Biomarkers and methods for assessing response to inflammatory disease therapy

1. A method for treating a subject for rheumatoid arthritis (RA), the method comprising:

i) performing at least one immunoassay on a blood sample from the subject to generate a dataset comprising protein level data for at least seven protein markers of a set comprising Serum Amyloid P-component (SAP), Cathepsin D (CPSD), Chemerin (TIG2), alpha-1-Microglobulin (A1 M), Haptoglobin (Hp), Pigment Epithelium Derived Factor (PEDF), Clusterin (CLU), Tissue type Plasminogen activator (tPA), C-reactive protein (CRP), Monocyte Chemotactic Protein 4 (MCP-4), Alpha-1-acid glycoprotein 1 (AGP-1), Connecting Peptide (C-Peptide), Complement Factor H (CFH), Pulmonary and Activation Regulated chemokine (PARC), growth-regulated alpha protein (GRO-alpha), Sex Hormone-Binding Globulin (SHBG), Matrix Metalloproteinase-7 (MMP-7), Growth/differentiation factor 15 (GDF-15), Fibroblast Growth Factor 21 (FGF-21), Angiopoietin-related protein 3 (ANGPTL3), Hemopexin (HPX), FASLG Receptor (FAS), Receptor for Advanced Glycosylation End products (RAGE), CD5 Antigen-like (CD5L), Endoglin (ENG), van Willebrand Factor (VWF), Apolipoprotein C-111 (Apo C-111), Interleukin-1 receptor antagonist (IL-1ra), Ficolin-3 (FCN3), Peroxiredoxin-4 (Prx-IV), ST2 cardiac biomarker (ST2), Sortilin (SORT1), Tumor necrosis factor ligand superfamily member 12 (Tweak), Phosphoserine Aminotrasferase (PSAT), Heparin-Binding EGF-Like Growth Factor (HB-EGF), Interleukin-8 (IL-8), Beta-2-Microglobulin (B2M), Apolipoprotein E (Apo E), Urokinase-type Plasminogen Activator (uPA), Adrenomedullin (ADM), Urokinase-type plasminogen, activator receptor (uPAR), Tetranectin (TN), E-Selectin (ESEL), Monokine Induced by Gamma Interferon (MIG), Glucagon-like Peptide 1, total (GLP-1 total), Interleukin-12 Subunit p40 (IL-12p40), Cartilage Oligomeric Matric protein (COMP), Apolipoprotein H (Apo H), Factor VII (F7), Interferon-inducible T-cell alpha chemoattractant (ITAC), Antileukoproteinase (ALP), Thymus and activation regulated chemokine (TARC), Plasminogen Activator Inhibitor 1 (PAI-1), Interleukin-15 (IL-15), Ceruloplasmin (CP), Complement Factor H-Related Protein 1 (CFHR1), Protein DJ-1 (DJ-1), Alpha-Fetoprotein (AFP), Chemokine CC-4 (HCC-4), Ferritin (FRTN), Immunoglobulin A (IgA), thrombin-Activatable Fibrinolysis (TAFT), Cystatin-B (CSTB), Alpha-1-Antichymotrypsin (AACT), Pancreatic Polypeptide (PPP), HeatShock Protein 70 (HSP-70), Transferrin Receptor Protein (TFR1), Tamm-Horsfall Urinary Glycoprotein (THP), Tenascin-C(TN-C), pepsinogen 1 (PG1), Hepatocyte Growth Factor (HGF), T-Cell-Specific Protein RANTES (RANTES), Tumor Necrosis Factor Receptor 2 (TNFR2), Macrophage Colony-Stimulating Factor 1 (M-CSF), Beta Amyloid 1-40 (AB-40), cystatin-C, Tissue Inhibitor of Metalloproteinases 3 (TIMP-3), Insulin-like Growth Factor binding Protein 4 (IGFBP4), Gastric Inhibitory Polypeptide (GIP), Midkine (MDK), Angiogenin (ANG), Stem Cell Factor (SCF), Myeloid Progenitor Inhibitory Factor 1 (MPIF-1), Osteoprotegerin (OPG), CD 40 antigen (CD40), Monocyte Chemotactic Protein 2 (MCP-2), Insulin-like Growth Factor-binding Protein 1 (GFBP-1), Vitamin K-Dependent Protein S (VKDPS), Hepatocyte Growth Factor Receptor (HGFR), Brain-Derived Neurotrophic Factor (BDNF), Macrophage-Stimulating Protein (MSP), and Monocyte Chemotactic Protein 1 (MCP-1),

wherein the at least seven protein markers comprise TIG2, PEDF, CPSD, SAP, C-Peptide, tPA, and FAS;

ii) calculating a biomarker disease activity score (BDAS) for the subject by applying the protein level data alone or in combination with a clinical parameter or assessment to an interpretation function, wherein the BDAS provides a quantitative measure of RA disease activity in the subject; and identifying the subject having the BDAS that indicates a need for therapy; and

iii) administering a therapy to the identified subject comprising one or more of:

administering a therapeutic compound selected from disease-modifying anti-rheumatic drugs (DMARDs), biologic DMARDs, non-steroidal anti-inflammatory drugs (NSAIDs), and corticosteroids; and

administering bariatric surgical intervention.

2. The method of claim 1 , wherein the at least seven protein markers comprise Tyk2, PEDF, CPSD, SAP, C-Peptide, tPA, and FAS, and one or more of A1M, SHBG, GDF-15, Hp, CD5L, AGP-1, CLU, CRP, CFH, RAGE, FGF-21, vWF, AACT, CSTB, ST2, TAFI, uPA, TN, Prx-IV, Tweak, PSAT, GLP-1 total, and IL-15.

3. The method of claim 1 , wherein the at least seven protein markers comprise TIG2, PEDF, CPSD, SAP, C-Peptide, tPA, and FAS, and one or more of SHBG, A1M, AGP-1, CD5L, CRP, PSAT, uPA, GIP, Prx-IV, HGF, and IL-15.

4. A method for treating a subject for rheumatoid arthritis (RA), the method comprising:

i) performing at least one immunoassay on a blood sample from the subject to generate a dataset comprising protein level data for at least seven protein markers of a set comprising Serum Amyloid P-component (SAP), Cathepsin D (CPSD), Chemerin (TIG2), alpha-1-Microglobulin (A1 M), Haptoglobin (Hp), Pigment Epithelium Derived Factor (PEDF), Clusterin (CLU), Tissue type Plasminogen activator (tPA), C-reactive protein (CRP), Monocyte Chemotactic Protein 4 (MCP-4), Alpha-1-acid glycoprotein 1 (AGP-1), Connecting Peptide (C-Peptide), Complement Factor H (CFH), Pulmonary and Activation Regulated chemokine (PARC), growth-regulated alpha protein (GRO-alpha), Sex Hormone-Binding Globulin (SHBG), Matrix Metalloproteinase-7 (MMP-7), Growth/differentiation factor 15 (GDF-15), Fibroblast Growth Factor 21 (FGF-21), Angiopoietin-related protein 3 (ANGPTL3), Hemopexin (HPX), FASLG Receptor (FAS), Receptor for Advanced Glycosylation End products (RAGE), CD5 Antigen-like (CD5L), Endoglin (ENG), van Willebrand Factor (VWF), Apolipoprotein C-111 (Apo C-111), Interleukin-1 receptor antagonist (IL-1ra), Ficolin-3 (FCN3), Peroxiredoxin-4 (Prx-IV), ST2 cardiac biomarker (ST2), Sortilin (SORT1), Tumor necrosis factor ligand superfamily member 12 (Tweak), Phosphoserine Aminotrasferase (PSAT), Heparin-Binding EGF-Like Growth Factor (HB-EGF), Interleukin-8 (IL-8), Beta-2-Microglobulin (B2M), Apolipoprotein E (Apo E), Urokinase-type Plasminogen Activator (uPA), Adrenomedullin (ADM), Urokinase-type plasminogen, activator receptor (uPAR), Tetranectin (TN), E-Selectin (ESEL), Monokine Induced by Gamma Interferon (MIG), Glucagon-like Peptide 1, total (GLP-1 total), Interleukin-12 Subunit p40 (IL-12p40), Cartilage Oligomeric Matric protein (COMP), Apolipoprotein H (Apo H), Factor VII (F7), Interferon-inducible T-cell alpha chemoattractant (ITAC), Antileukoproteinase (ALP), Thymus and activation regulated chemokine (TARC), Plasminogen Activator Inhibitor 1 (PAI-1), Interleukin-15 (IL-15), Ceruloplasmin (CP), Complement Factor H-Related Protein 1 (CFHR1), Protein DJ-1 (DJ-1), Alpha-Fetoprotein (AFP), Chemokine CC-4 (HCC-4), Ferritin (FRTN), Immunoglobulin A (IgA), thrombin-Activatable Fibrinolysis (TAFT), Cystatin-B (CSTB), Alpha-1-Antichymotrypsin (AACT), Pancreatic Polypeptide (PPP), HeatShock Protein 70 (HSP-70), Transferrin Receptor Protein (TFR1), Tamm-Horsfall Urinary Glycoprotein (THP), Tenascin-C(TN-C), pepsinogen 1 (PG1), Hepatocyte Growth Factor (HGF), T-Cell-Specific Protein RANTES (RANTES), Tumor Necrosis Factor Receptor 2 (TNFR2), Macrophage Colony-Stimulating Factor 1 (M-CSF), Beta Amyloid 1-40 (AB-40), cystatin-C, Tissue Inhibitor of Metalloproteinases 3 (TIMP-3), Insulin-like Growth Factor binding Protein 4 (IGFBP4), Gastric Inhibitory Polypeptide (GIP), Midkine (MDK), Angiogenin (ANG), Stem Cell Factor (SCF), Myeloid Progenitor Inhibitory Factor 1 (MPIF-1), Osteoprotegerin (OPG), CD 40 antigen (CD40), Monocyte Chemotactic Protein 2 (MCP-2), Insulin-like Growth Factor-binding Protein 1 (GFBP-1), Vitamin K-Dependent Protein S (VKDPS), Hepatocyte Growth Factor Receptor (HGFR), Brain-Derived Neurotrophic Factor (BDNF), Macrophage-Stimulating Protein (MSP), and Monocyte Chemotactic Protein 1 (MCP-1),

wherein the at least seven protein markers comprise TIG2, PEDF, CPSD, SAP, C-Peptide, tPA, and FAS;

ii) obtaining reference data from a reference group, the reference data comprising clinical assessment data for each member of the reference group and protein level data for each member of the reference group using the same markers as used for the subject,

wherein the clinical assessment data comprises one or more of DAS28, DAS28-ESR, DAS28-CRP, health assessment questionnaire (HAQ), modified HAQ (mHAQ), multi-dimensional HAQ (MDHAQ), visual analog scale (VAS), physician global assessment VAS, patient global assessment VAS, pain VAS, fatigue VAS, overall VAS, sleep VAS, simplified disease activity index (SDAI), clinical disease activity index (CDAI), routine assessment of patient index data (RAPID), RAPID3, RAPID4, RAPIDS, American College of Rheumatology (ACR), ACR20, ACR50, ACR70, SF-36, RA MRI score (RAMRIS), total Sharp score (TSS), van der Heijde-modified TSS, van der Heijde modified Sharp score (SHS), Larsen score, TJC, swollen joint count (SJC), CRP titer, and erythrocyte sedimentation rate (ESR);

iii) applying a statistical tool to the reference data for determining a coefficient in an interpretation function for each of the protein level data;

iv) calculating a biomarker disease activity score (BDAS) for the subject by applying the protein level data from the subject to the interpretation function, wherein the BDAS provides a quantitative measure of RA disease activity in the subject; and identifying the subject having the BDAS that indicates a need for therapy; and

v) administering a therapy to the identified subject comprising one or more of:

administering a therapeutic compound selected from disease-modifying anti-rheumatic drugs (DMARDs), biologic DMARDs, non-steroidal anti-inflammatory drugs (NSAIDs), and corticosteroids; and

administering bariatric surgical intervention.

5. The method of claim 4 , wherein the subject has one or more of RA radiographic progression, flare, or joint damage.

6. The method of claim 4 , wherein the at least seven protein markers comprise TIG2, PEDF, CPSD, SAP, C-Peptide, tPA, and FAS, and one or more of A1M, SHBG, GDF-15, Hp, CD5L, AGP-1, CLU, CRP, CFH, RAGE, FGF-21, vWF, AACT, CSTB, ST2, TAFI, uPA, TN, Prx-IV, Tweak, PSAT, GLP-1 total, and IL-15.

7. The method of claim 4 , wherein the at least seven protein markers comprise TIG2, PEDF, CPSD, SAP, C-Peptide, tPA, and FAS, one or more of SHBG, A1M, AGP-1, CD5L, CRP, PSAT, uPA, GIP, Prx-IV, HGF, and IL-15.