Multimodal CRISPR perturbations of GWAS loci associated with coronary artery disease in vascular endothelial cells.
Multimodal CRISPR perturbations of GWAS loci associated with coronary artery disease in vascular endothelial cells.
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DOI：
10.1371/journal.pgen.1010680
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发表时间：
2023-03
期刊：
影响因子：
4.5
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中科院分区：
文献类型：
--
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全基因组关联研究已经确定了250个与冠状动脉疾病(CAD)相关的遗传变异，但在大多数基因座上，原因变异、基因和分子机制仍不清楚。我们进行了集合CRISPR筛查，以测试位于或接近CAD相关遗传变异的序列对血管内皮细胞功能的影响。通过CRISPR基因敲除、抑制和激活，我们在83个CAD基因座上定位了1998个变异体，以评估它们对三种黏附蛋白(E-选择素、ICAM1、VCAM1)和三种关键内皮功能(一氧化氮和活性氧产生、钙信号传导)的影响。在错误发现率≤为10%的情况下，我们在26个CAD位点处的42个变异附近发现了显著的CRISPR扰动。我们使用碱基编辑来验证FES基因启动子中的一个假定的因果变体。虽然一些基因座包括以前在内皮细胞中具有特征的基因(如AIDA、ARHGEF26、ADAMTS7)，但大多数都是首次与内皮功能障碍有关。这些新基因中的一个的详细特征表明，RNA解旋酶DHX38与血管内皮细胞衰老有关。虽然我们的结果很有希望，但我们的结果也强调了使用CRISPR扰动来从功能上剖析Gwas基因座的几个局限性，包括未知的假阴性率和潜在的脱靶效应。全基因组关联研究是一种旨在识别会增加患心脏病或精神分裂症等常见人类疾病风险的基因变异的方法。虽然这种方法功能强大，但有一个主要局限性：它不能明确地定位导致疾病的基因。这一重要步骤要求研究人员对位于GWAS确定的变种附近的基因进行实验测试，以确定与感兴趣的疾病相关的功能。在这里，我们使用了一种名为CRISPR的技术来测试GWA在心脏病发作中所涉及的遗传变异附近的基因是否调节了血管内皮细胞的功能。内皮细胞形成血管内层，并在导致心脏病发作的病理(动脉粥样硬化)的发展中发挥关键作用。总体而言，我们在人类基因组中发现了26个区域，这些区域包括与心脏病发作相关的变异，并影响内皮细胞的功能。我们特别关注我们的一个发现，表明DHX38基因调控着一个称为衰老的过程，而衰老又调节着内皮细胞对促进心脏病发作的刺激的反应。
Genome-wide association studies have identified >250 genetic variants associated with coronary artery disease (CAD), but the causal variants, genes and molecular mechanisms remain unknown at most loci. We performed pooled CRISPR screens to test the impact of sequences at or near CAD-associated genetic variants on vascular endothelial cell functions. Using CRISPR knockout, inhibition and activation, we targeted 1998 variants at 83 CAD loci to assess their effect on three adhesion proteins (E-selectin, ICAM1, VCAM1) and three key endothelial functions (nitric oxide and reactive oxygen species production, calcium signalling). At a false discovery rate ≤10%, we identified significant CRISPR perturbations near 42 variants located within 26 CAD loci. We used base editing to validate a putative causal variant in the promoter of the FES gene. Although a few of the loci include genes previously characterized in endothelial cells (e.g. AIDA, ARHGEF26, ADAMTS7), most are implicated in endothelial dysfunction for the first time. Detailed characterization of one of these new loci implicated the RNA helicase DHX38 in vascular endothelial cell senescence. While promising, our results also highlighted several limitations in using CRISPR perturbations to functionally dissect GWAS loci, including an unknown false negative rate and potential off-target effects. Genome-wide association study (GWAS) is a method designed to identify genetic variants that increase the risk to develop common human diseases such as heart attacks or schizophrenia. While powerful, this method has one major limitation: it cannot unambiguously pinpoint the genes responsible for the diseases. This important step requires investigators to experimentally test genes located near the variants identified by GWAS for functions related to the diseases of interest. Here, we used a technique called CRISPR to test if genes near genetic variants implicated by GWAS in heart attacks modulate the functions of vascular endothelial cells. Endothelial cells form the inner layer of blood vessels, and play a critical role in the development of the pathology (atherosclerosis) that leads to heart attacks. In total, we found 26 regions in the human genome that include heart attacks-associated variants and that influence the functions of endothelial cells. Focusing specifically on one of our findings, we showed that the gene DHX38 regulates a process called senescence, which in turn modulates how endothelial cells respond to stimuli that promote heart attacks.
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影响因子：
4
作者：
Ajmal, Muhammad;Khan, Muhammad Imran;Cremers, Frans P. M.
通讯作者：
Cremers, Frans P. M.
影响因子：
64.8
作者：
Boix CA;James BT;Park YP;Meuleman W;Kellis M
通讯作者：
Kellis M
影响因子：
64.8
作者：
Graham SE;Clarke SL;Wu KH;Kanoni S;Zajac GJM;Ramdas S;Surakka I;Ntalla I;Vedantam S;Winkler TW;Locke AE;Marouli E;Hwang MY;Han S;Narita A;Choudhury A;Bentley AR;Ekoru K;Verma A;Trivedi B;Martin HC;Hunt KA;Hui Q;Klarin D;Zhu X;Thorleifsson G;Helgadottir A;Gudbjartsson DF;Holm H;Olafsson I;Akiyama M;Sakaue S;Terao C;Kanai M;Zhou W;Brumpton BM;Rasheed H;Ruotsalainen SE;Havulinna AS;Veturi Y;Feng Q;Rosenthal EA;Lingren T;Pacheco JA;Pendergrass SA;Haessler J;Giulianini F;Bradford Y;Miller JE;Campbell A;Lin K;Millwood IY;Hindy G;Rasheed A;Faul JD;Zhao W;Weir DR;Turman C;Huang H;Graff M;Mahajan A;Brown MR;Zhang W;Yu K;Schmidt EM;Pandit A;Gustafsson S;Yin X;Luan J;Zhao JH;Matsuda F;Jang HM;Yoon K;Medina-Gomez C;Pitsillides A;Hottenga JJ;Willemsen G;Wood AR;Ji Y;Gao Z;Haworth S;Mitchell RE;Chai JF;Aadahl M;Yao J;Manichaikul A;Warren HR;Ramirez J;Bork-Jensen J;Kårhus LL;Goel A;Sabater-Lleal M;Noordam R;Sidore C;Fiorillo E;McDaid AF;Marques-Vidal P;Wielscher M;Trompet S;Sattar N;Møllehave 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通讯作者：
Willer CJ
影响因子：
14.9
作者：
Bhasin, Jeffrey M.;Ting, Angela H.
通讯作者：
Ting, Angela H.
影响因子：
3.2
作者：
Goligorsky, Michael S.;Chen, Jun;Patschan, Susann
通讯作者：
Patschan, Susann