Transcriptomic profiling of human saphenous veins during ex vivo culture–induced neointima proliferation
Vein graft failure is a major limitation of coronary and peripheral bypass surgery, driven by neointima proliferation and smooth muscle cell (SMC) phenotypic modulation. To investigate the early molecular events underlying this process, we cultured segments of human saphenous veins ex vivo for seven days. Bulk RNA sequencing and 10x Visium spatial transcriptomics  were performed on paired fresh (Day 0) and cultured (Day 7) samples. Differential gene expression analysis revealed significant downregulation of contractile SMC markers and cytoskeletal genes, and upregulation of extracellular matrix (ECM), inflammatory, and stress-response pathways. Integration of both datasets highlighted coordinated suppression of SMC contractile phenotype and activation of matrix remodeling programs, consistent with early neointima development. These results provide a multi-omics resource defining molecular transitions that drive human vein graft remodeling. Overall design: Bulk RNA-seq profiling was performed on paired segments of human saphenous veins cultured ex vivo under serum-enriched conditions for 7 days (Day 7) compared with freshly isolated segments (Day 0).