Eleven clusters in RA synovium were identified and showed in uniform manifold approximation and projection (UAMP) (Fig. 1a) and defined as fibroblasts (PRG4 and PDPN), mural cells (THY1 and MCAM), endothelial cells (CD34 and VWF), CD4+ T cells (CD2 and CD4), CD8+ T cells (CD8A, GNLY, and GZMB), natural killer cells (LTB and CD3D), synovium macrophages (CD68 and LYZ), periperal blood macrophages (CD68 and LYZ), plasma cells, B cells (CD79A and CD37), and STMN1+ cells (STMN1) referring to the canonical marker genes (Fig. 1b). Here, CD68 is linked to rheumatoid arthritis.