Fig. 1
A comprehensive single-cell atlas of human synovial tissue by FCM and scRNA-seq analysis. a Schematic workflow of the experimental strategy, including “Biomarker Identification” and “Biomarker Verification.” Patients with ACL injury and loss of range of motion were treated properly in the ACL reconstruction surgery. After the initial surgery, patients underwent a year of rehabilitation were recruited, and those with knee arthrofibrosis were allocated in the AF group (arthrofibrosis) while others were allocated in the NC group (negative controls). Synovial tissues were obtained during the second surgery and digested to single-cell suspension. FCM and scRNA-seq analysis were performed to identify the biomarker of knee arthrofibrosis, which was further verified in cell lines and clinical patients. b Representative pre-reconstruction and post-reconstruction MRI figures of patients in AF and NC groups. c Percentages of major synovial cell types assesed by flow cytometry. d Cell clusters across 68 144 cells (six donors) shown on a UMAP visualization colored according to cell types. e Bubble plot of clustering analysis revealing six cell clusters defined in (d) with scaled expression of differentially expressed genes. f Cell clusters from six donors shown on a UMAP visualization colored by donors. g Cluster abundance of synovial tissue by scRNA-seq analysis. h UMAP plots showing subpopulations of fibroblasts, macrophages, FLS, endothelial cells, and VSMC by scRNA-seq. ACL, anterior cruciate ligament; FCM, flow cytometry; scRNA-seq, single-cell RNA sequencing; UMAP, uniform manifold approximation and projection; FLS, fibroblast-like synoviocytes; VSMC, vascular smooth muscle cells; ***P < 0.001
