Single cell RNA sequencing on synovium, meniscus and cartilage of rheumatoid arthritis

Rheumatoid arthritis (RA) induced destruction of knee joints is a common cause of total knee arthroplasty (TKA). Under single cell RNA sequencing generated by 10x Genomics, we identified CD142+ synovial fibroblasts as a novel cluster, located at the sublining layer in normal and osteoarthritis knee synovium, but elevated and distributed at the lining layer in RA knee synovium, and infiltrated in multiple RA joint synovia. Intra-articular injection of CD142+ synovial fibroblasts can quickly and drastically damage the meniscus but has a slight effect on cartilage.Long-term follow-up of the RA cohort indicated that enriched CD142+ synovial fibroblasts in the lining layer was a risk factor for severe joint destruction and eventually underwent TKA. Our results demonstrate that CD142+ synovial fibroblasts can be used as an indicator to assess prognosis and a therapeutic target to inhibit meniscal damage, thereby alleviating RA knee joint destruction. This dataset presents scRNA-seq raw and processed data files on RA cartilage, meniscus, and synovium. Fresh human cartilage, meniscus and synovial tissues obtained from the same RA knee by total knee arthroplasty were made into cell suspensions, and were captured with 10x Genomics based on the NovaSeq 6000 platform. For tsv.gz file, it is original processed matrix file. For RDS file, it is Seurat file that contains celltype reference.