Abstract 4142133: Variant-enhancer-gene mapping at the 9p21 locus in smooth muscle cells reveals new enhancer-gene pairs and mechanistic insights for coronary artery disease

Abstract

The majority of variants identified by genome-wide association studies (GWAS) that influence coronary artery disease (CAD) risk reside in noncoding regions of the genome, making it challenging to link them with the genes they regulate. The 9p21.3 locus is the most impactful genetic risk locus for CAD. Due to the complexity of this locus, the causal genes and molecular mechanisms are poorly understood. Enhancers are cell type specific, and vascular smooth muscle cells (SMC) are known to have the highest heritable risk for CAD and play a major role in the atherosclerotic plaque formation. Here, we report efforts to systematically map SMC specific enhancers to neighboring genes within the 9p21.3 locus by implementing single cell CRISPRi enhancer screens and validating single causal variants in these enhancers. First, we intersected CAD GWAS loci with human coronary artery SMC (HCASMC) ATAC-seq and H3K27ac ChIP-seq datasets to focus on the disease relevant SNPs. This analysis identified 27 SNPs in 11 enhancers, that we targeted with CRISPRi machinery and analyzed at 5- and 10-days post transduction. As target genes in the locus are lowly expressed, we employed the targeted Perturb-seq (TAP-seq) approach for library generation and sequencing. We identified several enhancer-gene -pairs, including a strong enhancer-gene connection to both CDKN2A and CDKN2B . Additionally, we identified multiple enhancer regions that control MTAP expression, with smaller but significant effects. We followed up with individual validation of enhancer-gene pairs through qPCR. Furthermore, these results are consistent with chromosomal interaction data obtained from our previous HiChIP. Notably, enhancers 5 and 6 were strong regulators of CDNK2B and CDKN2A expression, so we investigated how variants in these enhancers might directly disrupt transcription factor (TF) binding. By using luciferase enhancer assays, CHIPseq and phenotypic in vitro assays we linked this variation with TFs that drive vascular calcification in SMCs. Our results identify new variant to gene links and suggest how the genetic risk in 9p21 is mediated in the vascular wall, providing mechanistic understanding of vascular calcification and genetic risk of CAD and suggesting a novel mechanism of how 9p21.3 mediates disease risk.