eQTL mapping in iPSC-derived differentiated cardiomyocytes - Renewal 01 - Resubmi

iPSC 衍生的分化心肌细胞中的 eQTL 作图 - Renewal 01 - Resubmi

• 批准号: 8756985
• 负责人: Yoav Gilad
• 金额: $ 49.67万
• 依托单位: UNIVERSITY OF CHICAGO
• 依托单位国家: 美国
• 财政年份: 2009
• 资助国家: 美国
• 起止时间: 2009-04-15 至 2018-04-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8756985
• 关键词: B-Lymphocytes; Blood Cells; Blood Pressure; Cardiac Myocytes; Cardiovascular Diseases; Cardiovascular system; Cell Line; Cells; Complex; Data; Data Set; Disease; Eating; Environment; European; Family; Farming environment; Fibroblasts; Founder Generation; Functional RNA; Funding; Gene Expression; Gene Expression Regulation; Genes; Genetic; Genetic Variation; Genomics; Genotype; Grant; Heart; Heart Atrium; Heritability; Human; Human Genetics; Individual; Intuition; Knowledge; Left; Left Ventricular Mass; Life; Life Style; Light; Maps; Measurement; Methods; Methylation; Noise; Phenotype; Population; Quantitative Trait Loci; RNA Sequences; Regulator Genes; Risk; Role; Sampling; Site; Smoking; South Dakota; Testing; Thick; Time; Variant; Work; base; cardiovascular disorder risk; cell type; disorder risk; genome sequencing; genome wide association study; histone modification; human disease; hutterite; induced pluripotent stem cell; insight; interest; intima media; lymphoblastoid cell line; novel; public health relevance; trait

DESCRIPTION (provided by applicant): Genome-wide association studies (GWAS) have identified many variants associated with cardiovascular-related diseases, some of which are novel. However, similar to other common diseases, these identified risk-associated variants fail to explain a significant portion of the genetic heritability of cardiovascular disease (CVD). Moreover, many associated variants are non-coding with no obvious function, though putatively, these are involved in gene regulation. By combining results of GWAS with expression quantitative trait locus (eQTL) mapping one can identify functional variants that influence gene expression and are also associated with disease risk. Using such combination of approaches one can identify true weak associations that are otherwise difficult to distinguish from statistica noise using a GWAS approach alone, as well as develop an immediate intuition regarding both the function of associated variants and knowledge of the implicated genes. However, for this method to be most effective, eQTL studies should be performed in cells that are relevant to the phenotype of interest, which are often not easily accessible in population samples. Indeed, nearly all eQTL mapping studies in humans to date (including the studies we performed in the first term of this grant) used gene expression measurements from blood cell types, fibroblasts, or lymphoblastoid cell lines (LCLs). In that sense, induced pluripotent stem cells (iPSCs) can change human genetics in a profound way. The ability to differentiate iPSCs can allow us to perform functional studies in the most relevant cell types. We thus propose to map eQTLs and investigate the genetic basis of cardiovascular disease in cardiomyocytes, which will be differentiated from induced pluripotent stem cells (iPSCs) of 120 Hutterite individuals. The Hutterites are a founder population of European descent that practices a communal, farming lifestyle. The Hutterites of South Dakota, the subjects of our studies, live on communal (15-25 families) farms (called "colonies"), where all meals are prepared and eaten in a communal kitchen, smoking is prohibited (and rare), and early life environments are extremely uniform. Our specific aims are to reprogram iPSCs from the LCLs of 120 Hutterites and obtain differentiated cardiomyocytes from each individual (aim 1), map eQTLs in differentiated cardiomyocytes (aim 2), and integrate eQTL mapping with GWAS results to identify variants associated with CVD-related phenotypes (aim 3). At the conclusion of this work we expect to gain important insight on the genetic basis of gene regulation in the heart in general, as well as on gene regulatory variation that is associated with CVD risk.

描述（由申请人提供）：全基因组关联研究（GWAS）已经确定了许多与心血管相关疾病相关的变异，其中一些是新的。然而，与其他常见疾病类似，这些已确定的风险相关变异无法解释心血管疾病（CVD）遗传遗传性的很大一部分。此外，许多相关的变异是非编码的，没有明显的功能，尽管推测它们参与基因调控。通过将GWAS结果与表达数量性状位点（eQTL）定位相结合，可以确定影响基因表达并与疾病风险相关的功能变异。使用这种方法的组合，人们可以识别真正的弱关联，否则很难从单独使用GWAS方法的统计噪声中区分出来，并且可以对相关变体的功能和相关基因的知识产生直接的直觉。然而，为了使这种方法最有效，eQTL研究应该在与感兴趣的表型相关的细胞中进行，这些细胞通常不容易在总体样本中获得。事实上，迄今为止，几乎所有的人类eQTL定位研究（包括我们在本基金第一期进行的研究）都使用了来自血细胞类型、成纤维细胞或淋巴母细胞样细胞系（LCLs）的基因表达测量。从这个意义上说，诱导多能干细胞（iPSCs）可以深刻地改变人类遗传学。分化iPSCs的能力使我们能够在最相关的细胞类型中进行功能研究。因此，我们建议绘制eqtl图谱，并研究心血管疾病在心肌细胞中的遗传基础，这些心肌细胞将从120个huterite个体的诱导多能干细胞（iPSCs）中分化出来。赫特人是欧洲后裔的一个创始人，他们过着集体农耕的生活方式。南达科他州的Hutterites是我们研究的对象，他们生活在公共农场（15-25个家庭）（称为“殖民地”），所有的食物都在公共厨房里准备和吃，禁止吸烟（而且很少吸烟），早期生活环境极其统一。我们的具体目标是从120名hutterite人的LCLs中重编程iPSCs，并从每个人身上获得分化的心肌细胞（目标1），绘制分化心肌细胞中的eQTL图谱（目标2），并将eQTL图谱与GWAS结果相结合，以识别与cvd相关表型相关的变异（目标3）。在这项工作的结论中，我们期望对心脏基因调控的遗传基础以及与心血管疾病风险相关的基因调控变异获得重要的见解。