CAD variants act through ox-LDL-induced enhancer remodelling to alter VSMC gene programmes

Abstract

BackgroundVascular smooth muscle cells (VSMCs) play a central role in atherosclerotic coronary artery disease (CAD). Oxidised low-density lipoprotein cholesterol (ox-LDL) induces VSMCs dysfunction but the underlying molecular mechanisms are unclear. CAD genome-wide association studies (GWAS) have identified hundreds of disease-associated loci but their biological roles remain poorly defined. We hypothesised that ox-LDL drives pro-atherogenic changes in VSMCs by altering gene regulatory programs involving causal CAD variants. MethodsEx-vivo human coronary VSMCs were exposed to ox-LDL and profiled using RNA-seq, ATAC-seq, and H3K27ac ChIPmentation. Enhancer-gene links were inferred by integrating these data with Hi-C using the Activity-by-Contact (ABC) model. Variant effect predictions were done using AlphaGenome and key target genes functionally tested by CRISPR/Cas9 knockout. ResultsOx-LDL induced widespread transcriptional reprogramming in coronary VSMCs, with 1,487 upregulated and 1,864 downregulated genes (FDR < 0.05). Single-cell RNA-seq meta-analysis demonstrated that ox-LDL-associated programmes enriched in pro-inflammatory and synthetic-inflammatory VSMC clusters in vivo. ATAC-seq identified [~]22k differentially accessible regions following ox-LDL exposure (FDR < 0.05). Integration of ATAC-seq, H3K27ac, and Hi-C using the ABC framework showed that ox-LDL-driven chromatin remodelling was concentrated at distal enhancers, which linked to 2,008 differentially expressed genes via 4,243 peak-gene connections. ABC enhancers were significantly enriched for CAD variants compared with non-vascular disease controls, with stronger enrichment in dynamically accessible enhancers. AlphaGenome predicted larger regulatory effects of prioritised CAD variants in smooth muscle cells than in a non-vascular comparator, and motif analyses indicated allele-dependent transcription factor binding at prioritised enhancer variants. Locus-level prioritisation nominated candidate enhancer-mediated mechanisms at the SPECC1L and MAP1S loci, and CRISPR knockout of the target genes GUCD1 and BACH1 rescued ox-LDL-induced growth arrest/senescence phenotypes in human coronary artery VSMCs. ConclusionsOur unbiased multi-omics framework shows that ox-LDL rewires VSMC regulatory programmes that influence CAD genetic risk. Enhancer-gene mapping refines effector-gene assignment at CAD loci and prioritises regulatory targets in coronary VSMCs.