LncRNA Transcriptional Mechanisms of Coronary Artery Disease Risk

冠状动脉疾病风险的 LncRNA 转录机制

基本信息

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
项目类别：
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

项目摘要

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.

治疗危险因素的修饰已在冠状动脉疾病（CAD）中显着降低然而，西方人群的重大风险是由于影响疾病的常见遗传变异容器壁上的途径，并且在没有特定疗法的情况下保持较低的理解。促进我们的长期表征这种遗传风险的分子基础的目标，我们参与了全基因组协会研究（GWAS）确定与冠状动脉疾病（CAD）风险相关的等位基因变异，这些差异努力产生了数百个相关的基因座。但是，大多数确定的因果变异属于在蛋白质编码外显子之外，在理解不佳的基因组的调节区域中，进一步需要努力了解关联机制，从而了解疾病的风险。我们的中心假设是疾病等位基因变异的重要子集主要调节长的非编码RNA（LNCRNA）表达，具有调节因果蛋白编码基因（PCGENE）表达的作用基因组相互作用，例如染色体环。我们的目的是调查这些lncrnas的作用发挥介导CAD因果PCGENES的表达，以及实现这一目标的机制功能。我们的理由是，lncRNA是遗传和表观遗传学之间的关键中介信号传导以及阐明其功能机制是理解CAD风险的关键方面。获得有关这些分子在CAD背景下的基本信息，我们建议研究人类冠状动脉平滑肌细胞（HCASMC）LNCRNA。在AIM 1中，我们将确定lncrnas 通过与疾病相关的刺激在这些细胞中调节，并将其映射到CAD GWAS基因座。共表达网络分析将将这些LNCRNA连接到PCGENES，并启动网络和途径分析以开始建立他们的生物功能关联。在AIM 2中，我们将绘制表达式定量特质基因座变体（eqtls）对于每个LNCRNA，使用高通量等位基因特异性表达方法低丰度RNA的定量。将研究发现的lncRNA eqtls，以确定是否是否它们与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AIM 3中，我们将雇用CRISPR 抑制和单细胞RNA测序（perturbseq）以绘制由由与疾病相关的LNCRNA，还研究了它们的体外细胞对HCASMC的影响。这些研究将是在我们对主要培养的HCASMC的大量作品的帮助，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因果变体和基因的努力，这些变体和基因介导了风险该单元格类型。这项工作具有很高的创新性，因为它结合了一个高度开发的独特基因组数据集疾病相关的细胞类型，并且很重要，因为它将整合LNCRNA，其调节性变异和分子机制进入CAD风险的病因。

项目成果

期刊论文数量（6）

专著数量（0）

科研奖励数量（0）

会议论文数量（0）

专利数量（0）

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
影响因子：
0
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