Sho Sendo

Objective Rheumatoid arthritis (RA) is an autoimmune disease in which the joint lining, or synovium, becomes highly inflamed and majorly contributes to disease progression. Understanding pathogenic processes in RA synovium is critical for identifying therapeutic targets. We performed laser capture microscopy (LCM) followed by RNA sequencing (LCM‐RNAseq) to study regional transcriptomes throughout RA synovium. Methods Synovial lining, sublining, and vessels were captured by LCM from seven RA and seven osteoarthritis (OA) patients. RNAseq was performed on RNA extracted from captured tissue. Principal component analysis (PCA) was performed on the sample set by disease state. Differential expression analysis was performed between disease states based on log2 fold‐change and q ‐value parameters. Pathway analysis was performed using Reactome Pathway Database on differentially expressed genes (DEGs) between disease states. Significantly enriched pathways in each synovial region were selected based on false discovery rate (FDR). Results RA and OA transcriptomes were distinguishable by PCA. Pairwise comparisons of synovial lining, sublining, and vessels between RA and OA revealed substantial differences in transcriptional patterns throughout the synovium. Hierarchical clustering of pathways based on significance revealed a pattern of association between biological function and synovial topology. Analysis of pathways uniquely enriched in each region revealed distinct phenotypic abnormalities. As examples, RA lining was marked by anomalous immune cell signaling, RA sublining by aberrant cell cycle, and RA vessels by alterations in heme scavenging. Conclusion LCM‐RNAseq confirms reported transcriptional differences between RA and OA synovium and provides evidence supporting a relationship between synovial topology and molecular anomalies in RA.