LncRNA Transcriptional Mechanisms of Coronary Artery Disease Risk

冠状动脉疾病风险的 LncRNA 转录机制

• 批准号: 10327641
• 负责人: THOMAS QUERTERMOUS
• 金额: $ 39.1万
• 依托单位: STANFORD UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2019
• 资助国家: 美国
• 起止时间: 2019-01-18 至 2023-12-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10327641
• 关键词: Affect; Alleles; Biological; Biological Assay; Blood Vessels; Cardiovascular Diseases; Cell physiology; Cells; Chromatin; Clustered Regularly Interspaced Short Palindromic Repeats; Code; Complex; Coronary Arteriosclerosis; Coronary artery; Coupled; Development; Disease; Disease Pathway; Epigenetic Process; Etiology; Evaluation; Exons; Gene Expression; Genes; Genetic; Genetic Risk; Genetic Transcription; Genetic Variation; Genome; Genomics; Goals; Histones; Human; Human Genome; In Vitro; Inflammatory; Inherited; Link; Maps; Mediating; Methods; Modification; Molecular; Nucleic Acid Regulatory Sequences; Pathway Analysis; Pathway interactions; Phenotype; Play; Population; Post-Translational Protein Processing; Process; Proteins; Quantitative Trait Loci; RNA; Regulation; Research; Risk; Risk Assessment; Risk Factors; Role; Scientist; Signal Pathway; Signal Transduction; Smooth Muscle Myocytes; Specificity; Stimulus; Therapeutic; Untranslated RNA; Variant; Vascular Diseases; Work; base; causal variant; cell type; differential expression; disorder risk; epigenome; epigenomics; experimental study; functional genomics; genome editing; genome wide association study; genomic data; genomic locus; human disease; in vitro Assay; innovation; novel; programs; public health relevance; response; single-cell RNA sequencing; trait; transcriptome sequencing; vascular stress

Therapeutic risk factor modification has provided a significant decrease in coronary artery disease (CAD) in Western populations, however, significant risk is due to common inherited genetic variation that affects disease pathways in the vessel wall and remains poorly understood without specific therapies. To further our long-term goal of characterizing the molecular basis for this genetic risk, we have participated in genome-wide association studies (GWAS) identifying allelic variation linked to coronary artery disease (CAD) risk, and these efforts have yielded hundreds of associated loci. However, the majority of identified causal variation resides outside of protein coding exons, in regulatory regions of the genome that are poorly understood, and further efforts are required to understand the mechanisms of association and thus disease risk. Our central hypothesis is that an important subset of disease allelic variation primarily regulates long non-coding RNA (lncRNA) expression, with this effect modulating causal protein coding gene (pcGene) expression through functional genomic interactions such as chromosomal looping. Our objective here is to investigate the role these lncRNAs play in mediating expression of CAD causal pcGenes, and the mechanism by which they accomplish this function. Our rationale is that lncRNAs serve as a critical intermediary between genetic and epigenetic signaling, and that elucidating their mechanism of function is a key aspect of understanding CAD risk. To gain fundamental information regarding the mode of action of these molecules in the context of CAD, we propose to study human coronary artery smooth muscle cell (HCASMC) lncRNAs. In Aim 1, we will identify lncRNAs regulated in these cells by disease-related stimuli and that map to CAD GWAS loci. Co-expression network analyses will connect these lncRNAs to pcGenes, and initiate network and pathway analyses to begin to establish their biological functional associations. In Aim 2, we will map expression quantitative trait loci variants (eQTLs) for each of the lncRNAs, using a high-throughput allele-specific expression method that provides quantification of low abundance RNAs. Discovered lncRNA eQTLs will be investigated to determine whether they colocalize with CAD GWAS causal variation, as well as genomic molecular trait QTLs. CRISPR genome editing will be employed to validate the eQTLs, and confirm pcGene identity. In Aim 3, we will employ CRISPR inhibition and single cell RNA sequencing (PerturbSeq) to map the transcriptional networks regulated by the disease related lncRNAs, and also investigate their in vitro cellular effects on HCASMC. These studies will be aided by our extensive work with primary cultured HCASMC characterizing epigenome modification, chromatin accessibility, and looping, and our efforts to map CAD GWAS causal variants and genes that mediate risk in this cell type. This work is highly innovative in that it combines unique genomic datasets developed in a highly disease relevant cell type and significant since it will integrate lncRNAs, their regulatory variation, and molecular mechanisms into the etiology of CAD risk.

治疗危险因素的改变显着降低了冠状动脉疾病（CAD）的发病率 然而，西方人群的重大风险是由于影响疾病的共同遗传基因变异造成的 血管壁中的通路，并且在没有特定治疗的情况下仍然知之甚少。为了进一步推进我们的长期 为了表征这种遗传风险的分子基础，我们参与了全基因组研究 关联研究 (GWAS) 识别与冠状动脉疾病 (CAD) 风险相关的等位基因变异，这些 努力已经产生了数百个相关基因座。然而，大多数已确定的因果变异在于 在蛋白质编码外显子之外，在人们知之甚少的基因组调控区域，以及进一步 需要努力了解关联机制以及疾病风险。我们的中心假设 疾病等位基因变异的一个重要子集主要调节长非编码 RNA (lncRNA) 表达，这种效应通过功能性调节因果蛋白编码基因（pcGene）的表达 基因组相互作用，例如染色体环。我们的目标是研究这些 lncRNA 的作用 在介导 CAD 因果 pcGenes 表达中发挥的作用，以及它们实现这一目标的机制 功能。我们的理由是 lncRNA 作为遗传和表观遗传之间的关键中介 信号传导，阐明其功能机制是了解 CAD 风险的一个关键方面。为了获得 关于 CAD 背景下这些分子的作用模式的基本信息，我们建议 研究人冠状动脉平滑肌细胞 (HCASMC) lncRNA。在目标 1 中，我们将识别 lncRNA 这些细胞受到疾病相关刺激的调节，并且映射到 CAD GWAS 位点。共表达网络 分析将这些 lncRNA 连接到 pcGenes，并启动网络和通路分析以开始 建立它们的生物功能关联。在目标 2 中，我们将绘制表达数量性状基因座变异图 (eQTL) 对于每个 lncRNA，使用高通量等位基因特异性表达方法，提供 低丰度 RNA 的定量。将研究发现的 lncRNA eQTL 以确定是否 它们与 CAD GWAS 因果变异以及基因组分子性状 QTL 共定位。 CRISPR基因组 编辑将用于验证 eQTL，并确认 pcGene 身份。在目标 3 中，我们将采用 CRISPR 抑制和单细胞 RNA 测序 (PerturbSeq) 来绘制受 疾病相关的 lncRNA，并研究它们对 HCASMC 的体外细胞影响。这些研究将 得益于我们对原代培养的 HCASMC 的广泛研究，表征了表观基因组修饰、染色质 可访问性和循环，以及我们绘制 CAD GWAS 因果变异和介导风险的基因的努力 这种细胞类型。这项工作具有高度创新性，因为它结合了高度开发的独特基因组数据集。 疾病相关的细胞类型并且具有重要意义，因为它将整合 lncRNA、它们的调控变异，以及 CAD 风险病因学的分子机制。

项目成果

Single-cell transcriptome dataset of human and mouse in vitro adipogenesis models.

人类和小鼠体外脂肪形成模型的单细胞转录组数据集。

• DOI: 10.1101/2023.03.27.534456
• 发表时间: 2023
• 期刊: bioRxiv : the preprint server for biology
• 作者: Li,Jiehan;Jin,Christopher;Gustafsson,Stefan;Rao,Abhiram;Wabitsch,Martin;Park,ChongY;Quertermous,Thomas;Bielczyk-Maczynska,Ewa;Knowles,JoshuaW
• 通讯作者: Knowles,JoshuaW

Environment-Sensing Aryl Hydrocarbon Receptor Inhibits the Chondrogenic Fate of Modulated Smooth Muscle Cells in Atherosclerotic Lesions.

• DOI: 10.1161/circulationaha.120.045981
• 发表时间: 2020-08-11
• 期刊: Circulation
• 影响因子: 37.8
• 作者: Kim JB;Zhao Q;Nguyen T;Pjanic M;Cheng P;Wirka R;Travisano S;Nagao M;Kundu R;Quertermous T
• 通讯作者: Quertermous T