Functional Genomics of Tibetan Adaptations

西藏适应的功能基因组学

基本信息

批准号：
10116441
负责人：
Anna Di Rienzo
金额：
$ 75.76万
依托单位：
UNIVERSITY OF CHICAGO
依托单位国家：
美国
项目类别：
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/10116441
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 Gene set enrichment analysis 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 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 normoxia precise genome editing pressure reproductive outcome response single-cell RNA sequencing trait transcriptome sequencing

项目摘要

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.

抽象的尽管缺氧是人类生理的主要压力，但一些人群已经适应了高海拔（HA）缺氧环境。其中，对藏族人的研究最多它们的血红蛋白 (Hb) 水平相对较低。作为一个结果，他们严重缺氧，而且他们的生理机能如何应对缺氧仍然很差明白了。通过全基因组关联研究的独特组合，测试 Di Rienzo 实验室在多基因适应和功能性体外测定方面取得了两个主要成果观察结果：1) Hb 的最强关联信号和最强的选择性扫描在 EPAS1 位点发现的基因组信号影响内皮细胞的增强子活性（ECs），2）藏族人自然选择青睐较低的脉搏。这些发现提出了藏族人的心血管功能是否以及如何发生变化的问题对HA缺氧的适应。为了回答这些问题，我们提出以下具体目标：目标 1. 开发用于西藏适应功能表征的独特资源。我们将为 24 名藏人生成淋巴母细胞系并进行基因分型（待定），并将购买 24 来自千人基因组计划的汉族人 (CHB) 的拼箱。这些拼箱货将重新编程为诱导多能干细胞 (iPSC)，然后平行分化为心肌细胞 (CM) 和 EC。目标 2. 检验心血管功能是适应缺氧的目标这一假设藏族人。所有CM和EC均在常氧和缺氧条件下培养； RNA-seq 数据将是收集并分析以识别不同的基因和共表达模块 TBC 和 CHB 之间对缺氧的转录反应。顺式监管变体可能将使用以下方法来确定人群之间对缺氧反应的差异 RNA-seq 数据将被测试，以寻找藏族多基因适应的证据。目标 3. 通过编辑 iPSC 研究适应性等位基因的影响。我们将使用编辑技术删除 10 个增强子，包括 EPAS1 基因座上的增强子和其他在目标2.我们将通过精确的基因组编辑取代等位基因。我们还将培育转基因小鼠 EPAS1 增强子和人类相应增强子等位基因的缺失。总之，我们将描述心血管适应 HA 缺氧的机制通过独特的方法组合来阐明多基因的因果基础非欧洲人群对重要环境压力源的适应。