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-seq and flow cytometry to T cells, B cells, monocytes and fibroblasts from 51 samples of synovial tissue from patients with RA or osteoarthritis. 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 together 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 + T peripheral helper (Tph) and T follicular helper (Tfh). We defined distinct subsets of CD8 + T cells characterized by a GZMK + , GZMB + and GNLY + phenotype. 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.

Lupus nephritis is a potentially fatal autoimmune disease for which the current treatment is ineffective and often toxic. To develop mechanistic hypotheses of disease, we analyzed kidney samples from patients with lupus nephritis and from healthy control subjects using single-cell RNA sequencing. Our analysis revealed 21 subsets of leukocytes active in disease, including multiple populations of myeloid cells, T cells, natural killer cells and B cells that demonstrated both pro-inflammatory responses and inflammation-resolving responses. We found evidence of local activation of B cells correlated with an age-associated B-cell signature and evidence of progressive stages of monocyte differentiation within the kidney. A clear interferon response was observed in most cells. Two chemokine receptors, CXCR4 and CX3CR1 , were broadly expressed, implying a potentially central role in cell trafficking. Gene expression of immune cells in urine and kidney was highly correlated, which would suggest that urine might serve as a surrogate for kidney biopsies.

Wei, Slowikowski, Fonseka, Rao et al A single cell map of the RA joint Abstract 78 To define the cell populations in rheumatoid arthritis (RA) driving joint inflammation, we applied 79 single-cell RNA-seq (scRNA-seq), mass cytometry, bulk RNA-seq, and flow cytometry to sorted 80 T cells, B cells, monocytes, and fibroblasts from 51 synovial tissue RA and osteoarthritis (OA) 81 patient samples. Utilizing an integrated computational strategy based on canonical correlation 82 analysis to 5,452 scRNA-seq profiles, we identified 18 unique cell populations. Combining mass 83 cytometry and transcriptomics together revealed cell states expanded in RA synovia: 84 THY1 + HLA high sublining fibroblasts (OR=33.8), IL1B + pro-inflammatory monocytes (OR=7.8), 85 CD11c + T-bet + autoimmune-associated B cells (OR=5.7), and PD-1 + Tph/Tfh (OR=3.0). We also 86 defined CD8 + T cell subsets characterized by GZMK + , GZMB + , and GNLY + expression. Using 87 bulk and single-cell data, we mapped inflammatory mediators to source cell populations, for 88 example attributing IL6 production to THY1 + HLA high fibroblasts and naïve B cells, and IL1B to 89 pro-inflammatory monocytes. These populations are potentially key mediators of RA 90 pathogenesis. 91 92 93 94 95 96 97 98 99 100