Unveiling COL4A1 as a Key Driver Gene in scleroderma: Insights from Single-Cell and Bulk RNA Sequencing

Abstract Keloids and systemic sclerosis (SSc) are fibrotic disorders characterized by abnormal wound healing, leading to excessive collagen deposition and tissue fibrosis. The inflammatory and immune responses play critical roles in their pathogenesis, yet the molecular mechanisms remain elusive. We utilized high-throughput RNA sequencing (GSE130955) and single-cell RNA sequencing (GSE163973) datasets from the GEO database to explore gene expression profiles in scleroderma and keloid tissues. Differentially expressed genes (DEGs) were identified using the limma + voom package. Driver genes were detected through the SJARACNe algorithm, and functional enrichment was analyzed via GO and KEGG. Additionally, cell-cell communication networks were explored using the CellChat package, and gene expression validation was performed using qPCR and Western blot techniques. A total of 823 upregulated and 58 downregulated genes were identified in scleroderma scars, with significant enrichment in pathways related to extracellular matrix organization and immune responses. Key driver genes, including TCF23, PENK, and COL4A1, were identified, showing differential expression between scleroderma patients and controls. Single-cell RNA sequencing revealed key cell types involved in scar formation, particularly fibroblasts and endothelial cells, and highlighted the importance of intercellular signaling through collagen and laminin pathways. COL4A1 overexpression was shown to significantly enhance fibroblast proliferation and invasion in vitro. Our study uncovers novel molecular signatures and cellular interactions involved in the pathogenesis of keloids and scleroderma scars, providing potential therapeutic targets for these fibrotic conditions.