A multi-tissue human knee single-cell atlas identifies that osteoarthritis reduces regenerative tissue stem cells while increasing inflammatory pain macrophages

Osteoarthritis (OA) affects the entire knee joint; however, cross-tissue molecular mechanisms are poorly understood due to a lack of comprehensive, integrated analysis. We constructed the first comprehensive single-cell RNA sequencing knee OA atlas from articular cartilage, meniscus, synovium, and subchondral bone which showed active communication between them. Healthy synovium and meniscus contain the largest populations of tissue stem cells (TSCs) and immune cells that are altered in OA. The regenerative TSCs expressing SDF1, SOX9, CD146, PDGFRB, and CD105 decrease during OA, whereas osteogenic TSCs expressing osteogenic differentiation-related factor NT5E (CD73) are increased. In OA, the balance between regenerative and osteogenic TSCs shifts in the OA state with an increased number of osteogenic TSCs. We also report an increased level of quadruple-positive inflammatory (IL1B-IL6-NOS2-TNF) and pain marker (P2RX7) specific macrophages in OA. Fibroblasts are enriched in OA-synovium and may contribute to fibrosis. Importantly, OA cartilage contains unique MMP13-producing detrimental chondrocytes along with RUNX2-producing chondrocytes that worsen OA pathophysiology. This atlas provides a novel avenue for potential therapeutic applications in human knee OA and other musculoskeletal diseases and injuries, targeting synovium and meniscus to intervene in OA-specific molecular and cellular alterations.