Defining inflammatory cell states in rheumatoid arthritis joint synovial tissues by integrating single-cell transcriptomics and mass cytometry

To define the cell populations that drive joint inflammation in rheumatoid arthritis (RA), we applied single-cell RNA sequencing (scRNA-seq), mass cytometry, bulk RNA sequencing (RNA-seq) and flow cytometry to T cells, B cells, monocytes, and fibroblasts from 51 samples of synovial tissue from patients with RA or osteoarthritis (OA). Utilizing an integrated strategy based on canonical correlation analysis of 5,265 scRNA-seq profiles, we identified 18 unique cell populations. Combining mass cytometry and transcriptomics revealed cell states expanded in RA synovia: THY1(CD90)⁺HLA-DRA^hi sublining fibroblasts, IL1B⁺ pro-inflammatory monocytes, ITGAX⁺TBX21⁺ autoimmune-associated B cells and PDCD1⁺ peripheral helper T (T_PH) cells and follicular helper T (T_FH) cells. We defined distinct subsets of CD8⁺ T cells characterized by GZMK⁺, GZMB⁺, and GNLY⁺ phenotypes. We mapped inflammatory mediators to their source cell populations; for example, we attributed IL6 expression to THY1⁺HLA-DRA^hi fibroblasts and IL1B production to pro-inflammatory monocytes. These populations are potentially key mediators of RA pathogenesis.