Genetic regulatory mechanisms of smooth muscle cells map to coronary artery disease risk loci

Abstract

Coronary artery disease (CAD) is the leading cause of death globally. Genome-wide association studies (GWAS) have identified more than 95 independent loci that influence CAD risk, most of which reside in non-coding regions of the genome. To interpret these loci, we generated transcriptome and whole-genome datasets using human coronary artery smooth muscle cells (HCASMC) from 52 unrelated donors, as well as epigenomic datasets using ATAC-seq on a subset of 8 donors. Through systematic comparison with publicly available datasets from GTEx and ENCODE projects, we identified transcriptomic, epigenetic, and genetic regulatory mechanisms specific to HCASMC. We assessed the relevance of HCASMC to CAD risk using transcriptomic and epigenomic level analyses. By jointly modeling eQTL and GWAS datasets, we identified five genes (SIPA1, TCF21, SMAD3, FES, and PDGFRA) that modulate CAD risk through HCASMC, all of which have relevant functional roles in vascular remodeling. Comparison with GTEx data suggests that SIPA1 and PDGFRA influence CAD risk predominantly through HCASMC, while other annotated genes may have multiple cell and tissue targets. Together, these results provide new tissue-specific and mechanistic insights into the regulation of a critical vascular cell type associated with CAD in human populations.

Quantitative trait loci mapped for TCF21 binding, chromatin accessibility and chromosomal looping in coronary artery smooth muscle cells reveal molecular mechanisms of coronary disease loci

“…We obtained primary HCASMC lines from commercial vendors. Genotypes were called with whole genome sequencing or genotyping with Illumina chips, phased and imputed against 1000 Genome phase 3 data before merging [14]. We pooled 65 lines for TCF21 ChIPseq and Hi-C, and 71 lines for ATACseq experiments at passage 4-6 ( Fig.…”

“…QTLs of the CAD-associated transcription factor TCF21 were of particular interest because of the enrichment of its binding in other CAD loci [26] and contribution to the risk at these loci where it modulates the epigenome and thus expression of causal genes [15,27]. We have previously shown that CAD-associated variants are enriched in HCASMC regions of open chromatin [23], and that these cells contribute a significant portion of CAD risk [14]. There was at most 40% overlap of the HCASMC caQTLs with those reported previously for LCLs [9], suggesting that regulatory variation is quite different between these two cell types and underscoring the importance of these smooth muscle cell data for study of vascular disease genetics.…”

“…Our next goal was to characterize loci with bQTL, caQTL and clQTL colocalization. We first overlapped these QTLs to examine exact matching and included our published HCASMC eQTL data in this analysis [14]. The number of eQTLs (187299) was comparable to GTEx QTL numbers and QTL-gene pairs (Additional file 1: Suppl Figs.…”

“…The Hi-C protocol was modified from HiChIP with excluding the antibody purification [54]. Whole-genome sequencing data were processed with the GATK best practices pipeline [14] . cutadapt trimmed reads were aligned to the hg19 reference genome with bwa.…”

“…HCAMSC eQTL data came from a genome-wide association of gene expression with imputed common variation identified in 52 HCASMC lines [14] . CARDIoGRAMplusC4D variants data was from 1000 Genomes-based GWAS meta-analysis [18].…”