RU2815973C2 - Type i interferon mediated disorders - Google Patents

Abstract

FIELD: immunology.

SUBSTANCE: disclosed is use of a pharmaceutical composition containing an effective amount of anifrolumab, for treating systemic lupus erythematosus, myositis, scleroderma, lupus nephritis or cutaneous lupus erythematosus in a subject characterized by an increased expression profile of EPHB2, BLC, LAG-3 and IP-10 proteins.

EFFECT: invention makes it possible to effectively treat a unique subgroup of patients with potentially high activity of IFN type I and low levels of IFN-induced genes in blood.

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Description

The present invention relates to the identification and use of biomarkers to identify and/or monitor a subject suffering from a type I interferon-mediated disease or disorder, such as autoimmune diseases (eg, systemic lupus erythematosus). The present invention further relates to suitable methods of treatment and methods for identifying candidate therapeutic agents.

Type I interferon signaling contributes to pathology in a number of autoimmune diseases, particularly systemic lupus erythematosus (SLE), and can be monitored through type I IFN-induced transcripts present in whole blood that provide the type I IFN gene expression profile. As an example, in Yao et al. (Hum Genomics Proteomics 2009, pii: 374312) describes the identification of the expression profile of 21 IFNα/β genes and its use as a biomarker for type I IFN-related diseases or disorders.

This approach for determining gene expression profiling, however, has limited applicability due to the inconsistent correlation between the profiles of induced transcripts and the corresponding profiles of induced proteins.

Therefore, there is a need for an alternative, complementary or improved method for detecting and/or monitoring type I IFN activity in a subject.

The present invention solves one or more of the above problems and, for example, provides an accurate and/or reliable method for detecting a type 1 IFN-mediated disease or disorder in a subject.

In a first aspect, the present invention provides a method for identifying a subject suitable for treatment of a type I interferon-mediated disease or disorder with a therapeutic agent that modulates (eg, binds) the activity of type I interferon, comprising detecting an increased level of a first protein in a sample from the subject and an increased the level of the second protein in the sample from the subject,

where the first protein is EPHB2,

wherein the second protein exhibits type I interferon-induced gene expression and exhibits a Pearson correlation coefficient of greater than 0.3 compared to the type I interferon-associated gene expression profile, and

where the increased level of the first protein and the increased level of the second protein are compared with:

a) the level of the first protein and the level of the second protein, respectively, in a tissue sample or from a person not suffering from a type I interferon-mediated disease or disorder, or

b) the level of one or more control proteins in the sample from the subject.

In a second aspect, the present invention provides a method for identifying a subject suitable for treating a type I interferon-mediated disease or disorder with a therapeutic agent that modulates (eg binds) type I interferon activity, including:

i) detecting an increased level of a first protein in a sample from the subject and an increased level of a second protein in a sample from the subject,

where the first protein is EPHB2,

wherein the second protein exhibits type I interferon-induced gene expression and exhibits a Pearson correlation coefficient of greater than 0.3 compared to the type I interferon-associated gene expression profile, and

where the increased level of the first protein and the increased level of the second protein are compared with:

a) the level of the first protein and the level of the second protein, respectively, in a tissue sample or from a person not suffering from a type I interferon-mediated disease or disorder, or

b) the level of one or more control proteins in the sample from the subject; And

ii) administration of the therapeutic agent.

In a third aspect, the present invention provides an anti-type I interferon antibody or an anti-type I interferon receptor antibody that modulates (eg binds) type I interferon activity, for use in the treatment of a type I interferon-mediated disease or disorder in a subject, wherein the subject has been identified by detecting an increased level of a first protein in a sample from the subject and an increased level of a second protein in a sample from the subject,

where the first protein is EPHB2,

wherein the second protein exhibits type I interferon-induced gene expression and exhibits a Pearson correlation coefficient of greater than 0.3 compared to the type I interferon-associated gene expression profile, and

where the increased level of the first protein and the increased level of the second protein are compared with:

a) the level of the first protein and the level of the second protein, respectively, in a tissue sample or from a person not suffering from a type I interferon-mediated disease or disorder, or

b) the level of one or more control proteins in the sample from the subject.

In a fourth aspect, the present invention provides a method of treating a type I interferon-mediated disease or disorder in a subject, the method comprising administering an anti-type I interferon antibody or an anti-type I interferon receptor antibody that modulates (eg, binds) the activity of type I interferon, wherein the subject was identified by detecting an increased level of a first protein in a sample from the subject and an increased level of a second protein in a sample from the subject,

where the first protein is EPHB2,

wherein the second protein exhibits type I interferon-induced gene expression and exhibits a Pearson correlation coefficient of greater than 0.3 compared to the type I interferon-associated gene expression profile, and

where the increased level of the first protein and the increased level of the second protein are compared with:

a) the level of the first protein and the level of the second protein, respectively, in a tissue sample or from a person not suffering from a type I interferon-mediated disease or disorder, or

b) the level of one or more control proteins in the sample from the subject.

The present invention may further provide for detecting elevated levels of at least one other protein in a sample from a subject wherein the at least one other protein exhibits type I interferon-inducible gene expression and exhibits a Pearson correlation coefficient of greater than 0.3 compared to gene expression profile associated with type I interferon; and wherein the increased level of at least one other protein is compared to

a) the level of at least one other protein in a sample from a tissue or person not suffering from a type I interferon-mediated disease or disorder, or

b) the level of one or more control proteins in the sample from the subject.

In a fifth aspect, the present invention provides a method for monitoring or predicting the progression of a type I interferon-mediated disease or disorder in a subject, comprising:

i) identifying the expression level of the first protein in the original sample from the subject and the expression level of at least one other protein in the original sample from the subject; And

ii) identifying the expression level of the first protein in an additional sample (eg, taken at a later time compared to the original sample) from the subject and the expression level of at least one other protein in the additional sample from the subject;

wherein an increase in the expression level of the first protein and an increase in the expression level of at least one other protein in the additional sample compared to the original sample from the subject is predictive of disease progression; or

wherein a decrease in the expression level of the first protein and a decrease in the expression level of at least one other protein in the additional sample compared to the original sample from the subject predict regression of the disease;

where the first protein is EPHB2; And

wherein at least one other protein exhibits type I interferon-inducible gene expression and exhibits a Pearson correlation coefficient of greater than 0.3 relative to the type I interferon-associated gene expression profile.

In a sixth aspect, the present invention provides a method for monitoring the progression of a type I interferon-mediated disease or disorder in a subject receiving treatment with a therapeutic agent that modulates (eg binds) type I interferon activity, including:

i) identifying the expression level of the first protein in the original sample from the subject and the expression level of at least one other protein in the original sample from the subject;

ii) identifying the expression level of the first protein in an additional sample (eg, taken at a later time compared to the original sample) from the subject and the expression level of at least one other protein in the additional sample from the subject;

iii) administering to the subject a therapeutic agent that modulates the activity of type I interferon, wherein the therapeutic agent is administered before step i) or between steps i) and ii); And

iv) comparing the expression levels of the first protein and at least one other protein in the original sample from the subject with the expression levels of the first protein and at least one other protein, respectively, in the additional sample from the subject;

wherein the change in expression levels of the first protein and at least one other protein indicates the level of effectiveness of a therapeutic agent that modulates the activity of type I interferon;

where the first protein is EPHB2; And

wherein at least one other protein exhibits type I interferon-inducible gene expression and exhibits a Pearson correlation coefficient of greater than 0.3 relative to the type I interferon-associated gene expression profile.

In a seventh aspect, the present invention provides a method for identifying a therapeutic candidate for treating a type I interferon-mediated disease or disorder, comprising:

i) identifying the expression level of the first protein in the original sample from the subject and the expression level of at least one other protein in the original sample from the subject;

ii) administering the candidate therapeutic agent to the subject;

iii) identifying the expression level of the first protein in an additional sample (eg, taken at a later time compared to the original sample) from the subject and the expression level of at least one other protein in the additional sample from the subject; And

iv) comparing the expression levels of the first protein and at least one other protein in the original sample from the subject with the expression levels of the first protein and at least one other protein, respectively, in the additional sample from the subject;

wherein the change in the expression levels of the first protein and at least one other protein includes a decrease in the positive regulation of the expression levels of the first protein and at least one other protein, respectively, which indicates that the agent is a candidate therapeutic agent;

where the first protein is EPHB2; And

wherein at least one other protein exhibits type I interferon-inducible gene expression and exhibits a Pearson correlation coefficient of greater than 0.3 relative to the type I interferon-associated gene expression profile.

In the present invention, reference to a second protein and/or at least one other protein means a protein (each) independently selected from the group consisting of ALCAM; angiopoietin-2 (ANG-2); AREG; C1q; AXL receptor tyrosine kinase (AXL); B-cell activating factor (BAFF); B7-H1; beta-2-microglobulin (B2M); sCD163; CLM6; BLC; CD5L; ST4S6; SCGF-alpha; CO8A1; macrophage colony-stimulating factor 1 (M-CSF); R M-CSF; cathepsin S; soluble CXCL16; DLL1; DERM; monocyte chemotactic protein-4 (MCP-4); TIMD3; EMR2; intercellular adhesion molecule 1 (ICAM-1); Ra1 IL-13; interleukin-18 (IL-18); bFGF; IL-18 BPa; MIP-3b; MCP-1; VEGF sR3; TCCR; PHI; IGFBP-4; Ra IL-3; LAG-3; interleukin-1 receptor antagonist (IL-1Ra); JAG1; KYNU; macrophage inflammatory protein 3 beta (MIP-3 beta); LG3BP; ILT-4; MCP-3; fractalkine/CX3CL-1; interferon gamma inducible protein 10 (IP-10); MAPK14; monocyte chemotactic protein-2 (MCP-2); interferon-inducible alpha T cell chemoattractant (ITAC); monokine inducible interferon gamma (MIG); MMP-14; matrix metalloproteinase-7 (MMP-7); NAGK; Notch-3; LDH-H 1; glucocorticoid receptor; PDGF-CC; PLPP; NADPH-P450 oxidoreductase; SAA; a1-antitrypsin; PARK7; sialoadhesin; Siglec-7; SLAF7; osteopontin; PD-L2; BGH3; R III TGF-b; TNF-a; CD30; tenascin; tumor necrosis factor receptor 2 (TNFR2); TS; and SCGF-beta, or containing them.

In one embodiment, the second protein and/or at least one other protein forms part of a biological signaling pathway independent of the biological signaling pathway of the first protein.

Preferably, each of the second protein and/or at least one other protein is independently selected from BLC, LAG-3 and IP-10.

When measuring relative expression levels, in one embodiment, the level of at least one of:

first protein and

a second protein or at least one other protein

increased by at least 10%.

Alternatively, when measuring relative expression levels, in one embodiment the average value is:

level of the first protein and

level of a second protein and/or level of at least one other protein

increased by at least 10%.

The therapeutic agent used may be an anti-type I interferon antibody or an anti-type I interferon receptor antibody. In one embodiment, the therapeutic agent is an anti-type I interferon receptor antibody. Preferably, the anti-type I interferon receptor antibody is anifrolumab. In another embodiment, the therapeutic agent is an anti-type I interferon antibody. Preferably, the anti-type I interferon antibody is siphalumimab.

The subject to whom the present invention is directed generally requires treatment of a disease or disorder mediated by type I interferon selected from systemic lupus erythematosus, discoid lupus, lupus nephritis, dermatomyositis, polymyositis, psoriasis, SSc, vasculitis, sarcoidosis, Sjögren's syndrome and idiopathic inflammatory myositis. Preferably, the subject is in need of treatment for systemic lupus erythematosus.

Also provided is a method for recording data (eg, results) obtained by the methods of the present invention on a storage medium.

The following abbreviations are used in this document:

DM=dermatomyositis

HD=healthy donor

IBM = inclusion body myositis

IFN=interferon

IFNGS=interferon-related gene expression profile

IFNPS=interferon-related protein expression profile

LLOQ=lower limit of quantitation

PM=polymyositis

QC=quality control

RBM=rules based medicine

RFU=relative fluorescence units

SLE=systemic lupus erythematosus

SLEDAI=SLE Global Disease Activity Index

SOMAmer=modified aptamers with low dissociation rate

SSc=systemic sclerosis

WBC=white blood cell

The present inventors have used the measurement of circulating proteins that are capable of infiltrating the bloodstream (eg, from SLE-affected tissues) as a tool to detect/monitor global type I IFN activity.

Historically, the presence of DNA autoantibodies in patient serum has been a barrier to the effective use of SOMAmer to assess circulating protein levels in SLE. However, the present inventors have adapted protocols to reduce levels of these autoantibodies and report high reproducibility and accuracy with a QC pass rate of 100% and improved correlation with previously validated assay results using a multi-analyte platform. Using SOMAmer together with the expression profile of 21 IFNα/β genes (IFNGS) identified by Yao et al. (2009), the authors of the present invention obtained a protein expression profile associated with type I IFN, which may approach that of IFNGS. This type I IFN-associated protein expression profile represents a completely new approach for assessing type I IFN activity.

Thus, the present invention relates to methods for identifying, diagnosing, treating, and monitoring or predicting the progression of a disease or disorder in subjects. Subjects include any animal suffering from a type I IFN-mediated disease, disorder or condition. Subjects include any animal suffering from an autoimmune disease, disorder or condition. Subjects include humans, mice, rats, horses, pigs, cats, dogs, and any animal used for research.

The present invention further relates to methods for identifying therapeutic candidates.

Identification and measurement of protein levels that form type I IFNPS

The type I IFN-associated protein expression profile (IFNPS) of the present invention includes proteins characterized by type I interferon-induced gene expression and exhibiting a Pearson correlation coefficient of greater than 0.3 compared to the interferon-associated gene expression profile Type I Type I IFNGS may include the expression profile of 21 IFNα/β genes (IFNGS) identified by Yao et al. (2009). Circulating proteins used in the determination of the Pearson correlation can be identified by measurement using Somalogic, as described in Example 1.

Typically, the Pearson correlation coefficient is greater than 0.1 or greater than 0.15. In one embodiment, the Pearson correlation coefficient is greater than 0.2 or greater than 0.25. In one embodiment, the Pearson correlation coefficient is greater than 0.3 or greater than 0.35. In another embodiment, the Pearson correlation coefficient is greater than 0.4 or greater than 0.45. In another embodiment, the Pearson correlation coefficient is greater than 0.5 or greater than 0.6. In a preferred embodiment, the Pearson correlation coefficient is greater than 0.7.

According to the present invention, type I IFNPS typically consists of EPHB2 and one or more of ALCAM; angiopoietin-2 (ANG-2); AREG; C1q; AXL receptor tyrosine kinase (AXL); B-cell activating factor (BAFF); B7-H1; beta-2-microglobulin (B2M); sCD163; CLM6; BLC; CD5L; ST4S6; SCGF-alpha; CO8A1; macrophage colony-stimulating factor 1 (M-CSF); R M-CSF; cathepsin S; soluble CXCL16; DLL1; DERM; monocyte chemotactic protein-4 (MCP-4); TIMD3; EMR2; intercellular adhesion molecule 1 (ICAM-1); Ra1 IL-13; interleukin-18 (IL-18); bFGF; IL-18 BPa; MIP-3b; MCP-1; VEGF sR3; TCCR; PHI; IGFBP-4; Ra IL-3; LAG-3; interleukin-1 receptor antagonist (IL-1Ra); JAG1; KYNU; macrophage inflammatory protein 3 beta (MIP-3 beta); LG3BP; ILT-4; MCP-3; fractalkine/CX3CL-1; interferon gamma inducible protein 10 (IP-10); MAPK14; monocyte chemotactic protein-2 (MCP-2); interferon-inducible alpha T cell chemoattractant (ITAC); monokine inducible interferon gamma (MIG); MMP-14; matrix metalloproteinase-7 (MMP-7); NAGK; Notch-3; LDH-H 1; glucocorticoid receptor; PDGF-CC; PLPP; NADPH-P450 oxidoreductase; SAA; a1-antitrypsin; PARK7; sialoadhesin; Siglec-7; SLAF7; osteopontin; PD-L2; BGH3; R III TGF-b; TNF-a; CD30; tenascin; tumor necrosis factor receptor 2 (TNFR2); TS; and SCGF-beta, or contains them.

In one embodiment, type I IFNPS typically consists of EPHB2 and one or more of interferon-inducible chemokine, a marker of dendritic cell/T cell activation; or a B cell survival/differentiation marker or contains them. In one embodiment, type I IFNPS typically consists of or contains EPHB2 and an additional marker of inflammation/damage and tissue repair.

In one embodiment, type I IFNPS typically consists of or contains EPHB2 and a B cell survival/differentiation marker selected from the group consisting of B cell activating factor (BAFF), BLC, DLL1, and SLAF7.

In one embodiment, type I IFNPS typically consists of or contains EPHB2 and BLC.

In one embodiment, type I IFNPS typically consists of EPHB2 and a dendritic cell/T cell activation marker selected from the group consisting of receptor tyrosine kinase AXL (AXL), B7-H1, beta 2-microglobulin (B2M), SCGF-alpha, TIMD3, intercellular adhesion molecule 1 (ICAM-1), Ra1 IL-13, interleukin-18 (IL-18), IL-18 BPa, TCCR, Ra IL-3, LAG-3, LDH-H 1 , glucocorticoid receptor, PARK7, PD-L2, R III TGF-b, TNF-a, CD30 and SCGF-beta, or contains them.

In one embodiment, type I IFNPS typically consists of or contains EPHB2 and LAG-3.

In one embodiment, type I IFNPS typically consists of EPHB2 and an interferon-inducible chemokine selected from the group consisting of monocyte chemotactic protein 4 (MCP-4), MIP-3b, MCP-1, macrophage inflammatory protein 3 beta ( MIP-3 beta), MCP-3, fractalkine/CX3CL-1, interferon gamma inducible protein 10 (IP-10), monocyte chemotactic protein 2 (MCP-2), interferon inducible T cell chemoattractant (ITAC), and monokine inducible interferon gamma (MIG) or contains them.

In one embodiment, type I IFNPS typically consists of or contains EPHB2 and IP-10.

In one embodiment, type I IFNPS typically consists of EPHB2 and an additional marker of inflammation/damage and tissue repair selected from the group consisting of ALCAM, angiopoietin-2 (ANG-2), AREG, C1q, sCD163, CLM6, CD5L , ST4S6, CO8A1, macrophage colony stimulating factor 1 (M-CSF), R M-CSF, cathepsin S, soluble CXCL16, DERM, EMR2, bFGF, VEGF sR3, PHI, IGFBP-4, interleukin-1 receptor antagonist (IL-1Ra ), JAG1, KYNU, LG3BP, ILT-4, MAPK14, MMP-14, matrix metalloproteinase-7 (MMP-7), NAGK, Notch-3, PDGF-CC, PLPP, NADPH-P450 oxidoreductase, SAA, a1-antitrypsin , sialoadhesin, Siglec-7, osteopontin, BGH3, tenascin, tumor necrosis factor receptor 2 (TNFR2) and TS, or contains them.

In one embodiment, type I IFNPS consists of or contains EPHB2 and one or more of BLC, LAG-3, and IP-10.

In one embodiment, type I IFNPS consists of or contains EPHB2, BLC, LAG-3 and IP-10.

Reference herein to a protein (eg, a first protein, a second protein, and at least one other protein) includes structurally homologous proteins, such as naturally occurring isoforms or variants, or allelic variants and functional equivalents.

Positive or negative regulation of type I IFN-associated protein expression profile

The present invention provides methods for detecting or identifying type I IFN activity (eg protein levels). These methods of the present invention can use SOMAmers (modified low dissociation rate aptamers) to measure the levels of circulating proteins of interest in a sample (ie, proteins contained in type I IFNPS). SOMAmers are short, single-stranded deoxyoligonucleotides selected in vitro from libraries for their ability to bind to specific molecular targets modified with functional groups that mimic amino acid side chains. These modifications can interact with many epitopes from a larger range of target molecules, largely due to new secondary and tertiary structures formed within the SOMAmer reagent itself. In addition, SOMAmers are characterized by a low dissociation rate (low degree of dissociation) with their target. SOMAmers have higher affinity and specificity for a wider variety of proteins and are less susceptible to degradation by nucleases.

The subject may have a type I IFNPS profile. A type I IFNPS profile can be a strong profile, a moderate profile, or a weak profile. A type I IFNPS profile can be readily designated as strong, moderate, or weak by determining the fold dysregulation of the inducible type I IFNPS profile in a subject (eg, the fold increase in up-regulated type I IFNPS expression in a subject) relative to the control sample(s) or control subject(s) and comparing the subject's multiple degree of dysregulation with other subjects characterized by a type I IFNPS profile.

Positive or negative regulation (eg, increased levels) of a group of proteins included in the type I IFNPS profile can be determined by methods well known in the art. The up-regulation or down-regulation of type I IFNPS in a subject's expression profile may be of any degree relative to that of a control sample (which may be from a sample other than diseased tissue of the subject (eg skin of a psoriasis subject without lesions) or a human not suffering from a type I interferon-mediated disease or disorder), or may refer to proteins in a subject whose expression is not altered by the disease (control proteins).

The degree of positive regulation or negative regulation 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 85%, at least 90%, at least 95%, at least 100%, at least at least 125%, at least 150%, or at least 200%, or at least 300%, or at least 400%, or at least 500% or more than that of the control or control sample.

A type I IFNPS profile can be defined as the average fold increase in expression level for a set of proteins included in the protein expression profile. The average fold increase in expression level of a set of proteins may be from at least about 2 to at least about 15, from at least about 2 to at least about 10, or from at least about 2 to at least about 5. Average The fold increase in expression level of a set of genes may be at least about 2, at least about 2.5, at least about 3, at least about 3.5, at least about 4, at least about 4, 5, at least about 5, at least about 5.5, at least about 6, at least about 6.5, at least about 7, at least about 8, at least about 9 or at least at least about 10.

The degree of increase in expression level allows the identification of a fold change cutoff value for identifying expression profile positive and expression profile negative subjects suffering from autoimmune diseases. In one embodiment, the limit value is at least about 2. In another embodiment, the limit value is at least about 2.5. In another embodiment, the limit value is at least about 3. In another embodiment, the limit value is at least about 3.5. In another embodiment, the limit value is at least about 4. In another embodiment, the limit value is at least about 4.5. In another embodiment, the limit value is selected from at least 3.5, 3.6, 3.7, 3.8, 3.9, 4.0, 4.1, 4.2, 4.3, 4.4 and 4.5. In another embodiment, the cutoff value is from about 2 to about 8. In one embodiment, the cutoff value is the average of the increased expression levels of EPHB2 and at least one of BLC, LAG-3, and IP-10. In another embodiment, the cutoff value is the median value of the increased expression levels of EPHB2 and at least one of BLC, LAG-3 and IP-10.

Moreover, the subject may overexpress or have tissue that overexpresses the type I IFN subtype by 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% compared to the control. The type I IFN subtype may be any of IFNα1, IFNα2, IFNα4, IFNα5, IFNα6, IFNα7, IFNα8, IFNα10, IFNα14, IFNαl7, IFNα21, IFNβ, or IFNω. Type I IFN subtypes may include all of IFNαl, IFNα2, IFNα8, and IFNαl4.

In one embodiment, the level of at least one of (i) the first protein and (ii) the second protein or at least one other protein has an area under the curve (AUC) in SLE compared to a healthy donor (HD) of greater than 0. 5, regarding:

a) the level of the first protein or the level of the second protein or at least one other protein, respectively, in a sample from a tissue or from a person not suffering from a type I interferon-mediated disease or disorder, or

b) the level of one or more control proteins in the sample from the subject.

In embodiments, the AUC is greater than 0.6. In embodiments, the AUC is greater than 0.7. In embodiments, the AUC is greater than 0.8. In embodiments, the AUC is greater than 0.9. In embodiments, the AUC is greater than 0.95. In embodiments, the AUC is greater than 0.975. In embodiments, the AUC is greater than 0.99. In embodiments, the AUC is 1.

In one embodiment, the level of at least one of (i) the first protein and (ii) the second protein, or at least one other protein, differs by at least one standard deviation from the healthy donor mean relative to:

a) the level of the first protein or the level of the second protein or at least one other protein, respectively, in a sample from a tissue or from a person not suffering from a type I interferon-mediated disease or disorder, or

b) the level of one or more control proteins in the sample from the subject.

In embodiments, the level is within a range of at least two standard deviations from the mean value for a healthy donor. In embodiments, the level is within a range of at least two standard deviations from the mean value for a healthy donor.

In one embodiment, up- or down-regulation (eg, up-regulation) is calculated as the average of the fold change in expression levels in the expression profile of a group of at least two proteins, where the first protein is EPHB2, and where the second protein is characterized by interferon I-inducible gene expression type, and exhibits a Pearson correlation coefficient of greater than 0.3 compared to the type I interferon-associated gene expression profile (see, for example, Example 5). Positive or negative regulation (eg increased levels) of a group of proteins is measured relative to:

a) the level of the first protein and the level of the second protein, respectively, in a tissue sample or from a person not suffering from a type I interferon-mediated disease or disorder, or

b) the level of one or more control proteins in the sample from the subject.

In embodiments, the average of the level of the first protein and the level of the second protein and/or the level of at least one other protein is increased by at least Y% relative to:

a) the average level of the first protein and the level of the second protein, respectively, in a tissue sample or from a person not suffering from a type I interferon-mediated disease or disorder, or

b) the level of one or more control proteins in the sample from the subject.

In embodiments, Y is 10. In embodiments, Y is 15. In embodiments, Y is 20. In embodiments, Y is 25. In embodiments, Y is 30. In embodiments, Y is 40. In embodiments, Y is 50. In embodiments, Y is 60. In embodiments, Y is 70. In embodiments, Y is 80. In embodiments, Y is 90. In embodiments, Y is 100. In embodiments, Y is 125. In embodiments, Y is 150. In embodiments implementations, Y is 200. In embodiments, Y is 300. In embodiments, Y is 400. In embodiments, Y is 500. Preferably, Y is 10. More preferably, Y is 50.

Methods for detecting protein levels include immunoassays such as enzyme-linked immunosorbent assays, Western blotting, protein microarrays, and silver staining.

Positive or negative regulation of protein levels can be determined by detecting protein activity, including, but not limited to, detectable phosphorylation activity, dephosphorylation activity, or degradation activity.

The sample may be obtained from the subject, from a patient sample supplier, or may be a control sample used for calibration or as a control. If the sample is obtained from a subject, it may be any biological fluid or tissue such as whole blood, serum, saliva, urine, synovial fluid, bone marrow, cerebrospinal fluid, nasal secretions, sputum, amniotic fluid, bronchoalveolar lavage fluid, mononuclear cells peripheral blood cells, total white blood cells, lymph node cells, spleen cells, tonsil cells or skin. The sample can be obtained by any method known in the art. Preferably, the samples are whole blood or serum.

In one embodiment, the level of the first protein and the level of the second protein or at least one other protein in the method of the present invention can be detected in the same sample or in different samples. In one embodiment, the level of the first protein and the level of the second protein or at least one other protein are detected in the same sample. In another embodiment, the detected level of the first protein and the level of the second protein or at least one other protein are detected in different samples.

Methods for identifying, diagnosing and treating a subject

The present invention provides a method for identifying a subject suitable for treatment of a type I interferon-mediated disease or disorder with a therapeutic agent that modulates (eg, binds) the activity of type I interferon, the method comprising detecting an elevated level of a first protein in a sample from the subject and elevated levels of a second protein in a sample from a subject,

where the first protein is EPHB2,

wherein the second protein is characterized by type I interferon-induced gene expression and exhibits a Pearson correlation coefficient of greater than 0.3 compared with the type I interferon-associated gene expression profile, and wherein the increased level of the first protein and the increased level of the second protein are compared with :

a) the level of the first protein and the level of the second protein, respectively, in a tissue sample or from a person not suffering from a type I interferon-mediated disease or disorder, or

b) the level of one or more control proteins in the sample from the subject.

The present invention provides a method for identifying a subject suitable for treating a type I interferon-mediated disease or disorder with a therapeutic agent that modulates (eg binds) type I interferon activity, the method comprising detecting an increased level of a first protein in a sample from the subject and an increased level of a second protein in a sample from the subject,

where the first protein is EPHB2,

where the second protein is selected from ALCAM; angiopoietin-2 (ANG-2); AREG; C1q; AXL receptor tyrosine kinase (AXL); B-cell activating factor (BAFF); B7-H1; beta-2-microglobulin (B2M); sCD163; CLM6; BLC; CD5L; ST4S6; SCGF-alpha; CO8A1; macrophage colony-stimulating factor 1 (M-CSF); R M-CSF; cathepsin S; soluble CXCL16; DLL1; DERM; EPHB2; monocyte chemotactic protein 4 (MCP-4); TIMD3; EMR2; intercellular adhesion molecule 1 (ICAM-1); Ra1 IL-13; interleukin-18 (IL-18); bFGF; IL-18 BPa; MIP-3b; MCP-1; VEGF sR3; TCCR; PHI; IGFBP-4; Ra IL-3; LAG-3; interleukin-1 receptor antagonist (IL-1Ra); JAG1; KYNU; macrophage inflammatory protein 3 beta (MIP-3 beta); LG3BP; ILT-4; MCP-3; fractalkine/CX3CL-1; interferon gamma inducible protein 10 (IP-10); MAPK14; monocyte chemotactic protein-2 (MCP-2); interferon-inducible alpha T cell chemoattractant (ITAC); monokine inducible interferon gamma (MIG); MMP-14; matrix metalloproteinase-7 (MMP-7); NAGK; Notch-3; LDH-H 1; glucocorticoid receptor; PDGF-CC; PLPP; NADPH-P450 oxidoreductase; SAA; a1-antitrypsin; PARK7; sialoadhesin; Siglec-7; SLAF7; osteopontin; PD-L2; BGH3; R III TGF-b; TNF-a; CD30; tenascin; tumor necrosis factor receptor 2 (TNFR2); TS; and SCGF-beta, and where the increased level of the first protein and the increased level of the second protein are compared with:

a) the level of the first protein and the level of the second protein, respectively, in a tissue sample or from a person not suffering from a type I interferon-mediated disease or disorder, or

b) the level of one or more control proteins in the sample from the subject.

The present invention also provides a method for identifying a subject suitable for treating a type I interferon-mediated disease or disorder with a therapeutic agent that modulates (eg binds) type I interferon activity, including:

i) detecting an increased level of a first protein in a sample from the subject and an increased level of a second protein in a sample from the subject, wherein the first protein is EPHB2, wherein the second protein is characterized by type I interferon-inducible gene expression and exhibits a Pearson correlation coefficient of greater than 0, 3, compared with the gene expression profile associated with type I interferon, and where the increased level of the first protein and the increased level of the second protein are compared with:

a) the level of the first protein and the level of the second protein, respectively, in a tissue sample or from a person not suffering from a type I interferon-mediated disease or disorder, or

b) the level of one or more control proteins in the sample from the subject; And

ii) administration of the therapeutic agent.

The present invention provides a method for identifying a subject suitable for treating a type I interferon-mediated disease or disorder with a therapeutic agent that modulates (eg binds) type I interferon activity, including:

i) detecting an increased level of a first protein in a sample from the subject and an increased level of a second protein in a sample from the subject, wherein the first protein is EPHB2, wherein the second protein is selected from ALCAM; angiopoietin-2 (ANG-2); AREG; C1q; AXL receptor tyrosine kinase (AXL); B cell activating factor (BAFF); B7-H1; beta-2-microglobulin (B2M); sCD163; CLM6; BLC; CD5L; ST4S6; SCGF-alpha; CO8A1; macrophage colony-stimulating factor 1 (M-CSF); R M-CSF; cathepsin S; soluble CXCL16; DLL1; DERM; EPHB2; monocyte chemotactic protein 4 (MCP-4); TIMD3; EMR2; intercellular adhesion molecule 1 (ICAM-1); Ra1 IL-13; interleukin-18 (IL-18); bFGF; IL-18 BPa; MIP-3b; MCP-1; VEGF sR3; TCCR; PHI; IGFBP-4; Ra IL-3; LAG-3; interleukin-1 receptor antagonist (IL-1Ra); JAG1; KYNU; macrophage inflammatory protein 3 beta (MIP-3 beta); LG3BP; ILT-4; MCP-3; fractalkine/CX3CL-1; interferon gamma inducible protein 10 (IP-10); MAPK14; monocyte chemotactic protein-2 (MCP-2); interferon-inducible alpha T cell chemoattractant (ITAC); monokine inducible interferon gamma (MIG); MMP-14; matrix metalloproteinase-7 (MMP-7); NAGK; Notch-3; LDH-H 1; glucocorticoid receptor; PDGF-CC; PLPP; NADPH-P450 oxidoreductase; SAA; a1-antitrypsin; PARK7; sialoadhesin; Siglec-7; SLAF7; osteopontin; PD-L2; BGH3; R III TGF-b; TNF-a; CD30; tenascin; tumor necrosis factor receptor 2 (TNFR2); TS; and SCGF-beta, and where the increased level of the first protein and the increased level of the second protein are compared with:

a) the level of the first protein and the level of the second protein, respectively, in a tissue sample or from a person not suffering from a type I interferon-mediated disease or disorder, or

b) the level of one or more control proteins in the sample from the subject; And

ii) administration of the therapeutic agent.

The present invention further provides an anti-type I interferon antibody or an anti-type I interferon receptor antibody that modulates (eg binds) type I interferon activity, for use in the treatment of a type I interferon-mediated disease or disorder in a subject, wherein the subject has been identified by detecting an increased level of a first protein in a sample from the subject and an increased level of a second protein in a sample from the subject,

where the first protein is EPHB2,

wherein the second protein is characterized by type I interferon-induced gene expression and exhibits a Pearson correlation coefficient of greater than 0.3 compared with the type I interferon-associated gene expression profile, and wherein the increased level of the first protein and the increased level of the second protein are compared with :

a) the level of the first protein and the level of the second protein, respectively, in a tissue sample or from a person not suffering from a type I interferon-mediated disease or disorder, or

b) the level of one or more control proteins in the sample from the subject.

The present invention provides an anti-type I interferon antibody or an anti-type I interferon receptor antibody that modulates (eg binds) type I interferon activity, for use in the treatment of a type I interferon-mediated disease or disorder in a subject, wherein the subject has been identified by detecting an increased level of a first protein in a sample from the subject and an increased level of a second protein in a sample from the subject,

where the first protein is EPHB2,

where the second protein is selected from ALCAM; angiopoietin-2 (ANG-2); AREG; C1q; AXL receptor tyrosine kinase (AXL); B-cell activating factor (BAFF); B7-H1; beta-2-microglobulin (B2M); sCD163; CLM6; BLC; CD5L; ST4S6; SCGF-alpha; CO8A1; macrophage colony-stimulating factor 1 (M-CSF); R M-CSF; cathepsin S; soluble CXCL16; DLL1; DERM; EPHB2; monocyte chemotactic protein 4 (MCP-4); TIMD3; EMR2; intercellular adhesion molecule 1 (ICAM-1); Ra1 IL-13; interleukin-18 (IL-18); bFGF; IL-18 BPa; MIP-3b; MCP-1; VEGF sR3; TCCR; PHI; IGFBP-4; Ra IL-3; LAG-3; interleukin-1 receptor antagonist (IL-1Ra); JAG1; KYNU; macrophage inflammatory protein 3 beta (MIP-3 beta); LG3BP; ILT-4; MCP-3; fractalkine/CX3CL-1; interferon gamma inducible protein 10 (IP-10); MAPK14; monocyte chemotactic protein-2 (MCP-2); interferon-inducible alpha T cell chemoattractant (ITAC); monokine inducible interferon gamma (MIG); MMP-14; matrix metalloproteinase-7 (MMP-7); NAGK; Notch-3; LDH-H 1; glucocorticoid receptor; PDGF-CC; PLPP; NADPH-P450 oxidoreductase; SAA; a1-antitrypsin; PARK7; sialoadhesin; Siglec-7; SLAF7; osteopontin; PD-L2; BGH3; R III TGF-b; TNF-a; CD30; tenascin; tumor necrosis factor receptor 2 (TNFR2); TS; and SCGF-beta, and where the increased level of the first protein and the increased level of the second protein are compared with:

a) the level of the first protein and the level of the second protein, respectively, in a tissue sample or from a person not suffering from a type I interferon-mediated disease or disorder, or

b) the level of one or more control proteins in the sample from the subject.

The present invention also provides a method of treating a type I interferon-mediated disease or disorder in a subject, the method comprising administering an anti-type I interferon antibody or an anti-type I interferon receptor antibody that modulates (eg, binds) the activity of type I interferon where the subject has been identified by detecting an increased level of a first protein in a sample from the subject and an increased level of a second protein in a sample from the subject,

where the first protein is EPHB2,

wherein the second protein exhibits type I interferon-induced gene expression and exhibits a Pearson correlation coefficient of greater than 0.3 compared to the type I interferon-associated gene expression profile, and

where the increased level of the first protein and the increased level of the second protein are compared with:

a) the level of the first protein and the level of the second protein, respectively, in a tissue sample or from a person not suffering from a type I interferon-mediated disease or disorder, or

b) the level of one or more control proteins in the sample from the subject.

The present invention provides a method of treating a type I interferon-mediated disease or disorder in a subject, the method comprising administering an anti-type I interferon antibody or an anti-type I interferon receptor antibody that modulates (eg, binds) the activity of the type I interferon where the subject has been identified by detecting an increased level of a first protein in a sample from a subject and an increased level of a second protein in a sample from a subject,

where the first protein is EPHB2,

where the second protein is selected from ALCAM; angiopoietin-2 (ANG-2); AREG; C1q; AXL receptor tyrosine kinase (AXL); B-cell activating factor (BAFF); B7-H1; beta-2-microglobulin (B2M); sCD163; CLM6; BLC; CD5L; ST4S6; SCGF-alpha; CO8A1; macrophage colony-stimulating factor 1 (M-CSF); R M-CSF; cathepsin S; soluble CXCL16; DLL1; DERM; EPHB2; monocyte chemotactic protein 4 (MCP-4); TIMD3; EMR2; intercellular adhesion molecule 1 (ICAM-1); Ra1 IL-13; interleukin-18 (IL-18); bFGF; IL-18 BPa; MIP-3b; MCP-1; VEGF sR3; TCCR; PHI; IGFBP-4; Ra IL-3; LAG-3; interleukin-1 receptor antagonist (IL-1Ra); JAG1; KYNU; macrophage inflammatory protein 3 beta (MIP-3 beta); LG3BP; ILT-4; MCP-3; fractalkine/CX3CL-1; interferon gamma inducible protein 10 (IP-10); MAPK14; monocyte chemotactic protein-2 (MCP-2); interferon-inducible alpha T cell chemoattractant (ITAC); monokine inducible interferon gamma (MIG); MMP-14; matrix metalloproteinase-7 (MMP-7); NAGK; Notch-3; LDH-H 1; glucocorticoid receptor; PDGF-CC; PLPP; NADPH-P450 oxidoreductase; SAA; a1-antitrypsin; PARK7; sialoadhesin; Siglec-7; SLAF7; osteopontin; PD-L2; BGH3; R III TGF-b; TNF-a; CD30; tenascin; tumor necrosis factor receptor 2 (TNFR2); TS; and SCGF-beta; And

where the increased level of the first protein and the increased level of the second protein are compared with:

a) the level of the first protein and the level of the second protein, respectively, in a tissue sample or from a person not suffering from a type I interferon-mediated disease or disorder, or

b) the level of one or more control proteins in the sample from the subject.

Methods for monitoring or predicting the progression of a disease or disorder

It is possible to monitor the progression of a type I IFN-mediated disease or disorder in a subject using the methods covered by the present invention. In particular, the present invention provides a method for monitoring or predicting the progression of a type I interferon-mediated disease or disorder in a subject, comprising:

i) identifying the expression level of the first protein in the original sample from the subject and the expression level of at least one other protein in the original sample from the subject; And

ii) identifying the expression level of the first protein in an additional sample (eg, taken at a later time compared to the original sample) from the subject and the expression level of at least one other protein in the additional sample from the subject;

wherein an increase in the expression level of the first protein and an increase in the expression level of at least one other protein in the additional sample compared to the original sample from the subject is predictive of disease progression; or

wherein a decrease in the expression level of the first protein and a decrease in the expression level of at least one other protein in the additional sample compared to the original sample from the subject predict regression of the disease;

where the first protein is EPHB2; And

wherein at least one other protein exhibits type I interferon-inducible gene expression and exhibits a Pearson correlation coefficient of greater than 0.3 relative to the type I interferon-associated gene expression profile.

The present invention provides a method for monitoring or predicting the progression of a type I interferon-mediated disease or disorder in a subject, comprising:

i) identifying the expression level of the first protein in the original sample from the subject and the expression level of at least one other protein in the original sample from the subject; And

ii) identifying the expression level of the first protein in an additional sample (eg, taken at a later time compared to the original sample) from the subject and the expression level of at least one other protein in the additional sample from the subject;

wherein an increase in the expression level of the first protein and an increase in the expression level of at least one other protein in the additional sample compared to the original sample from the subject is predictive of disease progression; or

wherein a decrease in the expression level of the first protein and a decrease in the expression level of at least one other protein in the additional sample compared to the original sample from the subject predict regression of the disease;

where the first protein is EPHB2; And

wherein at least one other protein is selected from ALCAM; angiopoietin-2 (ANG-2); AREG; C1q; AXL receptor tyrosine kinase (AXL); B-cell activating factor (BAFF); B7-H1; beta-2-microglobulin (B2M); sCD163; CLM6; BLC; CD5L; ST4S6; SCGF-alpha; CO8A1; macrophage colony-stimulating factor 1 (M-CSF); R M-CSF; cathepsin S; soluble CXCL16; DLL1; DERM; EPHB2; monocyte chemotactic protein 4 (MCP-4); TIMD3; EMR2; intercellular adhesion molecule 1 (ICAM-1); Ra1 IL-13; interleukin-18 (IL-18); bFGF; IL-18 BPa; MIP-3b; MCP-1; VEGF sR3; TCCR; PHI; IGFBP-4; Ra IL-3; LAG-3; interleukin-1 receptor antagonist (IL-1Ra); JAG1; KYNU; macrophage inflammatory protein 3 beta (MIP-3 beta); LG3BP; ILT-4; MCP-3; fractalkine/CX3CL-1; interferon gamma inducible protein 10 (IP-10); MAPK14; monocyte chemotactic protein-2 (MCP-2); interferon-inducible alpha T cell chemoattractant (ITAC); monokine inducible interferon gamma (MIG); MMP-14; matrix metalloproteinase-7 (MMP-7); NAGK; Notch-3; LDH-H 1; glucocorticoid receptor; PDGF-CC; PLPP; NADPH-P450 oxidoreductase; SAA; a1-antitrypsin; PARK7; sialoadhesin; Siglec-7; SLAF7; osteopontin; PD-L2; BGH3; R III TGF-b; TNF-a; CD30; tenascin; tumor necrosis factor receptor 2 (TNFR2); TS; and SCGF-beta.

The present invention further provides a method of monitoring the progression of a disease or disorder mediated by type I interferon in a subject receiving treatment with a therapeutic agent that modulates (eg binds) type I interferon activity, including:

i) identifying the expression level of the first protein in the original sample from the subject and the expression level of at least one other protein in the original sample from the subject;

ii) identifying the expression level of the first protein in an additional sample (eg, taken at a later time compared to the original sample) from the subject and the expression level of at least one other protein in the additional sample from the subject;

iii) administering to the subject a therapeutic agent that modulates the activity of type I interferon, wherein the therapeutic agent is administered before step i) or between steps i) and ii); And

iv) comparing the expression levels of the first protein and at least one other protein in the original sample from the subject and the expression levels of the first protein and at least one other protein, respectively, in the additional sample from the subject;

wherein the change in expression levels of the first protein and at least one other protein indicates the level of effectiveness of a therapeutic agent that modulates the activity of type I interferon;

where the first protein is EPHB2; And

wherein at least one other protein exhibits type I interferon-inducible gene expression and exhibits a Pearson correlation coefficient of greater than 0.3 relative to the type I interferon-associated gene expression profile.

The present invention provides a method for monitoring the progression of a type I interferon-mediated disease or disorder in a subject receiving treatment with a therapeutic agent that modulates (eg binds) type I interferon activity, including:

i) identifying the expression level of the first protein in the original sample from the subject and the expression level of at least one other protein in the original sample from the subject;

ii) identifying the expression level of the first protein in an additional sample (eg, taken at a later time compared to the original sample) from the subject and the expression level of at least one other protein in the additional sample from the subject;

iii) administering to the subject a therapeutic agent that modulates the activity of type I interferon, wherein the therapeutic agent is administered before step i) or between steps i) and ii); And

iv) comparing the expression levels of the first protein and at least one other protein in the original sample from the subject and the expression levels of the first protein and at least one other protein, respectively, in the additional sample from the subject;

wherein the change in expression levels of the first protein and at least one other protein indicates the level of effectiveness of a therapeutic agent that modulates the activity of type I interferon;

where the first protein is EPHB2; And

wherein at least one other protein is selected from ALCAM; angiopoietin-2 (ANG-2); AREG; C1q; AXL receptor tyrosine kinase (AXL); B cell activating factor (BAFF); B7-H1; beta-2-microglobulin (B2M); sCD163; CLM6; BLC; CD5L; ST4S6; SCGF-alpha; CO8A1; macrophage colony-stimulating factor 1 (M-CSF); R M-CSF; cathepsin S; soluble CXCL16; DLL1; DERM; EPHB2; monocyte chemotactic protein 4 (MCP-4); TIMD3; EMR2; intercellular adhesion molecule 1 (ICAM-1); Ra1 IL-13; interleukin-18 (IL-18); bFGF; IL-18 BPa; MIP-3b; MCP-1; VEGF sR3; TCCR; PHI; IGFBP-4; Ra IL-3; LAG-3; interleukin-1 receptor antagonist (IL-1Ra); JAG1; KYNU; macrophage inflammatory protein 3 beta (MIP-3 beta); LG3BP; ILT-4; MCP-3; fractalkine/CX3CL-1; interferon gamma inducible protein 10 (IP-10); MAPK14; monocyte chemotactic protein-2 (MCP-2); interferon-inducible alpha T cell chemoattractant (ITAC); monokine inducible interferon gamma (MIG); MMP-14; matrix metalloproteinase-7 (MMP-7); NAGK; Notch-3; LDH-H 1; glucocorticoid receptor; PDGF-CC; PLPP; NADPH-P450 oxidoreductase; SAA; a1-antitrypsin; PARK7; sialoadhesin; Siglec-7; SLAF7; osteopontin; PD-L2; BGH3; R III TGF-b; TNF-a; CD30; tenascin; tumor necrosis factor receptor 2 (TNFR2); TS; and SCGF-beta.

In methods of monitoring or predicting the progression of a type I interferon-mediated disease or disorder in a subject, samples from the subject may be obtained at different time points, such as an initial sample and an additional sample. Optionally, samples from the subject may be obtained before and after administration of a therapeutic agent, such as an agent that binds to type I IFN and/or modulates its activity, or an agent that binds to type I IFN and does not modulate its activity, or a combination of agents that may or may not include an agent that binds to type I IFN and modulates its activity. Type I IFNPS profiles are obtained from pre- and post-administration samples. Type I IFNPS profiles across samples are compared.

The comparison can be made between the number of type I IFNPS proteins present in the samples, or the number of type I IFNPS proteins present in the samples, or any combination thereof.

Variation, which is an indicator of disease progression, can be indicated if the amount or level (or any combination thereof) of up-regulated type I IFNPS proteins is increased in the additional sample compared to the original sample.

Variation, which is an indicator of disease regression, can be indicated if the amount or level (or any combination thereof) of up-regulated type I IFNPS proteins is reduced in the additional sample compared to the original sample.

Variability, which indicates the effectiveness of a therapeutic agent, can be indicated if the amount or level (or any combination thereof) of up-regulated type I IFNPS proteins is reduced in a sample obtained after administration of the therapeutic agent compared to a sample obtained before administration of the therapeutic agent .

The number of up-regulated type I IFNPS proteins may be increased or decreased by a factor of at least 1, at least 2, at least 3, at least 4, at least 5, at least 6, at least 7, at least at least 8, at least 9 or at least 10 times. The level of any given up-regulated type I IFNPS protein may be reduced 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 IFNPS proteins whose levels are decreased may be at least 1, at least 2, at least 3, or at least 4. Any combination of decreased amount and decreased level of up-regulated type I IFNPS proteins may indicate effectiveness. Variability, which indicates the effectiveness of a therapeutic agent, can be indicated if the amount or level (or any combination thereof) of the down-regulated type I IFNPS protein is reduced in the sample obtained after administration of the therapeutic agent compared to the sample obtained before administration of the therapeutic agent .

The sample obtained from the subject may be obtained prior to the first administration of the agent, i.e., the subject has not previously been administered the agent. Alternatively, a sample obtained from the subject may be collected after administration of the agent during treatment. For example, the agent could be administered before the monitoring protocol began. After drug administration, an additional sample can be obtained from the subject and the type I IFNPS profiles of the samples are compared. The samples may be the same or different types, for example, each sample obtained may be a blood sample, or each sample obtained may be a blood serum sample. The type I IFNPS profiles identified in each sample may be the same, may overlap significantly, or may be similar.

Samples can be obtained at any time before and after administration of the therapeutic agent. The sample obtained after administration of the therapeutic agent may be obtained after 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. facilities. 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 after administration of the therapeutic agent.

Additional samples may be obtained from the subject 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 a subject to monitor the progression or regression of a disease or disorder over time. The progression of the disease or disorder may be monitored over a 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 for the life of the subject. Additional samples may be obtained from the subject at regular intervals, such as once a month, twice a month, once a quarter, twice a year, or at intervals of one year. Samples may be obtained from the subject after administration of the agent at regular intervals. For example, samples may be obtained from the subject one week after each administration of the agent, or two weeks after each administration of the agent, or three weeks after each administration of the agent, or one month after each administration of the agent, or two months after each administration facilities. Alternatively, multiple samples may be obtained from the subject after each administration of the agent.

The progression of a disease or disorder in a subject may similarly be monitored in the absence of administration of the agent. Samples may be obtained periodically from a subject suffering from a disease or disorder. Progression of a disease or disorder can be identified if the amount of up-regulated type I IFNPS proteins is increased in a later sample (eg, an additional sample) relative to an earlier sample (eg, an original sample). The number of up-regulated type I IFNPS proteins may be increased 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. Progression of a disease or disorder can be identified if the level of any of these up-regulated type I IFNPS proteins 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 according at least 95%. Progression of a disease or disorder can be identified if the level of any of these down-regulated type I IFNPS proteins 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 IFNPS proteins at elevated 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 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 IFNPS proteins with reduced 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 amounts and elevated levels of up-regulated type I IFNPS proteins may indicate progression of the disease or disorder. Alternatively or in combination, any combination of decreased amounts and decreased levels of down-regulated type I IFNPS proteins may indicate progression of the disease or disorder. Regression of the disease or disorder may also be identified in a subject suffering from the disease or disorder not treated with the agent. In this case, regression can be identified if the amount of type I IFNPS proteins is reduced in a later sample (eg, an additional sample) relative to an earlier sample (eg, an original sample). The number of type I IFNPS proteins may be reduced 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 at least 9 or at least 10. Regression of a disease or disorder can be identified if the level of any of these up-regulated type I IFNPS proteins is reduced by at least 10%, at least 20%, at least 25%, at least 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 %. Regression of a disease or disorder can be identified if the level of any of these down-regulated type I IFNPS proteins 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 IFNPS proteins with reduced 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 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 IFNPS proteins with elevated 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. Progression of a disease or disorder or regression of a disease or disorder may be monitored by obtaining samples for any period of time and at any time interval . Progression of the disease or disorder or regression of the disease or disorder may be monitored by obtaining samples over 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 for the life of the subject. Progression of the disease or disorder or regression of the disease or disorder may be monitored by obtaining samples at least once a month, twice a month, once a quarter, twice a year, or every year. There is no need to obtain samples at precise intervals.

Type I interferon-mediated disease, disorder, or conditions

A type I interferon-mediated disease, disorder, or condition is any condition that exhibits type I IFNPS. Such diseases, disorders or conditions include those with an autoimmune component, such as systemic lupus erythematosus (SLE), discoid lupus, insulin-dependent diabetes mellitus, inflammatory bowel disease (including Crohn's disease, ulcerative colitis and celiac disease), multiple sclerosis, psoriasis, autoimmune thyroiditis, scleroderma, rheumatoid arthritis, glomerulonephritis, idiopathic inflammatory myositis, Sjogren's syndrome, vasculitis, inclusion body myositis (IBM), dermatomyositis (DM), polymyositis (PM), sarcoidosis, scleroderma and lupus nephritis. Other diseases, disorders or conditions include graft-versus-host disease and graft rejection.

In the methods of the present invention, the subject may need treatment for a type I interferon-mediated disease or disorder selected from systemic lupus erythematosus, discoid lupus, lupus nephritis, dermatomyositis, polymyositis, psoriasis, SSc, vasculitis, sarcoidosis, Sjögren's syndrome, and idiopathic inflammatory myositis. Preferably, the subject is in need of treatment for systemic lupus erythematosus.

The subject may also exhibit any of a number of symptoms described, for example, in international publication No. WO 2008/070135, or may be characterized by the clinical SLEDAI score or BILAG score described in the same document. These symptoms may include fatigue, organ damage, malar rash and alopecia. The subject can be assessed using a known clinical scoring system, such as the SLEDAI, which is an indicator of SLE disease activity when measured and assessed over the past 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 according to the SLEDAI scoring system can range from 0 to 105. The following categories of SLEDAI activity were defined: no activity (SLEDAI equals 0); weak activity (SLEDAI equals 1-5); moderate activity (SLEDAI equals 6-10), high activity (SLEDAI equals 11-19); very high activity (SLEDAI equal to 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 index of SLE activity that is based on specific clinical manifestations in eight organ systems: general, mucocutaneous, neurological, musculoskeletal, cardiovascular, respiratory, renal and hematological findings. The 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 ranging from 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 Respondent Index (CRI), and the ANAM4™ test.

The methods described herein, for example a method for identifying a subject suitable for treatment of a type I IFN-mediated disease or disorder, can be used to identify the level of disease activity in a subject as measured by any classification methodology known in the art, e.g., mild, moderate , high or very high.

Therapeutics

The therapeutic agent may be administered to a subject, or the subject may be identified as a candidate for administration of the agent or therapeutic agent. The therapeutic agent is capable of modulating the activity of type I interferon. Suitable therapeutic agents include molecules that bind to type I IFN and modulate its activity. Suitable therapeutic agents include molecules that bind to type I interferon receptors and modulate their activity. The therapeutic agent may be a small molecule or a biological agent. In embodiments, the therapeutic agent is a small molecule. The small molecule may be synthesized or identified and isolated from a natural source. In other embodiments, the therapeutic agent is a biological agent. Preferably the biological agent is an antibody. The antibody may be an anti-type I interferon antibody or an anti-type I interferon receptor antibody.

The antibody may be an antibody specific for any type I IFN subtype(s). For example, the antibody may be specific for any of IFNα1, IFNα2, IFNα4, IFNα5, IFNα6, IFNα7, IFNα8, IFNα10, IFNαl4, IFNα17, IFNα21, IFΝβ, 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 subtypes. If the antibody is specific for more than one type I IFN subtype, the antibody may be specific for IFNα1, IFNα2, IFNα4, IFNα5, IFNα6, IFNα7, IFNα8, IFNα10, and IFNα21; or may be specific for IFNα1, IFNα2, IFNα4, IFNα5, IFNα8 and IFNα10; or may be specific for IFNα1, IFNα2, IFNα4, IFNα5, IFNα8 and IFNα21; or may be specific for IFNα1, IFNα2, IFNα4, IFNα5, IFNα10 and IFNα21. Antibodies specific for type I IFN include siphalumimab, any biologic or antibody other than siphalumimab, antibodies described in US patent application 11/009410, filed December 10, 2004, and 11/157494, filed June 20, 2005 , 9F3 and other antibodies described in US Pat. No. 7,087,726 (Example 1 and Example 2, the antibodies disclosed in Table 3 and Table 4, and/or the antibodies disclosed in the table entitled "Material Deposit" in lines 25-54, column 56), NK-2 and YOK5/19 (WO 84/03105), LO-22 (US Patent 4902618), 144 BS (US Patent 4885166) and EBI-1, EBI-2 and EBI-3 (EP 119476). A therapeutic agent that modulates IFNa activity can neutralize IFNa activity. The preparation and composition of such biological agents and methods of their administration are well known to one skilled in the art.

The antibody may be an anti-type I interferon receptor antibody, including those disclosed in US Patent Nos. 7,619,070 and 7,662,381 and International Publication No. WO 2009/100309.

The antibody may be a synthetic antibody, a monoclonal antibody, a polyclonal antibody, a recombinantly produced antibody, an intrabody, a multispecific antibody (including bispecific antibodies), a human antibody, a humanized antibody, a chimeric antibody, a single chain Fv (scFv) (including a bispecific scFv), a BiTE molecule, single-chain antibody, Fab fragments, F(ab') fragment, disulfide-linked Fv (sdFv) or epitope-binding fragment of any of the above. The antibody can be any immunoglobulin molecule or an immunologically active portion of an immunoglobulin molecule. In addition, the antibody can be of any isotype. For example, it may be any of the isotypes IgG1, IgG2, IgG3 or IgG4. The antibody may be a full-length antibody containing 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 bound to a therapeutic agent, such as a cytotoxin or radioactive isotope.

In methods of treating with a therapeutic agent (eg, anti-type I interferon antibodies or anti-type I interferon receptor antibodies that modulate the activity of type I interferon) or methods involving administering a therapeutic agent, a second agent other than an agent that binds to type I IFN to modulate its activity, or an agent that binds to the type I interferon receptor and modulates its activity, may be administered to a subject. The 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; antimalarial drugs such as hydroxychloroquine; corticosteroid hormones such as prednisone, hydrocortisone, methylprednisolone and dexamethasone; methotrexate; immunosuppressive agents such as azathioprine and cyclophosphamide; and biologics that, for example, target T cells, such as alefacept and efalizumab, or target TNFa, such as Enbrel, Remicade, and Humira.

Treatment with a therapeutic agent may result in neutralization of the type I IFNPS profile. Treatment with a therapeutic agent may result in a reduction in one or more symptoms of a type I IFN-mediated disease or disorder. Treatment with a therapeutic agent may result in a reduction in the number of exacerbations associated with a type I IFN-mediated disease or disorder. Treatment with the agent may result in an improved prognosis for a subject suffering from a type I IFN-mediated disease or disorder. Treatment with the remedy can lead to a higher quality of life for the subject. Treatment with a therapeutic agent may reduce the need for co-administration of second agents or may reduce the dosage of administration of a second agent to the subject. Treatment with a therapeutic agent may reduce the number of hospitalizations in a subject that are associated with a type I IFN-mediated disease or disorder.

A therapeutic agent that binds to type I IFN and modulates its activity may neutralize the type I IFNPS profile. Neutralization of the type I IFNPS profile may be a reduction in the level of at least one, at least two, at least three, at least four proteins. Neutralization of a Type I IFNPS profile represents 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%, according to at least 70%, at least 75%, at least 80%, or at least 90% of the level of any of at least one, at least two, at least three, at least two up-regulated proteins in the profile IFNPS type I. Alternatively, neutralization of a type I IFNPS profile refers to a reduction in the expression of up-regulated type I IFNPS proteins that is no more than 50%, no more than 45%, no more than 40%, no more than 35%, no more than 30%, no more than 25%, no more than 20%, no more than 15%, no more than 10%, no more than 5%, no more than 4%, no more than 3%, no more than 2% or no more than 1% of the expression levels of type I IFNPS proteins in the control sample. If the therapeutic agent that binds to type I IFN and modulates its activity is a biological agent, such as an antibody, then the agent can neutralize the protein expression profile associated with type I IFN at doses ranging from 0.3 to 30 mg/day. kg, from 0.3 to 10 mg/kg, from 0.3 to 3 mg/kg, from 0.3 to 1 mg/kg, from 1 to 30 mg/kg, from 3 to 30 mg/kg, from 5 up to 30 mg/kg, from 10 to 30 mg/kg, from 1 to 10 mg/kg, from 3 to 10 mg/kg or from 1 to 5 mg/kg.

A therapeutic agent that binds to type I IFN and modulates its activity may additionally or alternatively neutralize the expression of one or more type I IFN subtypes. 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 type I IFN subtypes . These subtypes may include IFNαl, IFNα2, IFNα4, IFNα5, IFNα6, IFNα7, IFNα8, IFNα10, IFNαl4, IFNαl7, IFNα21, IFNβ, or IFNω. These subtypes may include all of IFNα1, IFNα2, IFNα8 and IFNαl4. Alternatively, these subtypes may include IFNα1, IFNα2, IFNα4, IFNα5, IFNα8, IFNα10, IFNα21. Neutralization of 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 the level of any of at least one, at least two, at least three, at least five, at least seven , at least eight or at least ten subtypes. Neutralization of type I IFN subtypes may be a reduction in the expression of type I IFN subtype proteins that is within the range of no more than 50%, no more than 45%, no more than 40%, no more than 35%, no more than 30%, no more than 25%, no more than 20%, no more than 15%, no more than 10%, no more than 5%, no more than 4%, no more than 3%, no more than 2% or no more than 1% of the protein expression levels of type I IFN subtypes in the control sample. If the agent that binds to type I IFN and modulates its activity is a biological agent, such as an antibody, then the agent can neutralize subtypes of type I IFN at doses ranging from 0.3 to 30 mg/kg, from 0.3 to 10 mg/kg, from 0.3 to 3 mg/kg, from 0.3 to 1 mg/kg, from 1 to 30 mg/kg, from 3 to 30 mg/kg, from 5 to 30 mg/kg, from 10 to 30 mg/kg, 1 to 10 mg/kg, 3 to 10 mg/kg, or 1 to 5 mg/kg.

A therapeutic agent that binds to type I IFN and modulates its activity may additionally or alternatively neutralize the expression of IFNα receptors, or IFNARl or IFNAR2, or both, or TNFα, or IFNγ, or IFNγ receptors (either IFNGRl, IFNGR2, or both IFNGRl and IFNGR2). Neutralization of expression of IFNα receptors, or IFNARl or IFNAR2, or both, or TNFα, or IFNγ, or IFNγ receptors (either IFNGRl, IFNGR2, or both IFNGRl and IFNGR2) may represent 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%, according to 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% expression of any of at least one, at least two, at least three, at least five or at least six of these genes. Neutralization of the expression of IFNα receptors, or IFNARl or IFNAR2, or TNFα, or IFNγ, or IFNγ receptors (or IFNGRl, IFNGR2, or both IFNGRl and IFNGR2) is a decrease in expression by no more than 50%, no more than 45%, no more no more than 40%, no more than 35%, no more than 30%, no more than 25%, no more than 20%, no more than 15%, no more than 10%, no more than 5%, no more than 4 %, no more than 3%, no more than 2% or no more than 1% of the expression levels of these genes in the control sample. If the therapeutic agent that binds to type I IFN and modulates its activity is a biological agent, such as an antibody, then the agent can neutralize the expression of the IFNα receptors IFNARl or IFNAR2 or TNFα or IFNγ, or the IFNγ receptors IFNGRl or IFNGR2 at doses components from 0.3 to 30 mg/kg, from 0.3 to 10 mg/kg, from 0.3 to 3 mg/kg, from 0.3 to 1 mg/kg, from 1 to 30 mg/kg, from 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.

Identification of candidate therapeutic agents

A candidate therapeutic agent for treating a type I IFN-mediated disease or disorder may be identified through the methods covered by the present invention. In particular, the present invention provides a method for identifying a therapeutic candidate for the treatment of a type I interferon-mediated disease or disorder, comprising:

i) identifying the expression level of the first protein in the original sample from the subject and the expression level of at least one other protein in the original sample from the subject;

ii) administering the candidate therapeutic agent to the subject;

iii) identifying the expression level of the first protein in an additional sample (eg, taken at a later time compared to the original sample) from the subject and the expression level of at least one other protein in the additional sample from the subject; And

iv) comparing the expression levels of the first protein and at least one other protein in the original sample from the subject with the expression levels of the first protein and at least one other protein, respectively, in the additional sample from the subject;

wherein the change in the expression levels of the first protein and at least one other protein includes a decrease in the positive regulation of the expression levels of the first protein and at least one other protein, respectively, which indicates that the agent is a candidate therapeutic agent;

where the first protein is EPHB2; And

wherein at least one other protein exhibits type I interferon-inducible gene expression and exhibits a Pearson correlation coefficient of greater than 0.3 relative to the type I interferon-associated gene expression profile.

The present invention also provides a method for identifying a candidate therapeutic agent for the treatment of a type I interferon-mediated disease or disorder, comprising:

i) identifying the expression level of the first protein in the original sample from the subject and the expression level of at least one other protein in the original sample from the subject;

ii) administering the candidate therapeutic agent to the subject;

iii) identifying the expression level of the first protein in an additional sample (eg, taken at a later time compared to the original sample) from the subject and the expression level of at least one other protein in the additional sample from the subject; And

iv) comparing the expression levels of the first protein and at least one other protein in the original sample from the subject with the expression levels of the first protein and at least one other protein, respectively, in the additional sample from the subject;

wherein the change in the expression levels of the first protein and at least one other protein includes a decrease in the positive regulation of the expression levels of the first protein and at least one other protein, respectively, which indicates that the agent is a candidate therapeutic agent;

where the first protein is EPHB2; And

wherein at least one other protein is selected from ALCAM; angiopoietin-2 (ANG-2); AREG; C1q; AXL receptor tyrosine kinase (AXL); B-cell activating factor (BAFF); B7-H1; beta-2-microglobulin (B2M); sCD163; CLM6; BLC; CD5L; ST4S6; SCGF-alpha; CO8A1; macrophage colony-stimulating factor 1 (M-CSF); R M-CSF; cathepsin S; soluble CXCL16; DLL1; DERM; EPHB2; monocyte chemotactic protein 4 (MCP-4); TIMD3; EMR2; intercellular adhesion molecule 1 (ICAM-1); Ra1 IL-13; interleukin-18 (IL-18); bFGF; IL-18 BPa; MIP-3b; MCP-1; VEGF sR3; TCCR; PHI; IGFBP-4; Ra IL-3; LAG-3; interleukin-1 receptor antagonist (IL-1Ra); JAG1; KYNU; macrophage inflammatory protein 3 beta (MIP-3 beta); LG3BP; ILT-4; MCP-3; fractalkine/CX3CL-1; interferon gamma inducible protein 10 (IP-10); MAPK14; monocyte chemotactic protein-2 (MCP-2); interferon-inducible alpha T cell chemoattractant (ITAC); monokine inducible interferon gamma (MIG); MMP-14; matrix metalloproteinase-7 (MMP-7); NAGK; Notch-3; LDH-H 1; glucocorticoid receptor; PDGF-CC; PLPP; NADPH-P450 oxidoreductase; SAA; a1-antitrypsin; PARK7; sialoadhesin; Siglec-7; SLAF7; osteopontin; PD-L2; BGH3; R III TGF-b; TNF-a; CD30; tenascin; tumor necrosis factor receptor 2 (TNFR2); TS; and SCGF-beta.

Therapeutic candidates may be any type of molecule, including a small molecule or a biological agent. A therapeutic candidate identified through the methods covered by the present invention may be directly identified as useful as a therapeutic agent for a disease, disorder or condition. Alternatively, therapeutic candidates identified through the methods covered by the present invention may require further testing and/or modification before selection for treatment of subjects. Alternatively, a therapeutic candidate identified through the methods covered by the present invention may, upon further testing, be rejected as a molecule for treatment of subjects.

In methods by which candidate therapeutic agents are identified, samples (eg, cells) exhibiting a type I IFNPS profile are contacted with the agent. The cells may be any cell type, for example, commercially available immortalized cell lines that are characterized by a type I IFNPS profile, commercially available immortalized cell lines that have been treated with type I IFN to induce a type I IFNPS profile, cells isolated from a subject characterized by type I IFNPS profile, or cells isolated from a healthy subject and treated with type I IFN to induce a type I IFNPS profile.

The presence or absence of a change in the type I IFNPS profile in the sample is detected after contact of the sample with the product. The presence of a change may be any change in the type I IFNPS profile, including at least a 10% decrease in the up-regulated expression level of at least 2 type I IFNPS profile proteins, at least a 20% decrease in the expression of at least 2 up-regulated proteins proteins, at least 30% decrease in expression of at least 2 up-regulated proteins, at least 40% decrease in expression of at least 2 up-regulated proteins, at least 50% decrease in expression of at least 2 up-regulated proteins, at least 60% reduction in the expression of at least 2 up-regulated proteins, at least 70% reduction in the expression of at least 2 up-regulated proteins, at least 75% reduction in the expression of at least 2 up-regulated proteins, at least at least 80% reduction in expression of at least 2 up-regulated proteins, at least 85% reduction in expression of at least 2 up-regulated proteins, at least 90% reduction in expression of at least 2 up-regulated proteins, at least 95 % decrease in expression of at least 2 up-regulated proteins, at least 96% decrease in expression of at least 2 up-regulated proteins, at least 97% decrease in expression of at least 2 up-regulated proteins, at least 98% decrease expression of at least 2 up-regulated proteins, at least 99% reduction in expression of at least 2 up-regulated proteins, or 100% reduction in expression of at least 2 up-regulated proteins.

The present invention will now be described in more detail with reference to the following figures.

Examples

Example 1: Measurements with Somalogic using a shortened protocol

The SOMAscan multiplex assay includes 1.3 thousand individual affinity molecules called SOMAmer ^® (low dissociation rate modified aptamer) reagents, each of which has very high affinity for its target proteins (Rohloff JC et al., Nucleic Acid Ligands With Protein- like Side Chains: Modified Aptamers and Their Use as Diagnositc and Therapeutic Agents. Mol Ther Nucleic Acids 2014;3:e201; Gold L et al., Aptamer-based multiplexed proteomic technology for biomarker discovery. PLoS One . 2010;5:e15004) . Prior to SOMAscan analysis, biological samples were diluted using sample diluent containing buffers, salts, detergents, and competitors. For SLE samples, the competitors were a mixture of SomaLogic polyanionic competitors and single- and double-stranded herring sperm DNA. Diluted biological samples were incubated for 30 min before adding a 96-well plate containing a mixture of 1.3 thousand SOMAmer reagents to each well. After addition, the mixture of sample and SOMAmer reagents was incubated to form affinity complexes.

Two sequential bead immobilization and washing steps removed unbound or nonspecifically bound proteins and unbound SOMAmer reagents, leaving only target protein-bound SOMAmer reagents. These remaining SOMAmer reagents were isolated and each reagent was simultaneously quantified on a custom Agilent hybridization chip. The amount of each SOMAmer measured was quantitatively proportional to the protein concentration in the original sample. Somalogic measurements collected using this abbreviated protocol passed QC and were no longer elevated with a predominance of anti-dsDNA antibodies (Figure 1).

Data preparation

Developed data standardization procedures to ensure data consistency. In its simplest form, normalization procedures were controlled to account for inter-chip variation and were carried out in two steps. The first, using a set of hybridization control sequences introduced into the assay eluate prior to hybridization and measured independently for each sample microarray, which corrects for any systemic effects on data obtained during the readout phases of the assay. The second normalization scheme used all SOMAmer signals on a given microarray to allow comparison of samples within a plate or within similar groups. This corrected for variation that may have been introduced during the SOMAscan analysis and natural variation in the original sample concentration that may have occurred. Using normalization methods, scaling factors were calculated for each sample and subsequently applied to the signal for suitable features within the microarray. When establishing plate scaling and performing calibration, the endogenous control replicate signal obtained from each plate was used to calculate scaling factors for each plate and for each sequence within a plate to control for plate variation that may have occurred across multiple assays. .

Example 2: Somalogic measurements correlated with Rules Based Medicine measurements

To identify correlates of type I IFN protein activity from blood, a set of protein level measurements from Rules Based Medicine (RBM) and SOMAscan platforms were identified that correlated with type I IFN biology in microarrays for blood-derived samples and protein level measurements. To identify proteins correlated with type I IFN-dependent gene expression, 103 proteins were identified that correlated with the expression profile of 21 type I IFN genes with a Spearman correlation coefficient greater than 0.3. To identify proteins associated with a predominance of IFN-dependent proteins, a blind input separation algorithm, principal component analysis, followed by Promax rotation was used to identify a score highly correlated with the expression profile of 21 type I IFN genes and several measurements of IFN-inducible protein levels. -chemokines. 155 proteins were correlated with a Spearman rank correlation coefficient greater than 0.3. When examining the combination of the two lists, a total of 170 protein level measurements were found to be associated with type I IFN biology.

Table 2. Proteins known to have interferon-inducible transcripts as published in the Interferome database

Analyte name Platform Gene designation Biological signaling pathway SOMA-ALCAM SOMA ALCAM Inflammation/damage and tissue repair RBM - angiopoietin-2 (ANG-2) R.B.M. ANGPT2 Vascular damage/inflammation/tissue repair SOMA - angiopoietin-2 SOMA ANGPT2 Vascular damage/inflammation/tissue repair SOMA - AREG SOMA AREG Vascular damage/inflammation/tissue repair RBM - AXL receptor tyrosine kinase (AXL) R.B.M. AXL Dendritic cell/T cell activation SOMA - b2-microglobulin SOMA B2M Main correlates with IFN21GS RBM - beta 2 microglobulin (B2M) R.B.M. B2M Dendritic cell/T cell activation SOMA-C1q SOMA C1QA Inflammation/damage and tissue repair RBM - monocyte chemotactic protein-4 (MCP-4) R.B.M. CCL13 Interferon-inducible chemokine SOMA-MIP-3b SOMA CCL19 Interferon-inducible chemokine SOMA-MCP-1 SOMA CCL2 Interferon-inducible chemokine RBM - monocyte chemotactic protein 1 (MCP-1) R.B.M. CCL2 Interferon-inducible chemokine RBM - macrophage inflammatory protein 3 beta (MIP-3 beta) R.B.M. CCL23 Interferon-inducible chemokine SOMA-MCP-3 SOMA CCL7 Interferon-inducible chemokine RBM - monocyte chemotactic protein 2 (MCP-2) R.B.M. CCL8 Main correlates with IFN21GS SOMA-sCD163 SOMA CD163 Inflammation/damage and tissue repair SOMA-B7-H1 SOMA CD274 Main correlates with IFN21GS SOMA-CLM6 SOMA CD300C Inflammation/damage and tissue repair SOMA-CD5L SOMA CD5L Inflammation/damage and tissue repair RBM - CD5 antigen-like (CD5L) R.B.M. CD5L Inflammation/damage and tissue repair SOMA-ST4S6 SOMA CHST15 Inflammation/damage and tissue repair SOMA - SCGF-alpha SOMA CLEC11A Dendritic cell/T cell activation SOMA - SCGF-beta SOMA CLEC11A Dendritic cell/T cell activation SOMA - CO8A1 SOMA COL8A1 Inflammation/damage and tissue repair RBM - macrophage colony stimulating factor 1 (M-CSF) R.B.M. CSF1 Inflammation/damage and tissue repair SOMA-CSF-1 SOMA CSF1 Inflammation/damage and tissue repair SOMA-R M-CSF SOMA CSF1R Inflammation/damage and tissue repair SOMA - cathepsin S SOMA CTSS Inflammation/damage and tissue repair SOMA - fractalkine/CX3CL-1 SOMA CX3CL1 Interferon-inducible chemokine RBM - interferon gamma inducible protein 10 (IP-10) R.B.M. CXCL10 Interferon-inducible chemokine SOMA - IP-10 SOMA CXCL10 Interferon-inducible chemokine SOMA - I-TAC SOMA CXCL11 Interferon-inducible chemokine RBM - interferon-inducible alpha T cell chemoattractant (ITAC) R.B.M. CXCL11 Interferon-inducible chemokine SOMA - BLC SOMA CXCL13 B cell survival/differentiation RBM - B-Lymphocyte chemoattractant (BLC) R.B.M. CXCL13 B cell survival/differentiation SOMA - soluble CXCL16 SOMA CXCL16 Inflammation/damage and tissue repair RBM - monokine inducible interferon gamma (MIG) R.B.M. CXCL9 Interferon-inducible chemokine SOMA-DLL1 SOMA DLL1 B cell survival/differentiation SOMA - DERM SOMA DPT Inflammation/damage and tissue repair SOMA-EMR2 SOMA EMR2 Inflammation/damage and tissue repair SOMA-EPHB2 SOMA EPHB2 Major correlate of IFN21GS SOMA - bFGF SOMA FGF2 Inflammation/damage and tissue repair SOMA - VEGF sR3 SOMA FLT4 Inflammation/damage and tissue repair SOMA-PHI SOMA GPI Inflammation/damage and tissue repair SOMA - TIMD3 SOMA HAVCR2 Dendritic cell/T cell activation RBM - intercellular adhesion molecule 1 (ICAM-1) R.B.M. ICAM1 Dendritic cell/T cell activation SOMA-IGFBP-4 SOMA IGFBP4 Inflammation/damage and tissue repair SOMA - Ra1 IL-13 SOMA IL13RA1 Dendritic cell/T cell activation RBM - interleukin-18 (IL-18) R.B.M. IL18 Dendritic cell/T cell activation SOMA - IL-18 BPa SOMA IL18BP Dendritic cell/T cell activation RBM - interleukin-1 receptor antagonist (IL-1ra) R.B.M. IL1RN Inflammation/damage and tissue repair SOMA-TCCR SOMA IL27RA Dendritic cell/T cell activation SOMA - Ra IL-3 SOMA IL3RA Dendritic cell/T cell activation SOMA-JAG1 SOMA JAG1 Inflammation/damage and tissue repair SOMA - KYNU SOMA KYNU Inflammation/damage and tissue repair SOMA-LAG-3 SOMA LAG3 Dendritic cell/T cell activation SOMA-LDH-H 1 SOMA LDHB Dendritic cell/T cell activation SOMA - LG3BP SOMA LGALS3BP Inflammation/damage and tissue repair SOMA - ILT-4 SOMA LILRB2 Inflammation/damage and tissue repair SOMA-MAPK14 SOMA MAPK14 Inflammation/damage and tissue repair SOMA-MMP-14 SOMA MMP14 Inflammation/damage and tissue repair SOMA-MMP-7 SOMA MMP7 Inflammation/damage and tissue repair RBM - matrix metalloproteinase-7 (MMP-7) R.B.M. MMP7 Inflammation/damage and tissue repair SOMA - NAGK SOMA NAGK Inflammation/damage and tissue repair SOMA - Notch-3 SOMA NOTCH3 Inflammation/damage and tissue repair SOMA - glucocorticoid receptor SOMA NR3C1 Dendritic cell/T cell activation SOMA - PARK7 SOMA PARK7 Dendritic cell/T cell activation SOMA-PD-L2 SOMA PDCD1LG2 Dendritic cell/T cell activation SOMA - PDGF-CC SOMA P.D.G.F.C. Inflammation/damage and tissue repair SOMA-PLPP SOMA PDXP Inflammation/damage and tissue repair SOMA - NADPH-P450 oxidoreductase SOMA POR Inflammation/damage and tissue repair SOMA-SAA SOMA SAA1 Inflammation/damage and tissue repair SOMA - a1-antitrypsin SOMA SERPINA1 Inflammation/damage and tissue repair SOMA - sialoadhesin SOMA SIGLEC1 Inflammation/damage and tissue repair SOMA - Siglec-7 SOMA SIGLEC7 Inflammation/damage and tissue repair SOMA - SLAF7 SOMA SLAMF7 B cell survival/differentiation RBM - osteopontin R.B.M. SPP1 Inflammation/damage and tissue repair SOMA-BGH3 SOMA TGFBI Inflammation/damage and tissue repair SOMA - R III TGF-b SOMA TGFBR3 Dendritic cell/T cell activation SOMA - tenascin SOMA TNC Inflammation/damage and tissue repair SOMA - TNF-a SOMA TNF Dendritic cell/T cell activation RBM - tumor necrosis factor receptor 2 (TNFR2) R.B.M. TNFRSF1B Inflammation/damage and tissue repair SOMA - sR-II TNF SOMA TNFRSF1B Inflammation/damage and tissue repair SOMA-CD30 SOMA TNFRSF8 Dendritic cell/T cell activation RBM - B cell activating factor (BAFF) R.B.M. TNFSF13B B cell survival/differentiation SOMA - BAFF SOMA TNFSF13B B cell survival/differentiation SOMA-TS SOMA TYMS Inflammation/damage and tissue repair

Example 4: Independent Validation of IFNPS Components Using Microchips and Rules Based Medicine (RBM)

As an example of the utility of these 170 proteins, we selected a small sample for identification that can be used to generate an overall measure of type I IFN activity in the blood. We first filtered 170 proteins into a list of 87 protein level measurements from 75 unique proteins, 20 from Rules based Medicine and 67 from SOMAscan platforms known to have interferon-inducible transcripts as published in the Interferome database. The present inventors then used LASSO regression to select a small sample of SOMAscan measurements for use as a common metric. Measurements of protein levels obtained in 2013 and 2014. from the NIH-SLE cohort, was used as the training dataset to establish the linear model. Measurements of protein levels obtained in 2015 were used to validate the model. The cut parameter, λ, and the number of major correlates of IFN21GS by Pearson, k, for inclusion in the LASSO model were selected based on the values that minimized the mean square error (MSE) with the expression profile of 21 type I IFN genes after 10 iterations of 5-fold cross-validation . A linear combination of the top 4 proteins correlated with IFN21GS resulted in optimal prediction of IFN21GS in the training dataset. The present inventors re-fitted the 4-protein model using ordinary least squares (OLS) regression to obtain the final coefficient estimates. All measurements of protein levels were _log2 transformed, then scaled to the mean and standard deviation of the corresponding HD distribution in the training and testing datasets before fitting linear models.

Example 5: IFNPS Correlates with Global SLE Disease Activity (SLEDAI)

Scatterplots showing the correlation between IFNGS and SLEDAI, as well as the 4 protein expression profiles of type I IFN and SLEDAI of SLE patients are presented in Figure 6. The AUC for IFNGS and IFNPS was used to stratify SLE patients into those experiencing and not experiencing specific SLE symptoms ( Fig. 6 B). Scatterplots demonstrating the relationship between IFNGS and the 4 type I IFN expression profile proteins in non-lymphopenic and lymphopenic SLE patients are presented in Figure 6C.

Example 6: IFNPS Correlates with SLEDAI in SLE Patients with and without Lymphopenia

Correlations between IFNGS, SLEDAI, and 4 protein expression profiles of type I IFN and SLEDAI in non-lymphopenic and lymphopenic SLE patients were obtained as shown in Figure 6C.

All statistical analyzes were performed in R 3.1.1. Pairwise correlations were calculated using nonparametric Spearman correlation unless otherwise noted. Pairwise comparisons were calculated using the nonparametric Mann-Whitney U test method. The R package glmnet was used to establish the LASSO model.

In conclusion, in a cohort of 82 SLE patients and 48 healthy donors, it was found that the protein expression profile was higher compared to healthy donors for the majority of high IFNGS patients tested (49/55, 89%) and also in the case of a subset of patients tested with low IFNGS (7/27, 26%) (Fig. 5). The protein expression profile correlated with global disease activity (median SLEDAI score of 4 per cohort) in both lymphopenic and non-lymphopenic patients (Fig. 6). Significant associations with skin involvement, low levels of complement proteins, DNA autoantibodies, and thrombocytopenia were also observed. Thus, according to the results obtained by the present inventors, measurements of blood-derived protein levels can complement validated gene expression profiles for monitoring type I IFN activity.

Example 7: IFNPS Identifies a New Subgroup of Patients with Evidence of Type I IFN Activity

In patients with SLE, IFNGS shows a bimodal distribution and can be used to divide patients into two subgroups: those characterized by high IFNGS (high IFNGS) and those characterized by low levels (low IFNGS). The prevalence of IFNPS in HD was compared with SLE patients characterized by both high IFNGS and low IFNGS. IFNPS was found to be highly elevated in all patients with SLE. Of patients with SLE, 68% demonstrated an IFNPS greater than 2 standard deviations from the HD mean (AUC equal to 0.93, p less than 0.001). IFNPS was also significantly elevated in SLE patients with low IFNGS (AUC equal to 0.86, p less than 0.001), and a subgroup of 26% of SLE patients with low IFNGS was identified who similarly demonstrated an IFNPS greater than 2 standard deviations from the average value for HD (Fig. 3). Therefore, IFNPS can be used to identify a unique subgroup of patients with potentially high type I IFN activity and low levels of IFN-inducible genes in the blood.

Case Study 8: IFNPS and IFNGS Correlate with Global Disease Activity in SLE

The association between IFNPS and total disease activity in the training dataset was characterized to determine whether IFNPS correlated with overall disease activity. The Spearman correlation coefficient for IFNPS and IFNGS with the SLE Disease Activity Index (SLEDAI) was calculated and SLE disease activity was assessed in multiple organ systems. IFNPS was found to share a Spearman correlation coefficient of 0.45 (p equals 0.001) with SLEDAI, while IFNGS demonstrated a Spearman correlation coefficient of 0.19 (p equals 0.029) with SLEDAI, suggesting that that IFNPS may serve as a useful biomarker of overall disease in SLE (Figure 6A).

The prevalence of IFNPS and IFNGS was examined in patients positive and negative for each component of the SLEDAI. Both IFNGS and IFNPS were significantly increased in patients who had rash, low levels of complement proteins, and anti-dsDNA autoantibodies. IFNPS was also significantly elevated in SLE patients with thrombocytopenia, and IFNGS showed a similar trend. IFNPS also showed a numerical increase in SLE patients suffering from leukopenia (Fig. 6B). IFNPS is significantly correlated with SLEDAI in both SLE patients with leukopenia and SLE patients without leukopenia (p less than 0.05), providing further evidence that the expression profile reflects tissue biology that is insensitive to changes in blood composition (Fig. 6c).

To determine whether the results could be replicated in an independent cohort of patients with moderate to severe disease, the association between IFNPS and the SLEDAI composite score was assessed in both lymphopenic and non-lymphopenic patients in the MUSE cohort. In this cohort (), a significant association was found between IFNPS and hypocomplementemia, elevated anti-dsDNA antibodies, and leukopenia. In two patients with thrombocytopenia, IFNPS showed a positive correlation with the cutaneous lupus erythematosus prevalence and severity index (CLASI) (Spearman correlation coefficient 0.21, p less than 0.001), an alternative measure of skin disease activity that supports the association between IFNPS and skin lesions in SLE.

Thus, IFNPS reflects inflammation in multiple organ systems in patients with SLE, making IFNPS a useful biomarker of overall disease activity.

Example 9: IFNPS Associated with Type I IFN Signaling Pathway

Type I and type II IFNs play distinct roles in enhancing the immune response but induce largely overlapping transcriptional changes in cells. Moreover, type II IFNs are directly induced by type I IFNs. For these reasons, detecting differences between both types of responses during disease monitoring in humans is difficult. To confirm that the IFNPS identified by us reflects the biology associated with type I IFN, but not type II IFN, the correlation between IFNPS and the transcription of several components of the expression profiles of IFN-γ-inducible genes, IRF1, CXCL9, and SLAMF, was measured8,39. 41 and thus found no correlation between IFNPS and these genes in samples from patients with either SLE or myositis. In contrast, IFNPS correlated with all four components of the type I IFN-induced gene expression profile, IFI44L, IFI27, RSAD2, and IFI44, demonstrating that IFNPS is directly induced by type I IFN but not type II IFN.

To further evaluate whether IFNPS is specifically inducible by type I IFN, we examined whether IFNPS is suppressed by neutralizing IFNAR, a receptor required for type I IFN signaling. IFNPS was monitored in patients with SLE before and after treatment with anifrolumab, a monoclonal antibody that neutralizes IFNAR. The present inventors found that IFNPS was significantly reduced on days 169 and 365 compared to day 1 (p less than 0.001) in the group treated with 300 mg anifrolumab. In contrast, IFNPS did not show significant changes from baseline in the placebo group (p less than 0.05; Fig. 7a). Changes in IFNPS from day 1 to days 169 and 365 were also significant when compared between the anifrolumab 300 mg group and the placebo group (Fig. 7b). Therefore, after neutralization of IFNAR by anifrolumab, IFNPS was specifically suppressed, demonstrating that IFNPS reflects type I IFN-inducible biology.

Fig. 1. Circulating proteins provide data that are significantly different from those found when determining gene expression in whole blood. Spearman correlation density plots of pooled RBM and HGU133 Plus 2.0 measurements in 50 samples from HD and 143 samples from SLE patients. Analysis limited to analytes from RBM where 75% of measurements were above the LLOQ in a particular sample group. Somalogic measurement data collected using the new shortened protocol passes QC and is no longer elevated by anti-dsDNA antibodies. Boxplots showing the global signal distribution of 1129 protein measurements obtained using the standard Somalogic protocol (A) and the abbreviated protocol (B) with serum samples isolated from 143 samples obtained from SLE patients and 50 samples from HD. The minimum value, first quartile value, median value, third quartile value and maximum value in RFU per sample are indicated on each boxplot. The predominance of anti-dsDNA antibodies for each sample is shown in green in the graphs. C. Sample-specific median scaling factors used to normalize to the median of plates with samples obtained from SLE patients and samples from HD. Samples with a sample scaling factor less than 0.4, meaning the median RFU value is 2.5 times the median plate RFU value, failed quality control.

The shortened protocol improves correlation with Rules Based Medicine measurements. Density plots showing Spearman correlations of overall RBM and Somalogic measurements in 50 samples from HD, anti-dsDNA antibody negative for SLE, and anti-dsDNA antibody positive for SLE samples obtained using both standard and abbreviated protocols. Only analytes from RBM where 75% of measurements were above the LLOQ in a particular sample group were used for correlation analysis.

Most analytes show high reproducibility. A. Reproducibility of RFU values of samples analyzed in the same plate on the same day (A) and in different plates on different days (B) using an abbreviated protocol. Boxplots show the 10th and 90th percentiles, interquartile range, and median CV distributions from triplicate experiments with samples from HD, anti-dsDNA antibody-negative samples for SLE, and anti-dsDNA antibody-positive samples in regarding SLE.

Fig. 2. Identification of interferon-related protein expression profile (IFNPS). A. Venn diagram showing the selection of protein level measurements used for feature selection in LASSO regression. Somalogic measurements of 34 proteins demonstrated a Pearson correlation coefficient of greater than 0.3 compared with IFNGS and were known from in vitro or in vivo human experiments to be characterized by type I IFN-inducible gene expression. B. Mean Pearson correlation coefficient of type I IFN protein scores predicted after 10 iterations of 5-fold cross-validation with IFNGS varying the number of features entered into the LASSO regression model. The optimal value of λ was also selected through 10 iterations of 5-fold cross-validation. Feature selection was limited to proteins with positive independent associations with IFNGS. Proteins were scaled to HD mean and standard deviation before fitting the LASSO regression model. C. Regression coefficients of 4 protein expression profiles refitted to the expression profile of 21 IFNα/β genes with ordinary least squares regression. D. Scatterplot showing the correspondence between the 4 proteins of the type I IFN expression profile and IFNGS. R value calculated using the Pearson correlation coefficient.

Independent validation of IFNPS components using microchip and Rules Based Medicine (RBM). Validation of Somalogic level 4 protein measurement components of the type I IFN expression profile using independent platforms. For each expression profile component, pairwise Spearman correlations between Somalogic measurements and RBM protein level measurements or pairwise correlations between microarray-measured gene expression are indicated. All correlations were significant (p less than 0.001) except for the correlation between measurements of BLC protein levels using Somalogic and measurements of BLC gene expression performed using the HGU133 Plus 2.0 microarray.

Fig. 3. IFNPS increased compared to healthy donors for the majority of high IFNGS patients tested (89%), as well as for a subset of low IFNGS patients tested (26%). A Density plots showing the predominant expression profile of 21 IFNα/β genes in samples from SLE and HD patients. B. Expression profile of 4 type I IFN proteins in HD and SLE patients. C. Prevalence of IFNα/β gene expression profile in HD and SLE patients with low and high predominance of IFNα/β gene expression profile. D. Predominance of type I IFN-related protein expression profile in HD and SLE patients with low and high predominance of IFNα/β-related gene expression profile. Statistical comparisons within each group of SLE and HD patients were indicated by area under the curve (AUC) and p-value obtained using the Mann-Whitney U test.

Fig. 6. IFNPS correlates with global SLE disease activity (SLEDAI). Scatterplots showing the correlation between IFNGS and SLEDAI (A) and 4 protein expression profiles of type I IFN and SLEDAI in SLE patients. B. The AUC for IFNGS and IFNPS was used to stratify patients with SLE into those experiencing and not experiencing specific SLE symptoms. The threshold value for leukopenia is less than 3000 WBC/μl. P-values are reported using the Mann-Whitney U test (*** p less than 0.001, ** p less than 0.01, * p less than 0.05, p less than 0.10).

Fig. 6 continued: IFNPS correlates with SLEDAI in SLE patients with and without lymphopenia. C. Scatterplot showing the relationship between IFNGS and 4 type I IFN expression profile proteins in SLE non-lymphopenic and B. lymphopenic patients. The threshold value for leukopenia is less than 1000 lymphocytes/μl. Regression curve for both expression profiles fitted using ordinary least squares regression. The correlation coefficient and p-value were determined using the Spearman correlation coefficient.

Claims (8)

1. The use of a pharmaceutical composition for the treatment of systemic lupus erythematosus (SLE), myositis, scleroderma, lupus nephritis or cutaneous lupus erythematosus (CLE) in a subject, where the pharmaceutical composition contains a therapeutically effective amount of anifrolumab, and where the subject is identified as having an increased protein expression profile, associated with IFN (IFNPS), characterized by increased expression of EPHB2, BLC, LAG-3 and IP-10 proteins compared to the expression of EPHB2, BLC, LAG-3 and IP-10 proteins in a healthy donor. 2. Use according to claim 1, wherein increased IFNPS is characterized by the expression of EPHB2, BLC LAG-3 and IP-10 proteins compared to the average expression of EPHB2, BLC, LAG-3 and IP-10 proteins in a healthy donor. 3. Use according to claim 1 or 2, where the pharmaceutical composition contains 300 mg of anifrolumab. 4. The use of any of the preceding claims, where the use includes the administration of 300 mg of anifrolumab once every four weeks. 5. Use as claimed in any of the preceding claims, wherein the treatment suppresses elevated IFNPS in the subject. 6. Use of any of the preceding claims, wherein the treatment results in an improvement in the subject's SLE Disease Activity Index (SLEDAI). 7. Use of any of the preceding claims wherein the treatment results in an improvement in the cutaneous lupus erythematosus prevalence and severity index (CLASI) activity score in the subject. 8. Use as claimed in any of the preceding claims, wherein the subject is identified as a test patient with a low interferon gene expression profile (IFNGS).