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.

项目摘要为什么有些人似乎比其他人对环境扰动更敏感？答案这个问题具有广泛的含义，从我们从中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性的驱动因素。在这里，我们建议研究广泛的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发生有毒的环境暴露。具体来说，我们将研究环境暴露于六价铬[CR（VI）]无处不在的环境污染物。 Cr（vi）是有效的致癌物及其毒性远远超出其遗传毒性作用，包括神经毒性，线粒体缺陷，免疫像差和生殖缺陷，以列出一些。虽然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的敏感性或所涉及的分子途径。探索基因型的贡献在人类中，环境与个体变异的互动非常具有挑战性。解决这个问题我们创建了一种新的社区资源来研究果蝇中复杂性状变化的遗传基础 Melanogaster由大型，合成的杂种种群制成。有了这个新的多功能社区资源，我们可以从一个共同的遗传库中抬起数千种基因独特的果蝇，使它们暴露于一系列不同的环境[此处，CR（VI）]，并将随之而来的遗传体系结构对比。我们同时有开发了一种新的高吞吐量协议来对DNA进行测序并测定数千个的转录组以非常低的成本允许苍蝇进行预先的系统遗传分析。在AIM 1中使用此平台，我们将表型成千上万的个人苍蝇针对各种特征，都会受到CR（VI）暴露的影响。这设计改进和技术进步的结合在这两种统计能力方面都大大提高和遗传解决方案。它使我们能够询问某些人在下面经历的敏感性转变是否环境压力可以通过通过GXE释放遗传敏感性来解释。在目标2中，我们将从调节系统的角度使用系统遗传学方法研究的敏感性变化破坏。对环境压力更敏感的个体似乎已减少转录许多基因的鲁棒性。这种鲁棒性的这种差异似乎处于遗传控制之下，我们有开发了一个分析框架，以识别这种依赖上下文的转录网络及其遗传监管机构。最后，在AIM 3中，我们研究了环境敏感的等位基因如何取决于背景，并且哪些遗传因素调节其外观？我们将使用CRISPR/CAS9进行敲除和敲门等位基因进入AIM 1中鉴定的靶向基因，并将这些转基因线越过AIM 1的合成蝇 F1后代将进行基因分型和表型，以识别CR（VI）反应以识别修饰符。

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.