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Improved methods for inference of genotype-specific response to environmental toxins

推断对环境毒素的基因型特异性反应的改进方法

基本信息

批准号：
10557856
负责人：
Julien Ayroles
金额：
$ 69.02万
依托单位：
PRINCETON 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：
2019-02-01 至 2025-01-31
项目状态：
未结题

来源：
https://reporter.nih.gov/project-details/10557856
关键词：
Address Affect Alleles Behavioral Assay Biological Assay CRISPR/Cas technology Carcinogens Chromosome Mapping Clustered Regularly Interspaced Short Palindromic Repeats Communities Complex DNA Sequence Data Defect Disease Disease susceptibility Drosophila genus Drosophila melanogaster Environment Environmental Exposure Environmental Pollutants Exposure to Gene Expression Profiling Generations Genes Genetic Genetic Polymorphism Genetic Predisposition to Disease Genetic Transcription Genetic Variation Genetic study Genome Genotype Head Health Hazards Heavy Metals Household Human Immune Inbred Strain Individual Knock-in Knock-out Maps Measures Mediating Methods Mitochondria Modeling Molecular Mutation Oxidative Stress Oxidative Stress Induction Pathway interactions Penetrance Phenotype Population Predisposition Protocols documentation Reactive Oxygen Species Resolution Resources Risk Stress System Technology Toxic Environmental Substances Toxic effect Transgenic Organisms Variant Work advanced system biomarker identification carcinogenicity chromium hexavalent ion cost design disorder risk drinking water epidemiology study experience fly genetic analysis genetic approach genetic architecture genome wide association study genotoxicity improved individual variation inter-individual variation knock-down neurotoxicity pollutant reproductive response risk variant success trait transcriptome transcriptome sequencing

项目摘要

PROJECT SUMMARY Why do some individuals appear to be more sensitive than others to environmental perturbation? The answer to this question has broad implications ranging from our ability to make predictions about disease risk from genotype, to our ability to identify the drivers of inter-individual variability. Here, we propose to study the broad question of how the interplay between genetic and environmental variation mediates disease risk following a toxic environmental exposure. Specifically, we will examine the consequences of environmental exposure to hexavalent chromium [Cr(VI)] a ubiquitous environmental pollutant. Cr(VI) is a potent carcinogen and its toxicity extends far beyond its genotoxic effects, including neurotoxicity, mitochondrial defects, immune aberrations, and reproductive defects, to list a few. Although Cr(VI) is a common environmental and major health hazard, we know little about how genetic variation drives differential susceptibility to its toxicity, or the molecular pathways involved. Exploring the contribution of genotype-by- environment interactions to individual variation has been very challenging in humans. To address this problem we created a new community resource to study the genetic basis of complex trait variation in Drosophila melanogaster made of large, synthetic outbred populations. With this new and versatile community resource, we can rear thousands of genetically unique flies drawn from a common genetic pool, expose them to a range of different environments [here, Cr(VI)], and contrast the ensuing genetic architectures. We have simultaneously developed a new high throughput protocols to sequence the DNA and assay the transcriptome of thousands of flies at very low cost allowing for advance systems genetics analysis. Using this platform, in aim 1, we will phenotype thousands of individual flies for a variety of traits know to be impacted by Cr(VI) exposure. This combination of design improvements and technological advances produces a large boost in both statistical power and genetic resolution. It allows us to ask if the shift in sensitivity some individuals experience under environmental stress can be explained by the release of genetic susceptibility through of GxE. In aims 2, we will use a systems genetic approach study variation in sensitivity from the perspective of the regulatory systems disruption. Individuals more sensitive to environmental stress appear to have decreased transcriptional robustness for many genes. This variation in robustness appears to be under genetic control and we have developed an analytical framework to identify such context-dependent transcriptional networks and their genetic regulators. Finally, in aim 3, we examine how environmentally sensitive alleles are background-dependent, and what genetic factors modulate their penetrance? We will use CRISPR/Cas9 to knock-out and knock-in alleles into targeted genes identified in aim 1 and will crossed these transgenic lines to the synthetic flies from aim 1 and the F1 progeny will be genotyped and phenotyped for Cr(VI) responses to identify modifiers.

项目概要为什么有些人似乎比其他人对环境扰动更敏感？答案是这个问题具有广泛的影响，包括我们对疾病风险进行预测的能力基因型，我们有能力识别个体间变异的驱动因素。在此，我们建议广泛研究遗传和环境变异之间的相互作用如何介导疾病风险的问题暴露于有毒环境后。具体来说，我们将研究以下后果：六价铬 [Cr(VI)] 是一种普遍存在的环境污染物。 Cr(VI) 是一种强效致癌物，其毒性远远超出其基因毒性作用，包括神经毒性，线粒体缺陷、免疫畸变和生殖缺陷等等。尽管 Cr(VI) 是常见的环境和重大健康危害，我们对遗传变异如何驱动差异知之甚少对其毒性或所涉及的分子途径的敏感性。探索基因型的贡献环境与个体差异的相互作用对人类来说非常具有挑战性。为了解决这个问题我们创建了一个新的社区资源来研究果蝇复杂性状变异的遗传基础由大量合成的近交种群组成的黑腹果蝇。有了这个新的多功能社区资源，我们可以饲养数千只从共同基因库中提取的具有独特基因的果蝇，并将它们暴露于一系列不同的环境[此处为 Cr(VI)]，并对比随后的遗传结构。我们同时有开发了一种新的高通量方案来对 DNA 进行测序并分析数千个样本的转录组飞行成本非常低，可以进行先进的系统遗传学分析。利用这个平台，在目标 1 中，我们将对数千只果蝇个体进行了表型分析，了解其各种性状，这些性状均受到 Cr(VI) 暴露的影响。这设计改进和技术进步的结合大大提高了统计能力和遗传分辨率。它使我们能够询问某些人是否在以下情况下经历了敏感性的转变：环境压力可以通过 GxE 释放遗传易感性来解释。在目标 2 中，我们将使用系统遗传方法从监管系统的角度研究敏感性的变化扰乱。对环境压力更敏感的个体似乎转录水平下降许多基因的稳健性。这种鲁棒性的变化似乎受到遗传控制，我们有开发了一个分析框架来识别这种依赖于上下文的转录网络及其遗传监管机构。最后，在目标 3 中，我们研究了环境敏感等位基因如何依赖于背景，并且哪些遗传因素调节其外显率？我们将使用CRISPR/Cas9来敲除和敲入等位基因进入目标 1 中确定的目标基因，并将这些转基因品系与目标 1 中的合成果蝇杂交 F1 后代将对 Cr(VI) 反应进行基因分型和表型分析，以识别修饰因子。

项目成果

期刊论文数量（22）

专著数量（0）

科研奖励数量（0）

会议论文数量（0）

专利数量（0）

A model and test for coordinated polygenic epistasis in complex traits.

DOI：
10.1073/pnas.1922305118
发表时间：
2021-04-13
期刊：
Proceedings of the National Academy of Sciences of the United States of America
影响因子：
11.1
作者：
Sheppard B;Rappoport N;Loh PR;Sanders SJ;Zaitlen N;Dahl A
通讯作者：
Dahl A

Massively parallel analysis of human 3' UTRs reveals that AU-rich element length and registration predict mRNA destabilization.