Fig. 3

Gene signatures of different fibroblasts subset in LTS. (a) Volcano plot highlighted the top 5 differentially expressed genes (DEGs) in each cell type. The Y-axis represented the log2 fold change, indicating the magnitude of gene expression change, while the X-axis showed the percentage of cells expressing each DEG. (b) Ridge plots illustrated the expression profiles of 10 common Fibroblast lineage-specific markers across each cell type. The curves represented kernel density estimates (KDE), with the height of the curve corresponding to the density of gene expression within each region. (c) Violin plot showed the expression levels of selected marker genes in each fibroblast subpopulation. The width of the plot indicated the distribution of gene expression, reflecting the density of cells at different expression levels. (d) UMAP plot depicted 8 distinct fibroblast subpopulations identified during LTS progression, including fibrotic, inflammatory, stress-activated, proliferating, chondrocyte injury-related fibroblasts (CIRF), epithelial-mesenchymal transition (EMT)-related fibroblasts (EMTF), mesothelial, and “other.” Each subpopulation was annotated with a unique color. (e) Feature plots illustrated the expression of specific genes in fibrotic fibroblasts, alongside the spatial distribution of gene expression across the fibroblast population. The color intensity reflected the level of expression, ranging from low to high. (f) Feature plots illustrated the expression of specific genes in CIRF, alongside the spatial distribution of gene expression across the fibroblast population. The color intensity reflected the level of expression, ranging from low to high. (g) Feature plots illustrated the expression of specific genes in EMTF, alongside the spatial distribution of gene expression across the fibroblast population. The color intensity reflected the level of expression, ranging from low to high