Identification of smooth muscle cell genes causal in atherosclerotic plaque stability and cardiovascular disease risk

尽管有有效的LDL-C治疗，心血管疾病（CVD）风险仍然是一个主要的未满足的临床需求。我们 其他人已经确定了>300个冠状动脉疾病（CAD）的基因座。在血管平滑肌中起作用的基因 肌细胞（SMC）在几个位点上是致病的，但在大多数位点上的致病基因仍然未知。使用单 在小鼠模型中，我们通过细胞分析和SMC谱系追踪，发现SMC通过一个中间体转变， SMC衍生细胞（SDC）状态转化为调节疾病的保护性或有害表型。我们假设 SMC基因在斑块不稳定性和CVD风险中起着显著的因果作用，与脂蛋白基因无关。到 为了解决这个问题，我们将利用独特的小鼠模型和人力资源，包括巴基斯坦基因组学， 包括全球最大的人类基因敲除“科斯”队列的资源（PGR，研究n= 250，000） （完整科斯>5000;杂合科斯> 18，000个基因）以及慕尼黑血管生物库（MVB）， > 2，000个人类斑块和临床、组织学、转录组学和遗传数据。在目标1中，我们将整合SMC 在小鼠模型中进行谱系追踪，分析了> 100万名具有GWAS SNP，全外显子组（WES）的参与者 和全基因组（WGS）数据，消除与血浆脂蛋白相关的所有基因座/基因。实施 迄今为止最大的CAD罕见变异和基因负荷测试，我们将优先考虑可能的致病SMC/SDC基因 并揭示预测的功能丧失（pLoF）变体方向效应。为了使回调研究投入运作，我们 将限于PCR中具有至少5个pLoF载体的基因。基因优先权将通过多种族精细定位来完善， 共定位分析和生物相容性。我们希望优先考虑~30个SMC/SDC基因。所有人都将经历 大PheWAS用于多效性和安全性。对于前5个基因，回调研究将验证因果关系， 通过动脉粥样硬化特征、安全性和多效性标志物的深度表型分析， 在PGR家族中（每个家族n=200）。初步工作优先考虑了15个SMC/SDC基因，所有这些基因都具有很强的因果关系。 候选人，并且PCR中的初始回调扩大了最有希望的基因的大谱系（例如，PDE3A， SERPINH1、HHIPL1、ZEB2）。在目标2中，我们将使用RNA原位测序（HybRISS），RNA范围，邻近 连接试验（Myh 11-H3 K4 me 2 SMC/SDC标记）和组织学以确定SMC/SDC基因表达， 稳定与不稳定MVB斑块中约30个优先基因的位置。等位基因特异性表达的变化 稳定与不稳定MVB斑块中SDC类型的基因及其cis-eQTL与CAD SNP的共定位将 对菌斑稳定性的因果和方向影响。对于至少2个顶级基因，我们将使用Tet-on Dre/Cre 在晚期时间点用于SMC基因缺失的双重诱导型重组酶系统，以测试对 晚期病变斑块稳定性和疾病消退的特征。我们准备在小鼠模型中进行测试 如果PDE 3A，一个令人信服的例子，促进SMC增殖，衰老和血管重塑。总的来说， 我们提出了一个独特的整合平台，经人类遗传学验证，可以精细定位基因座，发现致病基因， 阐明SMC/SDC动脉粥样硬化稳定性和CVD风险因果通路中的安全治疗靶点。

Despite effective LDL-C therapies, cardiovascular disease (CVD) risk remains a major unmet clinical need. We and others have identified >300 loci for coronary artery disease (CAD). Genes that function in vascular smooth muscle cells (SMC) are causal at several loci yet the causal genes at most loci remain unknown. Using single cell profiling and SMC lineage-tracing in mouse models, we found that SMC transition through an intermediate SMC-derived cell (SDC) state into protective or harmful phenotypes that modulate disease. We hypothesize that SMC genes play a prominent causal role in plaque instability and CVD risk independent of lipoprotein genes. To address this, we will leverage unique mouse model and human resources, including the Pakistan Genomics Resource (PGR, n=250,000 for study) that includes the largest global cohort of human gene knockout “KOs” (complete KOs >5000; heterozygous KOs >18,000 genes) as well as the Munich Vascular Biobank (MVB) with >2,000 human plaques and clinical, histology, transcriptomics and genetic data. In Aim 1, we will integrate SMC lineage tracing in mouse models with analyses of >1 million participants with GWAS SNP, whole-exome (WES) and whole-genome (WGS) data, eliminating all loci/genes associated with plasma lipoproteins. Implementing the largest rare variant and gene burden testing for CAD to date, we will prioritize likely causal SMC/SDC genes and reveal predicted loss of function (pLoF) variant directional effects. To operationalize call-back studies, we will limit to genes with at least 5 pLoF carriers in PGR. Gene priority will be refined by multiethnic fine-mapping, co-localization analyses and biological plausibility. We expect to prioritize ~30 SMC/SDC genes. All will undergo large PheWAS for pleiotropy and safety. For the top 5 genes, call-back studies will validate causality and directionality and assess safety through deep phenotyping of atherosclerosis traits, safety and pleiotropy markers in PGR families (n=200 per family). Preliminary work prioritized 15 SMC/SDC genes, all strong causal candidates, and initial call-back in PGR expanded large pedigrees for the most promising genes (e.g., PDE3A, SERPINH1, HHIPL1, ZEB2). In Aim 2, we will use RNA in situ sequencing (HybRISS), RNA-scope, proximity ligation assays (Myh11-H3K4me2 SMC/SDC mark) and histology to define SMC/SDC gene expression and location for ~30 prioritized genes in stable vs. unstable MVB plaques. Change in allele specific expression for genes in SDC types in stable vs. unstable MVB plaques and co-localization of their cis-eQTLs to CAD SNPs will inform causal and directional effects on plaque stability. For at least 2 top genes, we will use a Tet-on Dre/Cre dual inducible recombinase system for SMC gene deletion at late time points to test effects and mechanisms on features of plaque stability in advanced lesions and disease regression. We are poised to test in mouse models if PDE3A, one compelling example, promotes SMC proliferation, senescence and vascular remodeling. Overall, we propose a unique integrative platform, validated by human genetics, to fine-map loci, discover causal genes and elucidate safe therapeutic targets in SMC/SDCs causal pathways for atherosclerosis stability and CVD risk.