A Systems-level Approach to Studying HIV/AIDS Susceptibility and Substance Abuse

描述（由申请人提供）：长期暴露于滥用药物与感染或艾滋病毒疾病进展的风险增加有关。遗传和环境因素在影响寄主易感性中起重要作用；并不是所有接触到这种病毒的人都会被感染，而那些被感染的人发展成艾滋病的速度也不同。常见的遗传变异只能解释艾滋病毒/艾滋病遗传风险的一小部分，因此，很大一部分风险可能是由于各种不同基因的许多低频变异的影响的总和，这些变异对风险的影响相对较大。为了确定特定的因果变异、它们影响的调节网络、它们引入的相关功能改变以及物质使用的影响，我们提出了一种系统生物学方法来识别与病毒生命周期和免疫相关的许多先天免疫反应因子。我们假设，具有强表型效应的先天免疫或炎症的调节因子或效应因子的多种尚未识别的罕见变异可能对宿主易感性有重要影响。为了解决这一假设，我们汇集了一个具有互补专业领域的多学科团队，采用系统生物学方法识别影响艾滋病毒/艾滋病易感性和药物滥用的具有不同和重叠功能的基因。网络分析将对来自大规模测量的数据进行，以破译支持细胞介导的抵抗和对艾滋病毒感染的反应的调节网络。多变量相关性分析基因模块对这些扰动的响应，根据它们对表型的附加或合作贡献，将提供对它们的协同相互作用的见解，并提供一个易于处理的、经过验证的数据集，用于识别具有高可信度的候选基因，以供进一步研究。候选基因的编码区和一致剪接位点的靶向捕获和大规模平行测序是一种经济有效的策略，用于鉴定碱基替换，小插入或缺失，以及外显子组中感兴趣的间隔及其剪接变异体的拷贝数变化。根据基于药物暴露和风险概况的表型进行极端定量性状采样，最大限度地提高了对测序人数的变异发现能力。来自MACS和WIHS个体的基因分型变异，所有这些个体都具有HIV疾病状态，遗传祖先和药物滥用史的特征，提供了一个发现样本量，可以确定易患疾病风险的特定变异的频率。对先天免疫反应因子预测的功能改变的功能验证将阐明它们影响HIV生命周期的机制，并更好地定义控制这些扰动反应的复杂网络及其特性。这个假设驱动的宿主易感性和药物滥用的系统级分析的结果应该增加我们对细胞对扰动反应的复杂特性的理解，并为HIV/AIDS的遗传学和发病机制提供见解。

DESCRIPTION (provided by applicant): Chronic exposure to drugs of abuse is associated with an increased risk for infection or HIV disease progression. Genetic and environment factors play an important role in influencing host susceptibility; not all people exposed to the virus become infected, and those who do progress to AIDS at different rates. Common genetic variants explain only a small fraction of the heritable risk for HIV/AIDS, and therefore a significant proportion of risk may be due to the summation of the effects of many low frequency variants of assorted different genes that have relatively large effects on risk. To determine specific causal variants, the regulatory networks they impact, the relevant functional alterations they introduce, and the influence of substance use, we propose a systems biology approach to identify the many innate immune response factors that are relevant to the virus life cycle and immunity. We hypothesize that multiple as-yet-unidentified rare variants of regulators or effectors of innate immunity or inflammation with strong phenotypic effects are likely to contribute significantly to host susceptibility. To address this hypothesis, we have brought together a multidisciplinary team with complementary areas of expertise for a systems biology approach to identify genes with distinct and overlapping functions that affect HIV/AIDS susceptibility and drug abuse. Network analysis will be performed on data from large-scale measurements to decipher regulatory networks underpinning cell-mediated resistance and responses to HIV infection. Multivariate correlations that analyze gene modules underlying the response to these perturbations in terms of their additive or cooperative contributions towards the phenotype will provide insight into their synergistic interactions and a tractable, validated dataset for identifying candidate genes with high-confidence for further study. Targeted capture and massively parallel sequencing of the coding regions and consensus splice sites of candidate genes is a cost-effective strategy for the identification of base substitutions, small insertions or deletions, and copy number changes within exome-containing intervals of interest and their splice variants. Extreme quantitative trait sampling according to phenotype based on both drug exposure and risk profiles maximizes power for variant discovery for the number of people sequenced. Genotyping variants across individuals from the MACS and the WIHS, all of who are characterized for their HIV disease status, genetic ancestries, and histories of substance abuse, gives a discovery sample size that could identify the frequency of specific variants that predispose to disease risk. Functional validation of the predicted function-altering changes in innate immune response factors will elucidate the mechanisms by which they affect the life cycle of HIV and better define the complex networks and their properties that govern responses to these perturbations. The results of this hypothesis-driven, systems-level analysis of host susceptibility and drug abuse should increase our understanding of the complex properties that underlie the cellular response to perturbation and provide insight into the genetics and pathogenesis of HIV/AIDS.