control of the IFN-stimulated response element (ISRE). Transfected cells were incubated with 50% patient sera and luciferase activity was detected in the culture supernatants 24 h later. Samples generating a signal greater than 1.5× negative control wells (normal human serum) were considered positive. To determine which class of type I IFN was responsible for the positive response, cells were treated with anti-type I and anti-type II IFN mAbs. FIG. 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 PBMCs were incubated with 25% SLE patient serum or with 25% autologous patient serum (as a negative control). Following the incubation, cells were harvested with Trizol LS and stored at −70° C. for RNA isolation. Total RNA was extracted and RNA purity and concentration were determined spectrophotometrically (260/280>1.9). The generation and hybridization of biotin-labeled amplified complementary RNA (cRNA) were conducted according to manufacturer's instructions (Affymetrix, Santa Clara, Calif.). Data was generated by implementing a 3-fold (up-regulation) expression cutoff between SLE serum stimulation compared to autologous serum control samples (q value≦0.05). FIG. 70b shows the number of probes detected as 3-fold or more upregulated in the healthy volunteer PBMCs by each of the four SLE patient serum samples. The number of probes detected as 3-fold or more upregulated by an SLE patient serum sample correspondingly increased with the level of type I IFN activity detected in the SLE serum sample.

The role of type I IFNs in inducing the 3-fold or more upregulation of probes by the SLE patient serum samples was next investigated. PBMCs isolated from a healthy volunteer, discussed above, were incubated with 25% SLE patient serum in the presence or absence of neutralizing antibodies against IFN-α, or irrelevant mAb, for 4 or 18 hours. As a negative control, PBMC were incubated with 25% of autologous patient serum. Following the incubation, cells were harvested with Trizol LS and stored at −70° C. for RNA isolation. Total RNA was extracted and RNA purity and concentration were determined spectrophotometrically (260/280>1.9). The generation and hybridization of biotin-labeled amplified complementary RNA (cRNA) were conducted according to manufacturer's instructions (Affymetrix, Santa Clara, Calif.). ARRAYASSIST® Lite software was used to calculate probe-level summaries from the array cell intensity files and R packages were used to identify differentially regulated genes (3-fold or greater upregulation in expression between SLE serum stimulation compared to autologous serum control samples (q value≦0.05); R Development Core Team, New Zealand). Percent neutralization was then determined by calculating the percent change for each upregulated probe treated with and without anti-IFNα antibody. FIG. 71a provides heat maps showing the percent neutralization of probes that were identified as upregulated following anti-IFNα treatment for type I IFN genes (689 probes) and non-type I IFN genes (probes induced by SLE serum outside of type I IFN gene list) 4 and 18 h post incubation. FIG. 710b shows, for each of the four SLE patient serum samples, the percentage of type I IFN gene signature or non-type I IFN gene signature probes that were neutralized by the anti-IFNα treatment following both the 4 and 18 hour incubations. It appears that the majority of genes neutralized by anti-IFNα treatment of SLE serum-treated healthy volunteer's PBMCs 4 hours post-incubation were type I IFN genes, while the majority of genes neutralized by anti-IFNα treatment of SLE serum-treated healthy volunteer's PBMCs 18 hours post-incubation were non-type I IFN genes.

Genes, whether type I IFN genes or non-type I IFN genes, that were both upregulated and neutralized by anti-IFNα treatment at 18 hours, but that were not upregulated at 4 hours (i.e., “unique genes”) were identified for each SLE patient serum sample. FIG. 72 provides the (a) type I IFN genes and (b) non-type I IFN genes that were identified as unique genes. Shaded areas indicate greater than 50% neutralization by anti-IFNα in that patient sample.

Cell pathways and processes neutralized by anti-IFNα treatment at the 18 hr time point are involved in cytokine and chemokine signaling pathways, immune regulation, cell adhesion, and cell survival. See FIG. 73, which provides a table showing the pathway analysis of altered genes and proteins at the 18 hr time point. Pathways highlighted in yellow were also significantly altered in SLE serum samples. The cell pathways and processes neutralized by anti-IFNα treatment at the 18 hr time point were analyzed with the METACORE integrated software suite from GENEGO, Inc. using the identified unique genes. Only pathways with p-values≦0.05 were considered significant. The pathways shown were altered in at least 2 out of 4 SLE serum samples.

Example 6
Administering MEDI-545 to Lupus Patients Neutralizes the IFNα-Inducible Candidate PD Marker Expression Pattern

Whole blood of lupus patients receiving placebo, 0.3 mg/kg, 1.0 mg/kg, and 3.0 mg/kg MEDI-545 were analyzed for expression of IFNα-inducible PD markers over the course of 28 days. Whole blood (˜2.5 mL) was drawn into PAXgene RNA tubes and processed as outlined above. With increasing doses of MEDI-545, up-regulated expression of the top 25 PD markers was neutralized. See FIG. 18, FIG. 23, and FIG. 24 which provide graphical representations of neutralization of these top 25 PD markers following administration of varying concentrations of the MEDI-545 IFNα Ab over various lengths of time. The top 25 PD markers measured in this study are provided in Table 19.

TABLE 19

Top 25 IFN-Induced PD Markers in Lupus Patients

UniGene

Gene

Probe ID
ID
Gene Title
Symbol

202086_at
Hs.517307
myxovirus (influenza virus) resistance 1, interferon-
MX1

inducible protein p78 (mouse) /// myxovirus (influenza

virus) resistance 1, interferon-inducible protein p78

(mouse)

202145_at
Hs.521903
lymphocyte antigen 6 complex, locus E
LY6E

202411_at
Hs.532634
interferon, alpha-inducible protein 27
IFI27

202869_at
Hs.524760
2′,5′-oligoadenylate synthetase 1, 40/46 kDa
OAS1

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
IFI6

204439_at
Hs.389724
interferon-induced protein 44-like
IFI44L

205483_s_at
Hs.458485
ISG15 ubiquitin-like modifier
ISG15

205569_at
Hs.518448
lysosomal-associated membrane protein 3
LAMP3

205660_at
Hs.118633
2′-5′-oligoadenylate synthetase-like
OASL

213797_at
Hs.17518
radical S-adenosyl methionine domain containing 2
RSAD2

214059_at
Hs.82316
Interferon-induced protein 44
IFI44

interferon-induced protein with tetratricopeptide

217502_at
Hs.437609
repeats 2
IFIT2

218400_at
Hs.528634
2′-5′-oligoadenylate synthetase 3, 100 kDa
OAS3

219211_at
Hs.38260
ubiquitin specific peptidase 18
USP18

sialic acid binding lg-like lectin 1, sialoadhesin /// sialic

219519_s_at
Hs.31869
acid binding lg-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)
EPSTI1

229450_at
—
—
—

235276_at
—
—
—

239979_at
Hs.546467
Epithelial stromal interaction 1 (breast)
EPSTI1

242234_at
Hs.441975
XIAP associated factor-1
BIRC4BP

44673_at
Hs.31869
sialic acid binding lg-like lectin 1, sialoadhesin
SIGLEC1

The neutralization of IFN-induced PD markers by MEDI-545 for several individual lupus patients was examined and is presented in FIGS. 19-21. FIGS. 19 and 20 are heatmaps showing the neutralization of the top 25 PD markers (see Table 19) for two individual lupus patients (FIG. 19, patient 1541; and FIG. 20, patient 1449). Each of these lupus patients received 3 mg/kg MEDI-545. Each exhibited neutralization of the top 25 inducible PD markers at 7 and 14 days post-MEDI-545 treatment.

Neutralization of the top 25 type I IFN inducible genes in whole blood of an SLE patient treated with high dose (30 mg/kg) MEDI-545 was also examined. A heatmap of neutralization of the top 25 type I IFN inducible genes at 1, 4, 7, and 14 days following administration of MEDI-545 is presented in FIG. 25(a). Neutralization of all genes can be seen following administration of MEDI-545. FIG. 25(b) is a PCA of target modulation based on the top 25 type I IFN inducible genes. The PCA diagram shows the progression of the treated SLE patient from a position directly opposite that of normal healthy donors prior to administration of MEDI-545 to a position where it clusters with the healthy donors after administration of MEDI-545.

The neutralization of 165 PD markers by MEDI-545 was examined in a further lupus patient dosed with a lower, 0.3 mg/kg dose, of Ab. See FIG. 21. MEDI-545 neutralized most of the 165 candidate PD markers in this lupus patient. The 165 candidate PD markers are shown as the first 165 entries of Table 20.

The neutralization of type I IFN inducible probes sets was not observed in SLE patients treated with placebo control. Compare PCA plots of SLE patients before (a) and after (b) dosing with placebo in FIG. 26. Thus, the neutralization of the type-I IFN PD markers was due to the MEDI-545 antibody.

Table 22 provides a list of the 63 type I IFN inducible probes upregulated in whole blood of lupus patients and neutralized by MEDI-545 or placebo by at least 30% at day 7, day 14, or day 28 post administration. Each set of columns provides neutralization data for each of the indicated genes at 7, 14, and 28 days post-administration. The first set of columns provides percentage neutralization of each of the indicated genes for lupus patients having a type I IFN signature and that were treated with MEDI-545. It can be noted that for each of the indicated genes, neutralization ranged from 30% to 68% at day 7 post-administration. Meanwhile, at day 7 in the placebo treated group, neutralization of the same genes ranged from 0% to 27%.

TABLE 22

Neutralization of 63 Type I IFN Inducible Probes in Whole Blood of Lupus

by MEDI-545

Lupus Sample With IFN
ALL Lupus Sample, (+) Medi-
Lupus Sample Without an IFN

text missing or illegible when filed

IFI44
214059_at
0.6871
0.6276
0.5047
0.3433
0.2657
0.2357
−0.0799
−0.2278
−0.0088

IFI44L
204439_at
0.6621
0.6193
0.5515
0.6662
0.5561
0.492
0.6713
0.4698
0.4379

RSAD2
213797_at
0.547
0.631
0.5213
0.6023
0.4611
0.4464
0.5377
0.2294
0.3783

G1P2
205483_s_at
0.6395
0.5954
0.5703
0.5404
0.4781
0.4148
0.4185
0.3181
0.2734

RSAD2
242625_at
0.6359
0.6123
0.4946
0.5607
0.541
0.3443
0.4681
0.4437
0.2077

USP18
219211_at
0.6305
0.6269
0.5577
0.4322
0.4423
0.4082
0.1882
0.1907
0.2723

IFI44
214453_s_at
0.626
0.5875
0.4223
0.4956
0.2741
0.2298
0.3352
−0.1532
0.0547

IFIT1
203153_at
0.6224
0.6093
0.5376
0.5442
0.4586
0.4182
0.448
0.2532
0.3097

IFIT3
204747_at
0.6213
0.5676
0.5638
0.5212
0.4174
0.3854
0.398
0.2124
0.2232

SERPING1
200986_at
0.617
0.6114
0.5974
0.4617
0.4294
0.3673
0.2706
0.1676
0.1582

HERC6
219352_at
0.5996
0.531
0.5352
0.3581
0.3678
0.4335
0.0609
0.1452
0.341

DNAPTP5
222154_s_at
0.5973
0.6223
0.5016
0.345
0.3819
0.2244
0.0345
0.0543
−0.0276

OASL

text missing or illegible when filed

0.5968
0.5529
0.5815
0.4715
0.3853
0.4208
0.3174
0.1569
0.2748

HERC5

text missing or illegible when filed

0.5948
0.5552
0.4997
0.4651
0.4521
0.3816
0.3054
0.3115
0.2742

OAS3

text missing or illegible when filed

0.589
0.5792
0.5062
0.4846

0.4039
0.3562
0.3065
0.311

IFRG28
219684_at
0.581
0.5218
0.4955
0.3014
0.3035
0.2441
−0.0427
0.0058
0.0155

MX1

text missing or illegible when filed

0.5817
0.5329
0.5073
0.512
0.4831
0.4001
0.4273
0.4152
0.3026

OAS1
202889_at
0.5761
0.5148
0.5652
0.4345
0.429
0.4373
0.2603
0.3119
0.3211

OASL

text missing or illegible when filed

0.5681
0.5549
0.5494
0.4814
0.4415
0.4046
0.3746
0.2868
0.2729

text missing or illegible when filed

205552_s_at
0.5678
0.5193
0.56
0.4796
0.4115
0.4196
0.3711
0.2644
0.292

LAMP3
205569_at
0.5531
0.6796
0.4871
0.3427
0.4182
0.2854
0.0838
0.0618
0.1021

text missing or illegible when filed

228439_at
0.535
0.50582
0.5093
0.359
0.2949
0.332
0.1424
0.0036
0.1709

SN
219619_s_at
0.5321
0.5639
0.5307
0.307
0.3711
0.212
0.03
0.1081
−0.0778

text missing or illegible when filed

228617_at
0.5317
0.503
0.4707
0.3942
0.3604
0.266
0.2249
0.1659
0.0799

IFITS
203598_s_at
0.5257
0.4922
0.3314
0.3004
0.1997
0.0723
0.023
−0.1991
−0.1633

IRF7

text missing or illegible when filed

0.5183
0.494
0.4717
0.4318
0.3509
0.301
0.3253
0.1557
0.1459

text missing or illegible when filed

0.517
0.5298
0.4999
0.3142
0.2662
0.2798
0.0646
−0.0932
0.0797

text missing or illegible when filed

0.5074
0.4803
0.553
0.3738
0.3527
0.3674
0.2093
0.1786
0.1987

ETV7

text missing or illegible when filed

0.5057
0.5101
0.3596
0.2965
0.2389
0.0985
0.039
−0.1308
−0.1389

IFIT5

text missing or illegible when filed

0.5056
0.4731
0.2902
0.2482
0.2263
0.028
−0.0685
−0.1102
−0.2105

HES4
227347_x_at
0.4998
0.4746
0.4266
0.3377
0.3141
0.2703
0.1383
0.0953
0.1283

ZC3HBC1
218543_s_at
0.4812
0.4274
0.4076
0.3058
0.2935
0.2109
0.0898
0.1109
0.0321

text missing or illegible when filed

230038_at
0.4636
0.4665
0.4025
0.3114
0.2848
0.2299
0.1241
0.037
0.073

text missing or illegible when filed

225503_at
0.4578
0.4242
0.3425
0.264
0.1555
0.1794
0.0253
−0.211
0.0312

OAS3

text missing or illegible when filed

0.4557
0.3628
0.4828
0.3165
0.2457
0.3356
0.1452
0.086
0.2018

OAS2
204372_at
0.4532
0.4503
0.3889
0.2963
0.3106
0.2084
0.1032
0.1202
0.0444

IFIT2
217502_at
0.4514
0.4519
0.1899
0.0857
−0.039
−0.4306
−0.3643
−0.7083
−0.9948

CXCL10
204533_at
0.4476
0.4647
0.262
0.1834
0.1911
0.1282
−0.1418
−0.1819
0.0066

LY6E
202145_at
0.4463
0.4582
0.4113
0.3404
0.3294
0.2612
0.21
0.1536
0.1247

HERC6

text missing or illegible when filed

0.4449
0.3726
0.3596
0.2954
0.2402
0.2433
0.1108
0.0596
0.1376

text missing or illegible when filed

204415_at
0.4421
0.3914
0.1018
0.152
0.3129
−0.3045
−0.205
0.2058
−0.6738

text missing or illegible when filed

243271_at
0.4419
0.4279
0.401
0.2663
0.2445
0.2165
0.0501
−0.0055
0.0488

OAS2
205553_at
0.4377
0.3721
0.2965
0.3008
0.2379
0.1882
0.1323
0.0548
0.0897

APOL6

text missing or illegible when filed

0.4264
0.063
0.4352
−0.0787
−0.5482
−0.2042
−0.7003
−1.3816
−0.7855

ZBP1
242020_s_at
0.4232
0.406
0.3729
0.0761
0.1281
0.2718
−0.3512
−0.2508
0.1799

PLSCR1
202446_s_at
0.4022
0.3948
0.2996
0.1919
0.1973
0.1063
−0.0668
−0.0719
−0.0694

OAS2

text missing or illegible when filed

0.3989
0.3655
0.3374
0.2712
0.2174
0.1639
0.114
0.0155
0.0061

TRIM6
223599_at
0.3896
0.3464
0.2669
0.2285
0.1987
0.1119
0.0303
−0.0027
−0.0289

ZCCHC2
233425_at
0.3891
0.429
0.3925
0.2541
0.2965
0.2822
0.088
0.1213
0.182

PLSCR1
202430_s_at
0.3847
0.3858
0.2706
−0.2032
−0.0283
−0.1714
0.9268
−0.5931
−0.5733

OLEC4D
1552773_at
0.3782
0.2012
0.1293
−0.5127
−0.9029
−0.5568
−1.6091
−2.4085
−1.1806

ECGF1
204858_s_at
0.3778
0.2403
0.2971
0.3178
0.1699
0.0019
0.244
0.0741
−0.2665

text missing or illegible when filed

233880_at
0.3658
0.3508
0.2804
0.2913
0.2599
0.108
0.1996
0.136
−0.0488

SN
44673_at
0.3642
0.3373
0.3736
0.2344
0.2522
0.1405
0.0747
0.1362
−0.0714

text missing or illegible when filed

228230_at
0.3636
0.4131
0.3363
0.2701
0.2731
0.1074
0.155
0.0822
−0.1008

PARP14
224701_at
0.3611
0.3765
0.3718
0.2737
0.2855
0.2267
0.1662
0.1614
0.0947

DNAPTP6
241812_at
0.3448
0.3672
0.2896
0.2048
0.2134
0.108
0.0325
0.0037
−0.0571

HSXIAPAF1
242234_at
0.3371
0.3793
0.1084
0.1586
0.1796
−0.2285
−0.0612
−0.0927
−0.05347

TNFAIP6
206025_s_at
0.336
0.3559
0.3269
0.1913
0.1909
0.1164
0.0133
−0.034
−0.0751

LGALS3BP

text missing or illegible when filed

0.3331
0.27
0.2644
−0.0457
0.1764
0.1032
−0.512
0.0787
−0.0434

CKS2
204170_s_at
0.3215
0.0604
0.0634
−0.2323
−0.5787
−1.1884
−0.914
−1.4502
−2.3265

STAT2

text missing or illegible when filed

0.3175
0.1781
0.1852
0.1643
−0.0318
−0.051
−0.0245
−0.318
−0.2675

EIF2AK2
204211_x_at
0.3094
0.3621
0.2577
0.2165
0.286
0.1441
0.1021
0.1822
0.0408

Samples Receiving Placebo

text missing or illegible when filed

IFI44
−0.1325
−1.91
−0.4165

IFI44L
0.007
−2.1816
0.036

RSAD2
−0.2332
−5.0172
−0.9617

G1P2
0.0423
−0.944
0.1706

RSAD2
−0.3537
−2.7176
−0.2632

USP18
−0.4424
−2.4219
−0.4972

IFI44
−0.2833
−1.0524
−2.4005

IFIT1
−0.1604
−1.1565
−0.436

IFIT3
−5.9101
−9.7543
−7.4011

SERPING1
−0.5973
−2.7824
0.4193

HERC6
−0.9901
−4.4468
1.6832

DNAPTP5
0.028
−1.947
0.007

OASL
−0.1014
−1.6808
0.1344

HERC5
−0.0955
−0.9446
0.1306

OAS3
−0.0945
−1.1786
0.1744

IFRG28
−2.1401
−2.8445
3.3644

MX1
−0.0951
−0.7789
0.01

OAS1
0.0389
−0.6246
0.0692

OASL
−0.0675
−0.9765
0.1773

text missing or illegible when filed

−0.1562
−1.7918
0.386

LAMP3
0.007
−1.4332
0.045

text missing or illegible when filed

−1.1629
−2.0558
0.5523

SN
−0.1736
−4.8297
0.1133

text missing or illegible when filed

−0.2206
−0.7607
0.1053

IFITS
0.0791
−0.2048
0.1939

IRF7
0.1162
−0.2791
0.2159

text missing or illegible when filed

0.0161
−1.0185
0.1578

text missing or illegible when filed

−0.6502
−1.8449
0.4875

ETV7
−0.5808
−1.3814
0.6834

IFIT5
−0.1956
−0.4059
0.6195

HES4
0.0775
−0.3688
0.2619

ZC3HBC1
0.055
−0.1726
0.1826

text missing or illegible when filed

0.0287
−0.4023
0.002

text missing or illegible when filed

−0.2153
−0.8023
0.4988

OAS3
−0.3754
−1.0637
0.0014

OAS2
−0.1067
−0.9025
0.1084

IFIT2
−0.7316
−0.9653
4.4123

CXCL10
−0.1664
−0.9562
0.1938

LY6E
−0.4715
−1.729
0.5955

HERC6
0.2771
−0.098
0.0584

text missing or illegible when filed

−0.3862
−0.3826
0.4763

text missing or illegible when filed

1.00E−04
−0.2487
0.116

OAS2
−0.0861
−1.1845
0.2322

APOL6
−1.0548
−2.225
0.0949

ZBP1
0.0954
−0.6879
0.0275

PLSCR1
0.0049
−0.5041
0.1826

OAS2
−0.026
−0.5978
0.0611

TRIM6
−0.4333
−0.2181
0.76

ZCCHC2
−0.1376
−0.4844
0.075

PLSCR1
−0.091
−0.5114
0.3841

OLEC4D
−0.0151
−0.298
0.9956

ECGF1
0.0637
−0.2711
0.1519

text missing or illegible when filed

−0.4266
−0.7606
0.4247

SN
−0.321
−1.2105
0.1766

text missing or illegible when filed

−0.5711
−0.6313
0.1671

PARP14
−0.0715
−0.3247
0.0835

DNAPTP6
−0.134
−0.5147
0.0613

HSXIAPAF1
−0.4102
−0.7359
0.0295

TNFAIP6
−0.3457
−0.7114
0.2343

LGALS3BP
0.111
−0.2857
0.3187

CKS2
−0.3697
0.1034
1.5141

STAT2
−0.0708
−0.6738
0.8915

EIF2AK2
−0.2044
−0.3038
0.2554

text missing or illegible when filed

indicates data missing or illegible when filed

Table 33 provides the results of a separate study which determined the top 50 genes neutralized in SLE patient whole blood 7 days after MEDI-545 treatment. Only three genes of the 50 genes, ZCCHC2, REC8L1, and GCLM, were not IFN-α/β-inducible.

TABLE 33

Top 50 probes neutralized 7 days post-dose in SLE patients receiving MEDI-545 treatment

Avg. Probe
Final

Probe
UniGene

Gene
Rank (By %
Probe

ID
ID
Gene Title
Symbol
Neutralization
Rank

219352_at
Hs.529317
hect domain and RLD 6
HERC6
2277.0
1

208436_s_at
Hs.166120
interferon regulatory factor 7
IRF7
2497.5
2

210797_s_at
Hs.118633
2′-5′-oligoadenylate synthetase-like
OASL
2708.2
3

205483_s_at
Hs.458485
ISG15 ubiquitin-like modifier
ISG15
2735.7
4

204439_at
Hs.389724
interferon-induced protein 44-like
IFI44L
3194.9
5

219211_at
Hs.38260
ubiquitin specific peptidase 18
USP18
3458.6
6

218543_s_at
Hs.12646
poly (ADP-ribose) polymerase family, member 12
PARP12
3472.3
7

205241_at
Hs.567405
SCO cytochrome oxidase deficient homolog 2 (yeast)
SCO2
3825.7
8

204747_at
Hs.47338
interferon-induced protein with tetratricopeptide repeats 3
IFIT3
3987.2
9

219519_s_at
Hs.31869
sialic acid binding lg-like lectin 1, sialoadhesin
SIGLEC1
4207.2
10

228230_at
Hs.517180
peroxisomal proliferator-activated receptor A interacting complex 285
PROC285
4373.1
11

235276_at
—
—
—
4438.7
12

214059_at
Hs.82316
Interferon-induced protein 44
IFI44
4477.4
13

222154_s_at
Hs.120323
DNA polymerase-transactivated protein 6
DNAPTP6
4531.3
14

202145_at
Hs.521903
lymphocyte antigen 6 complex, locus E
LY6E
4618.6
15

223849_s_at
Hs.514941
Mov10, Moloney leukemia virus 10, homolog (mouse)
MOV10
4691.0
16

219364_at
Hs.55918
likely ortholog of mouse D11lgp2
LGP2
4717.4
17

224503_s_at
Hs.114191
zinc finger, CCHC domain containing 2
ZCCHC2
4926.5
18

228617_at
Hs.441975
XIAP associated factor-1
BIRC4BP
4942.0
19

53720_at
—
hypothetical protein FLJ11286
FLJ11286
5046.2
20

218400_at
Hs.528634
2′-5′-oligoadenylate synthetase 3, 100 kDa
OAS3
5136.7
21

235508_at
Hs.526464
promyelocytic leukemia
PML
5328.7
22

232155_at
Hs.514554
KIAA1618
KIAA1618
5344.5
23

202086_at
Hs.517307
myxovirus (influenza virus) resistance 1, interferon-inducible protein p78 (mouse)
MX1
5484.4
24

242625_at
Hs.17518
radical S-adenosyl methionine domain containing 2
RSAD2
5522.4
25

209417_s_at
Hs.632258
interferon-induced protein 35
IFI35
5529.4
26

228439_at
Hs.124840
basic leucine zipper transcription factor, ATF-like 2
BATF2
5563.0
27

221766_s_at
Hs.10784
family with sequence similarity 46, member A
FAM46A
5607.1
28

202446_s_at
Hs.130759
phospholipid scramblase 1
PLSCR1
5911.3
29

205660_at
Hs.118633
2′-5′-oligoadenylate synthetase-like
OASL
6001.3
30

205875_s_at
Hs.344812
three prime repair exonuclease 1
TREX1
6062.0
31

34689_at
Hs.344812
three prime repair exonuclease 1
TREX1
6097.0
32

202869_at
Hs.524760
2′-5′-oligoadenylate synthetase 1, 40/46 kDa
OAS1
6101.5
33

214453_s_at
Hs.82316
interferon-induced protein 44
IFI44
6210.4
34

1555491_a_at
—
hypothetical protein FLJ11286
FLJ11286
6235.7
35

230036_at
Hs.489118
sterile alpha motif domain containing 9-like
SAMD9L
6254.1
36

222217_s_at
Hs.438723
solute carrier family 27 (fatty acid transporter), member 3
SLC27A3
6257.9
37

201641_at
Hs.118110
bone marrow stromal cell antigen 2
BST2
6371.4
38

218599_at
Hs.419259
REC8-like 1 (yeast)
REC8L1
6423.3
39

238327_at
Hs.531314
glutamate-cysteine ligase, modifier subunit
GCLM
6500.4
40

225291_at
Hs.388733
polyribonucleotide nucleotidyltransferase 1
PNPT1
6537.6
41

208581_x_at
Hs.374950
metallothionein 1X
MT1X
6541.4
42

212380_at
Hs.520102
KIAA0082
KIAA0082
6547.1
43

227347_x_at
Hs.154029
hairy and enhancer of split 4 (Drosophila)
HES4
6557.3
44

1557116_at
Hs.257352
apolipoprotein L, 6
APOL6
6571.1
45

231769_at
Hs.464419
F-box protein 6
FBXO6
6683.0
46

200986_at
Hs.384598
serpin peptidase inhibitor, clade G (C1 inhibitor), member 1, (angioedema, hereditary)
SERPING1
6688.7
47

33304_at
Hs.459265
interferon stimulated exonuclease gene 20 kDa
ISG20
6853.8
48

209593_s_at
Hs.252682
torsin family 1, member B (torsin B)
TOR1B
6866.4
49

202307_s_at
Hs.352018
transporter 1, ATP-binding cassette, sub-family B (MDR/TAP)
TAP1
6909.0
50

Example 7
The Majority of Lupus Patients Exhibit a Type I IFN-Inducible PD Marker Expression Pattern

Using 169 probe sets to detect expression of a number of PD markers, gene expression in whole blood samples of 35 lupus patients was analyzed using PCA (Principal Component Analysis). Principal component analysis is a statistical technique for simplifying a dataset, by reducing multidimensional datasets to lower dimensions for analysis. PCA was conducted on the filtered data set (169 probe sets) using the Spotfire statistical tool. The PCA determined that 24/35 of the lupus patients had a statistically significant PD marker signature. See FIG. 22 for PCA analysis results. The 169 probe sets used for this PCA analysis are provided in Table 20.

TABLE 20

Gene Expression Detected by 169 Probe Sets in 35 SLE Patients (Table 20 discloses

“DEAD (Asp-Glu-Ala-Asp)” as SEQ ID NO: 1)

Gene

Probe ID
UniGene ID
Gene Title
Symbol

1552772_at
Hs.3511811
C-type lectin domain family 4, member D
CLEC4D

1554343_a_at
Hs.435579
BCR downstream signaling 1
BRDG1

1555464_at
Hs.163173
interferon induced with helicase C domain 1
IFIH1

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
91 kDa
STAT1

lectin, galactoside-binding, soluble, 3 binding

200923_at
Hs.514535
protein
LGALS3BP

serpin peptidase inhibitor, clade G (C1 inhibitor),

200986_at
Hs.384598
member 1, (angioedema, hereditary)
SERPING1

201015_s_at
Hs.514174
junction plakoglobin
JUP

201324_at
Hs.436298
epithelial membrane protein 1
EMP1

201641_at
Hs.118110
bone marrow stromal cell antigen 2
BST2

201646_at
Hs.349656
scavenger receptor class B, member 2
SCARB2

methylenetetrahydrofolate dehydrogenase (NADP +

dependent) 2, methenyltetrahydrofolate

201761_at
Hs.469030
cyclohydrolase
MTHFD2

myxovirus (influenza virus) resistance 1,

interferon-inducible protein p78 (mouse) ///

myxovirus (influenza virus) resistance 1,

202086_at
Hs.517307
interferon-inducible protein p78 (mouse)
MX1

202145_at
Hs.521903
lymphocyte antigen 6 complex, locus E
LY6E

guanylate binding protein 1, interferon-inducible,

67 kDa /// guanylate binding protein 1, interferon-

202270_at
Hs.62661
inducible, 67 kDa
GBP1

202411_at
Hs.532634
interferon, alpha-inducible protein 27
IFI27

202430_s_at
Hs.130759
phospholipid scramblase 1
PLSCR1

202446_s_at
Hs.130759
phospholipid scramblase 1
PLSCR1

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, 40/46 kDa
OAS1

interferon-induced protein with tetratricopeptide

repeats 1 /// interferon-induced protein with

203153_at
Hs.20315
tetratricopeptide repeats 1
IFIT1

interferon-induced protein with tetratricopeptide

203595_s_at
Hs.252839
repeats 5
IFIT5

interferon-induced protein with tetratricopeptide

203596_s_at
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
IFI6

204439_at
Hs.389724
interferon-induced protein 44-like
IFI44L

204533_at
Hs.632586
chemokine (C-X-C motif) ligand 10
CXCL10

interferon-induced protein with tetratricopeptide

204747_at
Hs.47338
repeats 3
IFIT3

204972_at
Hs.414332
2′-5′-oligoadenylate synthetase 2, 69/71 kDa
OAS2

204994_at
Hs.926
myxovirus (influenza virus) resistance 2 (mouse)
MX2

205098_at
Hs.301921
chemokine (C-C motif) receptor 1
CCR1

205099_s_at
Hs.301921
chemokine (C-C motif) receptor 1
CCR1

signal transducer and activator of transcription 2,

205170_at
Hs.530595
113 kDa
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 1,40/46 kDa
OAS1

205569_at
Hs.518448
lysosomal-associated membrane protein 3
LAMP3

205660_at
Hs.118633
2′-5′-oligoadenylate synthetase-like
OASL

206025_s_at
Hs.437322
tumor necrosis factor, alpha-induced protein 6
TNFAIP6

206026_s_at
Hs.437322
tumor necrosis factor, alpha-induced protein 6
TNFAIP6

206133_at
Hs.441975
XIAP associated factor-1
BIRC4BP

206332_s_ata
—
interferon, gamma-inducible protein 16
IFI16

206513_at
Hs.281898
absent in melanoma 2
AIM2

206553_at
Hs.414332
2′-5′-oligoadenylate synthetase 2, 69/71 kDa
OAS2

carcinoembryonic antigen-related cell adhesion

206576_s_at
Hs.512682
molecule 1 (biliary glycoprotein)
CEACAM1

206715_at
Hs.125962
transcription factor EC
TFEC

Z-DNA binding protein 1 /// Z-DNA binding

208087_s_at
Hs.302123
protein 1
ZBP1

208436_s_at
Hs.166120
interferon regulatory factor 7
IRF7

208581_x_at
Hs.374950
metallothionein 1X
MT1X

208653_s_at
Hs.591335
CD164 molecule, sialomucin
CD164

208966_x_at
—
interferon, gamma-inducible protein 16
IFI16

209417_s_at
Hs.632258
interferon-induced protein 35
IFI35

carbinoembryonic antigen-related cell adhesion

209498_at
Hs.512682
molecule 1 (biliary glycoprotein)
CEACAM

209593_s_at
Hs.252682
torsin family 1, member B (torsin B)
TOR1B

210001_s_at
Hs.50640
suppressor of cytokine signaling 1
SOCS1

210705_s_at
Hs. 370515
tripartite motif-containing 5
TRIM5

210797_s_at
Hs.118633
2′-5′-oligoadenylate synthetase-like
OASL

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 /// hypthetical 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)
CEACAM1

212185_x_at
Hs.534330
metallothionein 2A
MT2A

212657_s_at
Hs.81134
interleukin 1 receptor antagonist
IL1RN

212659_s_at
Hs.81134
interleukin 1 receptor antagonist
IL1RN

212845_at
Hs.98259
sterile alpha motif domain containing 4A
SAMD4A

213293_s_at
Hs.501778
tripartite motif-containing 22
TRIM22

Full-length cDNA clone CS0DK002YF13 of HeLa

213294_at
Hs.546523
cells Cot 25-normalized of Homo sapiends (human)
—

213361_at
Hs.193842
tudor domain containing 7
TDRD7

213469_at
Hs.229988
GPI deacylase
PGAP1

213797_at
Hs.17518
radical S-adenosyl methionine domain containing 2
RSAD2

214059_at
Hs.82316
Interferon-induced protein 44
IFI44

tumor necrosis factor (ligand) superfamily, member

10 /// tumor necrosis factor (ligand) superfamily,

214329_x_at
Hs.478275
member 10
TNFSF10

214453_s_at
Hs.82316
interferon-induced protein 44
IFI44

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
IL1RN

216598_s_at
Hs.303649
chemokine (C-C motif) ligand 2
CCL2

217165_x_at
Hs.513626
metallothionein 1F (functional)
MT1F

interferon-induced protein with tetratricopeptide

217502_at
Hs.437609
repeats 2
IFIT2

217933_s_at
Hs.570791
leucine aminopeptidase 3
LAP3

218400_at
Hs.528634
2′-5′-oligoadenylate synthetase 3, 100 kDa
OAS3

218543_s_at
Hs.12646
poly (ADP-ribose) polymerase family, member 12
PARP12

218943_s_at
Hs.190622
DEAD (Asp-Glu-Ala-Asp) box polypeptide 58
DDX58

218986_s_at
Hs.591710
hypothetical protein FLJ20035
FLJ20035

219062_s_at
Hs.631682
zinc finger, CCHC domain containing 2
ZCCHC2

219209_at
Hs.163173
interferon induced with helicase C domain 1
IFIH1

219211_at
Hs.38260
ubiquitin specific peptidase 18
USP18

219352_at
Hs.529317
hect domain and RLD 6
HERC6

219364_at
Hs.55918
likely ortholog of mouse D11lgp2
LGP2

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_s_at
Hs.514941
(mouse)
MOV10

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
113 kDa
STAT2

hypothetical protein LOC652689 /// family with
LOC652689

sequence similarity 72, member A /// similar to
/// FAM72A

family with sequence similarity 72, member A ///
///

similar to family with sequence similarity 72,
LOC653594

225834_at
Hs.599880
member A
///

LOC653820

225869_s_at
Hs.502989
unc-93 homolog B1 (C. elegans)
UNC93B1

226103_at
Hs.632387
nexilin (F actin binding protein)
NEXN

226603_at
Hs.489118
sterile alpha motif domain containing 9-like
SAMD9L

226702_at
Hs.7155
hypothetical protein LOC129607
LOC129607

interferon-induced protein with tetratricopeptide

226757_at
Hs.437609
repeats 2
IFIT2

227458_at
—
—
—

227609_at
Hs.546467
epithelial stromal interaction 1 (breast)
EPSTI1

227697_at
Hs.527973
suppressor of cytokine signaling 3
SOCS3

228152_s_at
Hs.535011
hypothetical protein FLJ31033
FLJ31033

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, 69/71 kDa
OAS2

228617_at
Hs.441975
XIAP associated factor-1
BIRC4BP

229450_at
—
—
—

230036_at
Hs.489118
sterile alpha motif domain containing 9-like
SAMD9L

Transcribed locus, strongly similar to XP_511805.1

PREDICTED: hypothetical protein XP_511805

230314_at
Hs.112420
[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
91 kDa
STAT1

232666_at
Hs.528634
2′-5′-oligoadenylate synthetase 3, 100 kDa
OAS3

233425_at
Hs.631682
zinc finger, CCHC domain containing 2
ZCCHC2

233880_at
Hs.195642
chromosome 17 open reading frame 27
C17orf27

235061_at
Hs.291000
protein phosphatase 1K (PP2C domain containing)
PPM1K

235112_at
Hs.533491
KIAA1958
KIAA1958

235157_at
Hs.583792
Poly (ADP-ribose) polymerase family, member 14
PARP14

235276_at
—
—
—

235643_at
Hs.489118
sterile alpha motif domain containing 9-like
SAMD9L

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)
EPSTI1

241812_at
Hs.120323
DNA polymerase-transactivated protein 6
DNAPTP6

241916_at
Hs.130759
Phopholipid scramblase 1
PLSCR1

242020_s_at
Hs.302123
Z-DNA binding protein 1
ZBP1

242234_at
Hs.441975
XIAP associated factor-1
BIRC4BP

242625_at
Hs.17518
radical S-adenosyl methionine domain containing 2
RSAD2

242898_at
—
—
—

243271_at
Hs.489118
Sterile alpha motif domain containing 9-like
SAMD9L

44673_at
Hs.31869
sialic acid binding Ig-like lectin 1, sialoadhesin
SIGLEC1

AFFX-

signal transducer and activator of transcription 1,

HUMISGF3A/M97935_3_at
Hs.565365
91 kDa
STAT1

AFFX-

signal transducer and activator of transcription 1,

HUMISGF3A/M97935_5_at
Hs.565365
91 kDa
STAT1

AFFX-

signal transducer and activator of transcription 1,

HUMISGF3A/M97935_MB_at
Hs.565365
91 kDa
STAT1

Similarly, using 25 highly upregulated IFN-inducible genes, expression in whole blood samples of lupus patients and normal healthy donors was analyzed using PCA (Principal Component Analysis). The PCA determined that approximately 66% of the lupus patients had a strong/moderate type I IFN inducible signature. See FIG. 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 FIG. 65 provide further evidence that a high percentage of SLE patients share at least 2-fold overexpression of each individual type I IFN genes.

TABLE 23

Overexpressed Type-I IFN Genes in Whole Blood of Lupus Patients

Number Of Samples

Displaying A Fold-Change

Average log2

Probe.ID
Gene.Title
Gene.Symbol
>= 2
% of Samples
Fold-Change

222816_s_at
zinc finger, CCHC domain containing 2
ZCCHC2
70
79.55
2.124

204415_at
Interferon, alpha-inducible protein 6
IFI6
67
76.14
3.007

217502_at
interferon-induced protein with tetratricopeptide repeats 2
IFIT2
65
73.86
1.913

235643_at
sterile alpha motif domain containing 9-like
SAMD9L
65
73.06
2.020

213797_at
radical S-adenosyl methionine domain containing 2
RSAD2
62
70.45
2.978

214059_at
Interferon-induced protein 44
IFI44
61
69.32
3.050

202411_at
interferon alpha-inducible protein 27
IFI27
60
68.18
3.937

204439_at
interferon-induced protein 44-like
IFI44L
60
68.18
2.647

242625_at
radical S-adenosyl methionine domain containing 2
RSAD2
59
67.05
2.861

214453_s_at
interferon-induced protein 44
IFI44
59
67.05
2.463

203153_at
interferon-induced protein with tetratricopeptide repeats 1/// text missing or illegible when filed

IFIT1
59
67.05
2.034

242234_at
XIAP associated factor-1
BIRC4BP
59
67.05
2.066

203595_s_at
interon-induced protein with tetratricopeptide repeats 5
IFIT5
59
67.05
1.603

202086_at
myoxovirus (influenza virus) resistance 1, interferon-inducuble text missing or illegible when filed

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
IL1RN
58
65.91
1.278

219863_at
hect domain and RLD 5
HERC5
57
64.77
1.795

202869_at
2,5′-oligoadenylate synthetase 1, 40/46 kDa
OAS1
56
63.64
2.057

226702_at
hypothetical protein LOC129607
LOC129607
56
63.64
1.797

205483_s_at
ISG15 ubiquitin-like modifier
ISG15
56
63.64
1.979

204747_at
interferon-induced protein with 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 synthetase 3, 100 kDa
OAS3
55
62.50
1.932

227609_at
epithelial stromal interaction 1 (breast)
EPSTI1
55
62.50
1.788

200986_at
serpin peptidase inhibitor, clade G (C1 inhibitor), member 1 text missing or illegible when filed

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)
EPSTI1
54
61.36
1.895

205552_s_at
2′-5′-oligoadenylate synthetase 1, 40/46 kDa
OAS1
54
61.36
1.945

225929_s_at
chromosome 17 open reading frame 27
C17orf27
54
61.36
1.054

222154_s_at
DNA polymerase-transactivated protein 6
DNAPTP6
53
60.23
2.030

205569_at
lysosomal-associated membrane protein 3
LAMP3
53
60.23
1.813

205660_at
2′-5′-oligoadenylate synthetase-like
OASL
53
60.23
1.677

219352_at
hect domain and RLD 6
HERC6
52
59.09
1.663

210797_s_at
2′-5′-oligoadenylate synthetase-like
OASL
52
59.09
1.548

241916_at
Phospholipid scramblase 1
PLSCR1
52
59.09
1.396

208087_s_at
Z-DNA binding protein 1///Z-DNA 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_s_at
sialic acid binding Ig-like lectin 1, sialoadhesin///sialic acid text missing or illegible when filed

SIGLEC1
51
57.95
3.019

228617_at
XIAP associated factor-1
BIRC4BP
51
57.95
1.473

202446_s_at
phospholipid scramblase 1
PLSCR1
51
57.95
1.307

232095_at
SLIT-ROBO Rho GTPase activating protein 2
SRGAP2
50
56.82
1.155

232666_at
2′-5′-oligoadenylate synthetase 3, 100 kDa
OAS3
49
55.68
1.862

204972_at
2′-5′-oligoadenylate synthetase 2, 69/71 kDa
OAS2
49
55.68
1.642

202430_s_at
phospholipid scramblase 1
PLSCR1
49
55.68
1.209

224701_at
poly (ADP-ribose) polymerase family, member 14
PARP14
49
55.68
1.098

219211_at
ubiquitin specific peptidase 18
USP18
48
54.55
2.365

206553_at
2′-5′-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
C17orf27
47
53.41
0.936

44673_at
sialic acid binding Ig-like lectin 1, sialoadhesin
SIGLEC1
47
53.41
1.975

203596_s_at
interferon-induced protein with 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
IL1RN
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_s_at
dual adaptor of phosphotyrosine and 3-phosphoinositides
DAPP1
46
52.27
1.055

208436_s_at
interferon regulatory factor 7
IRF7
45
51.14
1.146

217933_s_at
leucine aminopeptidase 3
LAP3
45
51.14
0.807

228152_s_at
hypothetical protein FLJ31033
FLJ31033
45
51.14
0.834

230036_at
sterile alpha motif domain containing 9-like
SAMD9L
44
50.00
1.097

228607_at
2′-5′'-oligoadenylate synthetase 2, 69/71 kDa
OAS2
44
50.00
1.113

218543_s_at
poly (ADP-ribose) polymerase family, member 12
PARP12
44
50.00
1.111

226603_at
sterile alpha motif domain containing 9-like
SAMD9L
44
50.00
1.033

204211_x_at
eukaryotic translation initiation factor 2-alpha kinase 2
EIF2AK2
44
50.00
1.050

235157_at
Poly (ADP-ribose) polymerase family, member 14
PARP14
44
50.00
0.940

209417_s_at
interferon-induced protein 35
IFI35
44
50.00
0.957

text missing or illegible when filed

indicates data missing or illegible when filed

Based on the observations of different overexpressed type I IFN genes in SLE patients, described above, a set of 21 type I IFN genes in whole blood of lupus patients was identified as potentially useful. See Table 24.

TABLE 24

Twenty one potential overexpressed type I IFN genes useful as PD markers

DNA

SIG

PLSCR

Sample
IFI44
IFI27
IFI44L
PTP6
LAMP3
LY6E
RSAD2
HERC5
IFI6
ISG15
OAS3
LEC1
OAS2
USP18
RTP4
IFIT1
MX1
OAS1
EPSTI1
1
IFRG28

A_37329
23.67
3.34
23.45
7.63
6.75
7.25
26.21
8.12
5.53
7.47
4.82
5.16
5.22
7.14
3.94
15.26
4.98
7.75
6.57
3.69
3.71

A13

A_37330
5.31
4.33
6.28
2.80
4.23
1.44
8.14
2.76
2.39
3.44
3.48
2.26
2.63
2.12
1.82
4.83
2.77
2.06
2.48
3.65
2.17

A13

A_37343
10.70
1.41
10.31
2.51
2.23
2.94
11.76
2.52
1.25
1.97
2.63
0.96
2.38
2.85
2.73
7.39
2.82
3.78
2.97
2.12
2.89

A13

A_37345
37.55
30.71
28.86
5.28
3.94
4.30
35.61
1.88
1.85
3.73
2.26
0.92
3.03
2.54
3.70
21.92
2.66
4.51
10.06
2.48
3.92

A16

A_37360
10.72
4.62
7.36
2.42
1.34
3.38
14.35
2.07
3.34
2.46
2.55
2.81
2.17
2.01
1.12
13.79
2.32
2.30
3.51
1.40
1.29

A13

A_37361
4.19
0.83
5.32
2.51
4.13
1.27
7.01
3.64
4.67
3.08
4.16
6.38
2.97
2.43
1.46
4.55
2.40
2.02
2.40
2.43
1.41

A13

A_37365
24.79
8.25
26.45
15.76
18.11
11.33
54.51
13.72
15.37
16.02
10.79
10.33
8.85
9.57
7.07
23.56
8.22
11.56
16.51
5.93
7.49

A13

A_37473
0.88
0.96
0.53
0.63
0.65
0.85
0.27
0.39
0.48
0.70
0.25
0.26
0.50
0.96
1.35
0.31
0.77
0.68
0.59
1.45
1.48

A13

A_37475
0.85
0.17
0.67
0.89
0.14
0.36
0.36
0.32
0.18
0.27
0.42
0.12
0.73
0.43
0.69
0.32
0.23
0.92
0.50
2.97
0.82

A11

A_37476
1.25
4.20
0.83
2.71
2.19
2.82
0.95
1.97
0.70
1.78
0.93
0.45
2.15
2.94
4.70
0.49
1.76
1.54
1.01
7.92
4.96

A15

A_37477
0.78
17.78
0.54
0.37
0.40
2.26
0.11
0.28
0.65
1.99
0.28
0.57
0.35
1.18
3.44
0.23
0.96
1.65
0.51
2.05
3.50

A11

A_37478
1.53
5.56
0.98
1.90
2.24
1.89
0.82
1.65
0.71
2.89
0.50
1.00
1.64
1.86
4.20
0.39
1.73
2.40
1.23
8.18
4.51

A14

C_001
8.93
162.67
16.29
41.43
4.13
35.49
14.75
10.03
5.34
31.98
5.95
13.14
6.35
15.01
13.08
0.65
18.84
10.75
9.42
8.16
15.58

C_002
30.64
135.38
53.11
15.25
6.78
7.33
20.98
4.88
6.52
8.78
6.28
5.49
5.58
2.3.17
6.56
15.64
6.73
9.22
7.10
3.62
6.68

C_004
25.99
220.81
71.18
18.13
8.48
9.94
51.74
8.77
4.32
12.04
7.00
6.60
7.87
32.60
11.21
21.06
9.69
8.07
11.63
7.62
10.31

C_005
11.39
324.78
63.12
44.53
6.71
14.53
50.88
11.53
7.46
22.37
11.03
23.05
11.90
63.56
10.70
19.74
17.46
14.42
9.62
5.59
9.02

C_006b
0.48
0.57
0.47
0.55
0.25
0.73
0.27
0.33
1.20
0.70
0.21
0.31
0.34
0.38
0.81
0.33
0.38
0.52
0.60
0.37
0.67

C_007
63.08
498.86
71.47
31.25
9.75
25.15
124.43
17.25
12.01
30.68
4.98
4.68
11.92
37.94
14.21
32.73
13.92
12.20
14.28
45.35
11.18

C_009
30.12
209.75
46.29
15.46
6.63
11.07
32.35
8.07
4.71
10.17
6.77
8.67
9.57
21.00
8.07
14.25
9.04
9.53
8.01
7.63
7.49

C_010
24.31
85.83
42.22
21.61
10.78
15.14
49.98
12.94
7.29
19.29
10.90
7.34
10.34
18.34
7.80
12.47
8.32
11.58
12.30
7.21
7.03

C_011
26.17
160.53
30.34
57.41
32.45
29.58
45.36
35.18
2.66
14.93
44.32
25.28
27.10
51.74
26.85
9.19
15.63
17.96
15.00
19.29
28.84

C_012
48.84
131.90
85.63
15.28
7.85
10.17
57.95
8.19
5.21
8.71
7.76
4.55
10.17
31.27
10.46
27.35
8.32
7.66
12.35
6.33
9.08

C_013
3.14
2.21
4.97
1.84
1.79
0.73
6.65
2.66
1.34
1.02
1.05
0.74
1.41
2.45
2.69
3.55
2.14
1.32
3.19
2.30
2.31

C_017
21.09
256.30
48.34
18.49
5.74
9.18
35.38
7.79
4.91
13.13
6.54
4.77
6.67
16.58
4.91
18.66
5.69
10.37
8.29
5.62
5.43

C_118
71.14
177.60
97.17
41.72
11.95
28.82
98.76
16.75
10.97
27.33
18.71
9.84
16.48
75.02
18.41
44.09
23.41
12.66
18.71
12.52
15.53

C_019
75.89
362.67
158.96
30.47
16.33
17.58
113.44
17.70
16.63
29.09
7.39
5.29
15.13
61.50
21.00
22.61
21.25
19.06
18.93
12.46
19.78

C_020
49.27
149.00
96.50
40.29
13.89
23.41
77.48
16.52
10.21
30.40
6.26
5.94
11.57
48.59
13.57
34.76
13.99
11.76
13.89
8.63
13.38

C_10721
100.31
153.10
123.21
46.69
25.19
19.53
96.12
17.51
8.08
42.37
3.38
8.45
14.21
58.15
12.60
20.80
14.5
20.32
23.72
13.22
13.85

C_10722b
7.05
3.09
4.15
2.50
3.07
1.02
2.62
1.75
0.61
1.29
0.40
0.58
1.55
5.30
1.56
3.31
1.98
1.87
4.22
3.40
1.54

C_129141
49.92
189.36
47.56
32.63
11.54
24.45
50.52
15.98
15.19
50.39
12.14
6.27
13.98
26.94
12.80
33.17
10.47
17.41
16.85
8.43
13.53

C_19171
32.06
8.24
26.46
13.54
9.78
6.63
41.14
12.40
5.23
10.87
7.65
8.53
8.22
12.46
5.35
25.74
11.90
5.68
8.13
6.33
5.56

C_325532
77.48
163.43
90.25
236.52
162.67
30.05
73.47
26.40
26.86
193.45
36.73
130.31
28.23
71.53
23.96
33.26
13.14
20.71
25.62
12.29
27.39

C_45311
5.39
0.81
2.19
1.36
0.54
1.08
1.15
0.79
1.05
1.42
0.17
0.30
0.88
1.08
2.50
1.43
1.29
2.19
2.02
2.20
2.80

C_71277
15.15
7.55
19.03
7.33
3.59
3.65
14.39
3.88
1.82
4.00
3.85
3.76
4.75
7.54
3.43
7.76
4.15
3.10
6.32
2.90
3.76

C_72371
86.57
51.95
89.42
96.06
18.37
28.43
110.34
24.75
12.09
45.54
24.29
12.46
25.62
54.29
17.10
51.00
13.86
21.64
25.98
14.28
17.42

median
23.67
38.71

text missing or illegible when filed

15.25

8.07
4.71

text missing or illegible when filed

12.46

14.25

7.75

average
28.22
101.10

text missing or illegible when filed

25.02
12.14
11.17

text missing or illegible when filed

5.94

7.62
9.39
8.07
22.10
8.17

text missing or illegible when filed

7.95
8.32
9.27
6.55
8.16

sample
IFI44
IFI27
IFI44L
DNA
LAMP3
LY6E
RSAD2
HERC5
IFI6
ISG15
OAS3
SIG
OAS2
USP18
RTP4
IFIT1
MX1
OAS1
EPSTI1
PLSCR
IFRG28

PTP6

LEC1

1

text missing or illegible when filed

indicates data missing or illegible when filed

Overexpression of these genes, as detected initially using the Affymetrix arrays, was confirmed by FLUIDIGM dynamic array, validating their overexpression. See FIG. 69.

Example 8
MEDI-545 Considerably Neutralizes the Type I IFN Gene Signature of SLE Patients Having a Strong to Moderate Type I IFN Gene Signature

Patients in a clinical trial were identified as having a strong/moderate type I IFN gene, a weak type I IFN gene signature, or no type I IFN gene signature. These patients were designated into one of these groups based on 149 genes. Table 25 shows the number of lupus patients in the clinical trial that were designated in each of these three groups and indicates the treatment protocol they received.

TABLE 25

Patient distribution based on type-I IFN gene signature prior to treatment

Strong &

Group
moderate signature
Weak signature
No signature

PBO
10
5
2

0.3 mpk
5
0
1

1 mpk
2
2
2

3 mpk
3
2
1

10 mpk
4
3
0

30 mpk
3
2
1

Total
27
14
7

The SLE patients that were designated as having strong and moderate type-I IFN gene signatures all had: an average 4-fold increase in expression of the top 25 most upregulated type I IFN genes; an average 2-fold increase in expression of the top 50 most upregulated type I IFN genes; and a percentage of total examined disease genes being type I IFN inducible of 3.8. The average fold increase in the top 25 type I IFN inducible genes for each patient having a strong/moderate type I IFN signature or a weak signature in the trial is provided in FIG. 28.

Treatment of these different SLE patient groups provided evidence that neutralization of the type I IFN gene signature by MEDI-545 is drug specific. FIG. 29(a) shows that in a group of SLE patients having a type-I IFN gene signature, virtually all of the top 39 genes neutralized 14 days post-MEDI-545 treatment are type I IFN signature genes (see yellow highlighted genes; percentage inhibition of the type I IFN signature genes ranged from 30.5-64.7). By contrast, none of the top 39 neutralized genes in SLE patients who received placebo were type I IFN signature genes. See FIG. 29(c). The SLE patients who lacked a type I IFN signature and were treated with MEDI-545 displayed an intermediate neutralization pattern, with some type I IFN signature genes neutralized. (See FIG. 29(b); yellow highlighting indicates type I IFN signature genes, which were neutralized from 19%-44.9%).

Further break down of SLE patients into strong, moderate, and weak type-I IFN gene signatures was conducted. Briefly, the 25 most highly overexpressed type I IFN-inducible genes in individual SLE patients generated from the ex vivo stimulation of healthy donor WB with SLE patient sera study were selected and the median fold change of these 25 genes was used to construct a type I IFN gene signature score for each SLE patient. FIG. 84 shows the distribution of the type I IFN gene signature scores of the 46 SLE patients profiled. The SLE patients were profiled into 3 groups based on their type I IFN gene signature score: high type I IFN gene signature (score>10); moderate type I IFN gene signature (score 4-10); and weak type I IFN gene signature (score<4).

Selection of a Panel of 21 Type I IFN-Inducible Genes in WB of SLE Patients

To select a small, robust panel of type I IFN-inducible genes that could be developed into an HTP assay, the gene panel was narrowed to 21 genes. To identify the 21 potential PD and diagnostic markers, 807 IFN-α/β-inducible probes identified by ex vivo stimulation of healthy donor WB with 10 IFN-α subtypes (2a, 4b, 5, 6, 7, 8, 10, 14, 16, and 17) and IFN-β were used as a candidate marker starting point. The WB samples from a total of 46 SLE patients procured from commercial vendors and 24 healthy normal controls were used to determine the type I IFN-inducible probes that are upregulated in WB of SLE patients. 114 overexpressed probes (q≦0.05; fold change ≧2) were identified in WB of SLE patients were type I IFN-inducible using SAM and FDR.

To investigate whether these overexpressed type I IFN-inducible genes in WB of SLE patients were neutralizable by an anti-IFN-α mAb, one healthy donor PBMC was stimulated ex vivo with sera from six individual SLE patients. The healthy donor was prescreened to exclude those donors that might have viral infection. 161 type I IFN-inducible probes were upregulated by ≧2-fold in the PBMC of the healthy donor following stimulation with ≧1 SLE patient serum in which the overexpression of these genes was suppressed by ≧50% and ≧70% by an anti-IFN-α mAb and an anti-IFN-αR mAb, respectively.

The intersection between this list of 161 probes and previously determined list of 114 probes was 80 probes. Each of these 80 probes was ranked by both the average fold change magnitude across all SLE patients and the percentage of patients displaying a change 2-fold. Generally, the 21 most prevalently overexpressed type I IFN-inducible genes (that represent unique genes using the NetAffx annotation file for the Affymetrix U133 2.0 plus array; ESTs were excluded) from this ranking were retained for a static list of probes used to measure PD. The type I IFN signature score was then defined by the median of these 21 genes.

With these 21 genes, it was necessary to recalculate the thresholds that had been previously identified for partitioning SLE patients into type I IFN gene signature responses of strong, moderate, or weak (based on the Affymetrix platform) for a lower density platform (TAQMAN-based assay). A scaling method was required to convert the type I IFN signature score based on the top 25 differentially expressed genes (independent for each SLE patient) on the Affymetrix platform to the type I IFN signature score based on the 21 genes selected for the TAQMAN-based assay. This method was implemented to compensate for 3 primary differences between the 2 platforms: (1) the number of probes used for the type I IFN signature (25 genes dynamically determined for each patient on the Affymetrix platform versus a 21 static gene list on the TAQMAN-based assay), (2) the differences in sensitivity between the 2 platforms, and (3) the scales of the dynamic ranges within each platform. First, the fold change values were calculated (on a log₂scale) for the 155 type I-inducible probes between the 35 randomly selected SLE patients and the average of a set of normal healthy controls. The genes with the top 25-fold change values were determined for each patient on the Affymetrix platform (this gene set is allowed to vary from patient to patient depending on which type I IFN-inducible genes are most highly expressed). Next, the median fold change was calculated from the top 25 genes for each SLE patient. The same calculation was conducted across the same patients using the static 21 gene set on the TAQMAN-based assay. This gene set was identical for each patient and the median fold change was calculated based on 21 genes, rather than 25 dynamic genes, as was conducted for the Affymetrix platform. A simple regression model was then computed using these 2 vectors of equal length (35 median fold change values), and the coefficients from the model were used to calculate the conversion factor (from the Affymetrix platform to the TAQMAN-based assay) for the response threshold values to partition the SLE patients into a type I IFN gene signature category of strong (>10 on Affymetrix; >5.53 on TAQMAN), moderate (between 4 and 10 on Affymetrix; between 1.91 and 5.53 on TAQMAN), or weak (<4 on Affymetrix; <1.91 on TAQMAN). Using these scaled threshold values, for the purpose of stratifying SLE patients, the signature (ie, median fold change) that was calculated on the 21 genes from the TAQMAN-based assay was comparable to that from the top 25 upregulated type I IFN-inducible genes.

The prevalence and fold change (log₂based) of the 21 IFN α/β-inducible genes in whole blood of 111 SLE patients is provided in Table 32, below.

TABLE 32

Prevalence and fold chance in expression of 21 IFN α/β-inducible genes in SLE patient whole blood

Gene

Probe
Q value
Fold
Prevalence
Gene name
symbol

204415_at
qv < 1e−16
9.38
78.20
interferon, alpha-inducible protein 6
IFI6

213797_at
2.67E−12
8.27
71.80
radical S-adenosyl methionine domain
RSAD2

containing 2

214059_at
7.18E−14
7.93
70.90
Interferon-induced protein 44
IFI44

204439_at
5.85E−12
6.45
69.10
interferon-induced protein 44-like
IFI44L

202411_at
6.35E−12
14.42
67.30
interferon, alpha-inducible protein 27
IFI27

202086_at
1.09E−09
3.26
66.40
myxovirus (influenza virus) resistance 1,
MX1

interferon-inducible protein p78 (mouse)

203153_at
3.90E−07
3.52
65.50
interferon-induced protein with
IFIT1

tetratricopeptide repeats 1

219863_at
8.05E−11
3.27
64.50
hect domain and RLD 5
HERC5

205483_s_at
1.23E−13
3.71
63.60
ISG15 ubiquitin-like modifier
ISG15

205569_at
qv < 1e−16
3.91
62.70
lysosomal-associated membrane protein 3
LAMP3

218400_at
1.01E−10
3.65
62.70
2′-5′-oligoadenylate synthetase 3, 100 kDa
OAS3

202869_at
4.95E−11
3.77
61.80
2′,5′-oligoadenylate synthetase 1, 40/46 kDa
OAS1

227609_at
7.41E−10
3.16
60.90
epithelial stromal interaction 1 (breast)
EPSTI1

204747_at
9.78E−11
3.04
60.90
interferon-induced protein with
IFIT3

tetratricopeptide repeats 3

202145_at
qv < 1e−16
4.65
60.90
lymphocyte antigen 6 complex, locus E
LY6E

204972_at
qv < 1e−16
3.06
58.20
2′-5′-oligoadenylate synthetase 2, 69/71 kDa
OAS2

241916_at
6.29E−07
2.46
56.40
Phospholipid scramblase 1
PLSCR1

44673_at
qv < 1e−16
3.91
55.50
sialic acid binding Ig-like lectin 1,
SIGLEC1

sialoadhesin

219211_at
2.54E−13
4.83
55.50
ubiquitin specific peptidase 18
USP18

219684_at
2.75E−07
2.47
50.00
receptor (chemosensory) transporter
RTP4

protein 4

241812_at
5.25E−07
1.84
38.20
DNA polymerase-transactivated protein 6
DNAPTP6

These 21 genes were neutralized in a dose-dependent dependent fashion by MEDI-545. See FIGS. 86 and 89. Heatmap (FIG. 87a) and PCA calculations (FIG. 87b) using these 21 genes showed neutralization of the upregulated IFN α/β gene signature in an SLE patient treated with 30 mg/kg MEDI-545, but not in placebo-treated SLE patients (FIG. 88). Thus, it is evident that these genes could be used as a PD marker set.

Stratification of 35 Patients, by Strength of Type I IFN Gene Signature Using the 21 Genes

FIG. 85 shows the stratification of 35 SLE patients into groups of high (20 patients), moderate (8 patients), and weak (7 patients) type I IFN gene signatures based on the distribution of fold change values (log₂scale) of all 21 type I IFN-inducible genes and partitioned into each group by the median fold change of this distribution of 21 genes for each patient (vertical dashed lines), as measured by the dynamic array from FLUIDIGM. From FIG. 85, it is apparent that each patient distribution exhibits slight differences in skewness and basic shape/form, as this indicates the diversity in the various severity levels of SLE, based on the 21 type IFN-inducible gene selected. In a PCA plot for all SLE patients profiled in this study (n=100) and for the 24 healthy control samples using the 21 type I IFN-inducible genes, a clear distinction between SLE patients with an overexpressed type I IFN gene signature and those with weak or nondetectable type I IFN gene signatures is observed (FIG. 82C). Furthermore, the SLE patients with weak or nondetectable type I IFN gene signatures were clustered together with healthy donors. Importantly, the partitioning between these groups using the 21-gene panel of type I IFN-inducible genes was similar to that observed with the larger 114-gene set (FIGS. 81A and 81B).

Example 9
Multiple Type-I IFN Subtypes are Up-Regulated in Whole Blood of SLE Patients

To identify the type-I IFN subtypes responsible for the induction of the type-I IFN signature of SLE patients, mRNA levels of type-I IFN genes in SLE patient whole blood were measured.

Gene expression analysis was performed using a TAQMAN Low Density Array (TLDA) from Applied Biosystems. Expression of type-I IFNα subtypes 1, 2, 5, 6, 7, 8, 14, 17, and 21 was monitored and compared in whole blood of SLE patients relative to healthy volunteers.

Double-stranded cDNA for each patient sample was pre-amplified using the TAQMAN PreAmp Master Mix kit (Applied Biosystems). cDNA was pre-amplified by conducting 10 cycles of PCR on each patient sample using a pooled solution of primers, a pair for each gene analyzed on the array. The pre-amplified cDNA were diluted 1:5 with TE. A 50 μL volume of the diluted pre-amplified cDNA was added to a 50 μL volume of 2×TAQMAN Universal PCR Master Mix (Applied Biosystems) and mixed. The array was loaded with the mixture using standard procedures and the loaded array was run on a 7900HT Fast Real-Time PCR System (Applied Biosystems). Data analysis of the resulting Ct values was conducted with the SDSv2.2.2 software tool (Applied Biosystems).

FIG. 27 shows the relative overexpression of mRNA of nine IFNα subtypes in the whole blood of lupus patients relative to healthy volunteers. Many of these IFNα subtypes were upregulated at the mRNA level in the whole blood of SLE patients.

FIG. 66 shows that IFNβ, IFNω and IFNAR1 and IFNAR2 genes are also overexpressed in whole blood of lupus patients relative to healthy volunteers.

FIG. 82 shows that TNF-α, IFN-γ, IFN-γR1, and IFN-γR2 transcripts were also upregulated in WB of SLE patients (FIG. 82). However, the relative magnitude of overexpression of these transcripts was less than that of the type I IFN family members, especially the IFN-α subtypes.

Example 10
Ex Vivo IFN-Stimulated Whole Blood and Keratinocytes of Healthy Individuals Identifies a Panel of Type I IFN-Inducible Genes Relevant to Psoriasis

To identify type-I IFN inducible genes over-expressed in keratinocytes of lesions of psoriatic patients, whole blood and keratinocytes of healthy donors were stimulated ex vivo with a panel of IFNα subtypes, as well as IFNβ, IFNγ, and TNFα.

Whole Blood

Whole blood was collected from healthy donors in heparinized tubes. The total blood volume collected from each donor was pooled into a single culture flask and 3 mL of the total volume was aliquoted into a single well of a 6-well culture plate. Individual wells of blood were then exposed to a variety of treatments, including: vehicle (1×PBS), a panel of IFNα subtypes (IFNα2a, -4b, -5, -6, -7, -8, -10, -16, -17), IFNβ, IFNω, IFNλ, IFNγ, leukocyte IFN, or TNFα. Following exposure, the blood was gently mixed by pipetting and incubated at 37° C., 5% CO₂for 4 hrs (TNFα treatment was conducted for both 2 hrs and 4 hrs). Following the incubation period, 2.5 mL of blood was transferred to a PAXgene RNA tube and inverted 8-10 times. The PAXgene tubes were incubated at room temperature for two hours and then frozen (−20° C. overnight, −70° C. for long term storage) until further processing was required. Induction of gene expression by exposure to each of the treatment conditions was performed using Affymetrix GENECHIP® human genome U133 plus v2.0 arrays.

The various IFNα subtypes and IFNβ up-regulated 900-1200 probe sets by at least 2 fold. Of these, 689 probe sets (approximately 1.3% of all probe sets on the Affymetrix human genome U133 plus v2.0 array) were uniformly up-regulated by at least 2 fold in all donors by all ten IFNα subtypes and IFNβ. Using the same approach, 336 probe sets were identified as down-regulated by IFNα/β in the ex vivo stimulated whole blood.

Alterations in gene expression in healthy patient whole blood stimulated with TNFα were also observed at both the two and four hour time points. In all, 234 and 72 probe sets were up-regulated and down-regulated, respectively, by at least 2 fold in all donors. Furthermore, IFNγ challenge of whole blood for 4 hrs induced up-regulation of 304 probe sets and down-regulation of 52 probe sets by at least 2 fold. Little overlap was observed in the probe sets up-regulated by IFNα/β and TNFα (40 probes). By contrast, greater overlap was observed in the probe sets up-regulated by IFNα/β and IFNγ. 198 probes were up-regulated by at least 2-fold by both IFNα/β and IFNγ. Of the 198 probes up-regulated by at least 2-fold by both IFNα/β and IFNγ, the magnitude of up-regulation by IFNα/β was greater for about ⅔ of these probes (p value less than 0.05) than IFNγ.

FIG. 30 provides the hierarchical clustering of 1384 probe sets differentially regulated by either IFNα/β, or IFNγ, or TNFα in ex vivo stimulated whole blood. From this hierarchical clustering the similar response of whole blood to challenge with IFNα subtypes and IFNβ can easily be observed, as can the similar but distinctly different effect of IFNγ from IFNα/β, and the drastically different effect of TNFα from IFNα/β.

FIG. 31
a provides the hierarchical clustering of the relative expression of only the top 25 type-I IFN inducible probe sets identified in the ex vivo stimulated whole blood.

Keratinocytes

Normal human keratinocytes (EpiDerm system, MatTek, Inc.) were grown under serum-free conditions according to the manufacturers instructions. Briefly, keratinocytes were maintained on tissue culture inserts at the air-liquid interface to maintain a multilayered, fully differentiated epithelial phenotype. Keratinocytes were stimulated with human leukocyte IFN (15, 50, 150, IU/mL, PBL Biomedical Labs), human IFNα2a (15-350 IU/ml, PBL Biomedical Labs), recombinant human TNFα, (0.1 ng/ml, R+D Systems) or recombinant human IFNγ (3 ng/ml, R+D Systems). Epidermal cultures were harvested at 2, 4, or 18 hours post treatment for transcript analysis. Over 100 probe sets were identified as overexpressed in keratinocytes cultures stimulated with human IFNα2a and leukocyte IFN.

FIG. 31
b provides the hierarchical clustering of the relative expression of 25 type-I IFN inducible genes in ex vivo stimulated keratinocytes. The 25 type-I IFN inducible probe sets used to prepare the hierarchical clustering are the top 25 type-I IFN inducible probes identified in the ex vivo stimulated whole blood (those shown in FIG. 31a). Many of the top 25 type-I IFN inducible probe sets in ex vivo stimulated whole blood are also induced in ex vivo stimulated keratinocytes. See, e.g., MX1, IFI27, OAS1, IFI6, IFI44L, etc.

In addition, many of these genes were among those most overexpressed in the lesional skin of psoriasis patients. See discussion in Example 11, below.

Example 11
Whole Genome Array Profiling Identified IFNα/β Signaling Pathway as the Most Significantly Activated Pathway in Lesional Skin of Psoriasis Patients

A comparison of gene expression profiles of skin samples from healthy donors and paired non-lesional/lesional skin samples from psoriasis patients was performed to identify a type-I interferon induced gene expression signature associated with psoriatic skin lesions. Briefly, skin samples of 21 normal healthy control donors (5 samples obtained from Biochain, 14 from ILSbio, and 2 from Dr. James Krueger's lab) and 26 paired non-lesional/lesional skin samples of 24 psoriatic patients (21 pairs obtained from Asterand, and 5 from Dr. James Krueger's lab) were obtained. Three additional lesional skin samples from 3 psoriatic patients were obtained. These 3 additional lesional skin samples lacked a paired non-lesional skin sample because the non-lesional skin sample either did not yield sufficient cRNA for hybridization or the scanned array for the non-lesional skin sample had high scaling factors that were more than 3-fold of average.

Total RNA from the samples was extracted using the Qiagen RNAeasy-Mini kit (Hilden, Germany). The purity and concentration of the extracted RNA were determined spectrophotometrically (260/280>1.9). RNA quality was assessed on an Agilent 2100 Bioanalyzer using the RNA 6000 NANO LABCHIP®. Generation of biotin-labeled amplified cRNA, from 2 μg of total RNA, was accomplished using the Affymetrix GENECHIP® One-Cycle cDNA Synthesis kit and the AFFYMETRIX GENECHIP® WT Labeling kit. Concentration and purity of the cRNA product were determined spectrophotometrically.

Twenty micrograms of each biotin-labeled cRNA was fragmented for hybridization on Affymetrix GENECHIP® human genome U133 plus v2.0 arrays. Fragmented cRNA was prepared for hybridization as outlined in the Affymetrix GENECHIP® manual. Hybridization was conducted overnight in a model 320 rotating hybridization oven set at 45° C. All GENECHIP® wash and staining procedures were performed on an Affymetrix Model 450 Fluidics station. Arrays were scanned on an Affymetrix GENECHIP® Scanner 3000. Data capture and initial array quality assessment were performed with the GENECHIP Operating Software (GCOS) tool.

Stratagene's (La Jolla, Calif.) ARRAYASSIST® Lite software was used to calculate probe-level summaries (GC-RMA normalization algorithm) from the array CEL files. R packages (R development core team) samr & qvalue were used to generate differentially regulated genes. PCA and hierarchical clustering analyses were performed in both SpotFire and R (R Development Core Team). SAM & FDR were used to select differentially regulated genes (pairwise comparison between lesional and non-lesional skin, lesional and normal skin, and non-lesional and normal skin). Probe sets with a fold-change of at least 2 and q value less than or equal to 0.05 were considered to be differentially regulated. PCA and hierarchical clustering were performed in both SpotFire and bioconductor R.

Overall, 1408 probe sets were up-regulated and 1465 probe sets were down-regulated in lesional skin compared to non-lesional skin. Although the downregulated genes outnumbered the upregulated genes in the lesional skin, the magnitude of differential regulation of the upregulated genes was much greater as a whole. For example, 318 probe sets were upregulated by at least four fold in the lesional skin, while only 84 probe sets were downregulated by at least four fold in the lesional skin. Among them, 96 probe sets were upregulated by at least eight fold in the lesional skin, while only six probe sets were downregulated by at least eight fold.

463 probe sets were also up-regulated and 489 probe sets were down-regulated in non-lesional skin compared to normal skin. FIG. 45 provides a Venn diagram of the probe sets both upregulated (downregulated) in lesional skin and non-lesional skin relative to normal healthy skin. Only 70 of the 1408 upregulated probe sets in the lesional skin were also upregulated in non-lesional skin. Meanwhile, only 43 of the 1465 probe sets downregulated in the lesional skin were also downregulated in the non-lesional skin. These data suggested that the molecular events and biological changes from the non-lesional skin to lesional skin were quite different from those from the normal skin to the non-lesional skin.

To identify the most statistically significant signaling pathways altered in psoriasis, the list of differentially regulated genes were submitted to GENEGO for pathway and network analysis. Briefly, the pathway and network analysis was conducted with the MetaCore™ integrated software suite from GENEGO, Inc. (St. Joseph, Mich.). The significance, given a particular pathway or network, is approximated by a hypergeometric distribution where the p-value essentially represents the probability of a particular gene set mapping arising by chance, given the numbers of genes in the set of all genes on pathway maps, genes on a particular pathway map and genes in the experiment.

Fifty seven signaling pathways were significantly altered in lesional skin compared to non-lesional skin, a majority of which were involved in immune response and cell cycle. The IFNα/β signaling pathway was the most significantly altered in lesional skin with a p value of 3.8×10⁻¹³. IFNα/β signaling pathway members such as IFNα, IFNβ, IFNAR1, IFNAR2, STAT1, IRF1, MPL, ISG15, IFI6 were all significantly overexpressed in lesional skin compared to uninvolved skin.

Overall, 22 signaling pathways were activated and 37 signaling pathways were inhibited (p<0.05) in the lesional skin compared to non-lesional skin. All the putative signaling pathways activated were either cytokine and chemokine mediated signaling pathways or were involved in immune responses. For example, IFNγ, TNFα and onconstatin M signaling pathways were activated in the lesional skin of psoriatic patients. Of all the signaling pathways altered in lesional and non-lesional skin, IFNα/β signaling pathway topped the list with a p value of 6.6×10⁻²⁶(FIG. 46). Components of the pathway like IFNα subtypes, IFNβ, IFNAR1, IFNAR2, STAT1, IRF1, MPL, ISG15, IFI6 were all significantly overexpressed in lesional skin compared to non-lesional skin of psoriatic patients.

Using the list of probe sets identified to be type-I IFN inducible in the whole blood and keratinocyte ex vivo stimulation studies (Example 10), 164 of the 1408 (approximately 11.7%) probe sets upregulated in lesional relative to non-lesional skin were identified as type-I IFN inducible. Fisher's exact test calculated a p value (one-tailed t test) less than 0.0001, suggesting that the observed overexpression of type-I IFN genes in lesional skin of psoriatic patients was statistically significant. The type-I IFN induced genes were also many of the most highly upregulated genes in the lesional relative to non-lesional psoriatic skin. Nineteen percent of the top 100 and 200 most upregulated probe sets in lesional skin relative to non-lesional skin were type-I IFN genes. See FIGS. 47a and b for the top 100 upregulated probe sets in lesional skin. These genes included STAT1, a key component in forming the ISGF3 complex; IRF7, a master regulator of the IFNα/β mediated immune response; MYD88, which governs the induction of CD8⁺ T-cell responses with IRF7; IRF1, a transcriptional activator for the type-I IFN genes; OAS family members OAS1, OAS2, OAS3, mediators of resistance to virus infection; ISG15, a ubiquitin-like protein that becomes conjugated to many cellular proteins upon activation by IFNα/β; and members of the ISG15 signaling pathways such as USP18, UBE2L6, and HERC5. This enrichment of type I IFN genes indicated them as the most overexpressed genes in lesional skin of psoriatic patients.

Table 26 lists, in descending order, the top 50 IFN induced probes in lesional skin compared to non-lesional skin of psoriasis patients. Table 26 not only compares the log 2-based fold change (log 2 fc) and q value for each of the 50 most upregulated type I IFN inducible genes in lesional relative to non-lesional skin of psoriasis patients, it also compares the log 2-based fold change and q value for these 50 genes in non-lesional skin of psoriasis patients relative to healthy control patients.

TABLE 26

The frequency of upregulation of the top 50 type-I IFN induced probes in lesional relative to non-lesional skin in psoriasis patients

Probe ID
Unigene ID
Gene Title
Gene Symbol
log2 fc
q value
log2 fc
q value

219403_s_at
Hs.44227
heparanase
HPSE
4.598
4.46E−22
0.226
0.23589

204972_at
Hs.414332
2′-5′-oligoadenylate synthetase 2, 69/71 kDa
OAS2
4.098
8.57E−14
0.096
0.28896

205660_at
Hs.118633
2′-5′-oligoadenylate synthetase-like
OASL
4.030
1.34E−12
0.029
0.20341

227609_at
Hs.546467
epithelial stromal interaction 1 (breast)
EPSTI1
4.002
1.14E−14
0.254
0.10796

227458_at
—
—
—
3.859
9.31E−14
0.591
0.05449

219352_at
Hs.529317
hect domain and RLD 6
HERC6
3.842
9.49E−16
0.460
0.04810

216834_at
Hs.75256
regulator of G-protein signalling 1
RGS1
3.809
2.47E−17
5.269
0.00000

204533_at
Hs.632586
chemokine (C-X-C motif) ligand 10
CXCL10
3.697
2.97E−12
0.338
0.13024

226702_at
Hs.7155
hypothetical protein LOC129607
LOC129607
3.572
2.37E−16
0.156
0.26500

242625_at
Hs.17518
radical S-adenosyl methionine domain containing 2
RSAD2
3.403
1.65E−12
0.070
0.31309

213797_at
Hs.17518
radical S-adenosyl methionine domain containing 2
RSAD2
3.243
3.36E−10
0.004
0.36209

202086_at
Hs.517307
myxovirus (influenza virus) resistance 1, interferon-
MX1
3.235
5.28E−14
0.050
0.33453

inducible protein p78 (mouse)

205552_s_at
Hs.524760
2′-5′-oligoadenylate synthetase 1, 40/46 kDa
OAS1
3.222
2.41E−14
0.328
0.13669

210797_s_at
Hs.118633
2′-5′-oligoadenylate synthetase-like
OASL
3.216
1.63E−09
0.005
0.34940

204439_at
Hs.389724
interferon-induced protein 44-like
IFI44L
3.205
4.73E−13
0.120
0.30073

202411_at
Hs.532634
interferon, alpha-inducible protein 27
IFI27
3.165
4.81E−12
0.154
0.26878

202869_at
Hs.524760
2′-5′-oligoadenylate synthetase 1, 40/46 kDa
OA31
3.150
2.47E−14
0.248
0.21403

205483_s_at
Hs.458485
ISG15 ubiquitin-like modifier
ISG15
3.088
4.73E−13
0.273
0.11013

209969_s_at
Hs.565365
signal transducer and activator of transcription 1, 91 kDa
STAT1
2.993
7.95E−17
0.199
0.20072

228531_at
Hs.65641
sterile alpha motif domain containing 9
SAMD9
2.846
5.42E−14
0.033
0.35359

204415_at
Hs.523847
interferon, alpha-inducible protein 6
IFI6
2.769
7.23E−09
0.045
0.29074

214453_s_at
Hs.82316
interferon-induced protein 44
IFI44
2.679
1.94E−12
0.086
0.32618

222838_at
Hs.517265
SLAM family member 7
SLAMF7
2.659
1.60E−16
0.046
0.31222

219684_at
Hs.43388
receptor transporter protein 4
RTP4
2.649
3.73E−11
0.497
0.04912

203127_s_at
Hs.435661
serine palmitoyltransferase, long chain base subunit 2
SPTLC2
2.628
1.04E−20
1.016
0.00017

205569_at
Hs.518448
lysosomal-associated membrane protein 3
LAMP3
2.569
2.64E−09
0.293
0.22865

219691_at
Hs.65641
sterile alpha motif domain containing 9
SAMD9
2.559
1.30E−13
0.011
0.37349

223220_s_at
Hs.518200
poly (ADP-ribose) polymerase family, member 9
PARP9
2.553
1.08E−15
0.069
0.31416

AFFX-HUMISG
Hs.565365
signal transducer and activator of transcription 1, 91 kDa
STAT1
2.525
1.64E−10
0.706
0.03338

212268_at
Hs.381167
serpin peptidase inhibitor, clade B (ovalbumin), member 1
SERPINB1
2.510
3.02E−15
0.605
0.07749

216202_s_at
Hs.435661
serine palmitoyltransferase, long chain base subunit 2
SPTLC2
2.507
1.17E−13
0.682
0.01693

229450_at
—
—
—
2.492
1.50E−14
0.224
0.20674

208436_s_at
Hs.166120
interferon regulatory factor 7
IRF7
2.448
6.90E−15
0.578
0.01612

AFFX-HUMISG
Hs.565365
signal transducer and activator of transcription 1, 91 kDa
STAT1
2.444
3.03E−10
0.516
0.05854

204747_at
Hs.47338
interferon-induced protein with tetratricopeptide repeats 3
IFIT3
2.424
2.15E−14
0.365
0.07219

229390_at
Hs.381220
hypothetical protein LOC441168
RP1-93H18.5
2.400
2.59E−12
0.369
0.11426

218400_at
Hs.528634
2′-5′-oligoadenylate synthetase 3 100 kDa
OAS3
2.397
3.83E−14
0.179
0.11631

235276_at
—
—
—
2.386
3.61E−15
0.057
0.32771

203153_at
Hs.20315
interferon-induced protein with tetratricopeptide repeats 1
IFITI
2.351
1.17E−10
0.054
0.34454

210873_x_at
Hs.348983
apolipoprotein B m RNA editing enzyme, catalytic
APOBEC3A
2.348
1.35E−07
0.048
0.30119

polypeptide-like 3A

204698_at
Hs.459265
interferon stimulated exonuclease gene 20 kDa
ISG20
2.337
1.50E−12
0.644
0.05052

232666_at
Hs.528634
2′-5′-oligoadenylate synthetase 3, 100 kDa
OAS3
2.236
4.50E−10
0.077
0.04816

222881_at
Hs.44227
heparanase
HPSE
2.230
3.47E−15
0.221
0.17127

text missing or illegible when filed

indicates data missing or illegible when filed

Removal of ESTs, hypothetical proteins, and duplications of genes due to identification by multiple probe sets produced Table 27. Table 27 provides, in descending order, the top 50 most upregulated type-I IFN genes in lesional skin compared to non-lesional skin. For genes identified by more than one probe set, only the probe set detected as most upregulated is provided.

TABLE 27

Top 50 type-I IFN induced genes in lesional relative to non-lesional skin in psoriasis

patients (Table 27 discloses “DEAD (Asp-Glu-Ala-Asp)” as SEQ ID NO: 1)

Probe.ID
Unigene.ID
Gene.Title
Gene.Symbol
log2.fc
q.value(fdr)
% Prevalence

219403_s_at
Hs.44227
heparanase
HPSE
4.60
4.46E−22
100.00

204972_at
Hs.414332
2′-5′-oligoadenylate synthetase 2, 69/71 kDa
OAS2
4.10
8.57E−14
96.15

205660_at
Hs.118633
2′-5′-oligoadenylate synthetase-like
OASL
4.03
1.34E−12
96.15

227609_at
Hs.546467
epithelial stromal interaction 1 (breast)
EPSTI1
4.00
1.14E−14
92.31

219352_at
Hs.529317
hect domain and RLD 6
HERC6
3.84
9.49E−16
96.15

216834_at
Hs.75256
regulator of G-protein signalling 1
RGS1
3.81
2.47E−17
100.00

204533_at
Hs.632586
chemokine (C-X-C motif) ligand 10
CXCL10
3.70
2.97E−12
100.00

242625_at
Hs.17518
radical S-adenosyl methionine domain containing 2
RSAD2
3.40
1.65E−12
88.46

202086_at
Hs.517307
myxovirus (influenza virus) resistance 1, interferon-
MX1
3.24
5.28E−14
92.31

inducible protein p78 (mouse)

205552_s_at
Hs.524760
2′-5′-oligoadenylate synthetase 1, 40/46k Da
OAS1
3.22
2.41E−14
96.15

204439_at
Hs.389724
interferon-induced protein 44-like
IFI44L
3.21
4.73E−13
88.46

202411_at
Hs.532634
interferon, alpha-inducible protein 27
IFI27
3.17
4.81E−12
92.31

205483_s_at
Hs.458485
ISG15 ubiquitin-like modifier
ISG15
3.09
4.73E−13
92.31

209969_s_at
Hs.565365
signal transducer and activator of transcription 1, 91 kDa
STAT1
2.99
7.95E−17
96.15

228531_at
Hs.65641
sterile alpha motif domain containing 9
SAMD9
2.85
5.42E−14
92.31

204415_at
Hs.523847
interferon, alpha-inducible protein 6
IFI6
2.77
7.23E−09
84.62

214453_s_at
Hs.82316
interferon-induced protein 44
IFI44
2.68
1.94E−12
92.31

222838_at
Hs.517265
SLAM family member 7
SLAMF7
2.66
1.60E−16
92.31

219684_at
Hs.43388
receptor transporter protein 4
RTP4
2.65
3.73E−11
88.46

203127_s_at
Hs.435661
serine palmitoyltransferase, long chain base subunit 2
SPTLC2
2.63
1.04E−20
100.00

205569_at
Hs.518448
lysosomal-associated membrane protein 3
LAMP3
2.57
2.64E−09
96.15

223220_s_at
Hs.518200
poly (ADP-ribose) polymerase family, member 9
PARP9
2.55
1.08E−15
88.46

212268_at
Hs.381167
serpin peptidase inhibitor, clade B (ovalbumin), member 1
SERPINB1
2.51
3.02E−15
88.46

208436_s_at
Hs.166120
interferon regulatory factor 7
IRF7
2.45
6.90E−15
96.15

204747_at
Hs.47338
interferon-induced protein with tetratricopeptide repeats 3
IFIT3
2.42
2.15E−14
92.31

218400_at
Hs.528634
2′-5′-oligoadenylate synthetase 3, 100 kDa
OAS3
2.40
3.83E−14
100.00

203153_at
Hs.20315
interferon-induced protein with tetratricopeptide repeats 1
IFIT1
2.35
1.17E−10
84.62

210873_x_at
Hs.348983
apolipoprotein B mRNA editing enzyme, catalytic
APOBEC3A
2.35
1.35E−07
80.77

polypeptide-like 3A

204698_at
Hs.459265
interferon stimulated exonuclease gene 20 kDa
ISG20
2.34
1.50E−12
92.31

205241_at
Hs.567405
SCO cytochrome oxidase deficient homolog 2 (yeast)
SCO2
2.21
1.90E−17
96.15

207387_s_at
Hs.1466
glycerol kinase
GK
2.16
9.38E−14
92.31

219716_at
Hs.257352
apolipoprotein L, 6
APOL6
2.12
3.03E−11
92.31

202270_at
Hs.62661
guanylate binding protein 1, interferon-inducible, 67 kDa
GBP1
2.11
4.67E−14
92.31

229625_at
Hs.513726
Guanylate binding protein 5
GBP5
2.07
7.52E−10
88.46

228617_at
Hs.441975
XIAP associated factor-1
BIRC4BP
2.05
3.41E−12
84.62

206513_at
Hs.281898
absent in melanoma 2
AIM2
2.04
2.32E−08
76.92

218943_s_at
Hs.190622
DEAD (Asp-Glu-Ala-Asp) box polypeptide 58
DDX58
2.00
1.39E−10
88.46

203148_s_at
Hs.575631
tripartite motif-containing 14
TRIM14
1.94
2.17E−17
96.15

213293_s_at
Hs.501778
tripartite motif-containing 22
TRIM22
1.89
1.36E−12
88.46

214838_at
—
SFT2 domain containing 2
SFT2D2
1.88
5.30E−17
92.31

231769_at
Hs.464419
F-box protein 6
FBXO6
1.86
6.34E−14
88.46

227697_at
Hs.527973
suppressor of cytokine signaling 3
SOCS3
1.82
4.55E−10
88.46

206632_s_at
Hs.226307
apolipoprotein B mRNA editing enzyme, catalytic
APOBEC3B
1.81
9.42E−10
92.31

polypeptide-like 3B

201649_at
Hs.425777
ubiquitin-conjugating enzyme E2L 6
UBE2L6
1.81
2.15E−13
84.62

204702_s_at
Hs.404741
nuclear factor (erythroid-derived 2)-like 3
NFE2L3
1.80
1.71E−16
96.15

202531_at
Hs.436061
interferon regulatory factor 1
IRF1
1.79
2.13E−13
80.77

204994_at
Hs.926
myxovirus (influenza virus) resistance 2 (mouse)
MX2
1.75
7.99E−09
69.23

215966_x_at
—
glycerol kinase pseudogene 3
GKP3
1.73
3.33E−11
80.77

207655_s_at
Hs.444049
B-cell linker
BLNK
1.71
2.28E−14
96.15

216598_s_at
Hs.303649
chemokine (C-C motif) ligand 2
CCL2
1.71
4.80E−07
65.38

The fold changes (log 2 fc) were calculated based on relative transcript level between paired lesional skin and non-lesional skin. Q values were calculated based on FDR. Prevalence tabulated the percentage of the 26 paired lesional and non-lesional skin that had at least 2-fold overexpression of the genes listed in the table.

These top 50 type-I IFN induced genes in lesional relative to non-lesional skin in psoriasis patients were overexpressed, on average, 3.2-fold (CCL2 and BLNK) to 24-fold (HPSE) more in the lesional skin. In addition, all of the genes in the table, except CCL2 and AIM2, were upregulated in at least 84% of the paired lesional/non-lesional skin biopsies (23 of the 26 pairs) of the psoriasis patients. This robust upregulation of a large panel of type-I IFN genes across lesional versus non-lesional skin samples of psoriasis patients provided a strong rationale for their use as PD markers.

As briefly alluded to, above, upregulation of type-I interferon inducible genes was consistently observed across psoriasis patients. Table 28 provides the average and median fold change of the top 25 most upregulated type-I IFN probe sets for each paired lesional/non-lesional skin sample. The top 25 most upregulated type-I IFN probe sets were consistently observed to detect elevated gene expression in the lesional relative to non-lesional skin of each individual psoriasis patient.

TABLE 28

Average and median fold change of the top 25 most upregulated type-I IFN inducible

genes in 26 pairs of lesional skin compared to lesional skin

Gene

Probe ID
Unigene ID
Symbol
Pair 1
Pair 2
Pair 3
Pair 4
Pair 5
Pair 6
Pair 7
Pair 8
Pair 9

219403_s_at
Hs.44227
HPSE
67.78
24.31
35.28
27.94
37.31
28.56
236.24
128.77
10.29

204972_at
Hs.414332
OAS2
12.60
21.22
1.19
2.44
49.33
48.03
33.22
43.96
13.92

205660_at
Hs.118633
OASL
7.19
13.46
4.51
9.03
62.19
50.23
31.12
54.05
9.72

227609_at
Hs.546467
EPSTI1
11.25
20.34
−1.43
1.38
57.01
32.14
14.40
23.42
10.53

227458_at
—
—
16.69
10.94
19.35
3.11
54.31
23.30
30.76
10.59
3.25

219352_at
Hs.529317
HERC6
7.86
15.70
2.36
1.46
49.25
51.01
11.64
19.63
20.95

216834_at
Hs.75256
RGS1
27.92
8.50
17.90
6.81
58.42
16.25
4.97
20.52
10.02

204533_at
Hs.632586
CXCL10
3.92
3.01
8.72
3.91
249.60
13.12
13.37
15.14
4.75

226702_at
Hs.7155
LOC
3.59
5.77
3.10
1.27
60.00
12.76
14.72
22.00
9.53

129607

242625_at
Hs.17518
RSAD2
4.57
6.19
1.79
1.24
66.13
51.91
19.28
23.36
4.02

213797_at
Hs.17518
RSAD2
8.33
7.37
1.16
1.00
78.64
33.08
11.98
25.13
1.66

202086_at
Hs.517307
MX1
5.03
9.17
1.25
1.08
20.97
39.08
14.63
23.54
11.33

205552_s_at
Hs.524760
OAS1
5.93
11.05
1.19
2.76
21.03
29.00
11.76
27.37
7.71

210797_s_at
Hs.118633
OASL
2.04
6.90
1.32
1.34
45.94
31.06
16.86
66.61
9.25

204439_at
Hs.389724
IFI44L
4.52
6.71
−3.59
−1.06
14.49
58.16
9.25
32.21
6.68

202411_at
Hs.532634
IF127
10.97
15.52
1.94
2.66
12.02
38.87
14.83
27.63
17.02

202869_at
Hs.524760
OAS1
5.34
7.99
2.04
2.09
16.23
32.48
13.29
30.47
12.75

205483_s_at
Hs.458485
ISG15
5.64
4.37
1.65
1.10
19.82
40.24
8.30
13.89
7.00

209969_s_at
Hs.565365
STAT1
6.14
6.12
2.85
2.00
38.39
16.50
10.35
7.10
12.90

228531_at
Hs.65641
SAMD9
5.07
5.24
2.52
1.79
12.56
12.67
5.76
15.63
9.88

204415_at
Hs.523847
IFI6
1.62
6.53
−2.01
1.00
13.90
25.74
5.59
16.88
4.66

214453_s_at
Hs.82316
IFI44
2.60
6.23
−2.89
1.22
14.76
10.55
4.43
9.99
2.67

222838_at
Hs.517265
SLAMF7
5.26
7.36
1.70
1.97
10.55
8.75
5.56
9.97
6.78

219684_at
Hs.43388
RTP4
13.11
13.02
−3.07
−1.11
13.95
18.00
6.50
10.09
3.48

203127_s_at
Hs.435661
SPTLC2
6.06
5.07
4.11
3.50
8.18
5.50
11.49
8.25
2.73

Average fold change
10.04
9.92
4.12
3.20
43.40
29.08
22.41
37.45
8.55

Mediuan fold change
5.93
7.37
1.79
1.79
37.31
29.00
11.98
22.00
9.25

Probe ID
Pair 10
Pair 11
Pair 12
Pair 13
Pair 14
Pair 15
Pair 16
Pair 17
Pair 18
Pair 19

219403_s_at
7.12
19.62
25.78
30.21
24.01
56.80
10.70
35.20
11.42
5.86

204972_at
71.36
28.17
4.04
24.63
79.34
15.84
96.99
10.27
30.28
9.26

205660_at
9.94
1.10
2.31
24.75
44.70
11.91
45.98
17.46
14.66
33.60

227609_at
55.80
32.87
8.86
59.54
47.71
33.84
78.12
14.34
25.86
33.41

227458_at
40.43
41.37
6.70
26.83
23.19
37.88
70.78
75.98
19.04
26.19

219352_at
21.72
15.84
5.82
10.58
23.06
30.42
133.47
11.03
26.94
9.90

216834_at
24.32
19.50
9.91
94.41
14.83
23.00
15.64
13.95
31.90
100.03

204533_at
69.86
56.31
22.30
12.75
8.30
16.61
28.11
12.95
30.79
66.10

226702_at
58.99
27.55
2.99
5.99
39.75
25.66
225.39
19.79
30.96
4.88

242625_at
32.04
8.80
1.76
5.64
10.36
15.97
94.85
9.47
14.58
4.64

213797_at
21.73
8.43
2.73
3.23
31.91
12.04
49.52
8.11
12.61
11.92

202086_at
18.56
11.71
3.08
8.93
20.03
8.68
86.72
11.04
19.60
7.24

205552_s_at
19.23
20.14
3.49
2.82
37.85
21.91
39.43
6.13
24.10
6.86

210797_s_at
1.69
1.73
1.20
19.00
21.73
1.62
43.68
11.71
10.30
26.36

204439_at
37.49
31.82
3.96
19.43
16.66
23.81
253.56
6.81
20.34
3.18

202411_at
17.22
17.69
5.81
9.36
26.00
15.85
38.94
2.01
30.69
4.59

202869_at
49.00
10.15
5.52
2.31
16.94
19.52
36.57
4.58
16.19
4.81

205483_s_at
12.18
14.49
4.47
6.78
19.24
10.65
57.01
3.67
12.65
2.96

209969_s_at
17.32
12.41
3.77
14.31
7.49
25.00
18.73
5.45
9.63
9.16

228531_at
12.94
20.65
1.97
4.70
24.24
15.22
20.12
10.49
10.39
5.60

204415_at
11.65
6.45
3.30
5.43
30.76
3.29
38.93
4.08
20.01
2.08

214453_s_at
12.32
25.67
3.66
8.26
18.22
2.57
61.65
6.49
20.83
8.32

222838_at
10.62
15.91
5.44
19.09
5.39
14.93
6.86
10.10
8.69
15.42

219684_at
30.25
23.69
8.83
6.66
16.47
10.87
18.65
3.40
17.36
5.96

203127_s_at
4.53
6.24
5.67
5.61
11.38
8.26
7.73
10.92
7.32
4.82

Average fold
26.73
19.11
6.13
17.25
25.18
10.49
63.16
13.02
19.09
16.19

change

Mediuan fold
10.23
17.69
4.04
9.36
23.06
15.85
49.88
10.27
19.04
7.24

change

Probe ID
Pair 20
Pair 21
Pair 22
Pair 23
Pair 24
Pair 25
Pair 26

219403_s_at
12.73
25.78
30.81
32.26
24.58
48.50
105.13

204972_at
30.11
16.38
24.27
60.43
25.32
132.09
9.07

205660_at
17.27
84.97
24.22
92.12
46.44
54.96
39.66

227609_at
12.06
19.24
17.86
28.12
22.43
78.03
10.90

227458_at
49.50
5.43
24.89
24.13
11.46
26.05
9.87

219352_at
16.46
19.06
33.32
27.98
19.08
26.56
8.66

216834_at
8.02
2.44
13.49
15.83
22.64
29.15
14.83

204533_at
17.72
11.89
12.12
41.27
10.90
30.14
5.86

226702_at
45.30
14.42
7.91
32.87
14.50
19.85
3.13

242625_at
33.67
16.26
10.67
60.96
20.21
40.57
5.99

213797_at
24.02
25.00
10.04
75.04
17.36
28.33
6.29

202086_at
4.00
12.05
10.63
28.80
11.08
27.74
5.68

205552_s_at
2.63
4.18
13.46
21.42
9.30
32.15
16.09

210797_s_at
2.27
78.51
15.88
65.78
33.47
35.32
18.92

204439_at
17.90
12.16
7.60
18.42
4.52
25.93
1.12

202411_at
−4.73
3.46
10.59
22.17
7.00
50.18
7.37

202869_at
8.96
4.73
11.05
11.67
7.13
18.20
7.39

205483_s_at
2.57
11.30
5.71
34.41
18.06
30.48
5.07

209969_s_at
17.30
7.10
9.27
11.03
10.91
12.19
4.37

228531_at
14.30
6.80
6.38
16.24
12.46
13.49
6.75

204415_at
1.00
49.45
16.05
58.43
17.95
52.57
6.86

214453_s_at
10.76
4.93
5.66
13.27
8.02
26.71
2.03

222838_at
7.99
4.69
5.06
1.92
5.61
11.22
9.01

219684_at
1.92
5.90
8.90
4.55
4.92
28.75
3.91

203127_s_at
3.64
9.24
5.35
9.32
13.11
11.00
12.89

Average fold
11.30
18.21
13.65
32.82
15.91
35.61
13.07

change

Mediuan fold
12.00
11.89
19.67
27.98
13.11
28.75
7.37

change

FIG. 32 provides a graphic of the distribution of the average and median fold changes among the different pairs of lesional and non-lesional skin. The prevalent and uniform upregulation of the most overexpressed type-I IFN genes in lesional skin of psoriatic patients verified their usefulness as PD markers.

Seventeen probe sets were also observed as underexpressed in lesional skin that were also down-regulated by IFNα/β in the ex vivo stimulation studies described in Example 10. These genes include CYP1B1, TGST1, RRAGD, IRS2, MGST1, TGFBR3, and RGS2.

Example 12
Expression of Type-I IFN Genes is not Significantly Altered in Normal Skin Relative to Non-Lesional Skin of Psoriatic Patients

Although the array data obtained in Example 11 identified overexpression of numerous type-I IFN-inducible genes in lesional relative to non-lesional skin, it identified only 5 probe sets overexpressed in non-lesional skin relative to normal control skin. The p value of Fisher's exact test (two-tailed t-test) was 0.581, which suggested that the overexpression of the type-I IFN genes is not statistically significant in the non-lesional skin of the psoriasis patients over normal skin.

As shown in Table 26 (Example 11), most of the genes identified as being top 50 type-I IFN-induced genes in lesional relative to non-lesional skin were comparably expressed in non-lesional skin relative to normal skin controls (several genes, e.g., RGS1, SPTLC2, are downregulated in the non-lesional skin compared to normal skin). FIG. 33 provides a graphical representation of the relative expression of 3 type-I IFN inducible genes (HPSE, OASL, and HERC6; included as top 50 type-I IFN-induced probe sets in lesional relative to non-lesional skin), and 1 non type-I IFN inducible gene (SERPINB4) in both (a) lesional skin compared to non-lesional skin and (b) non-lesional skin compared to normal skin. The overexpression of genes HPSE, OASL, and HERC6 in lesional skin compared to non-lesional skin is both statistically significant (as evidenced by the very small p value) and large in scale (between 12-250 fold overexpression on average). SERPINB4 is overexpressed in non-lesional skin by about 3-4 fold compared to normal skin, but upregulated by well over 200 fold in lesional skin compared to non-lesional skin.

Analysis of normal healthy, lesional psoriasis, and non-lesional psoriasis skin samples using the 164 probe sets identified in Example 11 as type-I IFN inducible, showed a clustering of lesional psoriasis samples and a clustering of non-lesional psoriasis and normal healthy skin samples. FIG. 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. FIG. 34b provides a PCA plot of the skin samples using the same 164 upregulated type-I IFN inducible probe sets. Again, the normal skin samples and the non-lesional skin samples mostly clustered together, indicating similar levels of expression of the 164 genes. Also, the majority of the lesional skin samples were separated from the normal and non-lesional skin samples, indicating that the lesional samples exhibited a distinct overexpression of the type-I IFN inducible genes that was separable from the gene expression levels of the normal and non-lesional skin samples.

These observations were further confirmed by gene pathway analysis. GENEGO analysis showed that the possibility of an alteration in the IFNα/β signaling pathway of non-lesional skin of psoriasis patients relative to normal skin had a p value close to 1. A distinctive separation of lesional skin samples from non-lesional skin samples and normal skin samples was even observed when clustering samples based on the transcript profile of an entire genome array. See FIG. 47.

Example 13
Validation of Type-I IFN-Inducible Gene Up-Regulation in Psoriatic Lesional Skin Using TAQMAN-Based Assays

A BIOMARK™ 48.48 dynamic array (TAQMAN-based assay) from FLUIDIGM was used to validate the results of the Affymetrix GENECHIP® human genome U133 plus v2.0 arrays, results indicating that type-I IFN genes are up-regulated in lesional psoriatic relative to non-lesional psoriatic or normal skin samples.

Eighteen pairs of lesional and non-lesional skin samples from 18 psoriasis patients were used for the gene expression analysis. Twenty nine of these genes were type-I IFN inducible genes while 11 were highly upregulated in lesional skin but were not IFN-inducible genes, e.g., S100A9, S100A12, SERPINGB4, and KLK13. Each of these genes was selected based on prevalence and significance of overexpression in lesional skin. The overexpression of all genes in the lesional skin was confirmed by TAQMAN qRT-PCR, the majority of which showed very good correlation between microarray and TAQMAN assays. FIG. 35 provides TAQMAN data showing overexpression of each of ten (OAS2, OASL, EPSTI1, MX1, IFI44L, IFI44, HERC6, HPSE, ISG15, and STAT1) type-I IFN-inducible genes in lesional skin in the 18 paired lesional/non-lesional samples.

Overall, the TAQMAN-based assay and Affymetrix array results correlated well, validating the selected genes as overexpressed type-I IFN-induced genes in lesional psoriatic skin. The distribution of correlation coefficients between the TAQMAN-based assay and the Affymetrix array for the 40 overexpressed genes is provided in FIG. 36a. Nineteen of the overexpressed genes had correlation coefficients greater than 0.85, indicating excellent correlation between the microarray and TAQMAN-based assay. Another 17 genes had high correlation coefficients between the microarray and TAQMAN-based assay of 0.5-0.85. FIG. 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, many of the genes had high correlation coefficients, greater than 0.90. These genes include, inter alia, IFI27, CXCL10, ISG15, and MX1.

FIGS. 37
a-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 lesional/non-lesional samples. These data evidence that similar levels of overexpression of type-I IFN-induced genes in lesional psoriatic skin is detected between the TAQMAN and array assays, and thus the high correlation coefficients discussed above. FIGS. 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. FIGS. 37c and 37d show similar 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. FIG. 38 shows measurement of similar overexpression of type-I IFN-inducible genes IFI27 and CXCL10 by TAQMAN and microarray analysis in each if the 18 paired lesional/non-lesional skin samples. The correlation coefficient between the TAQMAN and microarray results for IFI27 and CXCL10 was 0.9456 and 0.9455, respectively.

Example 14
IFNα Ab Neutralizes Type-I IFNα-Induced Gene Expression in Ex Vivo Stimulated Keratinocytes of Healthy Volunteers

Keratinocytes of healthy volunteers were isolated and stimulated ex vivo with escalating doses of IFNα2a and leukocyte IFN to induce an escalating type I IFNα-induced gene expression pattern. Anti-IFNα antibody was able to neutralize the type I IFNα-induced gene expression pattern in a dose-dependent manner.

Normal human keratinocytes (EpiDerm system, MatTek, Inc.) were grown under serum-free conditions according to manufacturer's instructions. Briefly, keratinocytes were maintained on tissue culture inserts at the air-liquid interface to maintain a multilayered, fully differentiated epithelial phenotype. Keratinocytes were stimulated with human leukocyte IFN (15-150 IU/ml, PBL Biomedical Labs) and human IFNα2a (15-350 IU/ml, PBL Biomedical Labs). In some wells a humanized anti-human IFNα monoclonal antibody (0.01-100 μg/ml; MEDI-545, MedImmune, Inc) or isotype matched control antibody of irrelevant specificity (R347, MedImmune, Inc) was added simultaneously with cytokine stimulus. Epidermal cultures were harvested at 2, 4, or 18 hours post treatment for transcript analysis. Expression of type-I IFN-induced genes was measured using a BIOMARK™ 48.48 dynamic array.

Expression of a majority of type-I IFN-induced genes was upregulated in the IFNα2a and leukocyte interferon stimulated keratinocytes in a dose-dependent manner. This upregulation of type-I IFN-induced genes, by either IFNα2a or leukocyte interferon, was likewise inhibited in a dose-dependent manner by IFNα monoclonal antibody (MEDI-545). Control antibody, R347, did not have a significant effect on neutralization of the type-I IFN-induced genes.

Dose-dependent neutralization of three type-I IFN-induced genes (ISG15, USP18, and IFIT2) by MEDI-545 in IFNα2a or leukocyte IFN stimulated keratinocytes is provided in FIG. 39. FIGS. 39 (a), (c), and (e) show that MEDI-545 neutralizes overexpression of type-I IFN induced genes ISG15, USP18, and IFIT2, respectively, in keratinocytes stimulated with 350 IU/mL IFNα2a. Each of these genes was neutralized 100% by MEDI-545. FIGS. 39 (b), (d), and (f), show that MEDI-545 neutralizes overexpression of type-I IFN induced genes ISG15, USP18, and IFIT2, respectively, in keratinocytes stimulated with 150 I.U./mL leukocyte IFN. Neutralization of these genes by MEDI-545 was between 70 and 100%, which is not surprising because leukocyte IFN contains both IFNα and IFNβ. MEDI-545 neutralizes a majority of IFNα subtypes efficiently, but not IFNβ. These neutralization data provide further evidence that the type-I IFN-inducible genes identified in ex vivo stimulated whole blood and keratinocytes (Example 10) are type-I IFN-inducible genes. It also provides further support that upregulated expression of these genes in lesional psoriatic skin relative to non-lesional skin due to type-I IFN induction.

Example 15
Multiple Type-I IFN Subtypes are Up-Regulated in Lesional Skin of Psoriasis Patients

To identify the type-I IFN subtypes responsible for the induction of the type-I IFN signature in lesional skin of psoriasis patients, mRNA levels of type-I IFN genes in psoriatic lesions were measured.

Gene expression analysis was performed using a TAQMAN Low Density Array (TLDA) from Applied Biosystems. Expression of 23 genes, including type-I IFNα subtypes 1, 2, 5, 6, 7, 8, 14, 17, and 21; type-I IFNs IFNβ, κ, and ω; IFNγ; IFNα receptors IFNAR1 and IFNAR2; IFNγ receptors IFNGR1 and IFNGR2; type-I IFNα inducible genes RSAD2, OAS3, IFI44, MX1, and CXCL10; and TNFα was monitored and compared in paired lesional and non-lesional skin of 18 psoriasis patients.

FIG. 40
a shows the relative overexpression of mRNA of nine IFNα subtypes in the lesional skin compared to either non-lesional skin or normal skin. With the exception of IFNα5 (upregulated by about 4.6 fold; median fold change, p<0.001), none of the IFNα subtypes were significantly altered at the mRNA level in the non-lesional skin compared to that in the normal skin (p<0.05). However, all of these IFNα subtypes were upregulated at the mRNA level in the lesional skin compared to that in the normal skin (or non-lesional skin), with the overexpression of IFNα1, IFNα5, IFNα8, IFNα14, IFNα17, IFNα21 being statistically significant (p<0.05).

FIG. 40
b shows that the overexpression of other members of type I IFN family members, IFNβ, -κ, and -ω mRNA in the lesional skin compared to either non-lesional skin or normal skin. The alterations of IFNβ and IFNω mRNAs in the non-lesional skin were not significant. However, the upregulation of these mRNAs were significant in the lesional skin compared to normal skin (p values of 0.022 and 0.049 respectively). IFNκ mRNA was upregulated by about 1.6 fold (median fold change, p=0.03) in the non-lesional skin, and was sharply upregulated by 62.6 fold (median fold change) in the lesional skin compared to normal skin (p<0.001). Additionally, the receptors for type I IFN, IFNAR1 and IFNAR2 were also significantly overexpressed in the lesional skin of psoriatic patients at transcript level (p values<0.001; FIG. 40c). While IFNAR2 upregulation was significant in the non-lesional skin, IFNAR1 was not (FIG. 40c). Collectively, these data provided strong evidence that mRNA levels of type I IFN family members were comparable between the non-lesional skin and healthy normal skin (with the exception of IFNα5 and IFNκ), and were uniformly overexpressed in the lesional skin of psoriatic patients.

Table 29, lists the correlation coefficients of the overexpression of type-I IFN family member (type-I IFNα subtypes 1, 2, 5, 6, 7, 8, 14, 17, and 21; and IFNβ, IFNκ, and IFNω) mRNAs in lesional skin compared to non-lesional skin of psoriatic patients. Of the 12 type-I IFN family members measured, overexpression of IFNα1, 2, 8, and 14 in lesional skin correlated most consistently with overexpression of other members in the type-I IFN family, with the exception of IFNα5 which showed the weakest correlation with other type-I IFN family members.

TABLE 29

Correlation coefficient of overexpression of type-I IFN family members in lesional

skin of psoriasis patients

IFNA1
IFNA2
IFNA5
IFNA6
IFNA7
IFNA8
IFNA14
IFNA17
IFNA21
IFNB1
IFNK
IFNW1

INFA1
1

IFNA2
0.66
1

IFNA5
0.11
0.20
1

IFNA6
0.45
0.47
−0.01
1

IFNA7
0.77
0.79
0.09
0.68
1

IFNA8
0.64
0.99
0.19
0.49
0.84
1

IFNA14
0.84
0.94
0.26
0.44
0.72
0.94
1

IFNA17
1.00
0.96
0.15
0.07
0.77
0.97
0.94
1

IFNA21
0.71
0.49
0.50
0.42
0.81
0.49
0.61
0.75
1

IFNB1
0.54
0.86
0.28
0.33
0.69
0.96
0.80
0.93
0.54
1

IFNK
0.78
0.73
0.09
0.59
0.27
0.73
0.77
0.03
0.22
0.54
1

IFNW1
0.73
0.72
0.44
0.22
0.75
0.70
0.77
0.93
0.90
0.73
0.26
1

Example 16
Co-Overexpression of Type-I IFN, Type-II IFN, and TNFα and their Gene Signatures in Lesional Skin or Psoriasis Patients

The involvement of IFNγ and TNFα mRNA signaling pathways was also evaluated in the paired lesional/non-lesional psoriasis and normal skin samples. As discussed in Example 15, above, TLDA from Applied Biosciences was used to measure IFNγ, IFNGR1 and IFNGR2, and TNFα mRNA in lesional and non-lesional skin of psoriasis patients and in normal healthy skin.

Unlike the observations for type-I IFN mRNA expression levels, IFNγ, IFNGR1, IFNGR2, and TNFα mRNAs were significantly overexpressed in non-lesional skin compared to healthy normal skin (FIG. 41; p values of 0.02, <0.001, <0.001 and <0.001 respectively). TNFα mRNA was upregulated by about 5.7 fold, while IFNγ, IFNGR1 and IFNGR2 mRNAs were upregulated by about 1.5, 2.2, and 2.8 fold compared to that in the normal skin (median fold change; FIG. 41). However, like the type I IFNs, these genes were upregulated in the lesional skin compared to either non-lesional skin (p values of 0.04, 0.01, 0.001 and 0.007 respectively) or normal skin (p values<0.001 for all of them; FIG. 41). TNFα, IFNγ, IFNGR1 and IFNGR2 mRNAs were upregulated by about 33.5, 116.7, 11.6, and 8.4 fold in the lesional skin compared to that in the normal skin. These observations indicated that the mRNA expression patterns for IFNγ and TNFα are different from those of type I IFN family members, which were comparable between healthy skin and non-lesional skin (with the exception of IFNα5 and IFNκ), but upregulated in the lesional skin compared to non-lesional skin of psoriasis patients.

Example 17
Identification Genes Induced by Type II IFN and TNFα in Ex Vivo Stimulated Whole Blood and which are Induced in Skin Lesions of Psoriasis Patients

As described in Example 10, whole blood of healthy donors was stimulated ex vivo with a panel of IFNα subtypes, as well as IFNβ, IFNγ, and TNFα. Stimulating whole blood ex vivo with IFNγ or TNFα identified probe sets associated with potential IFNγ- or TNFα-inducible genes. Three hundred four probe sets were identified as at least 2-fold upregulated by IFNγ four hours post-stimulation. Two hundred thirty four probe sets were identified as at least 2-fold upregulated by TNFα both 2 and 4 hours post-stimulation.

The probe sets identified as associated with ex vivo IFNγ or TNFα induction were compared with the total 1408 probe sets (Example 11) found to be upregulated in lesional skin relative to non-lesional skin of psoriasis patients. Using this method, 106 and 35 of the probe sets included in the total 1408 upregulated in lesional skin were identified as IFNγ or TNFα inducible, respectively (FIG. 42). The 106 probe sets identified as IFNγ inducible are provided in FIG. 49. The 35 probe sets identified as TNFα inducible are provided in FIG. 50. The 164 probes sets shown in FIG. 42 as identified as type-I IFN inducible are provided in FIG. 51. The Fisher's exact test indicated that the p values (one-tailed t-test) of the overexpression of IFNγ or TNFα inducible genes in lesional skin were both less than 0.0001. The overexpression of IFNγ and TNFα inducible genes was significant.

Also using the list of probe sets identified to be type I IFN, IFNγ and TNFα inducible from the ex vivo studies, type I IFN, IFNγ and TNFα inducible genes upregulated at least 2-fold in each of the lesional relative to non-lesional skin sample were identified. FIG. 43 shows the number of type I IFN, IFNγ and TNFα inducible genes upregulated in each of the 26 paired lesional and non-lesional skin. The larger the number of type I IFN inducible genes upregulated in a particular lesional skin biopsy usually gave rise to the overexpression of larger numbers of IFNγ and TNFα inducible genes in the same lesional skin biopsy. This observation was confirmed by the strong correlation in the co-activation of these three sets of genes with correlation coefficients of 0.9811, 0.9179 and 0.9372 using two-tail paired t-test to compare the upregulation of type I IFN and IFNγ, type I IFN and TNFα, and IFNγ and TNFα inducible genes in lesional skin compared to non-lesional skin (FIG. 43a).

Similar analysis was carried out for the downregulated genes in the lesional skin compared to the non-lesional skin of psoriatic patients (FIG. 42). Of the 1465 total probe sets downregulated in lesional relative to non-lesional skin, only 17, 5, and 5 of them were type I IFN, IFNγ and TNFα inducible.

Although IFNγ and TNFα mRNAs were found to be upregulated in the non-lesional skin of psoriatic patients when compared to healthy normal skin, IFNγ and TNFα inducible genes did not appear to be significantly overexpressed in the non-lesional skin (FIG. 42). The absence of type I IFN, IFNγ and TNFα inducible gene signatures in the non-lesional skin compared to normal skin, even when IFNγ and TNFα mRNAs are overexpressed in the non-lesional skin, suggested that either IFNγ and TNFα proteins were not made in the non-lesional skin, or other signaling molecules might have inhibitory effect on the IFNγ and TNFα pathways in the non-lesional skin of psoriatic patients.

Example 18
Immunohistochemical Analysis of Biopsies from Lesional Psoriatic Skin, Non-Lesional Psoriatic Skin, and Skin from Normal Donors Shows Increased Protein Levels of Type I IFN-Induced Genes

To determine whether some of the highly overexpressed type I IFN inducible genes in psoriatic skin gave rise to similar changes in the expression of the proteins, immunohistochemical analyses were carried out to assess the presence of STAT1 and ISG15 protein in the skin. Furthermore, analysis of the cellular infiltrates (pDCs, mDCs and CD4-positive cells) was carried to compare the number of IFN-producing cell types and inflammatory cells in the biopsies of the lesional vs. non-lesional and normal skin.

Snap-frozen lesional psoriatic, non-lesional psoriatic, and normal skin biopsies were divided in half. One-half of each sample was embedded in O.C.T., sectioned at 5 μM, placed on a “plus” slide, and fixed in cold acetone. The sectioned samples were incubated with primary antibodies (specific for BDCA2, CD83, CD4, STAT1, and ISG15) for 4 hours and washed with TBS. The slides were then incubated with peroxidase-labeled polymer conjugated to goat anti-mouse immunoglobulin antibody (Envision+; Dakocytomation, Carpenteria, Calif.) for 30 minutes and washed with Tris-buffered saline, pH 7.2. Detection was performed with 3,3′-diaminobenzidiine tetrahydrochloride (DAB+; DakoCytomation) as the chromogen. Slides were washed with dH₂O), counterstained with hematoxylin, dehydrated and coverslipped.

In all psoriasis patients for which paired lesional/non-lesional samples could be evaluated, lesional skin contained increased numbers of pDCs, and/or mDCs, increased numbers of CD4+ cells, as well as the significant upregulation of STAT-1 and ISG15 protein in the epidermis and dermis compared to non-lesional biopsies. By contrast, skin biopsies from normal donors did not contain appreciable numbers of pDCs, mDCs or staining for STAT-1 and ISG15. See FIG. 44 for example immunohistochemistry slides.

Example 19
Immunohistochemical and Gene Expression Analysis of Biopsies from SLE Patient Skin Lesions Show Reduced Expression of Type I IFN-Induced Genes at the Protein and Transcript Level Following Treatment with MEDI-545

To determine whether transcripts of the top 25 type I IFN inducible genes in skin lesions of an SLE patient were neutralized by MEDI-545, biopsies from patients treated with 10 mg/kg MEDI-545 were examined. A heatmap of neutralization of the top 25 type I IFN inducible genes in skin lesions at 0 and 14 days post-treatment is provided in FIG. 58(a). All of the top 25 genes are neutralized 14 days following administration of MEDI-545. A PCA diagram of target modulation based on these top 25 type I IFN-inducible genes is provided in FIG. 58(b). The PCA diagram shows the progression of the treated SLE patient from a position directly opposite that of normal healthy donors prior to administration of MEDI-545 to a position nearing that of the healthy donors 14 days after administration of MEDI-545.

To determine whether levels of some of the proteins expressed from these highly overexpressed type I IFN inducible genes were also reduced by treatment with 10 mg/kg MEDI-545, immunohistochemical analyses were carried out to detect HERC5, ISG15, and IP10 protein in SLE skin lesions of patients treated with MEDI-545 and placebo. Furthermore, analysis of the cellular infiltrates (pDCs, mDCs and CD4-positive cells) was carried out to compare the number of IFN-producing cell types and inflammatory cells in the biopsies of the SLE skin lesions of MEDI-545 treated patients and placebo treated controls.

Snap-frozen skin lesion samples of MEDI-545 treated SLE patients and placebo treated SLE patients were divided in half. One-half of each sample was embedded in O.C.T., sectioned at 5 μM, placed on a “plus” slide, and fixed in cold acetone. The sectioned samples were incubated with primary antibodies (specific for BDCA2, CD83, CD4, IP10, and ISG15) for 4 hours and washed with TBS. The slides were then incubated with peroxidase-labeled polymer conjugated to goat anti-mouse immunoglobulin antibody (Envision+; Dakocytomation, Carpenteria, Calif.) for 30 minutes and washed with Tris-buffered saline, pH 7.2. Detection was performed with 3,3′-diaminobenzidiine tetrahydrochloride (DAB+; DakoCytomation) as the chromogen. Slides were washed with dH₂O), counterstained with hematoxylin, dehydrated and coverslipped.

In placebo-treated SLE patients both cellular infiltrates and levels of proteins expressed from overexpressed type I IFN inducible genes increased (or worsened) over the course of 14 days. See FIG. 52 which shows an increase in (worsening of) mDC (CD83 staining) and T cell (CD4 staining) infiltration in skin lesions. FIG. 52 also shows no change in pDC (BDCA2 staining) infiltration in the placebo-treated SLE patient skin lesions over the 14 days. See also FIG. 53 which shows an increase in staining for proteins expressed from overexpressed type I IFN inducible genes HERC and IP10. No change in staining for ISG15 was observed.

By contrast, in patients treated with 10 mg/kg MEDI-545 levels of infiltrates and proteins expressed from overexpressed type I IFN inducible genes were decreased by varying degrees. See FIGS. 54 and 55, which provide immunohistochemical data from a first SLE patient treated with MEDI-545 and FIGS. 56 and 57, which provide immunohistochemical data from a second SLE patient treated with MEDI-545.

Example 20
Assay for Sensitive Detection of Type I and Type II IFNs

To devise an assay to sensitively detect type I and type II IFNs a construct containing the gene for a luciferase enzyme isolated from the marine organism Gaussia princeps (Targeting Systems; Santee, Calif.) under the control of an interferon-stimulated response element (ISRE) (TAGTTTCACTTTCCC)₅(SEQ ID NO: 2); Biomyx; San Diego, Calif.) was cloned. HEK293H cells were stably transfected with the construct and these cells were used for the IFN detection assays.

25,000 of the stably transfected HEK293H cells were seeded per assay well in 50 uL of cell culture medium overnight in a CO₂incubator. The following day, patient serum samples (or normal pooled human serum spiked with the various sub-types of IFN alpha or IFN-beta, IFN-omega, IFN-gamma) were screened for detection of the various subtypes of IFN by adding 50 uL of undiluted patient or spiked serum to the assay wells containing the seeded cells (final concentration of 50% patient sera in the wells for 24 hours). IFN-induced luciferase activity was detected the following day, by observing chemiluminescence in the culture supernatants. Chemiluminescence was observed by transferring 50 uL of supernatant from the wells to a B&W Isoplate, adding 50 uL of chemiluminescent substrate, and detecting luminescence at 6 minutes. Samples generating a signal greater than 1.5-times the Negative Control wells on each assay plate are classified as Positive for IFN activity. See FIG. 59a-d, which provide detected levels of type I and type II IFN activity in the IFN bioassay for different plates of cells treated with patient serum and spiked control serum. Each of panels a-d show that increased dose of IFN in the assay results in increased detection of IFN activity.

In samples where IFN activity is detected, antibodies that specifically neutralize various Type I and Type II IFNs can then be used to determine which IFN was responsible for the positive response. Anti-IFN-type specific antibodies are 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 binds to the Type I interferon receptor on the HEK293H cells) followed by addition of the samples to the cells and chemiluminescence determination as above. Spiked samples that demonstrate lower chemiluminescence following specific antibody treatment are considered to be positive for the presence of the particular IFN(s) that is neutralized by the IFN-specific antibodies.

FIG. 60(
a) shows that increasing dose of MEDI-545 in the treated wells increasingly neutralizes of IFN activity as does increasing dose of MEDI-546 (FIG. 60(b)). FIGS. 61-63 show that IFNγ, IFNω, and IFNβ, respectively, are neutralized by antibodies specific for IFNγ, IFNω, and IFNβ, as expected.

Example 21
Alterations of Levels of Soluble Proteins in Serum of Lupus Patients

Serum was collected from SLE (n=40) and CLE (n=5) patients that had a history of at least 4 of 11 positive ACR classification criteria and demonstrated active disease manifestations at the time of sample collection. Ninety-five percent were female, with mean±SD age of 41±15 years. Seventy-six percent were currently receiving oral corticosteroids in doses ranging from 1 mg/d to 30 mg/d prednisone, with 2 SLE patients also receiving pulse intravenous steroids. Fifty-nine percent were receiving at least 1 potential disease-modifying medication other than corticosteroids. Luminex xMAP technology was used to detect changes in 89 analytes and was performed by Rules Based Medicine (see the world wide web at domain name rulesbasedmedicine.com). Results for each analyte were compared to the mean of a panel of normal human serum (n=17) and significance was determined using a paired t-test. FIG. 74 shows analytes whose levels were significantly (a) increased or (b) decreased from the mean of the normal serum (p value≧0.05). Significant alterations in levels of cytokines chemokines, metabolic proteins, and other soluble mediators were detected in serum of lupus patients.

Example 22
Alternative Assay, Panomics 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 IFNα2b. The 22 IFN-inducible transcripts detected by this initial QUANTIGENEPLEX assay were selected based on their consistent up-regulation in SLE patients and are shown on the x-axis of the graphs shown in FIGS. 75 and 76.

Stimulation of the whole blood was performed by incubating freshly drawn Na-EDTA whole blood from 5 healthy donors with 20 IU/mL IFNα2b for 4 hours. Following this incubation, 2.5 mL of the stimulated whole blood was added to PAXgene tubes, mixed, and held overnight at room temperature. After overnight incubation, the samples were frozen at −80° C. These sample-handling procedures were selected to mimic those to be used during clinical trials.

PAXgene blood was analyzed for expression levels of the IFN-inducible transcripts. PAXgene blood (500 μL) was pelleted and then lysed in 139 μL of buffer according to the QUANTIGENEPLEX PAXgene Blood Lysis Protocol. Processed blood from each donor was split into duplicate wells and hybridized overnight with a multiplex probe set for the 22 IFN-inducible genes. Gene expression was assessed the following day using a Luminex 100 instrument with BioRad BioPlex software. Fold changes were assessed for each individual based on the increase in signal observed between IFN-stimulated and PBS-stimulated control wells. FIG. 75 shows the fold-change in expression of each of the 22 IFN-inducible genes following IFN stimulation of each of the 5 healthy volunteer whole blood samples. The dashed line indicates a 2-fold change over PBS-stimulated control samples.

Whole blood of a single volunteer was further stimulated over a dose range of 0.2 to 200 IU/mL IFNα2b to determine whether upregulation of the IFN-inducible genes by IFNα2b was dose-dependent and could be detected by the QUANTIGENEPLEX assay. For each of the 22 transcripts, a dose-dependent induction was observed. See FIG. 76, which provides the fold change in expression for each of the 22 transcripts at each IFNα2b dosage. Maximal transcript induction of nearly 100-fold was observed for RSAD2, IFIT3, and MX1. Using a 2-fold increase over baseline as a cutoff criterion, 19/22 genes were detected in samples spiked with 2 IU/mL of IFN and 5/22 were detected in samples spiked with 0.2 IU/mL IFN. Expression of SIGLEC1, LY6E, SERPING1, OAS3 and IFI27 transcripts were poorly induced by IFNα2b stimulation. These low levels of induction may indicate a lack of sensitivity of the assay to these targets or differences in gene expression between actual SLE disease (from which this panel of transcripts was chosen) and ex vivo stimulation with a single IFNα subtype, IFNα2b. Dashed line indicates a 2-fold change over PBS-stimulated control samples.

Next, the QUANTIGENEPLEX assay was used to detect levels of IFN-inducible transcripts in whole blood of SLE patients. Twenty of the 22 probes from the original QUANTIGENEPLEX kit, probes identified in FIGS. 75 and 76, were retained in the QUANTIGENEPLEX assay used for this data analysis. Two probes, HSXIAPAF1 and GIP3, were substituted with different probes, XAF1 and IFI6. Using this panel of 22 probes, a baseline gene signature was established based on whole blood samples of ten healthy donors (blue bars in each panel). The baseline gene signature, based on the whole blood samples of the healthy donors, was compared to (1) the gene signature of an SLE patient that had detectable IFN serum activity and (2) the gene signature of an SLE patient that did not have detectable IFN serum activity. IFN serum activity was detected in the SLE patient serum samples using the assay described in Example 20. FIG. 77a shows a comparison of the gene signature of an SLE patient (red bars) having no detectable serum IFNα activity (i.e. serum IFN activity <2.5 IU/mL) relative to the baseline gene signature (blue bars). With the exception of LAMP3, all transcript levels were detected as elevated in blood from the SLE patient with no IFN serum activity. FIG. 77b shows a comparison of the gene signature of an SLE patient with high levels of serum IFNα activity (red bars) relative to the baseline gene signature (blue bars). All transcripts were elevated at least 2-fold in the blood of the patient with high IFN serum activity, with maximal inductions of nearly 80-fold for IFI27.

The data obtained from the QUANTIGENEPLEX assay was next evaluated for its comparability to data obtained from a FLUIDIGM Real-Time PCR assay. QUANTIGENEPLEX and FLUIDIGM methods were each used to analyze and compare transcript levels in PAXgene-preserved whole blood samples from 16 SLE patients participating in a Phase I clinical trial (of a monoclonal antibody against IFNα) relative to a composite median gene score from 10 healthy donors. FLUIDIGM analyses were carried out using a mixture of TAQMAN Gene Expression assays, including 4 reference control genes prepared using the TAQMAN PreAmp Master Mix Kit (Applied Biosystems). Dynamic arrays were loaded using a NanoFlex 4-IFC Controller (FLUIDIGM Corp) and real-time reactions were performed using a BIOMARK Real-Time PCR System. Results were analyzed using BIOMARK Real-Time PCR Analysis software. Delta-delta Cts (DDCt) were calculated using the mean of 4 reference genes (GAPDH, TFRC, b2M, and 18S) and a calibrator sample. The results obtained using whole blood samples from SLE patients demonstrated a high degree of correlation between QUANTIGENEPLEX and Real-Time PCR approaches to detect disease-related gene expression profiles. FIG. 78 shows the (a) composite median and (b) mean-fold changes of all genes in the panels that were calculated and compared by Pearson's correlation analysis. Significant correlation was observed between QUANTIGENEPLEX and FLUIDIGM when median (p=0.0002) and mean (p<0.0001) fold changes were compared for the panel of genes.

Data obtained from the QUANTIGENEPLEX and FLUIDIGM Real-Time PCR assays were further compared in their ability to detect changes in transcript levels in SLE patient samples over the course of treatment in a clinical trial. For this comparison, SLE patient samples were collected directly into PAXgene tubes on Day 0 (pre-dose) and multiple subsequent time points following administration of a single dose of an anti-IFNα monoclonal antibody or placebo. For each sample, an aggregate median fold-change was calculated from the panel of 22 genes and compared to the pre-dose sample for that patient. FIG. 79a shows the changes in gene signature for placebo- or antibody-treated SLE patients using FLUIDIGM technology. FIG. 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-administration were also highly similar between QUANTIGENEPLEX and FLUIDIGM technologies.

	Number	Date	Country
Parent	14330609	Jul 2014	US
Child	14606832		US
Parent	12517333	Feb 2010	US
Child	14330609		US

INTERFERON ALPHA-INDUCED PHARMACODYNAMIC MARKERS AND USES THEREOF

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