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.

治疗性危险因素调整可显著降低冠心病（CAD）发生率， 然而，西方人群的重大风险是由于共同的遗传基因变异，影响疾病 血管壁中的通路，并且在没有特定疗法的情况下仍然知之甚少。为了促进我们的长期发展 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）确定与冠状动脉疾病（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的基因座。然而，大多数已确定的因果变异存在于 在蛋白质编码外显子之外，在基因组的调控区域中，这些区域知之甚少，并且进一步 需要努力了解相关机制，从而了解疾病风险。我们的核心假设 疾病等位基因变异的一个重要子集主要调节长链非编码RNA（lncRNA）， 表达，这种作用通过功能性调节致病蛋白编码基因（pcGene）的表达 基因组相互作用，如染色体环。我们的目标是研究这些lncRNAs在 在介导CAD致病pcGenes表达中的作用，以及它们实现这一点的机制 功能我们的理论基础是lncRNA作为遗传和表观遗传之间的关键中介 信号，阐明其功能机制是理解CAD风险的关键方面。获得 关于这些分子在CAD背景下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）lncRNAs。在目标1中，我们将鉴定lncRNA 在这些细胞中由疾病相关刺激调节，并映射到CAD GWAS基因座。共表达网络 分析将这些lncRNA连接到pcGenes，并启动网络和途径分析，以开始 建立它们的生物功能联系。在目标2中，我们将定位表达数量性状基因座变体， 使用高通量等位基因特异性表达方法，对每个lncRNA的eQTL进行检测，该方法提供了 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，我们将使用CRISPR 抑制和单细胞RNA测序（PerturbSeq）来绘制由转录调控的转录网络。 疾病相关的lncRNA，并研究其对HCASMC的体外细胞作用。这些研究报告将 在我们对表征表观基因组修饰的原代培养的HCASMC的大量工作的帮助下， 可及性和循环，以及我们努力绘制CAD GWAS因果变异和介导风险的基因， 这种细胞类型。这项工作是高度创新的，因为它结合了独特的基因组数据集， 与疾病相关的细胞类型且意义重大，因为它将整合lncRNA、其调节变异，以及 分子机制的研究进展。

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