Defining Inflammatory Cell States in Rheumatoid Arthritis Joint Synovial Tissues by Integrating Single-cell Transcriptomics and Mass Cytometry

Abstract

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

Dendritic cells, T cells and their interaction in rheumatoid arthritis

“…These synovial DCs are generally mature and NF-κB is over-expressed. Multiple subsets of MHC class II + APCs are present in RA synovial tissue, including Toll-like receptor (TLR)-activated myeloid-derived cells, CD11c + CD20 + activated B cells and MHC class II hi fibroblast-like synoviocytes [30]. Multiple subsets of MHC class II + APCs are present in RA synovial tissue, including Toll-like receptor (TLR)-activated myeloid-derived cells, CD11c + CD20 + activated B cells and MHC class II hi fibroblast-like synoviocytes [30].…”

Tissue‐Resident Memory T Cells: Sequestered Immune Sensors and Effectors of Inflammation in Spondyloarthritis

“…In rheumatoid arthritis (RA), analysis of synovial tissue with single‐cell RNA sequencing and cytometry by time‐of‐flight mass spectrometry have revealed discrete cell subpopulations with transcriptomic and cell surface expression profiles linked to functional activities . These analyses, focused on the synovium and not the peripheral blood, provided new insights regarding key pathogenic cell–cell interactions and underscore the necessity of examining cellular and molecular events in the target tissue.…”

Advances in genetics toward identifying pathogenic cell states of rheumatoid arthritis

“…The ABF is defined as the likelihood ratio of the probability of observing an effect size according to a normal distribution (mean 0, variance equal to the variance of all effect sizes) to the probability of observing the same effect size according to a normal distribution with wider variance, eg adjusted for a prior of observing an odds ratio of 1.5. Of the RA‐associated putatively causal variants, we rediscovered missense variants in PTPN22 and TYK2 and found a novel missense variant rs35677470 in DNASE1L3 (expressed in stromal fibroblasts) and noncoding variants in CD28‐CTLA4 (rs55686954, rs117701653) and TNFAIP3 (rs35926684). The noncoding variants rs117701653 and rs35926684, near CD28‐CTLA4 and TNFAIP3 , respectively, exhibited allele‐specific protein binding activity (electrophoretic mobility shift assay (EMSA)) and CD4 + T cell specific differential enhancer activity (Luciferase reporter assay).…”

“…One such initiative is the Accelerating Medicines Partnership, which in its first phase profiled more than 5000 cells in 36 RA patients and 15 osteoarthritis (OA) controls. Our group developed a CCA graph‐based clustering strategy to identify single cell populations by leveraging correlated regulatory structure with bulk reference samples . As a result, 3 CD4 + T cell subtypes were identified with distinct expression profiles, CCR7+ T cells, Tregs, and a mix of T peripheral (Tph) and follicular (Tfh) helper cells.…”

“…Our group developed a CCA graphbased clustering strategy to identify single cell populations by leveraging correlated regulatory structure with bulk reference samples. 51 As a re-…”