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: 8890860
• 负责人: Yoav Gilad
• 金额: $ 57.84万
• 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/8890860
• 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; Funding; Gene Expression; Gene Expression Regulation; Genes; Genetic; Genetic Variation; Genetic study; Genomics; Genotype; Grant; Health; 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; Role; Sampling; Site; Smoking; South Dakota; Testing; Time; Untranslated RNA; 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; intimal medial thickening; lymphoblastoid cell line; novel; risk variant; trait; transcriptome sequencing

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）已经鉴定出许多与心血管相关疾病相关的变异，其中一些是新颖的。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) 遗传性的很大一部分。此外，许多相关变体是非编码的，没有明显的功能，尽管推测它们涉及基因调控。通过将 GWAS 的结果与表达数量性状基因座 (eQTL) 作图相结合，人们可以识别影响基因表达并与疾病风险相关的功能变异。使用这种方法组合，人们可以识别真正的弱关联，否则仅使用 GWAS 方法很难将其与统计噪音区分开来，并且可以对相关变体的功能和所涉及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，而这些细胞在群体样本中通常不容易获得。事实上，迄今为止几乎所有人类 eQTL 作图研究（包括我们在本次资助的第一期中进行的研究）都使用了血细胞类型、成纤维细胞或类淋巴母细胞系 (LCL) 的基因表达测量。从这个意义上说，诱导多能干细胞（iPSC）可以深刻地改变人类遗传学。分化 iPSC 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 图谱并研究心肌细胞中心血管疾病的遗传基础，该心肌细胞将与 120 名哈特派个体的诱导多能干细胞 (iPSC) 区分开来。哈特派是欧洲血统的创始人，他们过着公共的农业生活方式。我们的研究对象南达科他州的哈特派教徒生活在公共（15-25 个家庭）农场（称为“殖民地”），所有膳食均在公共厨房准备和食用，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 Hutterites 的 LCL 中重新编程 iPSC，并从每个个体中获得分化的心肌细胞（目标 1），绘制分化心肌细胞中的 eQTL（目标 2），并将 eQTL 定位与 GWAS 结果相结合，以识别与 CVD 相关表型相关的变异（目标 3）。在这项工作结束时，我们希望获得关于心脏基因调控的遗传基础以及与 CVD 风险相关的基因调控变异的重要见解。