Genomic profiling of human vascular cells identifies TWIST1 as a causal gene for common vascular diseases.

Sylvia Nürnberg ,Susannah Elwyn,John Pluta,Ulf Hedin,Yoseph Barash,Thomas Quertermous,Daniel J Rader,Scott Norton,Yoson Park,Yi-An Ko,Sanjay Sinha,Ting Wang,Stephanie Testa,Wei Zhao,Felipe Serrano,Milos Pjanic,Ljubica Perisic,Trieu Nguyen,Christopher D Brown,Harish Rao ,Marie Guerraty ,Robert Wirka

doi:10.1371/journal.pgen.1008538

Abstract

Genome-wide association studies have identified multiple novel genomic loci associated with vascular diseases. Many of these loci are common non-coding variants that affect the expression of disease-relevant genes within coronary vascular cells. To identify such genes on a genome-wide level, we performed deep transcriptomic analysis of genotyped primary human coronary artery smooth muscle cells (HCASMCs) and coronary endothelial cells (HCAECs) from the same subjects, including splicing Quantitative Trait Loci (sQTL), allele-specific expression (ASE), and colocalization analyses. We identified sQTLs for TARS2, YAP1, CFDP1, and STAT6 in HCASMCs and HCAECs, and 233 ASE genes, a subset of which are also GTEx eGenes in arterial tissues. Colocalization of GWAS association signals for coronary artery disease (CAD), migraine, stroke and abdominal aortic aneurysm with GTEx eGenes in aorta, coronary artery and tibial artery discovered novel candidate risk genes for these diseases. At the CAD and stroke locus tagged by rs2107595 we demonstrate colocalization with expression of the proximal gene TWIST1. We show that disrupting the rs2107595 locus alters TWIST1 expression and that the risk allele has increased binding of the NOTCH signaling protein RBPJ. Finally, we provide data that TWIST1 expression influences vascular SMC phenotypes, including proliferation and calcification, as a potential mechanism supporting a role for TWIST1 in CAD.

Highlights

Coronary artery disease (CAD) is a complex vascular wall process characterized by progressive development of atherosclerotic plaques involving multiple cell types
Genome-wide association studies (GWAS) have identified hundreds of genetic variants that are associated with human vascular disease including coronary artery disease
We perform deep transcriptomic profiling of genotyped human-derived vascular cells– endothelial cells and smooth muscle cells–and use splicing quantitative trait locus, allele-specific expression, and colocalization analyses to annotate genetic variants associated with vascular diseases and gain insight into their potential function in a cell-type specific manner

Summary

Introduction

Coronary artery disease (CAD) is a complex vascular wall process characterized by progressive development of atherosclerotic plaques involving multiple cell types. And twin studies estimate the heritability of risk for CAD at 40% to 60% [1]. Genome-wide Association Study (GWAS) meta-analyses have reported more than 160 genomic loci that are significantly associated with CAD [2,3,4,5]. The identified GWAS variants are predominantly common single nucleotide polymorphisms (SNPs) in non-coding regions, which makes the identification of the causal genes and their underlying connection to pathophysiology challenging. Mapping of expression quantitative trait loci (eQTLs) has been performed to associate GWAS SNPs with risk genes in vascular cells and tissues [10,11,12]. Atherosclerotic vascular tissues contain multiple cell types. Cell-specific analysis of eQTLs would considerably advance our understanding of the underlying biology

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