HK40020002A - Diagnostic and therapeutic methods for irak4-mediated disorders and conditions - Google Patents

Abstract

The present invention provides diagnostic and therapeutic methods and compositions for treating a patient suffering from an interleukin-1 receptor-associated kinase 4 (IRAK4)-mediated disorder or condition, such as an immune disorder (e.g., systemic lupus erythematosus (SLE)) or an inflammatory disorder (e.g., asthma). The invention provides diagnostic methods of monitoring the response of a patient having an IRAK4-mediated disorder or condition to treatment including an IRAK4 pathway inhibitor, methods of identifying a patient having an IRAK4-mediated disorder or condition who may benefit from treatment including an IRAK4 pathway inhibitor, and methods of selecting a therapy for a patient having an IRAK4-mediated disorder or condition based on the expression level of one or more IRAK4 biomarkers (e.g., one or more genes set forth in Table 1). Related therapeutic methods and compositions (e.g., diagnostic kits) are also provided.

Description

Methods of diagnosis and treatment of IRAK 4-mediated conditions and disorders

Cross Reference to Related Applications

This application claims the benefit of U.S. provisional application No.62/521,299 filed on 2017, 6, 16, which is incorporated herein by reference in its entirety.

Sequence listing

This application contains a sequence listing, filed electronically in ASCII format, and incorporated by reference herein in its entirety. The ASCII copy was created at 14.6.2018 under the name 50474- "170 WO2_ Sequence _ Listing _6.14.18_ ST25, size 142,784 bytes.

Technical Field

The present invention relates to diagnostic and therapeutic methods for treating interleukin-1 receptor associated kinase 4(IRAK4) -mediated disorders or conditions (e.g., immune disorders (e.g., Systemic Lupus Erythematosus (SLE)) or inflammatory disorders (e.g., asthma)) using IRAK4 pathway inhibitors (e.g., IRAK4 small molecule inhibitors). Related compositions (e.g., diagnostic kits) are also provided.

Background

The interleukin-1 receptor associated kinase (IRAK) family consists of four family members IRAK1, IRAK2, IRAK3 (also known as IRAK-M) and IRAK 4. These proteins are characterized by a typical N-terminal death domain that mediates interaction with MyD88 family aptamer proteins, and a centrally located kinase domain. IRAK1 and IRAK4 have kinase activity, whereas IRAK2 and IRAK3 have no catalytic activity. Upon activation of its upstream cognate receptor, IRAK4 is thought to phosphorylate IRAK1, resulting in activation and autophosphorylation of IRAK1, and subsequent phosphorylation of downstream substrates. Hyperphosphorylation of IRAK1 directs its dissociation from the receptor complex, as well as its eventual ubiquitination and proteasomal degradation. Phosphorylation of downstream substrates (e.g., Pellino-2) ultimately leads to the activation of MAPKs (e.g., p38, c-Jun N-terminal kinase (JNK), and NF-kB), followed by the production of pro-inflammatory cytokines, chemokines, and destructive enzymes.

The role of IRAK4, particularly in the pathogenesis of innate immunity and autoimmune and inflammatory disorders, is increasingly recognized, see, e.g., Li et al PNAS.99(8): 5567:. beta. 5572,2002 and Flannery et al biochem. Pharm.80(12):1981-1991, 2010. IRAK4 unstable or null mutant patients exhibit increased susceptibility to gram-positive bacterial infections, although generally resistant to gram-negative bacterial, viral and fungal infections, similarly IRAK4 deficient mice have deficiencies in TLR and IL-1 mediated cytokine production, and exhibit increased AK to infections, IRAK4 pathways are thought to be involved in a variety of disorders and conditions, including IRAK-mediated signal transduction and related cytokine production, and the development of appropriate therapeutic approaches to treat IRAK-related disorders, including small populations of IRAK4, including the development of immune-related inhibitors, including small groups of immune related inhibitors, and immune proliferation inhibitors (12).

Disclosure of Invention

The present invention provides diagnostic methods, therapeutic methods, and kits for treating IRAK 4-mediated disorders or conditions (e.g., immune disorders and inflammatory disorders).

In a fourth aspect, the invention features a method of monitoring the response of a patient suffering from an interleukin-1 receptor-associated kinase 4 (IRAK) -mediated disorder or condition to treatment comprising an IRAK pathway inhibitor, the method comprising (a) determining the expression level of 0 or more of the genes listed in table 1 (i.e., CD, SOCS, AQP, CDKN1, GADD45, B4GALT, IL15, TNFAIP, SOCS, IL1, PFKFB, BCL2A, CXCL, CCL, GPR, C15orf, DRAM, CXCL, TNFAIP, CSRNP, PLSCR, CLEC4, sn, and ACSL) in a sample obtained from the patient at a time point after administration of a first dose of an IRAK pathway inhibitor, and (B) comparing the expression level of 1 or more of the genes listed in table 1 with a reference expression level, whereby the response of the patient to treatment comprising an IRAK pathway inhibitor is monitored in an embodiment 2, a embodiment 3 or more of the genes listed in table 1, 5, 15, or more of the genes listed in a, 5, 15, or more of the genes selected from the genes listed in table 1, 5, 15, 5, or more of the genes selected from the genes listed.

In embodiments, the expression level of or more genes listed in table 1 in a sample obtained from the patient is reduced relative to a reference expression level in 0 embodiments, the expression level of or more genes listed in table 1 is reduced at least about 0.5 fold relative to the reference expression level in embodiments, the expression level of 3 or more genes listed in table 1 is reduced at least about 1 fold relative to the reference expression level in embodiments, the expression level of or more genes listed in table 1 is reduced at least about 2 fold relative to the reference expression level in 632 embodiments 6342 6 embodiments, the expression level of or more genes listed in table 1 is reduced at least about 3 fold relative to the reference expression level in embodiments, 8 embodiments, the expression level of or more genes listed in table 1 is reduced at least about 4 fold relative to the reference expression level in embodiments, the expression level of or more genes listed in table 1 is reduced at least about 4 fold relative to the reference expression level in embodiments, the expression level of at least about 595 or more genes listed in 59465 embodiments, the patient is reduced by at least about expression level of the reference expression level of the inhibitor listed in 59465 or the reference expression level listed in 598 embodiments.

In a second aspect, the invention features a method of treating a patient having an IRAK-mediated disorder or condition with an IRAK pathway inhibitor, the method comprising (a) determining the expression level of 0 or more genes listed in table 1 (i.e., CD, SOCS, AQP, CDKN1, GADD45, B4GALT, IL15, TNFAIP, SOCS, IL1, PFKFB, BCL2A, CXCL, CCL, GPR, C15orf, DRAM, CXCL, tnfa, CSRNP, PLSCR, CLEC4, SAMSN, and ACSL) in a sample at a time point after administration of a first dose of an IRAK pathway inhibitor, at a second dose of an inhibitor, at least one embodiment of a second dose of a inhibitor, at least one embodiment of a gak 4 genes listed in table 1, at a second dose of a pathway inhibitor, at least one dose of a second dose of a pathway inhibitor, and at least one dose of a second dose of a, wherein the second dose of the second.

In embodiments of any of the preceding aspects, the reference expression level is (i) an expression level of or more genes listed in table 1 in a patient sample obtained prior to administration of the th dose of the IRAK4 pathway inhibitor, (ii) an expression level of or more genes listed in table 1 in the reference population, (iii) a pre-specified expression level of or more genes listed in table 1, (iv) an expression level of or more genes listed in table 1 in a sample obtained from the patient at a previous time point, wherein the previous time point was after administration of the th dose of the IRAK4 pathway inhibitor, or (v) an expression level of or more genes listed in table 1 in a sample obtained from the patient at a subsequent time point.

In a third aspect, the invention features a method of identifying a patient having an IRAK 4-mediated condition or disorder that can benefit from treatment with an IRAK4 pathway inhibitor, the method comprising determining the expression level of or more genes listed in table 1 in a sample obtained from the patient (i.e., CD38, SOCS3, AQP9, CDKN1A, GADD45B, B4GALT5, IL15RA, TNFAIP3, SOCS1, IL1RN, PFKFB RN, BCL2a RN, CXCL RN, CCL RN, GPR RN, plsc 15orf RN, DRAM RN, CXCL RN, TNFAIP RN, CSRNP RN, cr RN, CLEC4 RN, SAMSN RN, and ACSL RN), wherein the expression level of the one or more genes listed in the sample compared to a reference expression level is identified as a patient that can benefit from treatment with an IRAK4 pathway inhibitor.

In a fourth aspect, the invention features methods of selecting a therapy for a patient having an IRAK 4-mediated disorder or condition, the method comprising determining in a sample obtained from the patient the expression levels of or more genes listed in table 1 (i.e., CD38, SOCS3, AQP9, CDKN1A, GADD45B, B4GALT5, IL15RA, TNFAIP3, SOCS1, IL1RN, PFKFB RN, BCL2a RN, CXCL RN, CCL RN, GPR RN, C15orf RN, DRAM RN, CXCL RN, TNFAIP RN, CSRNP RN, PLSCR RN, CLEC4 RN, SAMSN RN, and ACSL RN), wherein the expression levels of the one or more genes listed in table 1 in the sample are increased as compared to a reference expression level, identifying the patient as a treatment-pathway inhibitor for the IRAK RN.

In some embodiments of the third or fourth aspects, the one or more genes listed in table 1 comprise 0 or more genes selected from CD, SOCS, AQP, CDKN1, GADD45, B4GALT, IL15, TNFAIP, SOCS, IL1, PFKFB, and BCL2A in some embodiments, the 2 or more genes listed in table 1 comprise 3 or more genes selected from CD, SOCS, AQP, CDKN1, GADD45, B4GALT, IL15, TNFAIP, SOCS, IL1, and PFKFB in some embodiments, the 5or more genes listed in table 1 comprise 6 or more genes selected from CD, SOCS, AQP, CDKN1, GADD45, B4GALT, IL15, TNFAIP, and SOCS in some embodiments, the 7, the 8 or more genes listed in table 1, the 5or more genes listed in table 1, the 7, the 8 or more genes listed in table 1, the 5or more embodiments comprise at least one or more genes listed in table 1,2, the 1, 5, the 1, the 5or more genes listed in some embodiments, 2, the 7, 2, the 7, 5, 2, the 3, 5, or more genes listed in some embodiments, or 5, 2, including at least one more embodiments, 2, or more, 2, or more, 2, more, 2, or 4, more, 2, more, or 5, more, 2, or 1,2, more, 2, or 1, more, 2, or 1, more, or more, or more, or 1, more, or more, more.

In a fifth aspect, the invention features a method of treating a patient having an IRAK-mediated disorder or condition, the method comprising administering to the patient an IRAK pathway inhibitor, wherein the expression level of one or more genes listed in table 1 in a sample obtained from the patient (i.e., CD, SOCS, AQP, CDKN1, GADD45, B4GALT, IL15, TNFAIP, SOCS, IL1, PFKFB, BCL2A, CXCL, CCL, GPR, C15orf, DRAM, CXCL, TNFAIP, CSRNP, PLSCR, CLEC4, cusn, and ACSL) has been determined prior to treatment is increased relative to a reference expression level in at least one embodiment of the genes listed in table 1, a multiple embodiment of the genes listed in table 1, or multiple embodiment of the genes listed in table 1, GADD4, IL15, tnfp, SOCS, IL1, pfb 2A multiple embodiment of the genes listed in table 1, a multiple embodiment of the table 1, a multiple embodiment of the genes listed in table 1, a multiple embodiment of the genes listed in table 1, a multiple embodiment of the expression level listed in table 1, multiple embodiment of the multiple embodiments, a1, a, multiple embodiment of the genes listed in the multiple, a1, multiple embodiment of the expression level listed in the multiple embodiment of the multiple, multiple embodiment of the expression level listed in the multiple embodiment of the multiple, multiple embodiment of the multiple.

In embodiments of any of the third, fourth and fifth aspects, the reference expression level is (i) an expression level of or more genes listed in table 1 in the reference population or (ii) a pre-specified expression level of or more genes listed in table 1.

In embodiments of any of of the preceding aspects, the expression level of or more genes listed in table 1 in the reference population is the median expression level of or more genes listed in table 1 in the reference population.

In embodiments of any of the preceding aspects, the sample obtained from the patient is a tissue sample, a whole blood sample, a plasma sample, or a serum sample in embodiments, the sample obtained from the patient is a blood sample (e.g., a whole blood sample).

In embodiments of any of the preceding aspects, the expression level is an mRNA expression level in embodiments the mRNA expression level is determined by RNA-Seq, qPCR, microarray analysis, gene expression profiling, serial analysis of gene expression, or whole genome sequencing in embodiments the mRNA expression level is determined by qPCR in other embodiments of any of the preceding aspects, the expression level is a protein expression level.

In embodiments of any of the preceding aspects, the IRAK 4-mediated disorder or condition is selected from the group consisting of an immune disorder, an inflammatory disorder, a fibrotic disorder, an eosinophilic disorder, an infection, pain, a central nervous system disorder, acute kidney injury, a chronic kidney disorder, endometriosis, a non-alcoholic fatty liver disease, metabolic syndrome, and obesity in embodiments the immune disorder is lupus, asthma, atopic dermatitis, rheumatoid arthritis, Inflammatory Bowel Disease (IBD), crohn's disease, or ulcerative colitis in embodiments the inflammatory disorder is lupus, asthma, atopic dermatitis, rheumatoid arthritis, Inflammatory Bowel Disease (IBD), crohn's disease, or ulcerative colitis in embodiments the lupus is Systemic Lupus Erythematosus (SLE) in embodiments the lupus is lupus nephritis.

In embodiments of any one of items in the foregoing aspects, the IRAK4 pathway inhibitor is an IRAK4 inhibitor, an IRAK1 inhibitor, a toll-like receptor (TLR) inhibitor, an interleukin-1 receptor (IL-1R) inhibitor, an interleukin-33 receptor (IL-33R) inhibitor, or an inhibitor of myeloid differentiation major response gene 88(MyD88) in embodiments, an IRAK4 pathway inhibitor is an IRAK4 inhibitor in embodiments, an IRAK pathway inhibitor is a TLR inhibitor in embodiments, a TLR inhibitor, or an inhibitor of both TLR and in embodiments, an ak inhibitor is a TLR inhibitor in embodiments, an TLR inhibitor in a small TLR embodiment, an inhibitor of TLR is an inhibitor of a TLR .

In embodiments of any of the preceding aspects, the method further comprises step of administering to the patient an additional therapeutic agent in embodiments , the additional therapeutic agent is a corticosteroid, a non-steroidal anti-inflammatory drug (NSAID), chloroquine, hydroxychloroquineCyclosporine, azathioprine, methotrexate, mycophenolate mofetilOr cyclophosphamideIn some embodiments of , the IRAK4 pathway inhibitor and the additional therapeutic agent are co-administered in some embodiments of , the IRAK4 pathway inhibitor and the additional therapeutic agent are administered sequentially.

In another aspect, the invention features a kit for identifying a patient having an IRAK-mediated disorder or condition that may benefit from treatment with an IRAK pathway inhibitor, the kit comprising (a) a polypeptide or polynucleotide capable of determining the expression level of 0 or more of the genes listed in table 1 (i.e., CD, SOCS, AQP, CDKN1, GADD45, B4GALT, IL15, TNFAIP, SOCS, IL1, PFKFB, BCL2A, CXCL, CCL, GPR, C15orf, DRAM, CXCL, tnfp, CSRNP, PLSCR, CLEC4, gsn, and ACSL), and (B) instructions for using the polypeptide or polynucleotide to identify a patient having an IRAK-mediated disorder or condition that may benefit from treatment with an IRAK pathway inhibitor, in an embodiment 1,2 or more of the genes listed in table 1, SOCS, aqcs, aqdd, 1, GADD, or more of the genes listed in table 1, afcs, GADD4, afp, gab 5, gab, gac 4, or 5, or more of the genes listed in table 1, 5, or more of the genes selected from the table, C1, gab, 5, C, g, B, C, and g, C, B, C, B, C, B, C, and g, C, B, or C, B, C, and g, B, C, B, C, and g, C, B, C, B, C, B, and C, B, p, C, p, C, and p, C, B, C, B, C, p, and p, C, B, C, p, B, and p, p.

Drawings

Figure 1A is a heatmap showing a significant reduction in the induction of the TLR7/8 stimulator R848 (resiquimod) in whole blood of IRAK 4-deficient patients versus 285 genes from the microarray dataset for GEO accession GSE25742 (Alsina et al nat. immunol.15:1134-42,2014) compared to healthy patient controls (false discovery rate (FDR) < 0.05; Fold Change (FC) > 1.25).

FIG. 1B shows IRAK4 compared to R848-treated healthy patient controls^-/-And MyD88^-/-R848 (resiquimod) showed a relative signature score for 285 genes in patients that induced significantly lower.

FIG. 2 is a heat map showing IRAK4 compared to healthy patients^-/-Patients failed to upregulate type I IFNs and other TLR regulated genes in their response to R848.

FIG. 3 is a series of graphs showing three of the 44 genes (IL1RN, CLEC4E and SMSN1) p < 0.05; FC >1.2 identified as differentially upregulated in Systemic Lupus Erythematosus (SLE) patients from two extra-renal groups (university of Michigan group and ROSE phase II study group) compared to the corresponding group of healthy patients.

Fig. 4 is a series of graphs showing that IRAK4 kinase-deleted (IRAK4 kinase-dead) (KD) mice display significantly impaired IRAK4 pathway biomarker genes induced by R848 in bone marrow-derived macrophages (BMDM) compared to IRAK4 wild-type mice (CXCL 10 and CD38 are shown).

Fig. 5 shows that R848-induced IFN β 1 expression (extended) was significantly reduced in IRAK4KD mice compared to IRAK4 wild-type mouse macrophages (p ═ 0.02).

FIG. 6 is a table showing human IRAK4 compared to healthy and wild-type controls, respectively^-/-All 24 identified IRAK4 pathway biomarker genes and their respective expression levels following R848 induction in whole blood (left column) and IRAK4KD mouse macrophages (middle column).The right column shows the relative expression levels of each IRAK4 biomarker in SLE patients relative to healthy patient controls.

FIG. 7A shows that the induction of the expression level of IFN regulated gene OAS1A by R848 tends to be reduced in IRAK4KD mice compared to IRAK4 wild type mice (p < 0.15).

FIG. 7B shows that the induction of the expression level of IFN regulated gene OAS2 by R848 tends to be reduced in IRAK4KD mice compared to IRAK4 wild type mice (p < 0.15).

Figure 7C shows that the induction of the expression level of IFN regulated gene IFIT1 by R848 tends to be reduced (p <0.15) in IRAK4KD mice compared to IRAK4 wild type mice.

FIG. 7D shows that the induction of the expression level of the IFN regulated gene IFNA5 by R848 tends to be reduced in IRAK4KD mice compared to IRAK4 wild type mice (p < 0.15).

Figure 7E shows that the induction of the expression level of the IFN regulated gene MX1 by R848 tends to be reduced (p <0.15) in IRAK4KD mice compared to IRAK4 wild type mice.

FIG. 8 is a table showing the results of dose escalation experiments with and without R848 stimulation in human whole blood samples using two different IRAK4 small molecule inhibitors G03074387(G-4387) (BMS) and G03081557(G-1557) (Pfizer). Such IRAK4 biomarker genes that were shown to be dose-dependent downregulated by testing IRAK4 small molecule inhibitors were identified as "Y" in at least two of the three tested human donor samples.

Figure 9 is a series of graphs showing the percent reduction in expression of the first 9 IRAK4 biomarker genes that were dose-dependently down-regulated by two IRAK4 small molecule inhibitors, G-4387 and G-1557, the corresponding p-values are also shown.

Fig. 10A is a heat map showing the correlation coefficients for 12 IRAK4 biomarker genes represented as determined from SLE patient blood samples (whole blood samples) from the ROSE phase II study group described herein.

Fig. 10B is a heat map showing correlation coefficients for 12 IRAK4 biomarker genes represented as determined from SLE patient blood samples (PBMC samples) of the university of michigan group described herein.

Detailed Description

I. Introduction to the design reside in

The present invention is based, at least in part, on the discovery that the expression levels of specific IRAK4 pathway genes (e.g., CD4, SOCS 4, AQP 4, CDKN 14, GADD45 4, B4GALT 4, IL15 4, TNFAIP 4, SOCS 4, IL 14, PFKFB 4, BCL2A 4, CXCL 4, CCL 4, GPR 4, C15orf4, DRAM 4, CXCL 4, TNFAIP 4, CSRNP 4, CR4, CLEC 44, SAMSN 4, and ACSL 4) can be used as a biomarker (e.g., a prognostic biomarker and a predictive biomarker) or a predictive biomarker for a method of treating a patient suffering from an IRAK4 or a predictive response to a treatment of a disease or treatment pathway for a patient that would benefit from the IRAK4, including a method of diagnosing IRAK4, or predicting the response to a treatment of a patient suffering from an IRAK 4.

II definition

It is to be understood that the aspects and embodiments of the invention described herein include "comprising," "consisting of," and "consisting essentially of" the aspects and embodiments as used herein, the singular forms " (a)", " (an)" and "the" include plural references unless otherwise indicated.

As used herein, the term "about" refers to the usual error range for individual values as would be readily known to one skilled in the art. Reference herein to "about" a value or parameter includes (and describes) embodiments that are directed to that value or parameter itself. For example, a description referring to "about X" includes a description of "X".

The term "IRAK 4 pathway inhibitor" refers to a molecule that reduces, blocks, inhibits, eliminates, or interferes with signal transduction throughout the pathway in which IRAK4 functions in some embodiments of , an IRAK4 pathway inhibitor may inhibit the activity of or more proteins involved in the activation of IRAK4 signaling in some embodiments of , an IRAK4 signaling inhibitor may activate the activity of or more proteins involved in the inhibition of IRAK4 signaling in some embodiments an IRAK4 pathway inhibitor includes, but is not limited to, an IRAK4 inhibitor, an IRAK1 inhibitor, a toll-like receptor (TLR) inhibitor, an interleukin-1 receptor (IL-1R) inhibitor, an interleukin-33 receptor (IL-33R) inhibitor, or a myeloid differentiation primary response gene 88(MyD88) inhibitor.

The term "inhibitor of IRAK 4" or "antagonist of IRAK 4" refers to a molecule that reduces, blocks, inhibits, abrogates, or interferes with the activation or function of IRAK 4. in specific embodiments, the binding affinity (dissociation constant) of an IRAK4 inhibitor to IRAK4 is about 1,000nM or less. in another embodiments, the binding affinity of an IRAK4 inhibitor to IRAK4 is about 100nM or less. in another 0 embodiments, the binding affinity of an IRAK4 inhibitor to IRAK4 is about 50nM or less. in another embodiments, the binding affinity of an IRAK4 inhibitor to IRAK4 is about 10nM or less. in another embodiments, the binding affinity of an IRAK4 inhibitor to IRAK4 is about 1nM or less. in 4 specific embodiments, an IRAK4 inhibitor to inhibit the signal transduction of IRAK4 or less of IRAK4, or of an IRAK4, or a 4 nM signal transduction of an IRAK4 or a 4, or a 4 nM signal of an IRAK4 or a 4 signal of the other 4 or a smaller signal of the IRAK4 signal of the IRAK inhibitor is inhibited in another 4 or a 4 nM signal of the other 4 signal transduction embodiment.

The term "inhibitor of IRAK 1" or "antagonist of IRAK 1" refers to a molecule that reduces, blocks, inhibits, abrogates, or interferes with the activation or function of IRAK 1. in specific embodiments, the binding affinity (dissociation constant) of an IRAK1 inhibitor to IRAK1 is about 1,000nM or less. in another embodiments, the binding affinity of an IRAK1 inhibitor to IRAK1 is about 100nM or less. in another 0 embodiments, the binding affinity of an IRAK1 inhibitor to IRAK1 is about 50nM or less. in another embodiments, the binding affinity of an IRAK1 inhibitor to IRAK1 is about 10nM or less. in another embodiments, the binding affinity of an IRAK1 inhibitor to IRAK1 is about 1nM or less. in 1 specific embodiments, an IRAK1 inhibitor to inhibit the signal transduction of IRAK1 or less of IRAK1, or of an IRAK1, or a 1nM signal transduction of an IRAK1 or a1, or a 1nM signal of an IRAK1 or a1 signal of the other 1 or a smaller signal of the IRAK1 signal of the IRAK inhibitor is inhibited in another 1 or a 1nM signal of the other 1 signal transduction embodiment.

The term "toll-like receptor inhibitor", "toll-like receptor antagonist", "TLR inhibitor" or "TLR antagonist" refers to a molecule that reduces, blocks, inhibits, eliminates or interferes with TLR (e.g., TLR7, TLR8, TLR9, TLR1, TLR2, TLR4, TLR5, TLR6 and/or TLR10) activation or function in specific embodiments the binding affinity (dissociation constant) of the TLR inhibitor to TLR is about 1,000nM or less in another embodiments the binding affinity of the TLR inhibitor to TLR is about 100nM or less in another specific embodiments the binding affinity of the TLR inhibitor to TLR is about 50nM or less in another 1 embodiments the binding affinity of the TLR inhibitor to TLR is about 10nM or less in another 1 embodiment the binding affinity of the TLR inhibitor to TLR is about 1nM or less in another 639 embodiment the binding affinity of the TLR inhibitor to TLR is about 1nM or less in another embodiment the TLR 842 embodiment the TLR inhibitor inhibits signaling of TLR 72 nM or less in another or 8658 IC signaling in another embodiment the TLR 3655 nM or 869 embodiment the TLR 3655 nM inhibitor inhibits signaling in another embodiment the TLR 50nM or less signaling in another or less signaling in another embodiment.

The term "interleukin-1 receptor inhibitor", "interleukin-1 receptor antagonist", "IL-1R inhibitor" or "IL-1R antagonist" refers to a molecule that reduces, blocks, inhibits, eliminates or interferes with IL-1R activation or function in specific embodiments, the IL-1R inhibitor has a binding affinity (dissociation constant) for IL-1R of about 1,000nM or less in another embodiments, the IL-1R inhibitor has a binding affinity for IL-1R of about 100nM or less in another 0 embodiments, the IL-1R inhibitor has a binding affinity for IL-1R of about 50nM or less in another embodiments, the IL-1R inhibitor has a binding affinity for IL-1R of about 10nM or less in another embodiments, the IL-1R inhibitor has a binding affinity for IL-1R of about 1nM in another embodiments, the IL-1R inhibitor has a binding affinity for IL-1R of about 1nM or less in another 1nM 1 or less in another embodiments, the IL-1R inhibitor inhibits signaling by IL-1R inhibitor in another 68550 nM, or less than in another embodiment, the IL-1R inhibitor inhibits signaling by IL-1R signal transduction in another 6851R inhibitor, IC-1 nM, or less than in another 68550 nM, the other embodiments, the IL-1R inhibitor inhibits signaling in another 68550 nM, the IL-1R inhibitor of about 1R inhibitor in another 5 embodiment, the IL-1R inhibitor of about 1nM or less than the IL-1R inhibitor in another 600 embodiment, the IL-1R inhibitor inhibits signaling in another 6858 embodiment, the IL-1R inhibitor inhibits signaling in the IL-1R inhibitor of about 1R inhibitor of the IL-1R inhibitor of about 1nM or less than the IL-1R inhibitor of about.

The term "interleukin-33 receptor inhibitor", "interleukin-33 receptor antagonist", "IL-33R inhibitor" or "IL-33R antagonist" refers to a molecule that reduces, blocks, inhibits, eliminates or interferes with IL-33R activation or function in specific embodiments, the IL-33R inhibitor has a binding affinity (dissociation constant) for IL-33R of about 1000nM or less in another embodiments, the IL-33R inhibitor has a binding affinity for IL-33R of about 100nM or less in another 0 embodiments, the IL-33R inhibitor has a binding affinity for IL-33R of about 50nM or less in another embodiments, the IL-33R inhibitor has a binding affinity for IL-33R of about 10nM or less in another embodiments, the IL-33R inhibitor has a binding affinity for IL-33R of about 1nM or less in another embodiments, the IL-33R inhibitor has a binding affinity for IL-33R of about 1nM or less in another embodiments, the IL-33R inhibitor inhibits signaling by IL-33R inhibitor in IC 6333R 33 nM or IC 31, IC 42, IC 33R inhibitor inhibits signaling in another embodiment, IL-33R, IL-33R inhibitor, IC 31, or IC 33R 75 IC 31, or IC 31, IL-33R 75 IC7, or less in another embodiment, IL-33R 75 IC 42, IL-33R 75 IC7, IL-33R signal transduction, or IL-33R 75 IC 42, or less in another embodiment, IL-33R signal transduction inhibitors.

The term "inhibitor of a myeloid differentiation primary response gene 88", "antagonist of a myeloid differentiation primary response gene 88", "inhibitor of MyD 88", or "antagonist of MyD 88" refers to a molecule that reduces, blocks, inhibits, eliminates, or interferes with activation or function of MyD 88. in particular embodiments , the binding affinity (dissociation constant) of a MyD88 inhibitor for MyD88 is about 1,000nM or less. in other embodiments, the binding affinity of a MyD88 inhibitor for MyD88 is about 100nM or less. in other 0 embodiments, the binding affinity of a MyD88 inhibitor for MyD88 is about 50nM or less. in other embodiments, the binding affinity of a MyD88 inhibitor for MyD88 is about 10nM or less. in other embodiments, the binding affinity of a MyD88 inhibitor for MyD88 nM or less inhibits MyD88 nM or less signals in other embodiments of MyD88 nM or MyD88 nM signals in other embodiments, the MyD88 nM or less of MyD88 nM signal transduction inhibitor in other embodiments.

The term "CD 38" refers to cluster of differentiation 38 and includes homologs, mutations, and isoforms thereof. CD38 is also known in the art as ADPRC 1. The term includes unprocessed, full-length CD38, as well as any form of CD38 that is processed in a cell. The term includes naturally occurring variants (e.g., splice variants or allelic variants) of CD 38. The term includes, for example, the CD38 gene of human CD38, mRNA sequences (e.g., SEQ ID NO: 1; GenBank accession No. NM — 001775.3), and amino acid sequences of human CD38 (e.g., SEQ ID NO: 2; UniProtKB accession No. P28907), as well as CD38 DNA, mRNA, and amino acid sequences from any other vertebrate source, including mammals, such as primates and rodents (e.g., mice and rats).

The term "SOCS 3" refers to an inhibitor of cytokine signaling 3 and includes homologs, mutations, and isoforms thereof. SOCS3 is also known in the art as cytokine-induced SH2 protein 3(CIS3), STAT-induced STAT inhibitor 3(SSI3), and ATOD 4. The term includes unprocessed, full-length SOCS3, as well as any form of SOCS3 that is produced by processing in a cell. The term includes naturally occurring variants (e.g., splice variants or allelic variants) of SOCS 3. The term includes, for example, the SOCS3 gene of human SOCS3, the mRNA sequence (e.g., SEQ ID NO: 3; GenBank accession NM-003955.4) and the amino acid sequence of human SOCS3 (e.g., SEQ ID NO: 4; UniProtKB accession O14543), as well as SOCS3 DNA, mRNA and amino acid sequences from any other vertebrate source, including mammals, such as primates and rodents (e.g., mice and rats).

The term "AQP 9" refers to aquaporin 9 and includes homologs, mutations, and isoforms thereof. AQP9 is also known in the art as aquaglyceroporin 9, HsT17287, T17287, and small solute channel 1(SSC 1). The term includes unprocessed, full-length AQP9, as well as any form of AQP9 that is processed in a cell. The term includes naturally occurring variants (e.g., splice variants or allelic variants) of AQP 9. The term includes, for example, the AQP9 gene, mRNA sequences (e.g., SEQ ID NO: 5; GenBank accession NM-020980.4) of human AQP9 and the amino acid sequences (e.g., SEQ ID NO: 6; UniProtKB accession O43315) of human AQP9 as well as AQP9 DNA, mRNA and amino acid sequences from any other vertebrate source, including mammals such as primates and rodents (e.g., mice and rats).

The term "CDKN 1A" refers to cyclin-dependent kinase inhibitor 1A, and includes homologues, mutations and isoforms thereof. CDKN1A is also known in the art as CDK interacting protein 1(CIP1), melanoma differentiation associated protein 6(MDA-6), or wild-type P53 activating fragment 1 (WAF-1). The term includes unprocessed, full-length CDKN1A, as well as any form of CDKN1A that is processed in a cell. The term includes naturally occurring variants (e.g., splice variants or allelic variants) of CDKN 1A. The term includes, for example, the CDKN1A gene of human CDKN1A, the mRNA sequence (e.g., SEQ ID NO: 7; GenBank accession No. NM-000389) and the amino acid sequence of human CDKN1A (e.g., SEQ ID NO: 8; UniProtKB accession No. P38936), as well as the CDKN1A DNA, mRNA and amino acid sequences from any other vertebrate source, including mammals, such as primates and rodents (e.g., mice and rats).

The term "GADD 45B" refers to growth arrest and DNA damage-inducing Beta, and includes homologues, mutations and isoforms thereof. GADD45B is also known in the art as the myeloid differentiating primary response protein MyD118(MYD 118). The term includes unprocessed, full-length GADD45B, as well as any form of GADD45B that is processed in a cell. The term includes naturally occurring variants (e.g., splice variants or allelic variants) of GADD 45B. The term includes, for example, the GADD45B gene of human GADD45B, the mRNA sequences (e.g., SEQ ID NO: 9; GenBank accession No. NM-015675), and the amino acid sequences of human GADD45B (e.g., SEQ ID NO: 10; and UniProtKB accession No. O75293), as well as GADD45B DNA, mRNA and amino acid sequences from any other vertebrate source, including mammals, such as primates and rodents (e.g., mice and rats).

The term "B4 GALT 5" refers to β -1, 4-galactosyltransferase 5 and includes homologs, mutations, and isoforms thereof B4GALT5 is also known in the art as UDP-galactose: β -N-acetylglucosamine the term includes unprocessed full-length B4GALT5, as well as any form of b4galt5 that is produced by processing in a cell the term includes naturally occurring variants (e.g., splice variants or allelic variants) of B4GALT5 the term includes, for example, the B4GALT5 gene of human B4GALT5, mRNA sequences (e.g., SEQ ID NO: 11; GenBank accession No. NM _004776), and amino acid sequences of human B4GALT5 (e.g., SEQ ID NO: 12; UniProtKB accession No. O43286), as well as B4GALT5 DNA, mRNA and amino acid sequences from any other vertebrate sources, including mammals such as primates and rodents (e.g., mice and rats).

The term "IL 15 RA" refers to interleukin-15 receptor subunit α, and includes homologs, mutations, and isoforms thereof IL15RA is also known in the art as cd215. the term includes unprocessed, full-length IL15RA, as well as any form of il15ra that is produced by processing in a cell. the term includes naturally occurring variants (e.g., splice variants or allelic variants) of IL15 RA. the term includes, for example, the IL15RA gene of human IL15RA, mRNA sequences (e.g., SEQ ID NO: 13; GenBank accession No. NM — 008358), and amino acid sequences of human IL15RA (e.g., SEQ ID NO: 14; UniProtKB accession No. Q13261), as well as IL15RA DNA, mRNA, and amino acid sequences from any other vertebrate source, including mammals, such as primates and rodents (e.g., mice and rats).

The term "TNFAIP 3" refers to TNF α -induced protein 3 and includes homologs, mutations, and isoforms thereof TNFAIP3 is also referred to in the art as a20, OTUD7C, or aisbl. the term includes unprocessed full-length TNFAIP3, as well as any form of TNFAIP3 that is engineered into the cell-the term includes naturally occurring variants (e.g., splice variants or allelic variants) of TNFAIP 3-the term includes, for example, the TNFAIP3 gene of human TNFAIP3, mRNA sequences (e.g., SEQ ID NO: 15; GenBank accession No. NM — 001270508), and amino acid sequences of human TNFAIP3 (e.g., SEQ ID NO: 16; uniprot accession No. P21580), as well as TNFAIP3 DNA, mRNA, and amino acid sequences from any other vertebrate source, including mammals such as rodents and rats (e.g., mice and rats).

The term "SOCS 1" refers to an inhibitor of cytokine signaling 1 and includes homologs, mutations, and isoforms thereof. SOCS1 is also known in the art as STAT-induced STAT inhibitor 1(SSI1), Tec interacting protein 3(TIP3), cytokine-induced SH2 protein 1(CISH1), or JAK binding protein. This term includes unprocessed, full-length SOCS1 as well as any form of SOCS1 that is processed in a cell. The term includes naturally occurring variants (e.g., splice variants or allelic variants) of SOCS 1. The term includes, for example, the SOCS1 gene of human SOCS1, the mRNA sequence (e.g., SEQ ID NO: 17; GenBank accession NM-003745) and the amino acid sequence of human SOCS1 (e.g., SEQ ID NO: 18; UniProtKB accession O15524) as well as SOCS1DNA, mRNA and amino acid sequences from any other vertebrate source, including mammals such as primates and rodents (e.g., mice and rats).

The term "IL 1 RN" refers to an interleukin 1 receptor antagonist and includes homologs, mutations, and isoforms thereof. IL1RN is also known in the art as Anakinra, IRAP, DIRA, or MVCD 4. The term includes unprocessed, full-length IL1RN, as well as any form of IL1RN that is processed in a cell. The term includes naturally occurring variants (e.g., splice variants or allelic variants) of IL1 RN. The term includes, for example, the IL1RN gene of human IL1RN, the mRNA sequence (e.g., SEQ ID NO: 19; GenBank accession NM-173842) and the amino acid sequence of human IL1RN (e.g., SEQ ID NO: 20; UniProtKB accession P18510), as well as IL1RN DNA, mRNA and amino acid sequences from any other vertebrate source, including mammals, such as primates and rodents (e.g., mice and rats).

The term "PFKFB 3" refers to fructose-2-phosphate kinase/fructose-2, 6-bisphosphatase 3 and includes homologues, mutations and isoforms thereof. PFKFB3 is also known in the art as IPFK2, PFK2 or iPFK-2. The term includes unprocessed full-length PFKFB3, as well as any form of PFKFB3 that is processed in a cell. The term includes naturally occurring variants (e.g., splice variants or allelic variants) of PFKFB 3. The term includes, for example, the PFKFB3 gene, mRNA sequences (e.g., SEQ ID NO: 21; GenBank accession No. NM — 004566) of human PFKFB3 and amino acid sequences of human PFKFB3 (e.g., SEQ ID NO: 22; UniProtKB accession No. Q16875) as well as PFKFB3 DNA, mRNA and amino acid sequences from any other vertebrate source, including mammals, such as primates and rodents (e.g., mice and rats).

The term "BCL 2a 1" refers to BCL 2-related protein a1, and includes homologs, mutations, and isoforms thereof. BCL2A1 is also known in the art as GRS, ACC1, ACC2, BFL1, ACC-1, ACC-2, HBPA1, or BCL2L 5. The term includes unprocessed, full-length BCL2a1, as well as any form of BCL2a1 that is processed in a cell. The term includes naturally occurring variants (e.g., splice variants or allelic variants) of BCL2a 1. The term includes, for example, the BCL2a1 gene, mRNA sequences (e.g., SEQ ID NO: 23; GenBank accession No. NM — 004049) of human BCL2a1, and amino acid sequences (e.g., SEQ ID NO: 24; UniProtKB accession No. Q16548) of human BCL2a1, as well as BCL2a 1DNA, mRNA, and amino acid sequences from any other vertebrate source, including mammals, such as primates and rodents (e.g., mice and rats).

The term "CXCL 10" refers to C-X-C motif chemokine ligand 10 and includes homologs, mutations, and isoforms thereof. CXCL10 is also known in the art as C7, IFI10, INP10, IP-10, crg-2, mob-1, SCYB10 or glP-10. The term includes unprocessed, full-length CXCL10, as well as any form of CXCL10 that is produced by processing in a cell. The term includes naturally occurring variants (e.g., splice variants or allelic variants) of CXCL 10. The term includes, for example, the CXCL10 gene of human CXCL10, mRNA sequences (e.g., SEQ ID NO: 25; GenBank accession No. NM _001565) and amino acid sequences of human CXCL10 (e.g., SEQ ID NO: 26; UniProtKB accession No. P02778), as well as CXCL10 DNA, mRNA and amino acid sequences from any other vertebrate source, including mammals, such as primates and rodents (e.g., mice and rats).

The term "CCL 8" refers to C-C motif chemokine ligand 8, and includes homologs, mutations, and isoforms thereof. CCL8 is also known in the art as HC14, MCP2, MCP-2, SCYA8, or SCYA 10. The term includes unprocessed full-length CCL8, as well as any form of CCL8 that is processed in a cell. The term includes naturally occurring variants (e.g., splice variants or allelic variants) of CCL 8. The term includes, for example, the CCL8 gene of human CCL8, mRNA sequences (e.g., SEQ ID NO: 27; GenBank accession No. NM _005623), and amino acid sequences of human CCL8 (e.g., SEQ ID NO: 28; UniProtKB accession No. P80075), as well as CCL8 DNA, mRNA, and amino acid sequences from any other vertebrate source, including mammals, such as primates and rodents (e.g., mice and rats).

The term "GPR 84" refers to G protein-coupled receptor 84 and includes homologs, mutations, and isoforms thereof. GPR84 is also known in the art as EX33 or GPCR 4. The term includes unprocessed, full length GPR84, as well as any form of GPR84 that is processed in a cell. The term includes naturally occurring variants (e.g., splice variants or allelic variants) of GPR 84. The term includes, for example, the GPR84 gene of human GPR84, mRNA sequences (e.g., SEQ ID NO: 29; GenBank accession No. NM — 020370), and amino acid sequences of human GPR84 (e.g., SEQ ID NO: 30; UniProtKB accession No. Q9NQS5), as well as GPR84 DNA, mRNA and amino acid sequences from any other vertebrate source, including mammals such as primates and rodents (e.g., mice and rats).

The term "C15 orf 48" refers to chromosome 15 open reading frame 48 and includes homologs, mutations, and isoforms thereof. C15orf48 is also known in the art as NMES1 or FOAP-11. The term includes unprocessed, full-length C15orf48, as well as any form of C15orf48 that is processed in a cell. The term includes naturally occurring variants (e.g., splice variants or allelic variants) of C15orf 48. The term includes, for example, the C15orf48 gene of human C15orf48, the mRNA sequence (e.g., SEQ ID NO: 31; GenBank accession No. NM-197955), and the amino acid sequence of human C15orf48 (e.g., SEQ ID NO: 32; UniProtKB accession No. Q9C002), as well as any other vertebrate-derived C15orf48 DNA, mRNA, and amino acid sequences, including mammals, such as primates and rodents (e.g., mice and rats).

The term "DRAM 1" refers to DNA damage-regulated autophagy modulator 1 and includes homologs, mutations, and isoforms thereof. DRAM1 is also referred to in the art as DRAM. The term includes unprocessed full-length DRAM1, as well as any form of DRAM1 that is processed in a cell. The term includes naturally occurring variants (e.g., splice variants or allelic variants) of DRAM 1. The term includes, for example, the DRAM1 gene of human DRAM1, the mRNA sequence (e.g., SEQ ID NO: 33; GenBank accession No. NM-018370), and the amino acid sequence of human DRAM1 (e.g., SEQ ID NO: 34; UniProtKB accession No. Q8N682), as well as DRAM 1DNA, mRNA and amino acid sequences from any other vertebrate source, including mammals, such as primates and rodents (e.g., mice and rats).

The term "CXCL 11" refers to C-X-C motif chemokine ligand 11, and includes homologs, mutations, and isoforms thereof. CXCL11 is also known in the art as IP9, H174, IP-9, b-R1, I-TAC, SCYB11 or SCYB 9B. The term includes unprocessed, full-length CXCL11 as well as any form of CXCL11 that is processed in a cell. The term includes naturally occurring variants (e.g., splice variants or allelic variants) of CXCL 11. The term includes, for example, the CXCL11 gene of human CXCL11, mRNA sequences (e.g., SEQ ID NO: 35; GenBank accession No. NM — 005409) and amino acid sequences of human CXCL11 (e.g., SEQ ID NO: 36; UniProtKB accession No. O14625), as well as CXCL11DNA, mRNA and amino acid sequences from any other vertebrate source, including mammals, such as primates and rodents (e.g., mice and rats).

The term "TNFAIP 6" refers to TNF α -induced protein 6 and includes homologs, mutations, and isoforms thereof TNFAIP6 is also referred to in the art as TSG6 or TSG-6 the term includes unprocessed full-length TNFAIP6, as well as any form of TNFAIP6 that is produced by processing in a cell the term includes naturally occurring variants (e.g., splice variants or allelic variants) of TNFAIP6 the term includes, for example, the TNFAIP6 gene of human TNFAIP6, mRNA sequences (e.g., SEQ ID NO: 37; GenBank accession No. NM — 007115), and amino acid sequences of human TNFAIP6 (e.g., SEQ ID NO: 38; UniProtKB accession No. P98066), as well as TNFAIP6 DNA, mRNA, and amino acid sequences from any other vertebrate source, including mammals, such as primates and rodents (e.g., mice and rats).

The term "CSRNP 1" refers to cysteine-and serine-rich nucleoprotein 1, and includes homologues, mutations and isoforms thereof. CSRNP1 is also known in the art as AXUD1, URAX1, TAIP-3, CSRNP-1, or FAM 130B. The term includes unprocessed full-length CSRNP1, as well as any form of CSRNP1 that is processed in a cell. The term includes naturally occurring variants (e.g., splice variants or allelic variants) of CSRNP 1. The term includes, for example, the CSRNP1 gene of human CSRNP1, mRNA sequences (e.g., SEQ ID NO: 39; GenBank accession No. NM-033027) and amino acid sequences of human CSRNP1 (e.g., SEQ ID NO: 40; UniProtKB accession No. Q96S65), as well as CSRNP1DNA, mRNA and amino acid sequences from any other vertebrate source, including mammals, such as primates and rodents (e.g., mice and rats).

The term "PLSCR 1" refers to phospholipid scrambler (scramblase)1 and includes homologues, mutations and isoforms thereof. PLSCR1 is also known in the art as MMTRA 1B. The term includes unprocessed full-length PLSCR1, as well as any form of PLSCR1 that results from processing in cells. The term includes naturally occurring variants (e.g., splice variants or allelic variants) of PLSCR 1. The term includes, for example, the PLSCR1 gene of human PLSCR1, mRNA sequences (e.g., SEQ ID NO: 41; GenBank accession No. NM — 021105), and amino acid sequences of human PLSCR1 (e.g., SEQ ID NO: 42; UniProtKB accession No. 015162), as well as PLSCR 1DNA, mRNA, and amino acid sequences from any other vertebrate source, including mammals, such as primates and rodents (e.g., mice and rats).

The term "CLEC 4E" refers to C-type lectin domain family 4 member E, and includes homologs, mutations, and isoforms thereof. CLEC4E is also known in the art as minor or CLECSF 9. The term includes unprocessed, full-length CLEC4E, as well as any form of CLEC4E that is processed in a cell. The term includes naturally occurring variants (e.g., splice variants or allelic variants) of CLEC 4E. The term includes, for example, the CLEC4E gene of human CLEC4E, the mRNA sequence (e.g., SEQ ID NO: 43; GenBank accession No. NM-014358) and the amino acid sequence of human CLEC4E (e.g., SEQ ID NO: 44; UniProtKB accession No. Q9ULY5), as well as CLEC4E DNA, mRNA and amino acid sequences from any other vertebrate source, including mammals, such as primates and rodents (e.g., mice and rats).

The term "SAMSN 1" refers to the SAM domain, SH3 domain and nuclear localization signal 1, and includes homologues, mutations and isoforms thereof. SAMSN1 is also known in the art as SLy2, HACS1, NASH1, SASH2, or SH3D 6B. This term includes unprocessed, full-length SAMSN1, as well as any form of SAMSN1 that is processed in a cell. The term includes naturally occurring variants (e.g., splice variants or allelic variants) of SAMSN 1. The term includes, for example, the SAMSN1 gene of human SAMSN1, the mRNA sequence (e.g., SEQ ID NO: 45; GenBank accession NM-022136) and the amino acid sequence of human SAMSN1 (e.g., SEQ ID NO: 46; UniProtKB accession Q9NSI8), as well as SAMSN1DNA, mRNA and amino acid sequences from any other vertebrate source, including mammals, such as primates and rodents (e.g., mice and rats).

The term "ACSL 1" refers to acyl-coa synthetase long chain family member 1, and includes homologs, mutations, and isoforms thereof. ACSL1 is also known in the art as Acs, Acas, FACS, Acasl, Facl2 or LACS 1. The term includes unprocessed, full-length ACSL1, as well as any form of ACSLI that is produced by processing in a cell. The term includes naturally occurring variants (e.g., splice variants or allelic variants) of ACSL 1. The term includes, for example, the ACSLI gene of human ACSL1, the mRNA sequence (e.g., SEQ ID NO: 47; GenBank accession No. NM — 001286708), and the amino acid sequence of human ACSL1 (e.g., SEQ ID NO: 48; UniProtKB accession No. P33121), as well as ACSL 1DNA, mRNA, and amino acid sequences from any other vertebrate source, including mammals, such as primates and rodents (e.g., mice and rats).

As used herein, the terms "patient," "individual," and "subject" are used interchangeably and refer to any single animal, more preferably a mammal (including, e.g., non-human animals, such as cats, dogs, horses, rabbits, zoo animals, cattle, pigs, sheep, and non-human primates) for which treatment is desired, hi certain embodiments, the patient herein is a human, the patient may be a human having, suspected of having, or at risk of having an IRAK 4-mediated condition or disorder (e.g., immune disorders, inflammatory disorders, fibrotic disorders, eosinophilic disorders, infections, pain, central nervous system disorders, acute kidney injury, chronic kidney disease, endometriosis, non-alcoholic fatty liver disease, metabolic syndrome, and obesity.) the patient may have been previously treated with an IRAK4 pathway inhibitor, other drugs, or have not been previously treated.

The term "antibody" is used herein in the most sense and includes a variety of antibody structures including, but not limited to, monoclonal antibodies, polyclonal antibodies, multispecific antibodies (e.g., bispecific antibodies), and antibody fragments, so long as they exhibit the desired antigen binding activity.

Thus, for example, a polynucleotide as defined herein includes, but is not limited to, single-and double-stranded DNA, DNA comprising single-and double-stranded regions, single-and double-stranded RNA, and RNA comprising single-and double-stranded regions, hybrid molecules comprising DNA and RNA, which may be single-stranded, or more typically double-stranded or comprise regions that are single-and double-stranded.

Other types of modifications include, for example, "caps", substitution or more of the naturally occurring nucleotides with analogs, internucleotide modifications, for example, those modifications with uncharged linkages (e.g., methyl phosphonates, phosphotriesters, phosphoramidates, carbamates, etc.) and charged linkages (e.g., phosphorothioates, phosphorodithioates, etc.), those modifications containing pendant moieties such as proteins (e.g., nucleases, toxins, antibodies, signal peptides, poly-L-lysine, etc.), those modifications with intercalators (e.g., acridine, psoralen, etc.), those modifications containing chelators (e.g., metals, radioactive metals, boron, oxidative metals, etc.), those modifications containing alkylators, those modifications with modified linkages (e.g., α iso-nucleotide modifications, and other modified nucleotide residues), which may be substituted with a heterocyclic sugar protecting group, such as a 2-phosphate residue, or a sugar protecting group, such as a sugar residue, a phosphate residue, a sugar residue, a phosphate residue, a sugarEsters substituted with P (O) S ("thioesters"), P (S) S ("dithioates"), (O) NR₂("amic acid ester"), P (O) R, P (O) OR', CO OR CH₂("methylal") wherein each R or R' is independently H or substituted or unsubstituted alkyl (1-20C), optionally containing ether (-O-) linkages, aryl, alkenyl, cycloalkyl, cycloalkenyl, or aralkyl (araldyl) not all linkages in a polynucleotide need be the same.

As used herein, "oligonucleotide" generally refers to a short single-stranded polynucleotide that is less than about 250 nucleotides in length (but not necessarily). The oligonucleotide may be synthetic. The terms "oligonucleotide" and "polynucleotide" are not mutually exclusive. The above description of polynucleotides applies equally and fully to oligonucleotides.

The term "primer" refers to a single-stranded polynucleotide that is capable of hybridizing to a nucleic acid and allowing polymerization of the complementary nucleic acid, typically by providing a free 3' -OH group.

The term "small molecule" refers to any molecule having a molecular weight of about 2000 daltons or less, preferably about 500 daltons or less.

The term "detecting" includes any means of detection, including direct and indirect detection.

As used herein, the term "biomarker" refers to a set of indicator molecules or molecules (e.g., predictive, diagnostic, and/or prognostic indicators) that can be detected in a sample, including, for example, CD38, SOCS3, AQP9, CDKN1A, GADD45B, B4GALT5, IL15RA, TNFAIP3, SOCS1, IL1RN, PFKFB3, BCL2a1, CXCL10, CCL 9, GPR84, C15orf48, DRAM1, CXCL11, TNFAIP6, CSRNP1, PLSCR1, CLEC4E, sn E, and acsl1. biomarkers can be predictive biomarkers and used as indicator biomarkers for susceptibility to treatment or benefit of a patient suffering from a particular disorder or condition (e.g., an IRAK E-mediated disorder or condition) and include, for example, but are not limited to, as, a polynucleotide, a post-translational, polynucleotide, or post-copy number, e.g., a polynucleotide, a post-translational, or post-copy number, e.g., a polynucleotide, a polypeptide, such as a polypeptide (e.g., a) or a post-samak E).

As used herein, an "amount" or "level" of a biomarker is a detectable level in a biological sample. These can be measured by methods known to those skilled in the art and disclosed herein.

The term "expression level" or "level of expression" generally refers to the amount of a biomarker in a biological sample. "expression" generally refers to the process of converting information (e.g., gene coding and/or epigenetic gene information) into structures that exist and operate in a cell. Thus, as used herein, "expression" may refer to transcription into a polynucleotide, translation into a polypeptide, or even polynucleotide and/or polypeptide modifications (e.g., post-translational modifications of a polypeptide). Transcribed polynucleotides, translated polypeptides, or fragments of polynucleotide and/or polypeptide modifications (e.g., post-translational modifications of polypeptides) should also be considered as expressed, whether they are derived from transcripts generated by alternative splicing or degraded transcripts, or from post-translational processing of polypeptides (e.g., by proteolysis). "expressed genes" include those genes that are transcribed into mRNA polynucleotides and then translated into polypeptides, as well as those genes that are transcribed into RNA but not translated into polypeptides (e.g., transport and ribosomal RNA).

By "increased expression", "increased expression level", "increased expression level" or "increased level" is meant increased expression or increased level of a biomarker in an individual relative to a control, such as the median expression level of the biomarker in or more individuals (e.g., healthy individuals), an internal control (e.g., housekeeping biomarkers), or a sample from a patient group/cohort, without a disorder or condition (e.g., IRAK 4-mediated disorder or condition).

"reduced expression," "reduced expression level," "reduced expression level," or "reduced level" refers to reduced expression or reduced level of a biomarker in a control, such as the median expression level of the biomarker in or more individuals (e.g., healthy individuals) without a disorder or condition (e.g., an IRAK 4-mediated disorder or condition), an internal control (e.g., housekeeping biomarker), or a sample from a patient group/cohort.

The term "housekeeping gene" refers herein to a gene or genome encoding a protein, the activity of which is essential for maintaining cell function, and is typically similarly present in all cell types.

As used herein, "amplification" generally refers to a method of producing multiple copies of a desired sequence, "multiple copies" refers to at least two copies, "copies" do not mean complete sequence complementarity or identity to a template sequence.

As used herein, "polymerase chain reaction" or "PCR" techniques generally refer to procedures in which minute amounts of a particular fragment of nucleic acid, RNA and/or DNA are amplified as described, for example, in U.S. Pat. No.4,683,195. typically, sequence information needs to be obtained from the end of or beyond the region of interest so that oligonucleotide primers can be designed that are identical or similar in sequence to the opposite strands of the template to be amplified.the 5' terminal nucleotides of both primers can be brought to the end of the amplification material PCR can be used to amplify a particular RNA sequence from total genomic DNA, a particular DNA sequence, and cDNA transcribed from total cellular RNA, phage or plasmid sequences and the like-see generally Mullis et al, Cold Spring Harbor Symp. Quant. biol.51:263(1987) and Erlich, editorial, PCR Technology, (Stockton, NY, 1989.) PCR is considered as used herein to be a nucleic acid reaction method for amplifying a test sample, but the use of the particular RNA polymerase to generate a particular nucleic acid fragment or nucleic acid fragment using the polymerase 6332 and other methods known methods to amplify nucleic acids, including the particular nucleic acid fragment or nucleic acid(s) as described herein.

The technique has been described in various publications including, for example, Cronin et al, am.J.Pathol.164(1):35-42(2004) and Ma et al, Cancer Cell 5: 607-.

The term "microarray" refers to an ordered arrangement of hybridizable array elements, preferably polynucleotide probes, on a substrate.

As used herein, the term "sample" refers to a composition obtained or derived from a subject (e.g., an individual of interest) that comprises cells and/or other molecular entities to be characterized and/or identified, e.g., based on physical, biochemical, chemical, and/or physiological characteristics. For example, the phrase "disease sample" and variants thereof refers to any sample obtained from a subject of interest that is expected or known to comprise the cell and/or molecular entity to be characterized. Samples include, but are not limited to, tissue samples, primary or cultured cells or cell lines, cell supernatants, cell lysates, platelets, serum, plasma, vitreous humor, lymph fluid, synovial fluid, follicular fluid, semen, amniotic fluid, milk, whole blood, blood-derived cells, urine, cerebrospinal fluid, saliva, sputum, tears, sweat, mucus, tumor lysates and tissue culture media, tissue extracts (e.g., homogenized tissue, tumor tissue, cell extracts, and combinations thereof).

"tissue sample" or "cell sample" refers to a collection of similar cells obtained from a tissue of a subject or individual. The source of the tissue or cell sample may be from a fresh, frozen and/or preserved organ, a tissue sample, a biopsy and/or an aspirated solid tissue; blood or any blood component, such as plasma; body fluids, such as cerebrospinal fluid, amniotic fluid, peritoneal fluid or interstitial fluid; cells at any stage in the subject's pregnancy or development. The tissue sample may also be primary or cultured cells or cell lines. Optionally, the tissue or cell sample is obtained from a diseased tissue/organ. For example, a tumor sample is a tissue sample obtained from a tumor or other cancerous tissue.

As used herein, "reference sample," "reference cell," "reference tissue," "control sample," "control cell," or "control tissue" refers to a sample, cell, tissue, standard, or level used for comparison purposes in embodiments, the reference level, reference sample, reference cell, reference tissue, control sample, control cell, or control tissue is obtained from a healthy and/or non-diseased site (e.g., tissue or cell) of the body of the same subject or individual — for example, the reference level, reference sample, reference cell, reference tissue, control sample, control cell, or control tissue can be healthy and/or non-diseased cells or tissue adjacent to diseased cells or tissue.

For purposes herein, a "portion" of a tissue sample refers to a single portion or piece of the tissue sample, e.g., a thin section of tissue or cells cut from the tissue sample. It is understood that multiple portions of a tissue sample may be obtained and analyzed, provided that it is understood that the same portion of the tissue sample may be analyzed at the morphological and molecular level, or that polypeptides (e.g., by immunohistochemistry) and/or polynucleotides (e.g., by in situ hybridization) may be analyzed.

For example, the second assay or protocol may be performed using the results of a th assay or protocol, and/or the results of a th assay or protocol may be used to determine whether the second assay or protocol should be performed.

Any endpoint that is indicated as beneficial to an individual may be used to assess an "individual response" or "response" including, but not limited to, (1) inhibition of progression, including slowing or complete remission, of an IRAK 4-mediated disorder or condition at , (2) remission, at , of or more symptoms associated with an IRAK 4-mediated disorder or condition, (6) increase or prolong survival, including overall survival and progression-free survival, and/or (7) reduction of mortality at a given time point after treatment.

The term "survival" means that the patient is still alive and includes overall survival as well as progression-free survival.

As used herein, "progression-free survival" or "PFS" refers to the length of time that a treated disease (e.g., an IRAK 4-mediated disorder or condition (e.g., an immune disorder (e.g., Systemic Lupus Erythematosus (SLE)) or an inflammatory disorder (e.g., asthma)) does not progress or worsen during and after treatment.

As used herein, "overall survival" or "OS" refers to the percentage of subjects likely to survive in group after a particular period of time (e.g., 6 months, 1 year, 2 years, 3 years, 4 years, 5 years, 10 years, 15 years, 20 years, or more than 20 years from the time of diagnosis or treatment).

By "effective response" to a drug-treated patient or by "responsiveness" of a patient and like phrases, is meant conferring clinical or therapeutic benefit to a patient at risk of having or suffering from an IRAK 4-mediated disorder or condition, such as an immune disorder (e.g., Systemic Lupus Erythematosus (SLE)) or an inflammatory disorder (e.g., asthma) in embodiments or more genes listed in table 1 (e.g., 1,2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, or all 24 genes) are used to identify a patient that has an increased likelihood of treatment relative to a patient that does not express or more genes listed in table 1 (e.g., 1,2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, or all 24 genes), the predicted response to a drug (e.g., including an increase in the patient's) the likelihood of treatment including the same treatment of the IRAK4, e.g., 2, 3, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 3, or all 24 genes listed in table 1, 6, or all of the treatment pathways listed in table 1, 6, including the patient.

A "disorder" is any condition that would benefit from treatment, including but not limited to chronic and acute disorders or diseases, including those pathological conditions that predispose a mammal to the disorder in question.

The term "pharmaceutical formulation" refers to a formulation in a form that allows the biological activity of the active ingredient contained therein to be effective and that does not contain other components that have unacceptable toxicity to the subject to which the formulation is administered.

By "pharmaceutically acceptable excipient" is meant an ingredient of a pharmaceutical formulation other than the active ingredient that is not toxic to the subject. Pharmaceutically acceptable excipients include, but are not limited to, buffers, carriers, stabilizers, or preservatives.

The term "pharmaceutically acceptable salt" refers to salts that are not biologically or otherwise undesirable. Pharmaceutically acceptable salts include acid and base addition salts. The phrase "pharmaceutically acceptable" means that the substance or composition must be chemically and/or toxicologically compatible with the other ingredients forming the formulation and/or the mammal being treated therewith.

The term "pharmaceutically acceptable acid addition salts" refers to those pharmaceutically acceptable salts formed with inorganic acids such as hydrochloric acid, hydrobromic acid, sulfuric acid, nitric acid, carbonic acid, phosphoric acid, and organic acids selected from aliphatic, alicyclic, aromatic, araliphatic, heterocyclic, carboxylic and sulfonic organic acids such as formic acid, acetic acid, propionic acid, glycolic acid, gluconic acid, lactic acid, pyruvic acid, oxalic acid, malic acid, maleic acid, malonic acid, succinic acid, fumaric acid, tartaric acid, citric acid, aspartic acid, ascorbic acid, glutamic acid, anthranilic acid, benzoic acid, cinnamic acid, mandelic acid, pamoic acid, phenylacetic acid, methanesulfonic acid "methanesulfonate", ethanesulfonic acid, p-toluenesulfonic acid, and salicylic acid.

The term "pharmaceutically acceptable base addition salts" denotes those pharmaceutically acceptable salts formed with organic or inorganic bases. Examples of acceptable inorganic bases include sodium, potassium, ammonium, calcium, magnesium, iron, zinc, copper, manganese, and aluminum salts. Salts derived from pharmaceutically acceptable organic non-toxic bases include salts of primary, secondary and tertiary amines, substituted amines (including naturally occurring substituted amines), salts of cyclic amines, and salts of basic ion exchange resins, such as isopropylamine, trimethylamine, diethylamine, triethylamine, tripropylamine, ethanolamine, 2-diethylaminoethanol, trimethylamine, dicyclohexylamine, lysine, arginine, histidine, caffeine, procaine, hydrabamine, choline, betaine, ethylenediamine, glucosamine, methylglucamine, theobromine, purine, piperazine, piperidine, N-ethylpiperidine, and polyamine resins.

As used herein, "treatment" (and grammatical variations thereof, such as "treating" or "treatment") refers to clinical intervention in an attempt to alter the natural course of disease in the individual being treated, and may be used to prevent or to effect prophylaxis or during clinical pathology desirable therapeutic effects include, but are not limited to, preventing the occurrence or recurrence of disease, alleviating symptoms, reducing any direct or indirect pathological consequences of the disorder, preventing metastasis, reducing the rate of disease progression, alleviating or alleviating the state of the disease, and alleviating or improving prognosis. in embodiments, an IRAK4 pathway inhibitor (e.g., an IRAK4 inhibitor, an IRAK1 inhibitor, a toll-like receptor (TLR) inhibitor, an interleukin-1 receptor (IL-1R) inhibitor, an interleukin-33 receptor (IL-33R) inhibitor, or a myeloid differentiation primary response gene 88(MyD88) inhibitor) may be used to delay the development of an IRAK 4-mediated disorder or to slow the development of an IRAK 4-mediated disorder or condition.

As used herein, "administration" refers to a method of administering to a subject (e.g., a patient) a certain dose of a compound (e.g., an IRAK4 pathway inhibitor, such as an IRAK4 inhibitor or antagonist) or a pharmaceutical composition (e.g., a pharmaceutical composition comprising an inhibitor or antagonist).

Thus, simultaneous administration includes dosing regimens that continue administration of the one or more agents after cessation of administration of the one or more other agents.

By "reduce or inhibit" is meant the ability to cause an overall decrease of 10%, 20%, 30%, 40%, 50%, 60%, 70%, 75%, 80%, 85%, 90%, 95% or more. Reduction or inhibition may refer to, for example, reduction or inhibition of the activity and/or functional level of a protein in the IRAK4 pathway (e.g., the level of signal transduction through the IRAK4 pathway). Additionally, reducing or inhibiting may refer to, for example, reducing or inhibiting a symptom of the condition or disorder being treated (e.g., an IRAK 4-mediated condition or disorder).

The term "package insert" is used to refer to instructions typically contained in commercial packages of therapeutic products that contain information regarding the indications, usage, dosage, administration, combination therapy, contraindications and/or warnings for use of such therapeutic products.

An "article of manufacture" is any product (e.g., a package or container) or kit comprising at least agents, e.g., a medicament for treating a disorder or condition (e.g., an IRAK 4-mediated disorder or condition) or a probe for specifically detecting a biomarker described herein (e.g., CD38, SOCS3, AQP9, CDKN1A, GADD45B, B4GALT5, IL15RA, TNFAIP3, SOCS1, IL1RN, PFKFB3, BCL2a1, CXCL10, CCL8, GPR84, C15orf48, DRAM1, CXCL1, TNFAIP 1, CSRNP1, PLSCR1, CLEC 41, SAMSN1, and/or ACSL 1).

The phrase "based on" as used herein refers to information about or more biomarkers for informing diagnostic decisions, treatment decisions, information provided on a package insert or marketing/push guidelines, etc.

Method III

A. Diagnostic methods based on IRAK4 pathway biomarker expression levels

The present invention provides diagnostic methods wherein IRAK4 pathway biomarkers identified herein are used as pharmacodynamic biomarkers.

Accordingly, the invention features a diagnostic method of monitoring a patient having an interleukin-1 receptor-associated kinase 4(IRAK4) -mediated disorder or condition for a response to treatment including an IRAK4 pathway inhibitor, the method including (a) determining, in a sample obtained from the patient at a time point after administration of a -th dose of an IRAK4 pathway inhibitor, an expression level of or more genes listed in table 1 below (e.g., 1,2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, or all 24 genes), and (b) comparing the expression level of or more genes listed in table 1 in the sample to a reference expression level, thereby monitoring the patient's response to treatment including an IRAK4 pathway inhibitor.

TABLE 1 IRAK4 pathway biomarker genes

Gene

Gene
	CD38
SOCS3
	AQP9
CDKN1A
	GADD45B
B4GALT5
	IL15RA
TNFAIP3
	SOCS1
IL1RN
	PFKFB3
BCL2A1
	CXCL10
CCL8
	GPR84
C15orf48
	DRAM1
CXCL11
	TNFAIP6
CSRNP1
	PLSCR1
CLEC4E
	SAMSN1
ACSL1

Thus, the patient's response to treatment with a therapeutic comprising an IRAK4 pathway inhibitor can be monitored by determining the expression level of any combination of 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, or 23 genes selected from the genes listed in table 1 in a sample obtained from the patient at a time point after administration of the th dose of the IRAK4 pathway inhibitor, and then comparing the expression level of the combination of genes to a reference expression level (e.g., the median expression level of the same combination of genes in a reference population of individuals).

In certain instances, the method comprises determining from a patient obtained sample at a time point after administration of a third dose of an IRAK pathway inhibitor, an expression level of one or more genes (e.g., 0 gene, two genes, three genes, four genes, five genes, six genes, seven genes, eight genes, nine genes, ten genes, or all twelve genes) selected from CD, SOCS, AQP, CDKN1, GADD45, B4GALT, IL15, TNFAIP, SOCS, IL1, PFKFB, and bcl2a 1. for example, in certain instances, the method comprises determining from a patient obtained sample at a time point after administration of a third dose of an IRAK pathway inhibitor, an expression level of one or more genes selected from CD, SOCS, AQP, GADD45, GADD4 genes, four genes, five genes, six genes, seven genes, eight genes, nine genes, ten genes, or all ten genes selected from CD, SOCS, aqcs, AQP, GADD 1, GADD4 genes, tnfp, GADD, tnfp, IL 4 genes, and all three genes selected from the patient obtained sample at a time point after administration of a particular dose of an IRAK pathway inhibitor.

In some cases at , the expression level of or more genes listed in table 1 is reduced in a sample obtained from the patient at a time point after administration of the IRAK4 pathway inhibitor at the -fold relative to the reference expression level, e.g., the expression level of or more genes listed in table 1 is reduced in some cases at about 1% or more (e.g., the expression level of about 5or more genes listed in table 1 is reduced in a sample obtained from the patient before administration of the IRAK4 pathway inhibitor at the -fold, about 3% or more, about 4% or more, about 5% or more, about 6% or more, about 7% or more, about 8% or more, about 9% or more, about 10% or more, about 11% or more, about 12% or more, about 13% or more, about 14% or more, about 15% or more, about 20% or more, about 9% or more, about 10% or more, about 5% or about 5% to about 5% or more, about 5% or about 5.5% or more, about 5.5 to about 5% or more, about 5% or more, about 5% or about 5, about 5 to about 5% or more, about 5% or more, about 5% or more, about 5 to about 5% or more, about 5% or more, about 5, or more, about 5% or more of the expression level of the sample obtained at a time point after administration, about 5 to about 0 to about 5, about 5% or more, about 5 to about 5, about 5% or more, about 5 to about 5, about 0 to about 5% or more, about 5 to about 5% or more, about 5 to about 5, about 5% or more, about 5 to about 5% or more, about 5 to about 5, about 5 to about 5, about 0 to about 5, about 5% or more, about 5 to about 5% or more, about 5 to about 5, about 5% or more, about 5% to about 5% or more, about 5 to about 5, about 5% or more, about 5, about.

In embodiments, reduced or decreased expression refers to an overall reduction in the level of a biomarker (e.g., a protein or nucleic acid (e.g., a gene or mRNA)) by any of about 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 95%, 96%, 97%, 98%, 99%, or more, as compared to a reference level, reference sample, reference cell, reference tissue, control sample, control cell, or control tissue, as detected by methods known in the standard art as described herein.

Thus, in cases, the method further step includes administering at least a second dose (e.g., , two, three, four, five, six, seven, eight, nine, or ten or more additional doses) of an IRAK4 pathway inhibitor to the patient whose expression level of or more genes listed in table 1 is reduced relative to a reference expression level.

In any of the preceding embodiments, the reference expression level can be (i) an expression level of or more genes listed in Table 1 in a sample obtained from the patient prior to administration of the dose of the IRAK4 pathway inhibitor, (ii) an expression level of or more genes listed in Table 1 in a reference population (e.g., a median expression level of or more genes listed in Table 1 in the reference population), (iii) a pre-specified expression level of or more genes listed in Table 1, (iv) an expression level of or more genes listed in Table 1 in a sample obtained from the patient at a previous time point, wherein the previous time point was after administration of the dose of the IRAK4 pathway inhibitor, or (v) an expression level of or more genes listed in Table 1 in a sample obtained from the patient at a subsequent time point.

The present invention provides diagnostic methods wherein IRAK4 pathway biomarkers identified herein are used as predictive biomarkers.

Accordingly, the invention features a diagnostic method of identifying a patient having an IRAK 4-mediated disorder or condition that can benefit from treatment comprising an IRAK4 pathway inhibitor, the method comprising determining expression levels of or more genes listed in table 1 (e.g., 1,2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, or all 24 genes) in a sample obtained from the patient, wherein an increase in expression levels of or more genes listed in table 1 in the sample as compared to a reference expression level identifies the patient as a patient that can benefit from treatment comprising an IRAK4 pathway inhibitor.

The invention also features a diagnostic method of selecting a therapy for a patient having an IRAK 4-mediated condition or disorder, the method comprising determining expression levels of or more genes listed in table 1 (e.g., 1,2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, or all 24 genes) in a sample obtained from the patient, wherein an increase in expression levels of or more genes listed in table 1 in the sample as compared to a reference expression level identifies the patient as a patient who may benefit from treatment including an IRAK4 pathway inhibitor.

In certain instances, a method of identifying or selecting a therapy for a patient may comprise determining the expression level of one or more genes (e.g., one gene, two genes, three genes, four genes, five genes, six genes, seven genes, eight genes, nine genes, ten genes, or all twelve genes) selected from CD, SOCS, AQP, CDKN1, GADD45, B4GALT, IL15, TNFAIP, SOCS, IL1, PFKFB, and BCL2A 1. for example, in certain instances, the method comprises determining the expression level of one or more genes (e.g., one gene, two genes, three genes, four genes, five genes, six genes, seven genes, eight genes, nine genes, ten genes, or all ten genes) selected from CD, SOCS, AQP, CDKN1, GADD45, GAB 4GALT, IL15, TNFAIP, SOCS, and PFBKS 1. the method may comprise determining the expression level of one or more genes selected from the group consisting of CD, SODD 45, SODD, GADD4 genes, seven genes, and all twelve genes, three genes, four genes, five genes, four genes, or all.

In certain instances, an increase in expression level of or more genes listed in table 1 (e.g., 1,2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, or all 24 genes) relative to a reference expression level, e.g., an increase in expression level of or more genes listed in table 1 in a reference population, e.g., a median expression level of or more genes listed in table 1 in a reference population, e.g., about 2% or more (e.g., about 2% or more, about 3% or more, about 4% or more, about 5% or more, about 6% or about 0% or about 5% or more of about 0% or about 5% or about 10% more of the reference expression of the reference population, about 6 or about 10% of the reference expression of the reference population, about 7, about 6, about 10 or about 10% or about 10 or about 7, about 7 or about 10% of the reference population, about 7 or about 10% of the reference population, about 7 or about 10% or about 7, about 10% or about 10% or about 10 or about 7, about 10 or about 0% or about 10 or about 0% or about 10 or about 0% of the reference population, about 0% or about 7 or about 0% of the reference population, about 7 or about 0% or about 7 or about 0% or about 7 or about 0% or about 10 or about 0% or about 10% or about 10 or about 0% or about 10% or about 0% or about 10% or about 7 or about 10% or about 10 or about 0% or about 10% or about 0% or about 10% or about 10% of the reference population of.

In certain embodiments, increased or increased expression refers to an increase in the expression level (amount) of a biomarker in a sample, wherein the increase is at least any of about 1.5x, 1.75x, 2x, 3x, 4x, 5x, 6x, 7x, 8x, 9x, 10x, 25x, 50x, 75x, or 100x reference levels, reference samples, reference cells, reference tissues, control samples, control cells, or expression levels (amounts) of the respective biomarker in control tissues embodiments, increased expression refers to an overall increase of greater than about 1.5 fold, about 1.75 fold, about 2 fold, about 2.25 fold, about 2.5 fold, about 2.75 fold, about 3.0 fold, or about 3.25 fold over a reference sample, reference cells, reference tissues, control cells, control tissues, or internal controls (e.g., housekeeping genes) in cases, expression levels of the biomarker in a patient relative to the reference levels listed in the patient, 5 expression methods include administering an inhibitor to the patient at least one of the steps of the IRAK.

In some embodiments , the reference expression level can be (i) an expression level of or more genes listed in Table 1 in the reference population (e.g., the median expression level of or more genes listed in Table 1 in the reference population) or (ii) a pre-specified expression level of or more genes listed in Table 1.

The diagnostic methods described above provide a convenient, effective, and potentially cost-effective means to obtain data and information that can be used to assess an appropriate or effective therapy for treating a patient. For example, the sample obtained from the patient may be a tissue sample, a whole blood sample, a plasma sample, or a serum sample. Patients may be sampled before and/or after treatment with an IRAK4 pathway inhibitor, and the samples may be examined by various in vitro assays to determine whether the patient is likely to benefit from treatment comprising an IRAK4 pathway inhibitor, such as an IRAK4 inhibitor, an IRAK1 inhibitor, a toll-like receptor (TLR) inhibitor, an interleukin-1 receptor (IL-1R) inhibitor, an interleukin-33 receptor (IL-33R) inhibitor, or an inhibitor of myeloid differentiation primary response gene 88(MyD 88).

In another aspect, the invention also provides a method for monitoring a patient's sensitivity to an IRAK4 pathway inhibitor, which method may be performed in a variety of assay formats, including assays that detect gene or protein expression levels and biochemical assays that detect appropriate activity, determining that expression or presence of such biomarkers in a patient sample may predict whether the patient is sensitive to a biological effect of an IRAK4 pathway inhibitor, median expression levels of or more genes in samples of a patient group/cohort tested for sensitivity to an IRAK4 pathway inhibitor, or median expression levels of or more genes in samples of a patient group/cohort having a particular IRAK 4-mediated disorder or condition, median expression levels of or more genes in samples of table 1 obtained from the patient at a time point after administration of a dose of an IRAK4 pathway inhibitor, i.e., the difference in the efficacy of the patient with the relevant treatment pathway 16, 19, 16, 19, 16, 9, 19, 16, 8, or 16 of the patient in the samples obtained from table 1.

In another aspect, the present invention provides methods of optimizing therapeutic efficacy for therapy of a patient having an IRAK 4-mediated disorder or condition, comprising detecting or more genes listed in table 1 in a sample obtained from the patient (e.g., 1,2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, or all 24 genes) comprising a decrease in the level of expression of an IRAK2 or more genes listed in table 1 in a sample obtained prior to administration of an IRAK4 pathway signaling inhibitor to the patient, (ii) a sample obtained from the patient after administration of an IRAK4 pathway signaling inhibitor to the patient, or (iii) a sample obtained from the patient before and after such treatment, a sample obtained from the patient after administration of an IRAK4 pathway inhibitor to the patient, a decrease in the sample listed in table 1 (e.g., 1,2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 15, 14, 15, or all of the patient may be treated for whom a response to an IRAK 6314, 16, or 16, including a treatment that the patient may be indicated by a treatment with a decrease in response to a treatment pathway or a treatment that the patient may be indicated by a treatment pathway or a treatment of an IRAK2 or a treatment pathway inhibitor, including a treatment that the patient.

In any of the methods described herein, the expression level of any combination of 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, or 23 genes selected from the genes listed in table 1 in a sample obtained from the patient can be determined.

In embodiments of the diagnostic methods described herein, the expression levels of two combinations of genes listed in table 1 can be determined, such as any of the exemplary combinations shown in table 2.

Table 2 exemplary two gene combinations for IRAK4 biomarkers

In embodiments of the diagnostic methods described herein, the expression levels of the three combinations of genes listed in table 1 can be determined, such as any of the exemplary combinations shown in table 3.

Table 3 exemplary three-gene combinations of IRAK4 biomarkers

In embodiments of the diagnostic methods described herein, the expression levels of the four combinations of genes listed in table 1 can be determined, such as any of the exemplary combinations shown in table 4.

Table 4 exemplary four gene combinations for IRAK4 biomarkers

In embodiments of the diagnostic methods described herein, the expression levels of the five combinations of genes listed in table 1 can be determined, such as any of the exemplary combinations shown in table 5.

Table 5 exemplary five gene combinations for IRAK4 biomarkers

In embodiments of the diagnostic methods described herein, the expression levels of the six combinations of genes listed in table 1 can be determined, such as any of the exemplary combinations shown in table 6.

Table 6 exemplary six gene combinations of IRAK4 biomarkers

In embodiments of the diagnostic methods described herein, the expression levels of the seven combinations of genes listed in table 1 can be determined, such as any of the exemplary combinations shown in table 7.

Table 7 exemplary seven gene combinations of IRAK4 biomarkers

In embodiments of the diagnostic methods described herein, the expression levels of the eight combinations of genes listed in table 1 can be determined, such as any of the exemplary combinations shown in table 8.

Table 8 exemplary eight gene combinations for IRAK4 biomarkers

The presence and/or expression levels (amounts) of IRAK4 pathway biomarkers described herein In a sample can be analyzed by a variety of methods, many of which are known In the art and understood by the skilled artisan, including, but not limited to, immunohistochemistry ("IHC"), western blot analysis, immunoprecipitation, molecular binding assays, enzyme-linked immunosorbent assays (ELISA), enzyme-linked immunosorbent assays (ELIFA), fluorescence activated cell sorting ("FACS"), massabray, proteomics, blood Based quantification assays (e.g., serum ELISA), biochemical enzyme activity assays, In situ hybridization, Fluorescence In Situ Hybridization (FISH), Southern analysis, Northern analysis, whole genome sequencing, Polymerase Chain Reaction (PCR) (including quantitative PCR)) and other amplification type detection methods, such as branched dna (branched dna), SISBA, TMA, etc.), RNA-Seq, microarray analysis, serial analysis of gene expression profiling and/or gene expression ("SAGE"), and any of a variety of gene expression profiling and/or gene expression In a variety of gene array analyses that can be performed by protein, gene and/or tissue array analysis, such as Southern analysis, dna sequencing, western Blotting, etc., for evaluation of products, e.g. 3, western Blotting, for example, western Blotting, western Blotting, etc., using a unit, typically for example, a multiple immunoblotting unit, a unit, see e.g. 3.

In any of the foregoing methods, the presence and/or level (amount) of expression of a biomarker (e.g., CD38, SOCS3, AQP9, CDKN1A, GADD45B, B4GALT5, IL15RA, TNFAIP3, SOCS1, IL1RN, PFKFB3, BCL2a1, CXCL10, CCL8, GPR84, C15orf48, DRAM1, CXCL11, TNFAIP6, CSRNP1, cr1, CLEC4E, SAMSN1, and/or ACSL1) can be a nucleic acid expression level in some cases , qPCR, RT-PCR, RNA-Seq, multiplex qPCR or RT-qPCR, microarray analysis, SAGE, massaay techniques, or in situ hybridization (e.g., FISH).

In certain instances, biomarkers (e.g., CD38, SOCS3, AQP9, CDKN1A, GADD45B, B4GALT5, IL15RA, TNFAIP3, SOCS1, IL1RN, PFKFB3, BCL2a1, CXCL10, CCL8, GPR84, C15orf48, DRAM 48, CXCL 48, TNFAIP 48, CSRNP 48, cr 48, CLEC4 48, sam 48, and/or ACSL 48) are expressed at levels of mRNA in a particular case, a biomarker (e.g., CD, RNA-Seq (e.g., whole transcriptome shotgun sequencing) using a secondary sequencing technique, a hybridization assay using a complementary DNA probe (e.g., using a probe labeled for one or more genes for a probe for a given gene in a particular case, a probe for a particular mRNA family of interest, such as a target mRNA, or a probe for a target mRNA, or a target mRNA can be detected by a solid-array-based on a solid-array-sample-probe amplification protocol such as a solid-array-sample, or a probe-based on-probe-amplification protocol, such as a solid-array-or a probe-based on-probe-amplification protocol that can be detected at a clinical-target sequence, such as a mRNA expression level that is determined by a target sequence that is an mRNA expression level that is increased in a mRNA expression level that is an mRNA expression or a clinical-specific for a mRNA expression test, or a target molecule, including a target molecule, or a target molecule, such as a target, or a target molecule, such as a target molecule, a target, or a target, such as a target, or a kit, including a kit.

In any of the foregoing methods, the presence and/or level (amount) of expression of a biomarker (e.g., CD38, SOCS3, AQP9, CDKN1A, GADD45B, B4GALT5, IL15RA, TNFAIP3, SOCS1, IL1RN, PFKFB3, BCL2a GPR 1, CXCL10, CCL8, CCL 84, C15orf48, DRAM1, CXCL11, TNFAIP6, CSRNP1, PLSCR1, CLEC4E, SAMSN1, and/or ACSL1) is measured by determining the level of protein expression of the biomarker. In certain instances, the method comprises contacting the biological sample with an antibody that specifically binds to a biomarker described herein under conditions that allow binding of the biomarker, and detecting whether a complex is formed between the antibody and the biomarker. Such methods may be in vitro or in vivo. Any method known in the art for measuring the expression level of a protein can be used. For example, in certain instances, the level of protein expression of a biomarker (e.g., CD38, SOCS3, AQP9, CDKN1A, GADD45B, B4GALT5, IL15RA, TNFAIP3, SOCS1, IL1RN, PFKFB3, BCL2a1, CXCL10, CCL8, GPR84, C15orf48, DRAM1, CXCL11, TNFAIP6, CSRNP1, cscr 1, CLEC4E, SAMSN1, and/or acpsl 1) is determined using a method selected from the group consisting of: flow cytometry (e.g., Fluorescence Activated Cell Sorting (FACS)^TM) Western blot, ELISA, ELIFA, immunoprecipitation, Immunohistochemistry (IHC), immunofluorescence, radioimmunoassay, dot blot, immunodetection methods, HPLC, surface plasmon resonance, spectroscopy, mass spectrometry, and HPLC.

In certain instances, a reference level, reference sample, reference cell, reference tissue, control sample, control cell, or control tissue is a single sample or a combination of multiple samples from the same subject or individual that are obtained at or more different time points than the test sample is obtained.

In certain embodiments, the reference level, reference sample, reference cell, reference tissue, control sample, control cell, or control tissue is a combination of multiple samples from or more healthy individuals who are not patients, hi certain embodiments, the reference level, reference sample, reference cell, reference tissue, control sample, control cell, or control tissue is a combination of multiple samples from or more individuals who are not patients or patients who have a disorder or condition (e.g., an IRAK 4-mediated disorder or condition), hi certain embodiments, the reference level, reference sample, reference cell, reference tissue, control sample, control cell, or control tissue is a pooled RNA sample from normal tissue or a pooled plasma or serum sample from or more individuals who are not patients, hi certain embodiments, the reference level, reference sample, reference cell, reference tissue, control sample, control cell, or control tissue is a pooled RNA sample from an IRAK 4-mediated disorder or condition (e.g., an inflammatory disorder or immune disorder) from a patient who is not suffering from an IRAK 4-mediated disorder or condition (e.g., an inflammatory disorder or immune disorder) or a pooled plasma or serum sample from a pooled sample of, in certain embodiments, the reference level is a reference sample of an IRAK 4-mediated disorder or a reference sample, or a pooled RNA sample of a reference sample, in certain embodiments, or a reference sample of a reference sample, or a reference sample of a reference sample.

In any of the foregoing diagnostic methods, the IRAK 4-mediated condition or disorder is selected from the group consisting of an immune condition, an inflammatory condition, a fibrotic condition, an eosinophilic condition, an infection, pain, a central nervous system condition, an acute kidney injury, a chronic kidney condition, endometriosis, a non-alcoholic fatty liver disease, a metabolic syndrome, and obesity.

In certain instances, the immune disorder is allergic airway syndrome, allergic rhinitis, allograft rejection, asthma, atopic dermatitis, contact dermatitis, crohn's disease, cutaneous lupus, delayed hypersensitivity, diabetes, gout, graft versus host disease, graft rejection, Inflammatory Bowel Disease (IBD), inflammatory myositis (e.g., polymyositis, dermatomyositis), lupus nephritis, multiple sclerosis, psoriasis, rheumatoid arthritis, scleroderma, sepsis, systemic lupus erythematosus, systemic sclerosis, or ulcerative colitis.

In certain instances, the inflammatory condition is acute respiratory distress syndrome, acute lung injury, adult still's disease, allergic airway syndrome, allergic rhinitis, asthma, atherosclerosis, atopic dermatitis, bronchitis, calcium pyrophosphate deposition disease (CPPD), cerebrovascular accidents (e.g., stroke), Chronic Obstructive Pulmonary Disease (COPD), contact dermatitis, crohn's disease, cryoprotein-associated periodic syndrome (CAPS), cutaneous lupus, delayed hypersensitivity, gout, graft-versus-host disease, Inflammatory Bowel Disease (IBD), inflammatory myositis (e.g., polymyositis, dermatomyositis), lupus nephritis, rheumatoid arthritis, rhinitis, scleroderma, sepsis, systemic lupus erythematosus, systemic onset juvenile idiopathic arthritis, systemic sclerosis, or ulcerative colitis.

In some cases, the eosinophilic disorder is allergic rhinitis, asthma, atopic dermatitis, Chronic Obstructive Pulmonary Disease (COPD), or contact dermatitis.

In some cases, the fibrotic disorder is atherosclerosis, scleroderma, or systemic sclerosis.

In some cases, the central nervous system disorder is a cerebrovascular accident (e.g., stroke), multiple sclerosis, or neurodegeneration.

In some cases, the pain is neuropathic pain.

In some cases, the infection is bronchitis or sepsis.

In any of the foregoing diagnostic methods of the invention, the IRAK4 pathway inhibitor is an IRAK4 inhibitor, an IRAK1 inhibitor, a toll-like receptor (TLR) inhibitor, an interleukin-1 receptor (IL-1R) inhibitor, an interleukin-33 receptor (IL-33R) inhibitor, or an inhibitor of the myeloid differentiation major response gene 88(MyD88) inhibitor in instances IRAK4 pathway inhibitor is an IRAK4 inhibitor in instances, an IRAK4 pathway inhibitor is a TLR inhibitor in instances, a TLR inhibitor is a TLR7 inhibitor, a TLR8 inhibitor, a TLR9 inhibitor, a TLR1 inhibitor, a TLR2 inhibitor, a TLR4 inhibitor, or a TLR4 inhibitor in some instances, an IRAK4 pathway inhibitor is a TLR 8472 inhibitor, a TLR4 inhibitor, or an inhibitor of both TLR4 and a TLR4 inhibitor in some instances, an IRAK4 pathway inhibitor is an IRAK4 inhibitor, an IRAK4 inhibitor in any of embodiments, a protein complex, a small molecule, such as a small molecule.

B. Methods of treatment using IRAK4 pathway inhibitors

The invention also provides methods for treating a patient having an IRAK 4-mediated disorder or condition, such as an immune disorder (e.g., Systemic Lupus Erythematosus (SLE)) or an inflammatory disorder (e.g., asthma). Thus, in certain instances, the methods of the invention comprise administering an IRAK4 pathway inhibitor to a patient. Any IRAK4 pathway inhibitor described above or known in the art may be used in conjunction with this method.

In aspects, the invention features methods of treating a patient having an IRAK 4-mediated condition or disorder with an IRAK4 pathway inhibitor by (a) determining the expression level of or more genes listed in Table 1 (e.g., 1,2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, or all 24 genes) in a sample obtained from the patient at a time point after administration of the th dose of the IRAK4 pathway inhibitor, (b) comparing the expression level of or more genes listed in Table 1 in the sample to a reference expression level, and (c) administering to the patient at least a second dose of the IRAK4 pathway inhibitor based on a decrease in the expression level of the or more genes listed in Table 1 relative to the reference expression level.

In some cases at , the expression level of or more genes listed in table 1 is reduced in a sample obtained from the patient at a time point after administration of the IRAK4 pathway inhibitor at the -fold relative to the reference expression level, e.g., the expression level of or more genes listed in table 1 is reduced in some cases at about 1% or more (e.g., about 2% or more, about 3% or more, about 4% or more, about 5% or more, about 6% or more, about 7% or more, about 8% or more, about 9% or more, about 10% or more, about 11% or more, about 12% or more, about 13% or more, about 14% or more, about 15% or more, about 20% or more, about 9% or more, about 10% or more, about 5% or more, about 5.5% or more, about 5% or more, about 5.5.5% or more, about 5.70% or more genes listed in a sample obtained at a time point after administration of the IRAK -fold, 7, e.1, about 5, about 0.1, about 5, e.1, e.g., the reference expression level of the or more genes, or more, about 5, about 70, about 5, or more genes, about 5 to about 5, about 5 to about 5, about 5% or more, about 5 to about 5% or more, about 5% or more, about 5 to about 5% or more, about 5% or more, about 5 to about 5, about 5% or more, about 5 to about 5, about 5 to about 5% or more, about 5 to about 5, about 5% or more, about 5 to about 5% or more, about 5 to about 5, about 5% or more, about 5% or more, about 5 to about 5, about 5% or more, about 5 to about 5, about 5.

In embodiments, reduced or decreased expression refers to an overall reduction in the level of a biomarker (e.g., a protein or nucleic acid (e.g., a gene or mRNA)) by any of about 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 95%, 96%, 97%, 98%, 99%, or more, as detected by standard art-known methods as described herein, in certain embodiments, reduced expression refers to a reduction in the level (amount) of expression of the biomarker in a sample, wherein the reduction is at least about any of the level (amount) of expression of the corresponding biomarker in a reference level, a reference sample, a reference cell, a reference tissue, a control sample, a control cell, or a control tissue.

In certain instances, the method comprises administering at least a second dose of an IRAK pathway inhibitor to a patient suffering from an IRAK-mediated disorder or condition who has received a second dose of an IRAK pathway inhibitor based on a reduced level of expression of one or more genes listed in table 1 relative to a reference level of expression, in 0 cases, the method comprises administering at least a second dose of an IRAK pathway inhibitor to a patient suffering from an IRAK-mediated disorder or condition selected from the group consisting of CD, SOCS, AQP, CDKN1, GADD45, B4GALT, IL15, TNFAIP, SOCS, IL1, PFKFB, and BCL2A based on a reduced level of expression of 1 or more genes (e.g., 2 genes, two genes, three genes, four genes, five genes, six genes, seven genes, eight genes, nine genes, ten genes, twelve genes) relative to a reference level of expression, CD, SOCS, AQP, CDKN1, GADD45, B4GALT, IL15, TNFAIP, GADD, gab, and BCL2A, administering at least a second dose of an IRAK pathway inhibitor to a patient suffering from an IRAK-mediated disorder or condition that has received a reduced level of at least four genes (e.g., four genes, seven genes, GADD, gacs, GADD, gaq 1, GADD, gaq, a reduced level relative to a patient who has received a reference level of an IRAK pathway inhibitor based on a reduced level of an IRAK pathway inhibitor, a reduced level of a reference level of an IRAK pathway inhibitor, a gene, a reference level of a gene, a reduced level of a reference level of a patient including a gene, a reference level of a gene, a reduced level of an IRAK pathway inhibitor, a patient including a reference level of a gene, a reduced level of a patient, a reference level of a target gene, a patient, a target gene, a reduced level of a patient, a reduced level of at least two gene, a patient, a reduced level of a patient, a reduced level.

In any of the foregoing embodiments, the reference expression level can be (i) an expression level of or more genes listed in table 1 in a sample obtained from the patient prior to administration of an th dose of the IRAK4 pathway inhibitor, (ii) an expression level of or more genes listed in table 1 in a reference population (e.g., a median expression level of or more genes listed in table 1 in the reference population), (iii) a pre-specified expression level of or more genes listed in table 1, (iv) an expression level of or more genes listed in table 1 in a sample obtained from the patient at a previous time point, wherein the previous time point is after administration of an th dose of the IRAK4 pathway inhibitor, or (v) an expression level of or more genes listed in table 1 in a sample obtained from the patient at a subsequent time point.

In another aspect, the invention features a method of treatment of a patient having an IRAK 4-mediated disorder or condition, the method including administering an IRAK4 pathway inhibitor to the patient, wherein the level of expression of or more genes (e.g., 1,2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, or all 24 genes) listed in table 1 in a sample obtained from the patient relative to a reference level of expression has been determined prior to treatment.

In certain instances, an increase in expression level of or more genes listed in table 1 (e.g., 1,2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, or all 24 genes) in a sample obtained from a patient relative to a reference expression level has been determined, e.g., an increase in expression level of or more genes listed in table 1 in a reference population, e.g., a median expression level of or more genes listed in table 1 in a reference population, is determined, e.g., about 1% or more (e.g., about 2% or more, about 3% or more, about 4% or more, about 5% or more, about 6% or more genes in a reference population, about 1% or about 5% or more of about 0% to about 5% or about 10% or more of the reference expression level of the reference expression of the gene or about 6.7, about 10% or more, about 10% or about 10% or more of the reference population, about 10% or about 10 or more of the reference expression of the reference population, about 7.7, about 7.60, about 0.60, about 0.7, about 10.7, about 10% or about 10% or more of the reference population, about 10% or about 10% or more of the reference population, about 10 or more of the reference expression of the reference population, about 10% or about 10 or about 0 or about 10% or about 0 or about 10% or about 10% or about 10% or about 7 or about 0 or more of the reference population, about 10 or about 0 or about 10% or about 10 or more of the reference population, about 0 or about 10 or about 7 or about 10% or about 7 or about 10% or about 10% or about 10% or about 10% or about 0 or about 10% or about 10% or more of the reference protein in the reference population, about 10 or about 10% or about 10 or more of the reference population, about 0 or about 10% or about 10% or more of the reference population, about 10% or about 0 or about 10% or about 10 or more of the reference population, about 10 or more of the reference population.

In certain embodiments, increased or increased expression refers to an increase in the level (amount) of expression of a biomarker in a sample, wherein the increase is at least about 1.5x, 1.75x, 2x, 3x, 4x, 5x, 6x, 7x, 8x, 9x, 10x, 25x, 50x, 75x, or 100x reference level, the level (amount) of expression of the corresponding biomarker in a reference sample, reference cell, reference tissue, control sample, control cell, or control tissue in embodiments, increased expression refers to an overall increase of greater than about 1.5 fold, about 1.75 fold, about 2 fold, about 2.25 fold, about 2.5 fold, about 2.75 fold, about 3.0 fold, or about 3.25 fold as compared to the reference sample, reference cell, reference tissue, control sample, control cell, control tissue, or internal control (e.g., housekeeping gene).

In certain embodiments, when a patient is identified as having an increased likelihood of benefit from treatment with an IRAK4 pathway inhibitor relative to an increased expression level of or more genes (e.g., 1,2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, or all 24 genes) listed in table 1 relative to a reference expression level, the method comprises administering an IRAK4 pathway inhibitor to the patient.

In certain instances, when a patient is identified as having an increased likelihood of benefit from treatment with an IRAK pathway inhibitor relative to a reference expression level of one or more genes (e.g., one gene, two genes, three genes, four genes, five genes, six genes, seven genes, eight genes, nine genes, ten genes, or all twelve genes) selected from CD, SOCS, AQP, CDKN1, GADD45, B4GALT, IL15, TNFAIP, SOCS, IL1, PFKFB, and BCL2A, the method comprises administering an IRAK pathway inhibitor to the patient having an IRAK-mediated disorder or condition, in some cases, when the reference expression level is selected from CD, SOCS, AQP, CDKN1, GADD45, B4GALT, IL15, TNFAIP, SOCS, IL1, and pfak B, the one or more genes (e.g., one gene, two genes, three genes, four genes, seven genes, six genes, five genes, six genes, five genes, seven genes, five genes, six genes, seven genes, five genes, six genes, five genes, six genes, five genes, six genes, or all three genes, six genes, three genes.

In some embodiments , the reference expression level can be (i) an expression level of or more genes listed in Table 1 in the reference population (e.g., the median expression level of or more genes listed in Table 1 in the reference population) or (ii) a pre-specified expression level of or more genes listed in Table 1.

In any of the above methods, administration of an IRAK4 pathway inhibitor may have the following therapeutic effects (i.e., benefits): as a result of, or as a result of, treatment with an IRAK4 pathway inhibitor, the patient has a cellular or biological response, a complete response, a partial response, a stable disease (no progression or recurrence), or a later-stage relapsed response. For specific conditions or disorders mediated by IRAK4, responsiveness to treatment with an IRAK4 pathway inhibitor was assessed and evaluated in different ways according to standard medical practice. Often, the skilled physician will seek relief from the signs and symptoms of a particular disease. The following are examples.

For IRAK 4-mediated lupus and SLE disorders, the SLEDAI score provides a numerical quantification of disease activity. SLEDAI is a weighted index of 24 clinical and laboratory parameters known to be associated with disease activity, ranging from 0 to 103. See Bryan Gescuk & John Davis, "Novel thermal agent for system viral perfusion in Rheumatology 2002,14: 515-. Antibodies to double stranded DNA are believed to cause kidney damage (flare) and other manifestations of lupus. The time to renal injury in patients receiving antibody therapy can be monitored, which refers to a significant reproducible increase in serum creatinine, urine protein, or blood in the urine. Alternatively or additionally, the patient may be monitored for antinuclear antibody levels and for antibodies to double-stranded DNA.

For IRAK 4-mediated Rheumatoid Arthritis (RA) conditions, measurements of treatment progress may include the number of swollen and painful joints and the length of morning stiffness by using X-rays and a scoring system called the Sharp score, the extent of erosion of the patient's joints in the hands and feet can be examined.Another scoring system is based on the American college of rheumatology to assess the criteria for treatment response. methods to assess the efficacy of RA treatment are based on the American society of rheumatology (ACR) criteria which measures, among others, the percentage of improvement in pain and swollen joints.compared to no antibody treatment (e.g., baseline before treatment) or treatment with placebo, RA patients are scored, for example, ACR20 (20% improvement). other methods to assess the efficacy of antibody treatment include X-ray scores such as for structural damage (e.g., bone erosion and narrowing of joint spaces) and Sharp X-ray scores such as for assessing the efficacy of structural damage (e.g., bone erosion and narrowing of joint spaces) can also be assessed according to the health assessment questionnaire [ HAQ ] score, AIMS score, SF-36, the pain or disability score for patients can be assessed during or for the following measures 20% improvement and the other methods include at least 20% improvement in joint count of joint count:

1. the pain of the patient is assessed by a Visual Analog Scale (VAS),

2. patient global assessment of disease activity (VAS),

3. physician global assessment of disease activity (VAS),

4. measuring the patient's self-assessed disability via a health assessment questionnaire, and

5. acute phase reactant, CRP, or ESR.

ACR50 and 70 are similarly defined preferably quantitative amounts of the CD20 binding antibody of the invention are administered to the patient to effectively obtain a score of at least ACR20, preferably at least ACR30, more preferably at least ACR50, even more preferably at least ACR70, most preferably at least ACR 75 and higher.

In cases, administration of an IRAK4 pathway inhibitor has a therapeutic effect of reducing or delaying progression of an IRAK 4-mediated disorder or condition by 1 day or more (e.g., 2 days, 3 days, 4 days, 5 days, 6 days, 1 week, 2 weeks, 3 weeks, 1 month, 2 months, 3 months, 4 months, 5 months, 6 months, 7 months, 8 months, 9 months, 10 months, 11 months, or 1 year or more) as compared to treatment that does not comprise an IRAK4 pathway inhibitor.

In any of the foregoing methods of treatment, the IRAK 4-mediated disorder or condition is selected from the group consisting of an immune disorder, an inflammatory disorder, a fibrotic disorder, an eosinophilic disorder, an infection, pain, a central nervous system disorder, acute kidney injury, chronic kidney disease, endometriosis, a non-alcoholic fatty liver disease, metabolic syndrome, and obesity.

In certain instances, the immune disorder is allergic airway syndrome, allergic rhinitis, allograft rejection, asthma, atopic dermatitis, contact dermatitis, crohn's disease, cutaneous lupus, delayed hypersensitivity, diabetes, gout, graft versus host disease, graft rejection, Inflammatory Bowel Disease (IBD), inflammatory myositis (e.g., polymyositis, dermatomyositis), lupus nephritis, multiple sclerosis, psoriasis, rheumatoid arthritis, scleroderma, sepsis, systemic lupus erythematosus, systemic sclerosis, or ulcerative colitis.

In certain instances, the inflammatory condition is acute respiratory distress syndrome, acute lung injury, adult still's disease, allergic airway syndrome, allergic rhinitis, asthma, atherosclerosis, atopic dermatitis, bronchitis, calcium pyrophosphate deposition disease (CPPD), cerebrovascular accidents (e.g., stroke), Chronic Obstructive Pulmonary Disease (COPD), contact dermatitis, crohn's disease, cryoprotein-associated periodic syndrome (CAPS), cutaneous lupus, delayed hypersensitivity, gout, graft-versus-host disease, Inflammatory Bowel Disease (IBD), inflammatory myositis (e.g., polymyositis, dermatomyositis), lupus nephritis, rheumatoid arthritis, rhinitis, scleroderma, sepsis, systemic lupus erythematosus, systemic onset juvenile idiopathic arthritis, systemic sclerosis, or ulcerative colitis.

In some cases, the eosinophilic disorder is allergic rhinitis, asthma, atopic dermatitis, Chronic Obstructive Pulmonary Disease (COPD), or contact dermatitis.

In some cases, the fibrotic disorder is atherosclerosis, scleroderma, or systemic sclerosis.

In some cases, the central nervous system disorder is a cerebrovascular accident (e.g., stroke), multiple sclerosis, or neurodegeneration.

In some cases, the pain is neuropathic pain.

In some cases, the infection is bronchitis or sepsis.

As described above, an IRAK4 pathway inhibitor may be an IRAK4 inhibitor, an IRAK1 inhibitor, a toll-like receptor (TLR) inhibitor, an interleukin-1 receptor (IL-1R) inhibitor, an interleukin-33 receptor (IL-33R) inhibitor, or an inhibitor of the myeloid major differentiation responsive gene 88(MyD88) in cases, an IRAK4 pathway inhibitor is an IRAK4 inhibitor in cases, an IRAK4 pathway inhibitor is a TLR inhibitor in cases, a TLR inhibitor is a TLR7 inhibitor, a TLR8 inhibitor, a TLR9 inhibitor, a TLR1 inhibitor, a TLR2 inhibitor, a TLR4 inhibitor, or a TLR4 inhibitor in certain cases, an IRAK4 pathway inhibitor is a TLR4 inhibitor, or both a TLR4 inhibitor and a TLR4 inhibitor, in certain cases, an IRAK4 pathway inhibitor is an IRAK4 inhibitor, a multi-molecule inhibitor, such as a multi-molecule antibody, or a multi-molecule.

Dosage and administration

patients who respond to or are susceptible to treatment with an IRAK4 pathway inhibitor may be treated with an IRAK4 pathway inhibitor alone or in combination with other therapeutic agents, such treatment may result in, for example, a reduction or delay in the progression of an IRAK 4-mediated condition or disorder by 1 day or more (e.g., 2 days, 3 days, 4 days, 5 days, 6 days, 1 week, 2 weeks, 3 weeks, 1 month, 2 months, 3 months, 4 months, 5 months, 6 months, 7 months, 8 months, 9 months, 10 months, 11 months, or 1 year or more) as compared to treatment that does not include an IRAK4 pathway inhibitor.

One skilled in the art will appreciate that, upon diagnosing a patient as likely to respond to an IRAK4 pathway inhibitor, the exact manner in which a therapeutically effective amount of an IRAK4 pathway inhibitor is administered will be determined by the attending physician. The diagnosis of a patient's possible response to such IRAK4 pathway inhibitors, as well as the patient's condition and medical history, may affect the mode of administration, including dosage, combination with other agents, timing and frequency of administration, and the like. Thus, even if a patient with an IRAK 4-mediated disorder or condition (e.g., an immune disorder (e.g., SLE) or an inflammatory disorder (e.g., asthma)) is predicted to be relatively insensitive to an IRAK4 pathway inhibitor, it may still benefit from treatment with the IRAK4 pathway inhibitor, particularly in combination with other agents, including agents that may alter the patient's responsiveness to antagonists.

Compositions comprising an IRAK4 pathway inhibitor are formulated, administered and administered in a manner that meets good medical specifications. Factors considered in this context include the particular type of IRAK 4-mediated condition or disorder being treated (e.g., immune disorder, inflammatory disorder, fibrotic disorder, eosinophilic disorder, infection, pain, central nervous system disorder, acute kidney injury, chronic kidney disease, endometriosis, non-alcoholic fatty liver disease, metabolic syndrome, and obesity), the particular mammal being treated (e.g., a human), the clinical condition of the individual patient, the cause of IRAK 4-mediated condition or disorder, the site of substance delivery, possible side effects, the type of inhibitor, the method of administration, the schedule of administration, and other factors known to medical practitioners. The effective amount of IRAK4 pathway inhibitor administered will be determined by such considerations.

For example, a physician may start at a dose of an IRAK4 pathway inhibitor used in a pharmaceutical composition that is below the level required to achieve the desired therapeutic effect and gradually increase the dose until the desired effect is achieved.

In certain examples, the IRAK4 pathway inhibitor may be the only agent administered to the subject (i.e., as a single therapy).

Thus, the and second doses of an IRAK4 pathway inhibitor preferably use the same IRAK4 pathway inhibitor (or at least the same species/type of an IRAK4 pathway inhibitor, e.g., using the same or different doses of an IRAK4 inhibitor), more preferably the same IRAK4 pathway inhibitor for all doses of an IRAK4 pathway inhibitor, i.e., the same species/type of an IRAK4 pathway inhibitor for both the first two doses (preferably all doses) of treatment (e.g., the same or different IRAK4 inhibitor for all doses).

Treatment with an IRAK4 pathway inhibitor or a pharmaceutically acceptable salt thereof may be carried out according to standard methods.

In one embodiment, the IRAK4 pathway inhibitor is administered orally in embodiments each dose is administered intravenously in embodiments each dose is administered subcutaneously in another embodiments each dose is administered by subcutaneous administration in another embodiments the dose is administered by intravenous and subcutaneous administration.

The duration of treatment, or the duration of treatment, can be continued for as long as medically indicated, until a desired therapeutic effect (e.g., those described herein) is obtained in certain embodiments, the treatment is continued for 1 month, 2 months, 4 months, 6 months, 8 months, 10 months, 1 year, 2 years, 3 years, 4 years, 5 years, or for up to several years, until years of the subject.

In some embodiments , the IRAK4 pathway inhibitor is administered as close as possible to the first sign, diagnosis, manifestation, or occurrence of an IRAK 4-mediated disorder or condition being treated (e.g., immune disorders, inflammatory disorders, fibrotic disorders, eosinophilic disorders, infection, pain, central nervous system disorders, acute kidney injury, chronic kidney disease, endometriosis, nonalcoholic fatty liver disease, metabolic syndrome, and obesity).

1. Route of administration

Factors contemplated in this instance include the particular IRAK 4-mediated disorder or condition being treated (e.g., immune disorder, inflammatory disorder, fibrotic disorder, eosinophilic disorder, infection, pain, central nervous system disorder, acute kidney injury, chronic kidney disease, endometriosis, non-alcoholic fatty liver disease, metabolic syndrome, and obesity), the clinical condition of the individual patient, the cause of the disorder, the site of substance delivery, the method of administration, the schedule of administration, and other factors known to the medical practitioner the IRAK4 pathway inhibitor is optionally, but not necessarily, formulated with or more agents currently used to prevent or treat the IRAK 4-mediated disorder or condition being treated (e.g., immune disorder, inflammatory disorder, fibrotic disorder, eosinophilic disorder, infection, pain, central nervous system disorder, acute injury to the kidney, chronic kidney disease, endometriosis, non-alcoholic fatty liver disease, metabolic syndrome, obesity-causing agent, , and/or obesity ).

For the prevention or treatment of an IRAK 4-mediated disorder or condition being treated (e.g., an immune disorder, an inflammatory disorder, a fibrotic disorder, an eosinophilic disorder, an infection, pain, a central nervous system disorder, acute kidney injury, chronic kidney disease, endometriosis, non-alcoholic fatty liver disease, metabolic syndrome, and obesity), the appropriate dosage of an IRAK4 pathway inhibitor described herein (when used alone or in combination with or more other therapeutic agents) will depend on the type of disease being treated, the severity and course of the disease, whether the IRAK4 pathway inhibitor is administered for prophylactic or therapeutic purposes, previous therapy, the clinical history of the patient and response to an IRAK4 pathway inhibitor, and the judgment of the attending physician, the IRAK4 pathway inhibitor is suitable for times or is administered to the patient by a series of treatments .

The IRAK4 pathway inhibitor may be administered by any suitable means, including oral, parenteral, topical, subcutaneous, intraperitoneal, intrapulmonary, intranasal, and/or intralesional administration. Parenteral infusion includes intramuscular, intravenous, intraarterial, intraperitoneal or subcutaneous administration. Intrathecal administration is also contemplated. Additionally, the IRAK4 pathway inhibitor may suitably be administered by pulsed infusion, for example with a decreasing dose of an IRAK4 pathway inhibitor.

In another embodiments, each exposure is given by subcutaneous (s.c.) administration, in yet another embodiments, the exposures are given by both intravenous and subcutaneous administration.

2. Combination therapy

The method may further include steps including administering an effective amount of an IRAK4 pathway inhibitor in combination with another therapeutic agent to the patientCyclosporine, azathioprine, methotrexate, mycophenolate mofetilOr cyclophosphamideAt a certain pointIn some cases, an IRAK4 pathway inhibitor may be used in combination with surgery.

Combination therapy can provide "synergy" and prove "synergistic," i.e., the effect achieved when is used is greater than the sum of the effects produced by the compounds used alone, synergy can be achieved when the active ingredients are (1) co-formulated and administered or delivered simultaneously in a combined unit dose formulation, (2) delivered alternately or in parallel as separate formulations, or (3) delivered by other regimens when the compounds are administered or delivered sequentially when delivered in alternation therapy, generally, an effective dose of each active ingredient is administered sequentially (i.e., one after the other) during alternation therapy, while serves to administer an effective dose of two or more active ingredients in combination therapy.

As described above, a method of treatment may comprise administering a combination of two or more (e.g., three or more) IRAK4 pathway inhibitors in some cases, e.g., two IRAK4 inhibitors in combination (or sequentially or concomitantly), in some cases, e.g., two IRAK1 inhibitors in combination (or sequentially or concomitantly), in some cases, e.g., two TLR inhibitors in combination (or sequentially or concomitantly).

In general, for the prevention or treatment of disease, the appropriate dosage of other therapeutic agents will depend on the type of disease to be treated, the type of antibody, the severity and course of the disease, whether the IRAK4 pathway inhibitor and other agent (e.g., corticosteroid) are administered for prophylactic or therapeutic purposes, previous therapy, the clinical history of the patient, and the response to the IRAK4 pathway inhibitor and other agent, as well as the discretion of the attending physician, IRAK4 pathway inhibitor and other agent are administered to the patient times or by series of treatments, IRAK4 pathway inhibitor is typically administered as described above, depending on the diseaseType and severity of (1), about 20mg/m²To 600mg/m²Whether administered individually times or multiple times, or by continuous infusion typical daily dosage ranges may be about 20mg/m²、85mg/m²、90mg/m²、125mg/m²、200mg/m²、400mg/m²、500mg/m²Or higher depending on the factors mentioned above. For repeated administrations over several days or longer, depending on the condition, the treatment is continued until the desired suppression of disease symptoms occurs. Thus, about 20mg/m may be administered to the patient²、85mg/m²、90mg/m²、125mg/m²、200mg/m²、400mg/m²、500mg/m²、600mg/m²Such doses may be administered intermittently (e.g., such that the patient receives about two to about twenty doses, e.g., about six doses of the other agent), for example, weekly or every two, three, four, five or six weeks.

In another embodiments, the patient has previously been administered or more drugs to treat an IRAK4 mediated disorder or condition in another embodiments, the patient is not responsive to or more drugs that have previously been administered to treat an IRAK4 mediated disorder or conditionCyclosporine, azathioprine, methotrexate, mycophenolate mofetilAnd/or cyclophosphamideIt was not administered in combination with an IRAK4 pathway inhibitor.

Diagnostic kit and composition

The present invention further provides -steps diagnostic kits and compositions comprising or more agents (e.g., polypeptides [ such as antibodies or antigen binding fragments thereof ] or polynucleotides [ such as probes or primers ]) for determining the level of expression of or more genes listed in table 1 (e.g., immune disorders, inflammatory disorders, fibrotic disorders, eosinophilic disorders, infections, pain, central nervous system disorders, acute kidney injury, chronic kidney disease, endometriosis, non-alcoholic fatty liver disease, metabolic syndrome, and obesity) in a subject or patient sample having an IRAK 4-mediated disorder or condition (e.g., an immune disorder, an inflammatory disorder, an eosinophilic disorder, an infection, pain, a central nervous system disorder, acute kidney injury, chronic kidney disease, endometriosis, non-alcoholic fatty liver disease, metabolic syndrome, and obesity) including or more genes listed in a patient having an IRAK -mediated disorder or condition (e.g., an immune disorder, an acute renal disorder, chronic kidney disease, an endometrial disorder, endometriosis, a non-alcoholic fatty liver disease, metabolic syndrome, and obesity) under conditions where the expression of or more genes listed in a patient may be increased relative to a further therapeutic response to an IRAK 72-like receptor expression of an inhibitor or a drug (e.g., if the expression of an IRAK 72-receptor-like inhibitor or a drug is included in a patient having an IRAK 72- -like receptor (e.g., a receptor- -receptor-like inhibitor or a receptor, including a receptor- -like inhibitor or a receptor that is included in a further drug that has been included in a further therapeutic agent or a further included in a further therapeutic agent that the drug (e.g., a further includes a further therapeutic agent or a further therapeutic agent that the expression of an IRAK 72 or a receptor that the expression of an IRAK 72- or a receptor that has been included in a receptor that the drug that the expression of a receptor that has been included in a receptor that the expression of an IRAK 72- or a receptor that the drug (e.g., a receptor that the drug that the expression of an inhibitor or a receptor that the drug that the expression of a receptor that the expression of an inhibitor or a receptor that the expression of an IRAK 72 or a receptor that the expression of a receptor that the drug that the expression of a receptor that the receptor that has been included in a receptor that has been included a receptor that the receptor that has been included in a receptor that the drug (e.g., a receptor that the expression of an IRak 72 or a receptor that has been included in a receptor that the expression of an IRak 72 or a receptor that the drug that has been included in a receptor that the drug that the receptor that.

The compositions of the invention include polypeptides (e.g., antibodies or antigen-binding fragments thereof) or polynucleotides (e.g., probes and/or primers) capable of determining the expression level of RNASE4 and optionally or more other biomarkers (e.g., PSA and/or ANG).

Examples

The following examples are provided to illustrate but not limit the invention.

Example 1 identification of genes impaired in response to TLR7/8 stimulation in patients deficient in IRAK4

To determine candidate IRAK4 biomarker genes that can be used as drug efficacy and predictive biomarkers, genes that show a significant reduction in induction after TLR stimulation in patients carrying IRAK4 loss of function mutations compared to healthy patients were first identified. To this end, an analysis of the microarray dataset of GEO accession number GSE25742 (Alsina et al nat. Immunol.15:1134-42,2014), which is a study of the genome-wide microarray expression profiles of whole blood from patients with Toll-like receptor (TLR) and interleukin-1 receptor (IL-1R), i.e.toll/IL-1 receptor (TIR) pathway, signaling defects, was performed. Analysis of the microarray dataset determined 285 genes showing a significant reduction in the induction of TLR7/8 stimulator R848 (resiquimod) in whole blood from IRAK4 deficient patients compared to healthy patient controls (false discovery rate (FDR)<0.05; fold Change (FC)>1.25) (fig. 1A-1B and 6). Although healthy patients were found to upregulate type I interferon in a control response R848(IFN), but IRAK4^-/-Patients failed to upregulate type I IFNs and other TLR regulated genes in response to R848 (figure 2).

Example 2 identification of genes upregulated in Systemic Lupus Erythematosus (SLE) patients

An analysis of two groups of extrarenal Systemic Lupus Erythematosus (SLE) patients was performed to determine which of the 285 differentially expressed genes identified in example 1 also showed increased baseline expression in SLE patients. Two datasets of Peripheral Blood Mononuclear Cell (PBMC) microarray data (university of michigan group; SLE (n 61), Healthy Control (HC) (n 20)) and whole blood RNA sequencing data (ROSE phase II study (kalusian et al ann. rheum. dis.75: 196-. Subsequently in both datasets, 44 of the 285 differentially expressed genes were identified as being up-regulated (p < 0.05; FC >1.2) in SLE patients compared to healthy patients (FIGS. 3 and 6).

Example 3 characterization of IRAK4 pathway genes using IRAK4 kinase-deficient mice.

The putative IRAK4 pathway genes identified in example 2 were characterized at steps by generating IRAK4 kinase-deleted (KD) mice using the 5' end of the mouse IRAK4 complementary DNA as a probe, isolating genomic DNA of IRAK4 from 129/J mouse genomic libraries using standard cloning techniques, designing targeting constructs to disrupt the ATG initiation codon and replacing the portion of exon 2 of the IRAK4 gene with the PGK-Neo cassette, linearizing and transfecting the targeting plasmids into 129/Ola background embryonic stem cells (E14 clone), injecting the homologously recombined embryonic stem cell line into 3.5 day C57BL/6J (B6) blastocysts, which are subsequently transferred into CD1 pseudopregnant mothers to produce chimeric male progeny, backcrossing the chimeras with C57BL/6J to produce male progeny for male progeny of the thorns, verifying F1 by Southern blot analysis, germ line transferring the chimeras and crossing the F1 mutants to obtain homozygous mice.

Bone marrow-derived macrophages (BMDM) from IRAK4KD mice (n ═ 5) and wild-type control mice (n ═ 5) were harvested and stimulated in vitro with the TLR7 agonist R848 for four hours. Gene expression analysis by Fluidigm from IRAK4KD and wild type control miceOf non-stimulated and stimulated BMDM, putative IRAK4 pathway biomarker genes. Gene expression analysis showed that the putative IRAK4 pathway biomarker genes showed TLR 7-induced impaired induction in BMDM from IRAK4KD mice compared to IRAK4 wild-type mice (fig. 4 and 6). From human IRAK4^-/-Similar gene expression analysis of patient whole blood indicated that certain putative IRAK4 pathway biomarker genes also showed TLR 7-induced impaired induction (figure 6). In particular, 24 genes out of a total of 44 putative IRAK pathway biomarker genes were found to show TLR 7-induced impaired induction in both humans and mice. These 24 IRAK4 pathway biomarkers are listed in table 1 and described herein, highlighting the commonality between human and mouse systems.

Other gene expression analyses showed that IFN β showed lower R848 induction (p ═ 0.02) in IRAK4KD mice compared to IRAK4 wild type mice (fig. 5) other IFN regulatory genes (OAS1A, OAS2, IFIT1, IFNA5 and MX1) showed the same trend, i.e. a reduction in R848 induction (p <0.15) compared to IRAK4 wild type mice (fig. 7A-7E).

Example 4 dose-dependent downregulation of IRAK4 pathway biomarker genes by IRAK4 small molecule inhibitors.

Subsequently in human whole blood samples 24 IRAK4 pathway biomarker genes were characterized based on the inducibility of R848 and dose-dependent downregulation of two different IRAK4 small molecule inhibitors test compounds G03074387(G-4387) (BMS) and G03081557(G-1557) (Pfizer). Whole blood samples from three healthy donors were divided into six groups: (1) not stimulating; (2) stimulation with 1.25. mu.M (. about.440 ng/ml) R848; (3) g-4387 at IC50(268nM) for 1 hr + R848 stimulation for 3.5 hr; (4) g-4387 at IC70(553nM) for 1 hr + R848 stimulation for 3.5 hr; (5) g-4387 at IC90(1.75 μ M) for 1 hr + R848 stimulation for 3.5 hr; (6) g-4387 was left at 5. mu.M for 1 hr + R848 stimulation for 3.5 hr. Similar experiments were performed on G-1557 using whole blood samples from the same three healthy donors, except that the doses of G-1557 in groups (3) - (6) were as follows: (3) g-1557, IC50(13 nM); (4) g-1557, IC70(25 nM); (5) g-1557, IC90(70 nM); and (6) G-1557, 200 nM. For both experiments, RNA was subsequently extracted and the transcript levels of the 24 IRAK4 pathway biomarker genes were measured by qPCR. The results of these experiments are shown in figures 8 and 9. Of the 24 IRAK4 pathway biomarker genes, 9 genes in whole blood (CD38, SOCS3, AQP9, CDKN1A, GADD45B, B4GALT5, IL15RA, TNFAIP3, and SOCS1) were dose-dependently downregulated by G-4387 and G-1557 (fig. 9). In addition, in the ROSE phase II and university of michigan SLE group described in example 2 above, correlated features were observed in SLE patient blood for these IRAK4 biomarker genes (fig. 10A-10B). A significant positive correlation was also observed between IRAK4 pathway biomarker gene and Interferon Signature Metrics (ISM) and anti-dsDNA status and BAFF, anti-RNP antibody and anti-Sm antibody levels. A significant negative correlation was observed between IRAK4 biomarker genes and levels of complement component 3(C3) and complement component 4(C4) in both SLE datasets.

Taken together, the data indicate that coordinated expression of these IRAK4 regulatory genes reflects TLR and other upstream stimuli, and thus IRAK pathway activity, supporting the identified IRAK4 pathway biomarker genes as biomarkers for pharmacodynamics and prognostic diagnostics for patients likely to respond to treatment including IRAK4 pathway inhibitors (e.g., IRAK4 small molecule inhibitors).

Other embodiments

Although the foregoing invention has been described in some detail by way of illustration and example for purposes of clarity of understanding, these descriptions and examples should not be construed as limiting the scope of the invention. The disclosures of all patent and scientific literature cited herein are expressly incorporated by reference in their entirety.

Claims (98)

1. A method of monitoring the response of a patient having an interleukin-1 receptor associated kinase 4(IRAK4) -mediated disorder or condition to a treatment comprising an IRAK4 pathway inhibitor, the method comprising:

   (a) determining expression levels of or more genes listed in Table 1 in a sample obtained from the patient at a time point after administration of the th dose of the IRAK4 pathway inhibitor, and

   (b) comparing the expression level of or more genes listed in table 1 in the sample to a reference expression level, thereby monitoring the patient's response to a treatment comprising an IRAK4 pathway inhibitor.
2. 2. The method of claim 1, wherein the or more genes listed in table 1 comprise or more genes selected from the group consisting of CD38, SOCS3, AQP9, CDKN1A, GADD45B, B4GALT5, IL15RA, TNFAIP3, SOCS1, IL1RN, PFKFB3, and BCL2a 1.
3. 3. The method of claim 2, wherein the or more genes listed in table 1 comprise or more genes selected from the group consisting of CD38, SOCS3, AQP9, CDKN1A, GADD45B, B4GALT5, IL15RA, TNFAIP3, SOCS1, IL1RN, and PFKFB 3.
4. 4. The method of claim 3, wherein the or more genes listed in Table 1 comprise or more genes selected from CD38, SOCS3, AQP9, CDKN1A, GADD45B, B4GALT5, IL15RA, TNFAIP3, and SOCS 1.
5. 5. The method of claim 4, wherein the or more genes listed in Table 1 comprise all 9 of CD38, SOCS3, AQP9, CDKN1A, GADD45B, B4GALT5, IL15RA, TNFAIP3, and SOCS 1.
6. 6. The method of claim 5, wherein the or more genes listed in Table 1 comprise all 11 of CD38, SOCS3, AQP9, CDKN1A, GADD45B, B4GALT5, IL15RA, TNFAIP3, SOCS1, IL1RN, and PFKFB 3.
7. 7. The method of claim 6, wherein the or more genes listed in Table 1 comprise all 12 of CD38, SOCS3, AQP9, CDKN1A, GADD45B, B4GALT5, IL15RA, TNFAIP3, SOCS1, IL1RN, PFKFB3, and BCL2A 1.
8. 8. The method of claim 7, wherein the or more genes listed in Table 1 are all 24 genes listed in Table 1.
9. 9. The method of , wherein the expression level of or more genes listed in table 1 in a sample obtained from the patient is reduced relative to a reference expression level.
10. 10. The method of claim 9, wherein the expression level of or more genes listed in table 1 is reduced at least about 0.5-fold relative to a reference expression level.
11. 11. The method of claim 10, wherein the expression level of or more genes listed in table 1 is reduced at least about 1-fold relative to a reference expression level.
12. 12. The method of claim 11, wherein the expression level of or more genes listed in table 1 is reduced at least about 2-fold relative to a reference expression level.
13. 13. The method of claim 12, wherein the expression level of or more genes listed in table 1 is reduced at least about 3-fold relative to a reference expression level.
14. 14. The method of claim 13, wherein the expression level of or more genes listed in table 1 is reduced at least about 4-fold relative to a reference expression level.
15. 15. The method of claim 14, wherein the expression level of or more genes listed in table 1 is reduced at least about 5-fold relative to a reference expression level.
16. 16. The method of claim 15, wherein the expression level of or more genes listed in table 1 is reduced at least about 10-fold relative to a reference expression level.
17. 17. The method of any of claims 9-16, wherein a decreased expression level of or more genes listed in table 1 indicates that the patient is responsive to an IRAK4 pathway inhibitor.
18. 18. The method of claim 17, further comprising administering at least a second dose of an IRAK4 pathway inhibitor to a patient having a reduced expression level of or more genes listed in table 1 relative to a reference expression level.
19. A method of treating a patient having an IRAK 4-mediated condition or disorder with an IRAK4 pathway inhibitor, the method comprising:

    (a) determining expression levels of or more genes listed in table 1 in samples obtained from the patient at a time point after administration of an dose of IRAK4 pathway inhibitor;

    (b) comparing the expression level of or more genes listed in Table 1 in the sample with a reference expression level, and

    (c) administering to the patient at least a second dose of an IRAK4 pathway inhibitor based on a decrease in the expression level of or more genes listed in table 1 relative to a reference expression level.
20. 20. The method of claim 19, wherein the or more genes listed in table 1 comprise or more genes selected from CD38, SOCS3, AQP9, CDKN1A, GADD45B, B4GALT5, IL15RA, TNFAIP3, SOCS1, IL1RN, PFKFB3, and BCL2a 1.
21. 21. The method of claim 20, wherein the or more genes listed in table 1 comprise or more genes selected from CD38, SOCS3, AQP9, CDKN1A, GADD45B, B4GALT5, IL15RA, TNFAIP3, SOCS1, IL1RN, and PFKFB 3.
22. 22. The method of claim 21, wherein the or more genes listed in table 1 comprise or more genes selected from CD38, SOCS3, AQP9, CDKN1A, GADD45B, B4GALT5, IL15RA, TNFAIP3, and SOCS 1.
23. 23. The method of claim 22, wherein the or more genes listed in table 1 comprise all 9 of CD38, SOCS3, AQP9, CDKN1A, GADD45B, B4GALT5, IL15RA, TNFAIP3, and SOCS 1.
24. 24. The method of claim 23, wherein the or more genes listed in table 1 comprise all 11 of CD38, SOCS3, AQP9, CDKN1A, GADD45B, B4GALT5, IL15RA, TNFAIP3, SOCS1, IL1RN, and PFKFB 3.
25. 25. The method of claim 24, wherein the or more genes listed in table 1 comprise all 12 of CD38, SOCS3, AQP9, CDKN1A, GADD45B, B4GALT5, IL15RA, TNFAIP3, SOCS1, IL1RN, PFKFB3, and BCL2a 1.
26. 26. The method of claim 25, wherein the or more genes listed in table 1 are all 24 genes listed in table 1.
27. 27. The method of any , wherein the expression level of or more genes listed in table 1 is reduced at least about 0.5-fold relative to a reference expression level.
28. 28. The method of claim 27, wherein the expression level of or more genes listed in table 1 is reduced at least about 1-fold relative to a reference expression level.
29. 29. The method of claim 28, wherein the expression level of or more genes listed in table 1 is reduced at least about 2-fold relative to a reference expression level.
30. 30. The method of claim 29, wherein the expression level of or more genes listed in table 1 is reduced at least about 3-fold relative to a reference expression level.
31. 31. The method of claim 30, wherein the expression level of or more genes listed in table 1 is reduced at least about 4-fold relative to a reference expression level.
32. 32. The method of claim 31, wherein the expression level of or more genes listed in table 1 is reduced at least about 5-fold relative to a reference expression level.
33. 33. The method of claim 32, wherein the expression level of or more genes listed in table 1 is reduced at least about 10-fold relative to a reference expression level.
34. 34. The method of any of claims 1-33, wherein the reference expression level is:

    (i) expression levels of or more genes listed in table 1 in patient samples obtained prior to administration of dose of the IRAK4 pathway inhibitor;

    (ii) the expression level of or more genes listed in table 1 in a reference population;

    (iii) pre-specified expression levels of or more genes listed in table 1;

    (iv) expression levels of or more genes listed in Table 1 in samples obtained from the patient at prior time points after administration of doses of IRAK4 pathway inhibitor, or

    (v) The expression levels of or more genes listed in table 1 in samples obtained from patients at subsequent time points.
35. 35, a method of identifying a patient having an IRAK 4-mediated condition or disorder that would benefit from treatment comprising an IRAK4 pathway inhibitor, the method comprising determining expression levels of or more genes listed in table 1 in a sample obtained from the patient, wherein an increased expression level of or more genes listed in table 1 in the sample as compared to a reference expression level identifies the patient as a patient who would benefit from treatment comprising an IRAK4 pathway inhibitor.
36. 36. A method of selecting a therapy for a patient having an IRAK 4-mediated condition or disorder, the method comprising determining expression levels of or more genes listed in table 1 in a sample obtained from the patient, wherein increased expression levels of or more genes listed in table 1 in the sample as compared to a reference expression level identifies the patient as a patient who may benefit from treatment comprising an IRAK4 pathway inhibitor.
37. 37. The method of claim 35 or 36, wherein the or more genes listed in table 1 comprise or more genes selected from CD38, SOCS3, AQP9, CDKN1A, GADD45B, B4GALT5, IL15RA, TNFAIP3, SOCS1, IL1RN, PFKFB3, and BCL2a 1.
38. 38. The method of claim 37, wherein the or more genes listed in table 1 comprise or more genes selected from CD38, SOCS3, AQP9, CDKN1A, GADD45B, B4GALT5, IL15RA, TNFAIP3, SOCS1, IL1RN, and PFKFB 3.
39. 39. The method of claim 38, wherein the or more genes listed in table 1 comprise or more genes selected from CD38, SOCS3, AQP9, CDKN1A, GADD45B, B4GALT5, IL15RA, TNFAIP3, and SOCS 1.
40. 40. The method of claim 39, wherein the or more genes listed in Table 1 comprise all 9 of CD38, SOCS3, AQP9, CDKN1A, GADD45B, B4GALT5, IL15RA, TNFAIP3, and SOCS 1.
41. 41. The method of claim 40, wherein the or more genes listed in Table 1 comprise all 11 of CD38, SOCS3, AQP9, CDKN1A, GADD45B, B4GALT5, IL15RA, TNFAIP3, SOCS1, IL1RN, and PFKFB 3.
42. 42. The method of claim 41, wherein the or more genes listed in Table 1 comprise all 12 of CD38, SOCS3, AQP9, CDKN1A, GADD45B, B4GALT5, IL15RA, TNFAIP3, SOCS1, IL1RN, PFKFB3, and BCL2A 1.
43. 43. The method of claim 42, wherein the or more genes listed in Table 1 are all 24 genes listed in Table 1.
44. 44. The method of any of claims 35-43, wherein the expression level of or more genes listed in Table 1 in the sample obtained from the patient is increased relative to a reference expression level.
45. 45. The method of claim 44, wherein the expression level of or more genes listed in Table 1 is increased at least about 0.5-fold relative to a reference expression level.
46. 46. The method of claim 45, wherein the expression level of or more genes listed in Table 1 is increased at least about 1-fold relative to a reference expression level.
47. 47. The method of claim 46, wherein the expression level of or more genes listed in Table 1 is increased at least about 2-fold relative to a reference expression level.
48. 48. The method of claim 47, wherein the expression level of or more genes listed in Table 1 is increased at least about 3-fold relative to a reference expression level.
49. 49. The method of claim 48, wherein the expression level of or more genes listed in Table 1 is increased at least about 4-fold relative to a reference expression level.
50. 50. The method of claim 49, wherein the expression level of or more genes listed in Table 1 is increased at least about 5-fold relative to a reference expression level.
51. 51. The method of claim 50, wherein the expression level of or more genes listed in Table 1 is increased at least about 10-fold relative to a reference expression level.
52. 52. The method of any of claims 35-51, wherein the patient has increased expression levels of or more genes listed in Table 1 relative to a reference expression level, and the method further comprises administering an IRAK4 pathway inhibitor to the patient.
53. 53. A method of treating a patient having an IRAK 4-mediated condition or disorder, the method comprising administering to the patient an IRAK4 pathway inhibitor, wherein an increase in the expression level of or more genes listed in Table 1 in a sample obtained from the patient relative to a reference expression level has been determined prior to treatment.
54. 54. The method of claim 53, wherein the or more genes listed in Table 1 comprise or more genes selected from CD38, SOCS3, AQP9, CDKN1A, GADD45B, B4GALT5, IL15RA, TNFAIP3, SOCS1, IL1RN, PFKFB3, and BCL2A 1.
55. 55. The method of claim 54, wherein the or more genes listed in Table 1 comprise or more genes selected from CD38, SOCS3, AQP9, CDKN1A, GADD45B, B4GALT5, IL15RA, TNFAIP3, SOCS1, IL1RN, and PFKFB 3.
56. 56. The method of claim 55, wherein the or more genes listed in Table 1 comprise or more genes selected from CD38, SOCS3, AQP9, CDKN1A, GADD45B, B4GALT5, IL15RA, TNFAIP3, and SOCS 1.
57. 57. The method of claim 56, wherein the or more genes listed in Table 1 comprise all nine of CD38, SOCS3, AQP9, CDKN1A, GADD45B, B4GALT5, IL15RA, TNFAIP3, and SOCS 1.
58. 58. The method of claim 57, wherein the or more genes listed in Table 1 comprise all 11 of CD38, SOCS3, AQP9, CDKN1A, GADD45B, B4GALT5, IL15RA, TNFAIP3, SOCS1, IL1RN, and PFKFB 3.
59. 59. The method of claim 58, wherein the or more genes listed in Table 1 comprise all 12 of CD38, SOCS3, AQP9, CDKN1A, GADD45B, B4GALT5, IL15RA, TNFAIP3, SOCS1, IL1RN, PFKFB3, and BCL2A 1.
60. 60. The method of claim 59, wherein the or more genes listed in Table 1 are all 24 genes listed in Table 1.
61. 61. The method of any , wherein the increase in expression level of or more genes listed in Table 1 relative to a reference expression level has been determined to be at least about 0.5-fold.
62. 62. The method of claim 61, wherein the expression level of or more genes listed in Table 1 has been determined to be increased at least about 1-fold relative to a reference expression level.
63. 63. The method of claim 62, wherein the expression level of or more genes listed in Table 1 has been determined to be increased at least about 2-fold relative to a reference expression level.
64. 64. The method of claim 63, wherein the expression level of or more genes listed in Table 1 has been determined to be increased at least about 3-fold relative to a reference expression level.
65. 65. The method of claim 64, wherein the expression level of or more genes listed in Table 1 has been determined to be increased at least about 4-fold relative to a reference expression level.
66. 66. The method of claim 65, wherein the expression level of or more genes listed in Table 1 has been determined to be increased at least about 5-fold relative to a reference expression level.
67. 67. The method of claim 66, wherein the expression level of or more genes listed in Table 1 has been determined to be increased at least about 10-fold relative to a reference expression level.
68. 68. The method of any of claims 35 to 67, wherein the reference expression level is:

    (i) the expression level of or more genes listed in Table 1 in the reference population, or

    (ii) Pre-specified expression levels of or more genes listed in table 1.
69. 69. The method of claim 34 or 68, wherein the expression level of or more genes listed in Table 1 in the reference population is the median expression level of or more genes listed in Table 1 in the reference population.
70. 70. The method of any of claims 1-69, wherein the sample obtained from the patient is a tissue sample, a whole blood sample, a plasma sample, or a serum sample.
71. 71. The method of any of claims 1-70, wherein the expression level is an mRNA expression level.
72. 72. The method of claim 71, wherein mRNA expression levels are determined by RNA-Seq, qPCR, microarray analysis, gene expression profiling, serial analysis of gene expression, or whole genome sequencing.
73. 73. The method of claim 72, wherein mRNA expression levels are determined by qPCR.
74. 74. The method of any of claims 1-70, wherein the expression level is a protein expression level.
75. 75. The method of of any one of claims 1-74, wherein the IRAK4 mediated disorder or condition is selected from the group consisting of an immune disorder, an inflammatory disorder, a fibrotic disorder, an eosinophilic disorder, an infection, pain, a central nervous system disorder, acute kidney injury, a chronic kidney disorder, endometriosis, a non-alcoholic fatty liver disease, metabolic syndrome, and obesity.
76. 76. The method of claim 75, wherein the immune disorder is lupus, asthma, atopic dermatitis, rheumatoid arthritis, Inflammatory Bowel Disease (IBD), Crohn's disease, or ulcerative colitis.
77. 77. The method of claim 75, wherein the inflammatory condition is lupus, asthma, atopic dermatitis, rheumatoid arthritis, Inflammatory Bowel Disease (IBD), Crohn's disease, or ulcerative colitis.
78. 78. The method of claim 76 or 77, wherein the lupus is Systemic Lupus Erythematosus (SLE).
79. 79. The method of claim 76 or 77, wherein the lupus is lupus nephritis.
80. 80. The method of any of claims 1-79, wherein the IRAK4 pathway inhibitor is an IRAK4 inhibitor, an IRAK1 inhibitor, a toll-like receptor (TLR) inhibitor, an interleukin-1 receptor (IL-1R) inhibitor, an interleukin-33 receptor (IL-33R) inhibitor, or a myeloid differentiation major response gene 88(MyD88) inhibitor.
81. 81. The method of claim 80, wherein the IRAK4 pathway inhibitor is an IRAK4 inhibitor.
82. 82. The method according to claim 80, wherein the IRAK4 pathway inhibitor is a TLR inhibitor.
83. 83. The method as claimed in claim 82, wherein the TLR inhibitor is a TLR7 inhibitor, a TLR8 inhibitor, a TLR9 inhibitor, a TLR1 inhibitor, a TLR2 inhibitor, a TLR4 inhibitor, a TLR5 inhibitor, a TLR6 inhibitor, or a TLR10 inhibitor.
84. 84. The method of claim 83, wherein the TLR inhibitor is a TLR7 inhibitor, a TLR8 inhibitor, or both a TLR7 inhibitor and a TLR8 inhibitor.
85. 85. The method as claimed in claim 83 wherein the TLR inhibitor is a TLR9 inhibitor.
86. 86. The method of any of claims 80-85, wherein the IRAK4 pathway inhibitor is a small molecule inhibitor.
87. 87. The method of of any of claims 18-34 and 52-86, further step comprising administering an additional therapeutic agent to the patient.
88. 88. The method of claim 87, wherein the additional therapeutic agent is a corticosteroid, a nonsteroidal anti-inflammatory drug (NSAID), chloroquine, hydroxychloroquineCyclosporine, azathioprine, methotrexate, mycophenolate mofetilOr cyclophosphamide
89. 89. The method of claim 87 or 88, wherein the IRAK4 pathway inhibitor and the other therapeutic agent are co-administered.
90. 90. The method of claim 87 or 88, wherein the IRAK4 pathway inhibitor and the other therapeutic agent are administered sequentially.
91. A kit of parts 91, for use in identifying a patient having an IRAK 4-mediated condition or disorder that may benefit from treatment with an IRAK4 pathway inhibitor, the kit comprising:

    (a) a polypeptide or polynucleotide capable of determining the expression level of or more genes listed in Table 1, and

    (b) instructions for using the polypeptide or polynucleotide to identify a patient having an IRAK 4-mediated disorder or condition that may benefit from treatment comprising an IRAK4 pathway inhibitor.
92. 92. The kit of claim 91, wherein the or more genes listed in Table 1 comprise or more genes selected from CD38, SOCS3, AQP9, CDKN1A, GADD45B, B4GALT5, IL15RA, TNFAIP3, SOCS1, IL1RN, PFKFB3, and BCL2A 1.
93. 93. The kit of claim 92, wherein the or more genes listed in Table 1 comprise or more genes selected from CD38, SOCS3, AQP9, CDKN1A, GADD45B, B4GALT5, IL15RA, TNFAIP3, SOCS1, IL1RN, and PFKFB 3.
94. 94. The kit of claim 93, wherein the or more genes listed in table 1 comprise or more genes selected from CD38, SOCS3, AQP9, CDKN1A, GADD45B, B4GALT5, IL15RA, TNFAIP3, and SOCS 1.
95. 95. The kit of claim 94, wherein the or more genes listed in Table 1 comprise all nine selected from CD38, SOCS3, AQP9, CDKN1A, GADD45B, B4GALT5, IL15RA, TNFAIP3, and SOCS 1.
96. 96. The kit of claim 95, wherein the or more genes listed in table 1 comprise all 11 selected from the group consisting of CD38, SOCS3, AQP9, CDKN1A, GADD45B, B4GALT5, IL15RA, TNFAIP3, SOCS1, IL1RN, and PFKFB 3.
97. 97. The kit of claim 96, wherein the or more genes listed in table 1 comprise all 12 selected from the group consisting of CD38, SOCS3, AQP9, CDKN1A, GADD45B, B4GALT5, IL15RA, TNFAIP3, SOCS1, IL1RN, PFKFB3, and BCL2a 1.
98. 98. The kit of claim 97, wherein the or more genes listed in table 1 are all 24 genes listed in table 1.