Genomic profiling of human vascular cells identifies TWIST1 as a causal gene for common vascular diseases
Genomic profiling of human vascular cells identifies TWIST1 as a causal gene for common vascular diseases
复制标题
DOI：
10.1371/journal.pgen.1008538
复制
发表时间：
2020-01-01
期刊：
影响因子：
4.5
通讯作者：
Rader, Daniel J.
中科院分区：
文献类型：
--
作者：
Nurnberg, Sylvia T.;Guerraty, Marie A.;Rader, Daniel J.
全基因组关联研究（GWAS）已经确定了数百种与人类血管疾病（包括冠状动脉疾病）相关的遗传变异。这些主要是非编码区中常见的单核苷酸多态性（SNP），这使得鉴定致病基因及其与病理生理学的潜在联系具有挑战性。已经进行了表达数量性状基因座（eQTL）的定位，以将GWAS SNP与血管细胞和组织中的风险基因相关联。然而，动脉粥样硬化血管组织含有多种细胞类型。我们对基因分型的人源性血管细胞（内皮细胞和平滑肌细胞）进行深度转录组学分析，并使用剪接数量性状位点、等位基因特异性表达和共定位分析来注释与血管疾病相关的遗传变异，并以细胞类型特异性方式深入了解其潜在功能。基于这些分析，我们确定计算，然后实验验证CAD风险位点rs2107595和基因TWIST 1之间的关联。我们建议，这个位点的次要等位基因可以影响转录因子的结合，并提供数据支持TWIST 1在调节平滑肌细胞表型的作用。全基因组关联研究已经确定了多个新的基因组位点与血管疾病。其中许多基因座是常见的非编码变体，会影响冠状血管细胞内疾病相关基因的表达。为了在全基因组水平上识别这些基因，我们对来自相同受试者的基因分型的原代人冠状动脉平滑肌细胞（HCASMC）和冠状动脉内皮细胞（HCAEC）进行了深度转录组学分析，包括剪接定量性状位点（sQTL），等位基因特异性表达（ASE）和共定位分析。我们在HCASMC和HCAEC中鉴定了TARS2、YAP1、CFDP1和STAT6的sQTL，以及233个ASE基因，其中一个子集也是动脉组织中的GTEx eGene。冠状动脉疾病（CAD）、偏头痛、中风和腹主动脉瘤的GWAS关联信号与主动脉、冠状动脉和胫动脉中的GTEx eGenes的共定位发现了这些疾病的新的候选风险基因。在CAD和中风位点标记的rs2107595，我们证明了共定位与近端基因TWIST 1的表达。我们表明，破坏rs2107595位点改变TWIST 1的表达和风险等位基因增加了NOTCH信号蛋白RBPJ的结合。最后，我们提供的数据表明，TWIST 1表达影响血管SMC表型，包括增殖和钙化，作为一个潜在的机制，支持TWIST 1在CAD中的作用。
Author summaryGenome-wide association studies (GWAS) have identified hundreds of genetic variants that are associated with human vascular disease including coronary artery disease. These 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. However, atherosclerotic vascular tissues contain multiple cell types. 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. Based on these analyses, we identified computationally and then validate experimentally an association between the CAD risk locus rs2107595 and the gene TWIST1. We propose that the minor allele for this locus can affect transcription factor binding and provide data supporting a role for TWIST1 in modulating smooth muscle cell phenotype.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.