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

F Zhang, K Wei, K Slowikowski, CY Fonseka… - Nature …, 2019 - nature.com
F Zhang, K Wei, K Slowikowski, CY Fonseka, DA Rao, S Kelly, SM Goodman, D Tabechian…
Nature immunology, 2019nature.com
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 …
Abstract
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.
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