Functional Genomics of Tibetan Adaptations

西藏适应的功能基因组学

• 批准号: 9883985
• 负责人: Anna Di Rienzo
• 金额: $ 68.47万
• 依托单位: UNIVERSITY OF CHICAGO
• 依托单位国家: 美国
• 财政年份: 2014
• 资助国家: 美国
• 起止时间: 2014-04-01 至 2024-02-29
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/9883985
• 关键词: ATAC-seq; Acclimatization; Alleles; Altitude; Biology; Cardiac Myocytes; Cardiovascular Diseases; Cardiovascular Physiology; Cardiovascular system; Chicago; Chinese People; Chromatin; Clustered Regularly Interspaced Short Palindromic Repeats; Cultured Cells; Data; Endothelial Cells; Endothelium; Enhancers; Environment; Frequencies; Genes; Genetic; Genetic Enhancer Element; Genetic Transcription; Genome; Genotype; Hemoglobin; Hemoglobin concentration result; Human; Hypoxemia; Hypoxia; Lung diseases; Maps; Mediator of activation protein; Molecular; Mus; Natural Selections; Outcome; Oxygen; Pathway interactions; Phenotype; Physiologic pulse; Physiological; Physiology; Population; Quantitative Trait Loci; Research Design; Resolution; Resources; Signal Transduction; Stress; System; Technology; Testing; Time; Transgenic Mice; Variant; Work; base; cell type; environmental stressor; experience; experimental study; functional genomics; genetic testing; genome wide association study; heart function; humanized mouse; in vitro Assay; indexing; induced pluripotent stem cell; insight; lymphoblastoid cell line; multidisciplinary; precise genome editing; pressure; reproductive; response; single-cell RNA sequencing; trait; transcriptome sequencing

ABSTRACT Although hypoxia is a major stress on human physiology, several populations have adapted to high altitude (HA) hypoxic environments. Among them, Tibetans have been studied most extensively and they have been shown to have relatively low hemoglobin (Hb) levels. As a result, they are severely hypoxemic and how their physiology copes with hypoxia remains poorly understood. Through a unique combination of genome-wide association studies, tests for polygenic adaptation and functional in vitro assays, the Di Rienzo lab has made two major observations: 1) the strongest association signals for Hb and the strongest selective sweep signals in the genome, found at the EPAS1 locus, influence enhancer activity in endothelial cells (ECs), and 2) lower pulse was favored by natural selection in Tibetans. These findings raise the questions of whether and how cardiovascular functions changed in Tibetans as a result of adaptations to HA hypoxia. To answer them, we propose the following specific aims: Aim 1. Develop a unique resource for the functional characterization of Tibetan adaptations. We will generate and genotype lymphoblastoid cell lines for 24 Tibetans (TBC) and will purchase 24 LCLs from Han Chinese (CHB) from the 1000 genome project. These LCLs will be reprogrammed to induced pluripotent stem cells (iPSCs) and then differentiated in parallel into cardiomyocytes (CMs) and ECs. Aim 2. Test the hypothesis that cardiovascular functions were targets of adaptation to hypoxia in Tibetans. All the CMs and ECs will be cultured in normoxia and hypoxia; RNA-seq data will be collected and analyzed to identify genes and co-expression modules that differ in the transcriptional response to hypoxia between TBC and CHB. Cis-regulatory variants that may account for between-population differences in response to hypoxia will be identified using the RNA-seq data and, in turn, will be tested for evidence of polygenic adaptations in Tibetans. Aim 3. Investigate the effects of adaptive alleles by editing iPSCs. We will use editing technologies to delete 10 enhancers including those at the EPAS1 locus and others identified in Aim 2. We will replace alleles by precise genome editing. We will also generate transgenic mice with deletion of EPAS1 enhancer and with the corresponding enhancer alleles in humans. In summary, we will characterize the mechanisms of cardiovascular adaptations to HA hypoxia through a unique combination of approaches to elucidate the causal basis of a polygenic adaptation to an important environmental stressor, in a non-European population.

抽象的 尽管缺氧是对人类生理学的主要压力，但有几个人口已适应 高海拔（HA）低氧环境。其中，藏人研究了最多 广泛的，它们的血红蛋白（Hb）水平相对较低。作为 结果，它们严重低氧，其生理学如何与缺氧保持较差 理解。通过全基因组关联研究的独特组合，测试 多基因适应和在体外测定中功能性，Di Rienzo实验室已成为两个主要的 观察：1）HB的最强关联信号和最强的选择性扫描 在EPAS1基因座中发现的基因组中的信号会影响内皮细胞中增强子活性 （EC）和2）藏在藏族中的自然选择有利于较低的脉冲。这些发现提出了 由于藏族功能是否以及如何在藏族中发生变化的问题 适应HA缺氧。为了回答它们，我们提出以下具体目的： 目标1。为藏族适应的功能表征开发独特的资源。我们 将生成24个藏族（TBC）的基因型淋巴细胞细胞系，并将购买24 来自1000基因组项目的Han Chinese（CHB）的LCL。这些LCL将是 重新编程为诱导的多能干细胞（IPSC），然后并行分化为 心肌细胞（CMS）和ECS。 AIM 2。测试心血管功能是适应缺氧的靶标的假设 藏人。所有CMS和EC将在常规氧和缺氧中培养； RNA-seq数据将是 收集和分析以鉴定基因和共表达模块在 对TBC和CHB之间缺氧的转录反应。顺式调节变体可能 考虑到对缺氧的响应中人口间差异的解释 RNA-seq数据又将测试藏族中多基因适应的证据。 AIM 3。通过编辑IPSC来研究自适应等位基因的影响。我们将使用编辑 删除10个增强剂的技术，包括EPAS1基因座和其他确定的技术 目标2。我们将通过精确的基因组编辑代替等位基因。我们还将生成转基因小鼠 随着EPAS1增强子的删除以及人类中相应的增强等位基因。 总而言之，我们将表征心血管适应HA缺氧的机制 通过独特的方法组合，以阐明多基因的因果关系 在非欧洲人口中适应重要的环境压力源。