- Zhang, Fan;
- Wei, Kevin;
- Slowikowski, Kamil;
- Fonseka, Chamith Y;
- Rao, Deepak A;
- Kelly, Stephen;
- Goodman, Susan M;
- Tabechian, Darren;
- Hughes, Laura B;
- Salomon-Escoto, Karen;
- Watts, Gerald FM;
- Jonsson, A Helena;
- Rangel-Moreno, Javier;
- Meednu, Nida;
- Rozo, Cristina;
- Apruzzese, William;
- Eisenhaure, Thomas M;
- Lieb, David J;
- Boyle, David L;
- Mandelin, Arthur M;
- Boyce, Brendan F;
- DiCarlo, Edward;
- Gravallese, Ellen M;
- Gregersen, Peter K;
- Moreland, Larry;
- Firestein, Gary S;
- Hacohen, Nir;
- Nusbaum, Chad;
- Lederer, James A;
- Perlman, Harris;
- Pitzalis, Costantino;
- Filer, Andrew;
- Holers, V Michael;
- Bykerk, Vivian P;
- Donlin, Laura T;
- Anolik, Jennifer H;
- Brenner, Michael B;
- Raychaudhuri, Soumya
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-DRAhi sublining fibroblasts, IL1B+ pro-inflammatory monocytes, ITGAX+TBX21+ autoimmune-associated B cells and PDCD1+ peripheral helper T (TPH) cells and follicular helper T (TFH) 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-DRAhi fibroblasts and IL1B production to pro-inflammatory monocytes. These populations are potentially key mediators of RA pathogenesis.