Biomarkers and methods for assessing psoriatic arthritis disease activity
Provided herein are biomarkers and methods for generating scores useful for assessing psoriatic arthritis (PsA) disease activity in subjects previously diagnosed with PsA. The invention also provides predictive model methods based on the biomarkers, as well as computer systems, software embodiments of the models for scoring and optionally classifying samples, and methods of recommending optimal therapeutic regimens.
1. A method for treating a subject having psoriatic arthritis (PsA), the method comprising:
performing at least one immunoassay on a blood sample from the subject to generate a dataset comprising protein level data for protein markers from a set 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);
calculating, using the protein level data, a PsA disease activity, wherein the PsA disease activity is significantly greater than found for a combination of control biomarkers that are indicative of PsA; and
administering a PsA therapeutic regimen to the subject in need thereof, wherein the therapeutic regimen comprises one or more of:
administering a therapeutic compound selected from disease-modifying antirheumatic drugs (DMARDs), biologic DMARDs, non-steroidal anti-inflammatory drugs (NSAIDs), and corticosteroids;
administering physical therapy, dietary modification and/or supplementation; and
administering bariatric surgical intervention.
2. The method of claim 1 , wherein performance of the at least one immunoassay comprises:
obtaining a blood sample from the subject, 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 the protein markers; and
detecting the complexes to generate the protein level data.
3. The method of claim 1 , wherein the at least one immunoassay comprises a multiplex assay.
4. The method of claim 1 , wherein the protein markers consist of at most 500 protein markers.
5. The method of claim 4 , wherein the protein markers consist of at most 250 protein markers.
6. The method of claim 4 , wherein the protein markers consist of at most 100 protein markers.
7. The method of claim 4 , wherein the protein markers consist of at most 50 protein markers.
8. The method of claim 4 , wherein the protein markers consist of at most 25 protein markers.
9. The method of claim 4 , wherein the protein markers consist of 12 protein markers.
10. The method of claim 1 , wherein the PsA disease activity is calculated using an interpretation function comprising the protein level data and values of one or more clinical assessments of the subject.
11. The method of claim 10 , wherein the interpretation function comprises a predicted Tender Joint Count 28 (TJC28) value, a predicted Swollen Joint Count28 (SJC28) value, and a predicted Patient Global Health (PGA) value.
12. The method of claim 11 , wherein the predicted values were obtained by Curds and Whey and Lasso (CW-Lasso).
13. The method of claim 11 , wherein the interpretation function is given by the formula: score=((0.56×(predicted TJC28) 0.5 +0.28×(predicted SJC28) 0.5 +0.36×log(CRP×10 −6 +1)+(0.14×(predicted PGA))+0.96)×10.53)+1.