To systematically identify causal genetic mechanisms that confer risk for coronary artery disease (CAD) in GWAS loci, we mapped genome-wide variant-to-enhancer-to-gene (V2E2G) links in vascular smooth muscle cells (SMC). Enhancers identified by active chromatin features, and further prioritized by base-resolution deep learning models of chromatin accessibility in 108 CAD loci, were studied with CRISPRi targeting and Direct-Capture Targeted Perturb-seq (DC-TAP-seq) evaluation of 470 genes. Seventy-six V2E2G links were identified for 59 candidate CAD genes representing gene programs including epithelial-mesenchymal transformation, ubiquitination, and protein folding as well as BMP and TGFB signaling. Similar methods employed with an independent focused screen targeting one candidate locus at 9p21.3 identified 10 enhancers regulating expression of multiple genes at this location. Detailed molecular studies revealed that two enhancers mediating transcription factor binding and transcriptional regulation contribute to ancestry-specific and sex-specific risk for CAD and the surrogate biomarker vascular calcification. Together, these studies advance our identification of GWAS CAD V2E2G links across the genome, and specific mechanisms of risk at the complex 9p21.3 locus.

J.M.E. has received materials from 10x Genomics unrelated to this study, and received speaking honoraria from GSK plc, Roche Genentech, and Amgen.

https://github.com/EngreitzLab/DC_TAP_Paper/tree/main

This work was supported by National Institutes of Health grants R01 HL171045 (TQ), R01HL134817 (TQ), R01HL139478 (TQ), R01HL156846 (TQ), R01HL158525 (TQ), UM1 HG011972 (TQ, JME), and the William G. Irwin Foundation (TQ), as well as a Human Cell Atlas grant (ZF2019-002437) from the Chan Zuckerberg Foundation (TQ). M.R. received support from the Sigrid Juselius Foundation and the Emil Aaltonen Foundation. This work was also supported by American Heart Association grant 24POST1193881. E.J. and J.R. were supported by the Novo Nordisk Foundation Center for Genomic Mechanisms of Disease (NNF21SA0072102). J.M.E. was also supported by NHLBI R01HL159176, the Applebaum Foundation, and the BASE Research Initiative at the Lucile Packard Childrens Hospital at Stanford University. M.U.K. was supported by the European Union (ERC, SECRET, 101125115).

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