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

鉴定导致动脉粥样硬化斑块稳定性和心血管疾病风险的平滑肌细胞基因

• 批准号: 10720225
• 负责人: Muredach P Reilly
• 金额: $ 69.24万
• 依托单位: COLUMBIA UNIVERSITY HEALTH SCIENCES
• 依托单位国家: 美国
• 财政年份: 2023
• 资助国家: 美国
• 起止时间: 2023-08-10 至 2027-06-30
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10720225
• 关键词: Acceleration; Address; Affect; Alleles; Arterial Fatty Streak; Arteries; Atherosclerosis; Biological; Biological Assay; Blood; Blood Vessels; Callback; Cardiovascular Diseases; Carotid Arteries; Carotid Artery Plaques; Cell Aging; Cell Lineage; Cell Proliferation; Cells; Cholesterol; Clinical; Coronary Arteriosclerosis; Data; Disease; Disease regression; Etiology; Family; Gene Deletion; Gene Expression; Genes; Genetic; Genetic Variation; Genome Mappings; Heterozygote; Histology; Human; Human Genetics; Human Resources; Knock-out; Lesion; Ligation; Lipids; Lipoproteins; Location; Low-Density Lipoproteins; Maps; Meta-Analysis; Mus; Mutation; Pakistan; Participant; Pathway interactions; Phenotype; Plasma; Play; Population Genetics; RNA; Residual state; Resolution; Resources; Role; Safety; Signal Transduction; Smooth Muscle Myocytes; Stable Disease; System; Testing; Time; Tretinoin; Variant; Vascular Smooth Muscle; Vascular remodeling; Work; biobank; cardiovascular disorder risk; causal variant; cell type; cohort; conditional knockout; coronary artery calcium; exome; fine art; gene function; genetic analysis; genetic pedigree; genome resource; genome sequencing; genome wide association study; human model; improved; in situ sequencing; intimal medial thickening; knockout gene; loss of function; mouse model; multi-ethnic; pleiotropism; programs; rare variant; recombinase; safety assessment; senescence; single-cell RNA sequencing; therapeutic target; trait; transcriptome sequencing; transcriptomic profiling; transcriptomics; whole genome

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.

尽管 LDL-C 治疗有效，但心血管疾病 (CVD) 风险仍然是一个未满足的主要临床需求。 等人已经鉴定出超过 300 个在血管平滑肌中发挥作用的冠状动脉疾病 (CAD) 基因位点。 肌肉细胞（SMC）在多个位点上有因果关系，但大多数位点的因果基因仍然未知。 通过对小鼠模型中的细胞分析和 SMC 谱系追踪，我们发现 SMC 通过中间体转变 SMC 衍生细胞 (SDC) 状态为调节疾病的保护性或有害表型。 SMC 基因在斑块不稳定和 CVD 风险中发挥着重要的因果作用，与脂蛋白基因无关。 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 资源（PGR，n=250,000 用于研究），包括全球最大的人类基因敲除“KO”队列 （完整 KO > 5000 个；杂合 KO > 18,000 个基因）以及慕尼黑血管生物库 (MVB) >2,000 个人类斑块以及临床、组织学、转录组学和遗传数据 在目标 1 中，我们将整合 SMC。 小鼠模型中的谱系追踪，通过 GWAS SNP、全外显子组 (WES) 对超过 100 万参与者进行分析 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。 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致病的 SMC/SDC 基因 并揭示预测的功能丧失（pLoF）变异方向效应为了实施回调研究，我们。 将限制在 PGR 中具有至少 5 个 pLoF 携带者的基因 基因优先级将通过多种族精细映射进行细化， 我们预计将优先考虑约 30 个 SMC/SDC 基因。 对于前 5 个基因，回调研究将验证因果关系和安全性。 通过动脉粥样硬化特征、安全性和多效性标记物的深度表型分析来确定方向性并评估安全性 在 PGR 家族中（每个家族 n = 200），初步工作优先考虑 15 个 SMC/SDC 基因，所有基因均具有强因果关系。 候选基因，以及 PGR 中的初始回调扩大了最有希望的基因（例如 PDE3A、 在目标 2 中，我们将使用 RNA 原位测序 (HybRISS)、RNA 范围、邻近性。 连接测定（Myh11-H3K4me2 SMC/SDC 标记）和组织学来定义 SMC/SDC 基因表达和 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 类型中的基因及其顺式 eQTL 与 CAD SNP 的共定位将 对于至少 2 个顶级基因，我们将使用 Tet-on Dre/Cre 来了解对斑块稳定性的因果和方向影响。 双诱导重组酶系统用于在晚期时间点删除 SMC 基因，以测试对 SMC 基因删除的影响和机制 我们准备在小鼠模型中测试晚期病变和疾病消退中斑块稳定性的特征。 PDE3A 是一个令人信服的例子，它促进 SMC 增殖、衰老和血管重塑。 我们提出了一个经过人类遗传学验证的独特综合平台，用于精细定位基因座、发现因果基因 阐明 SMC/SDC 因果通路中动脉粥样硬化稳定性和 CVD 风险的安全治疗靶点。