Fig. 3

Cell-type-resolved expression differences between the SVF from nonlesional sites of patients with LoS and healthy donors. A Differentially expressed genes that were identified in each major cell type between LoS and CTRL. The likelihood-ratio test implemented in Seurat was applied. A statistical threshold was set to an absolute log2-fold change > 0.25 and an adjusted P-value < 0.05. B Dysregulated pathways in ASCs from nonlesional sites of patients with LoS identified through gene set enrichment analysis (GSEA). A statistically significant threshold was established with an FDR q value < 0.05. C Enrichment plots (upper panel) and leading-edge gene expression heatmaps (lower panel; the top 20 genes) for representative pathways dysregulated in ASCs. Normalized enrichment score (NES) was employed to compare analysis outcomes across gene sets. A positive NES indicates that the pathway is upregulated, while a negative score indicates that the pathway is downregulated. The vertical lines depicted in the enrichment plot indicate where the members of the gene set are positioned in the ranked gene list. The subset of genes in the gene set that make the greatest contribution to the enrichment are known as leading-edge genes. The heatmap displays the average expression across cells in each group. CTRL control, FDR false discovery rate, LoS localized scleroderma