Molecular architecture of human atherosclerosis revealed through integrative human genetics

Current genetic discovery methods are largely restricted to profiling circulating molecules or genetic architecture, limited in use of tissue-based molecular genetics to identify pathogenic and therapeutic targets. Here, we leverage a multi-level genetic discovery platform integrating population-level proteomics with functional genomic analyses based on human coronary artery tissue to reveal determinants of coronary disease susceptibility. Using aptamer-based proteomics ({approx}7,000 aptamers) across {approx}3,000 individuals, we first identified the circulating proteome of prevalent and incident coronary artery calcium (CAC)--a sensitive marker of subclinical coronary artery disease (CAD)--with causal implication in calcified plaque formation or disease phenotypes via parallel genetic approaches (Mendelian randomization, MR) and proteome-wide association (PWAS). Identified proteins specified pathways of extracellular matrix remodeling, immune cell function, lipid metabolism, and inflammation. To resolve findings at a coronary tissue level, we performed the largest to date coronary artery-specific transcriptome-wide association study for CAC (TWAS; based on RNA-seq from 268 human coronary arteries) in >35,000 individuals, demonstrating enrichment of targets from the circulating proteome with supportive evidence by traditional MR approaches (NOTCH3, SPINK2, S100A12, RPP25, OAF, HS6ST3, TNFSF12, GPC6), several implicated in CVD-adjacent biological mechanisms. Phenome-wide association and single cell transcriptomics in human coronary arteries across atherosclerosis implicated targets in tissue-specific disease mechanisms. Finally, using coronary artery-specific functional genomic annotations of chromatin structure, conformation, and accessibility, we identified trans regulation of two of these genes (GPC6, RPP25) by CAC GWAS-significant SNPs, resolving targets for previously "orphan" genome-wide significant loci. These multi-level findings furnish a resource for pathobiology of CAC, atherosclerosis, and establish an adaptable framework applicable to all organ systems to parse precision targets for prevention, surveillance, and therapy of cardiovascular disease.