Biomarkers and methods for assessing myocardial infarction and serious infection risk in rheumatoid arthritis patients

1. A method for treating cardiovascular disease (CVD) or infection in a subject with rheumatoid arthritis (RA), the method comprising:

performing an immunoassay on a sample from the subject to generate a dataset comprising protein level data for at least four protein markers of the group comprising chitinase 3-like 1 (cartilage glycoprotein-39) (CHI3L1); C-reactive protein, pentraxin-related (CRP); epidermal growth factor (beta-urogastrone) (EGF); interleukin 6 (interferon, beta 2) (IL6); leptin (LEP); matrix metallopeptidase 1 (interstitial collagenase) (MMP1); matrix metallopeptidase 3 (stromelysin 1, progelatinase) (MMP3); resistin (RETN); serum amyloid A1 (SAA1); tumor necrosis factor receptor superfamily, member 1A (TNFRSF1A); vascular cell adhesion molecule 1 (VCAM1); and, vascular endothelial growth factor A (VEGFA), wherein the at least four protein markers comprise LEP, CRP, CHI3L1, and MMP1; and

calculating a risk score for the sample indicating CVD or infection present in the subject by combining the dataset with a clinical parameter and a clinical assessment; and

administering a therapeutic regimen to the subject comprising one or more of:

administering a therapeutic compound selected from a Disease-modifying antirheumatic drug (DMARD), a biologic DMARD, a non-steroidal anti-inflammatory drug (NSAID), and a corticosteroid;

administering dietary modification and/or supplementation; and

administering bariatric surgical intervention.

2. The method of claim 1 , wherein the infection is associated with rheumatoid arthritis (RA).

3. The method of claim 1 , wherein the infection is a serious infection event.

4. The method of claim 1 , wherein the DMARD is selected from methotrexate (MTX), azathioprine (AZA), bucillamine (BUC), chloroquine (CQ), cyclosporine, doxycycline (DOXY), hydroxychloroquine (HCQ), intramuscular gold (IM gold), leflunomide (LEF), levofloxacin (LEV), sulfasalazine (SSZ), folinic acid, D-pencillamine, gold auranofin, gold aurothioglucose, gold thiomalate, cyclophosphamide, chlorambucil, infliximab, adalimumab, etanercept, golimumab, anakinra, abatacept, rituximab, and tocilizumab.

5. The method of claim 1 , wherein the clinical parameter is a selected from age, sex, smoking status, adiposity, body mass index (BMI), and race/ethnicity.

6. The method of claim 5 , wherein the clinical parameters are age, sex, and race/ethnicity.

7. The method of claim 1 , further comprising a period of monitoring the subject's symptoms before administering treatment.

8. The method of claim 1 , wherein the clinical assessment is selected from a Disease Activity Score (DAS), a DAS28, a DAS28-CRP, a DAS28-ESR, a Sharp score, a tender joint count (TJC), a swollen joint count (SJC), a Health assessment questionnaire (HAQ), a modified HAQ (mHAQ), a multi-dimensional HAQ (MD HAQ), a visual analog scale (VAS), a physician global assessment VAS, a patient global assessment VAS, a pain VAS, a fatigue VAS, an overall VAS, a sleep VAS, a simplified disease activity index (SDAI), a clinical disease activity index (CDAI), a routine assessment of patient index data (RAPID), a RAPID3, a RAPID4, a RAPID5, an American College of Rheumatology score (ACR), an ACR20, an ACR50, an ACR70, a SF-36, a RA MRI score (RAMRIS), a total Sharp score (TSS), a van der Heijde-modified TSS, a Sharp-van der Heijde score (SHS), a Larsen score, a CRP titer, and an erythrocyte sedimentation rate (ESR).

9. The method of claim 1 , wherein the immunoassay comprises a multiplex assay.

10. The method of claim 1 , wherein the immunoassay comprises:

obtaining the blood sample, wherein the blood sample comprises the protein markers;

contacting the blood sample with a plurality of distinct reagents;

generating a plurality of distinct complexes between the reagents and markers; and

detecting the complexes to generate the data.

11. The method of claim 1 , wherein the calculating a risk score uses a reference group of at least 10,000 patients.

12. The method of claim 1 , wherein the cardiovascular disease is a coronary heart disease (CHD).

13. The method of claim 12 , wherein the CHD is one or more of myocardial infarction (MI), percutaneous coronary intervention (PCI), and coronary artery bypass grafting (CABG).

14. The method of claim 1 , wherein the risk score is adjusted to a scale of 1-100.

15. The method of claim 14 , wherein a threshold for indicating risk of CVD or infection is 30.

16. The method of claim 1 , further comprising monitoring a response of the subject to a treatment by obtaining one or more additional risk scores for the subject after the treatment.

17. The method of claim 1 , wherein the calculating a risk score uses a statistical tool to derive an interpretation function based on a predictive model of the subject's inflammatory disease.

18. The method of claim 17 , wherein the statistical tool comprises one or more of Cox proportional hazards, clustering algorithms, analysis of variants (ANOVA), Ada-boosting, Classification and Regression Trees (CART), boosted CART, Random Forest (RF), Recursive Partitioning Trees (RPART), Curds and Whey (CW), Curds and Whey-Lasso, principal component analysis (PCA), factor rotation analysis, Linear Discriminant Analysis (LDA), Eigengene Linear Discriminant Analysis (ELDA), quadratic discriminant analysis, Discriminant Function Analysis (DFA), Hidden Markov Models, kernel density estimation, kernel partial least squares algorithm, kernel matching pursuit algorithm, kernel Fisher's discriminate analysis algorithm, kernel principal components analysis algorithm; linear regression, Stepwise Regression, Forward-Backward Variable Stepwise Regression, Lasso shrinkage and selection, Elastic Net regularization and selection, Lasso and Elastic Net-regularized generalized linear model, Logistic Regression (LogReg), Kth-nearest neighbor (KNN), non-linear regression, classification, neural networks, partial least square, rules based classification, shrunken centroids (SC), sliced inverse regression, Standard for the Exchange of Product model data, Application Interpreted Constructs (StepAIC), super principal component (SPC) regression, Support Vector Machines (SVM), and Recursive Support Vector Machines (RSVM).