Transcriptomic analysis of synovial cells derived from collagen-induced arthritis mice treated with a JAK inhibitor, upadacitinib

In rheumatoid arthritis (RA), inflammation and joint destruction are exacerbated by a complicated interaction among immune cells, synovial fibroblasts and bone cells. It remains to be elucidated which cell-cell interaction critically drives the pathogenesis of RA and serves as a therapeutic target for synthetic disease modifying antirheumatic drugs (DMARDs) such as janus kinase (JAK) inhibitors. we performed a scRNA-seq analysis of the synovium of collagen-induced arthritis (CIA) mice treated with JAK inhibitor, followed by a computational analysis to identify the drug target cells and signaling pathways in vivo scRNA-seq analysis was performed on synovial cells which were isolated from the knee joints of CIA mice treated with a JAK inhibitor, upadacitinib (n=6). Alignment, quantitation and aggregation of the sample count matrices were performed using the 10x Genomics Cell Ranger pipeline (v.3.0) according to the manufacturer’s protocol (GENEWIZ).