Mazzucco, M. R.; Mehta, B.; Ruiz-Ortiz, J.; Hale, C.; Omi, F.; Singh, P.; Yuan, R.; Lessard, S.; Song, E. K.; Zhang, M.; Younis, S.; Robinson, W. H.; Ramirez, D.; DiCarlo, E.; Wang, W.; Carroll, T.; Rodriguez, J.; Sculco, P.; Li, X.; Wu, Y.; Darnell, R. B.; Lotz, M.; Miller, R. E.; Maerz, T.; Malfait, A.-M.; Otero, M.; Orange, D. E.

Objectives: To identify synovial transcriptional clusters in human knee osteoarthritis (OA) and determine how these relate to synovial histologic features, cell-type-associated gene expression, and cartilage degeneration severity. Methods: Bulk RNA sequencing (RNA-seq) of synovial tissue from n = 135 patients with knee OA was analyzed using consensus clustering. Clusters were compared by clinical and histologic features, including cartilage degeneration severity (OARSI score). Single-cell RNA-seq (n = 18) and spatial transcriptomics were used to relate cartilage degeneration-associated gene expression patterns to synovial cell populations. Results: Four synovial transcriptional clusters that differed in synovial histologic features and cartilage degeneration severity were identified. Greater cartilage degeneration was associated with enrichment of lining fibroblast- and inflammatory myeloid-associated gene expression, whereas lesser cartilage degeneration was associated with enrichment of sublining fibroblast, endothelial, mural cell, and adipocyte-associated gene expression. Conclusions: Human knee OA synovium segregates into transcriptional clusters associated with cartilage degeneration severity. Synovial transcriptional heterogeneity corresponds to cell-type-associated gene expression.