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; 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.

尽管有效的LDL-C疗法，心血管疾病（CVD）的风险仍然是主要的未满足临床需求。我们 其他人已经确定了冠状动脉疾病（CAD）的300个地方。在血管平滑中起作用的基因 肌肉细胞（SMC）在几个基因座是因果关系，但最多基因座的因果基因仍然未知。使用单个 小鼠模型中的细胞分析和SMC谱系追踪，我们发现SMC通过中间体过渡 SMC衍生的细胞（SDC）状态为调节疾病的保护性或有害表型。我们假设这一点 SMC基因在斑块不稳定性中起着重要的因果作用，而CVD风险独立于脂蛋白基因。到 解决这个问题，我们将利用独特的鼠标模型和人力资源，包括巴基斯坦基因组学 资源（PGR，n = 250,000的研究），其中包括最大的全球人类基因敲除“ KOS” （完整的KOS> 5000；杂合KOS> 18,000个基因）以及带有慕尼黑血管生物库（MVB） > 2,000人斑块和临床，组织学，转录组学和遗传数据。在AIM 1中，我们将整合SMC 用GWAS SNP，全象征（WES）分析鼠标模型中的谱系跟踪。 和全基因组（WGS）数据，消除了与血浆脂蛋白相关的所有局部/基因。实施 迄今为止，最大的稀有变体和基因Burnen测试了CAD，我们将优先考虑可能因果SMC/SDC基因 并揭示了预测的功能丧失（PLOF）变体方向性效应。为了实现呼叫研究，我们 将限制在PGR中至少有5个plof载体的基因。基因优先级将通过多民族精细映射来完善， 共定位分析和生物学合理性。我们希望优先考虑约30个SMC/SDC基因。所有人都会经历 大型Phewas用于多效和安全性。对于前5个基因，呼叫研究将验证休闲性和 方向性和评估安全性通过动脉粥样硬化特征，安全性和多效标志物的深层表型来安全性 在PGR家族中（每个家庭n = 200）。初步工作优先考虑15个SMC/SDC基因，所有强大因果 候选人和PGR中的初始呼叫向最有前途的基因扩展了大型谱系（例如，PDE3A， serpinh1，hhipl1，zeb2）。在AIM 2中，我们将使用RNA原位测序（hybriss），RNA-SCOPE，接近度 连接测定（MYH11-H3K4ME2 SMC/SDC标记）和组织学以定义SMC/SDC基因表达和 稳定与不稳定的MVB斑块中约30个优先基因的位置。更改等位基因的特定表达式 稳定与不稳定的MVB斑块中的SDC类型中的基因以及其顺式EQTL的共定位为CAD SNP将 告知因果关系对牙菌斑稳定性的影响。对于至少2个顶部基因，我们将使用Tet-On Dre/Cre 在较晚的时间点进行SMC基因缺失的双重诱导重组酶系统，以测试效果和机制对 晚期病变和疾病回归中斑块稳定的特征。我们被中毒用于在鼠标模型中进行测试 如果PDE3A（一个引人注目的例子）促进了SMC增殖，感应和血管重塑。全面的， 我们提出了一个由人类遗传学验证的独特集成平台，以细地局部发现catusal基因 并在SMC/SDCS因果关系途径中阐明了安全的治疗靶标，以实现动脉粥样硬化稳定性和CVD风险。