Compendium of Synovial Signatures Identifies Pathologic Characteristics for Predicting Treatment Response in Rheumatoid Arthritis

Abstract

1Treatment of patients with rheumatoid arthritis (RA) is challenging due to clinical heterogeneity 2 and variability. Integration of RA synovial genome-scale transcriptomic profiling of different 3 patient cohorts can provide insights on the causal basis of drug responses. A normalized 4 compendium was built that consists of 256 RA synovial samples that cover an intersection of 5 11,769 genes from 11 datasets. Differentially expression genes (DEGs) that were identified in 6 three independent methods were fed into functional network analysis, with subsequent grouping 7 of the samples based on a non-negative matrix factorization method. Finally, we built a predictive 8 model for treatment response by using RA-relevant pathway activation scores and four machine 9 learning classification techniques. We identified 876 up-regulated DEGs including 24 known 10 genetic risk factors and 8 drug targets. DEG-based subgrouping revealed 3 distinct RA patient 11 clusters with distinct activity signatures for RA-relevant pathways. In the case of infliximab, we 12 constructed a classifier of drug response that was highly accurate with an AUC/AUPR of 0.92/0.86. 13The most informative pathways in achieving this performance were the NFB-, FcRI-TCR-, and 14 TNF signaling pathways. Similarly, the expression of the HMMR, PRPF4B, EVI2A, RAB27A, 15 MALT1, SNX6, and IFIH1 genes contributed in predicting the patient outcome. Construction and 16 analysis of normalized synovial transcriptomic compendia can provide useful insights for 17 understanding RA-related pathway involvement and drug responses for individual patients. The 18 efficacy of a predictive model for personalized drug response has been demonstrated and can be 19 generalized to several drugs, co-morbidities, and other relevant features.20 21 22