A comprehensive single-cell atlas of freshly-dissociated human synovium in inflammatory arthritis with an optimized dissociation protocol for prospective fresh synovial biopsy collection

Abstract Single-cell RNA-sequencing is advancing our understanding of synovial pathobiology in inflammatory arthritis. Here, we optimized the protocol for dissociation of synovial biopsies and created a comprehensive reference single-cell atlas of fresh human synovium in inflammatory arthritis. We derived our protocol from the published dissociation method for cryopreserved synovium (Donlin L. et al. Arthritis Res. Ther. 2019) with modifications to enrich synovial cells and minimize cell loss. These modifications enabled consistently high cell yield and viability, thereby minimizing the rate of synovial tissue sample dropout. Our single-cell atlas of the human synovium comprised more than 100’000 unsorted single-cell profiles from 27 synovia of patients with inflammatory arthritis. Synovial cells formed ten lymphoid, 14 myeloid and 17 stromal cell clusters, including IFITM2+ synovial neutrophils. We identified lining SOD2highSAA1+SAA2+ and transitional SERPINE1+COL5A3+ synovial fibroblasts, exhibiting gene signatures linked to cartilage breakdown (SDC4) and extracellular matrix remodelling (LOXL2, TGFBI, TGFB1), respectively. We uncovered synovial endothelial cell diversity and broadened the transcriptional characterization of tissue-resident FOLR2+ COLEC12+ and SLC40A1+ synovial macrophages, inferring their extracellular matrix sensing and iron recycling activities. Our research brings an efficient synovium dissociation protocol for prospectively collected fresh synovial biopsies and expands the knowledge about human synovium composition in inflammatory arthritis.