Multi-omics and GWAS Integration Identifies Novel OxLDL-driven Pro-atherogenic Programs in Coronary Artery Smooth Muscle Cells

Objectives: Phenotypic changes in vascular smooth muscle cells (VSMCs) are implicated in atherosclerosis leading to coronary artery disease (CAD). Oxidized low-density lipoprotein cholesterol (oxLDL) induces VSMCs dysfunction but the underlying molecular mechanisms are unclear. CAD genome-wide association studies (GWAS) have identified hundreds of loci but their biological roles remain poorly defined. We aimed to understand whether the effect of oxLDL is mediated in part through CAD-associated genetic variants. Hypothesis: oxLDL drives pro-atherogenic changes in VSMCs by altering gene regulatory programs involving causal CAD variants. Methods: LDL was isolated from plasma of healthy adult donors by density-gradient ultracentrifugation, oxidized, and dialyzed against PBS. VSMCs from human coronary arteries were treated with dialysate (buffer controls) or 100 µg/mL oxLDL for 48 h (n=4–6 per group). RNA sequencing (RNA-seq), assay for transposase-accessible chromatin sequencing (ATAC-seq), and H3K27ac ChIPmentation were performed. Integration of our multiomic data with CAD GWAS were undertaken. Results: OxLDL significantly altered gene expression (Benjamini-Hochberg adjusted p-value [ P.adj] <0.05) with 1,487 upregulated and 1,864 downregulated genes. Upregulated genes were enriched for autophagy, response to ischemia, oxidative stress, and lipid modification, whereas downregulated genes were enriched for extracellular matrix assembly, regulation of DNA repair, and vasculogenesis. ATAC-seq identified >169k open chromatin regions, of which >63k had active H3K27ac histone marks. OxLDL treatment altered chromatin accessibility at ~10k active enhancers and promoters ( P.adj < 0.05). There was significant concordance between chromatin accessibility and H3K27ac signal at promoters of differentially expressed genes (r 0.56, p-value < 0.001). Motif enrichment analysis of dynamic enhancers and promoters revealed enriched transcription factor (TFs) binding motifs that were also differentially expressed. Enriched TFs showed master regulatory roles on expression of genes not previously reported in atherosclerosis. Integration of our multiomic data with GWAS results prioritized CAD variants in 22 dynamic enhancers and 13 dynamic promoters, with several in binding sites for prioritized TFs. Conclusions: OxLDL alters gene expression in VSMCs by altering chromatin accessibility and activity of associated regulatory elements. We show that these dynamic regulatory elements are enriched with CAD risk variants with capacity to alter TF binding and thereby impact gene expression. Our unbiased, multiomic approach demonstrates that oxLDL alters novel gene regulatory programs in VSMCs that are critical for CAD risk. Funding Source Novo Nordisk This abstract was presented at the American Physiology Summit 2025 and is only available in HTML format. There is no downloadable file or PDF version. The Physiology editorial board was not involved in the peer review process.