Functional Genomics and Epigenomics in HIV of Longitudinal Injection Drug Use Trajectory

 描述（由申请人提供）：我们建议对ALIVE队列中表观遗传变异（DNA甲基化、组蛋白甲基化和乙酰化）、全基因组和静脉用药变异之间的关系进行全面调查。艾滋病与静脉注射经历（ALIVE）研究是一项在巴尔的摩开展的以社区为基础的静脉注射吸毒者（IDUs）前瞻性队列研究，始于1988年，最终招募了3,500多名IDUs。随后的两年期随访包括对风险行为和药物使用的全面评估。我们的工作重点将放在样本中已使用Affytek 6.0平台进行基因分型的HIV受试者（N~1200）上。这个样本是>95%的非裔美国人，解决了基因组学研究中的一个共同缺点。在目标1中，我们建议在长期长期使用期间的可用纵向生物样本的子集中，然后在完全戒除所有非法药物后> 1年，检查DNA甲基化（使用Illumina甲基化450 k微珠芯片在全基因组范围内评估）与静脉内药物使用之间的关系。这是研究计划中提出的一项初步研究的延伸，我们发现IDU对全基因组甲基化有显著影响。我们还将对随后复发的子样本进行这项工作，以揭示复发者（目标1.2）和继续戒烟者之间不同的甲基化信号，并检查甲基化在早期药物使用停止中的作用（目标1.3）。在目标2中，我们将这项工作扩展到研究长期慢性使用（操作为“注射年”）对全基因组甲基化信号的影响。目的3：利用ChIP Seq技术研究组蛋白甲基化（H3 K9 me 2）和乙酰化（H3 K9 ac）之间的关系。与目标1一样，我们将从慢性IDU和完全戒断期间的相同个体中选择纵向样本，以最大限度地提高我们发现差异的可能性。我们还将尝试在死后的大脑样本中复制最重要的发现，将阿片类药物使用者与对照组进行比较。这项工作是新颖和创新的几个原因。这项拟议中的工作是对非裔美国人样本中任何疾病或特征进行的最大规模的表观遗传研究之一。这项工作建立在大量文献的基础上，这些文献基于药物暴露的动物模型，人类数据集数量有限，在长期使用和完全禁欲期间可以尝试类似的工作。最后，考虑到我们已有的GWAS数据，这项工作将是真正的整合，跨越生物学的许多领域（遗传，表观遗传和表型）。

 DESCRIPTION (provided by applicant): We propose a comprehensive investigation into the relationship between epigenetic variation (DNA Methylation, Histone Methylation and Acetylation), genome-wide, and variation in intravenous drug use in the ALIVE cohort. The AIDS Linked to the Intravenous Experience (ALIVE) study is a prospective community-based cohort of intravenous drug users (IDUs) in Baltimore that commenced in 1988, eventually enrolling more than 3,500 IDUs. Subsequent biennial follow-up included comprehensive assessment of risk behaviors and drug use. We will focus our work on the HIV- subjects in the sample who were already genotyped using the Affymetrix 6.0 platform (N~1200). This sample is >95% African- American addressing a common shortcoming in genomics research. In Aim 1, we propose to examine the relationship between DNA methylation, assessed genome-wide using the Illumina Methylation 450k bead chip, and intravenous drug use, in a subset with available longitudinal biological samples during extended periods of chronic use and then again > 1 year after complete abstinence from all illicit drugs. This is an extension of a preliminary study, presented in the Research Plan, where we found a significant impact of IDU on genome-wide methylation. We will also perform this work on a subsample with subsequent relapse to uncover methylation signals which differ between those who relapse (Aim 1.2) and those who continue to abstain as well as examine the role of methylation in early drug use cessation (Aim 1.3). In Aim 2, we extend this work to examine the impact of long-term chronic use, operationalized as `injection years', on genome-wide methylation signals. Aim 3, we examine the relationship between Histone Methylation (H3K9me2) and Acetylation (H3K9ac) using ChIP Seq technology. As in Aim 1, we will select longitudinal samples from the same individuals during periods of chronic IDU and complete abstinence to maximize the likelihood that we will find differences. We will also attempt to replicate the top findings in a post-mortem brain sample comparing opiate users to controls. This work is novel and innovative for several reasons. The proposed work is among the largest epigenetic studies for any disease or trait in an African American sample. The work builds on a large literature based on animal models of drug exposure for which there are a limited number of human datasets, with available biological samples during periods of chronic use and complete abstinence that could attempt similar work. Lastly, given that we have existing GWAS data, this work will be truly integrative, across many domains of biology (genetic, epigenetic, and phenotypic).