Mapping atherogenesis mechanisms in smooth muscle cells by targeting genes linked to coronary artery disease.

Genome-wide association studies (GWASs) have linked numerous genetic loci active in vascular cells to coronary artery disease (CAD), implicating smooth muscle cells (SMCs) and SMC-derived mesenchymal cells as potential mediators. We combined CAD GWAS with single-cell RNA sequencing (scRNA-seq) from human atherosclerotic plaques to identify 20 risk genes with putative action in SMCs, and then performed in vitro perturbation experiments in SMCs driven toward plaque-relevant phenotypes. Although the genes encode diverse proteins, their perturbations converged on shared transcriptional programs regulating contractile machinery, cell-cycle progression, nuclear factor κB (NF-κB), and type I interferon signaling. Integrating GWAS effect-direction with cholesterol- and stretch-responsive gene modules suggest that cholesterol-induced signaling promotes pro-atherogenic SMC states and is differentially modulated by risk versus protective variants. These results delineate polygenic regulation of SMC disease mechanisms and show that GWAS effect-directionality can help prioritize cellular pathways for follow-up functional studies across genes and cell types.