Impact of Methamphetamine Use on the HIV Nucleome in Individuals on Antiretroviral Therapy

使用甲基苯丙胺对接受抗逆转录病毒治疗的个体 HIV 核组的影响

• 批准号: 9764331
• 负责人: Zhijun Duan
• 金额: $ 101.99万
• 依托单位: UNIVERSITY OF WASHINGTON
• 依托单位国家: 美国
• 财政年份: 2018
• 资助国家: 美国
• 起止时间: 2018-08-15 至 2021-05-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/9764331
• 关键词: 3-Dimensional; Acquired Immunodeficiency Syndrome; Adherence; Affect; Architecture; BACH2 gene; CD4 Positive T Lymphocytes; CRISPR/Cas technology; Cell Culture Techniques; Cell Nucleus; Cell Proliferation; Cell Survival; Cells; ChIP-seq; Chromatin; Chronic; Comorbidity; DNA; DNA biosynthesis; Deoxyribonucleases; Development; Disease Progression; Enhancers; Epigenetic Process; Exposure to; Expression Profiling; Gene Expression; Genes; Genome; Genome engineering; Genomics; Glean; HIV; HIV Infections; HIV resistance; HIV-1; Human; Human Genome; Individual; Inflammation; Insertional Mutagenesis; Investigation; Latent Virus; Lead; Life Expectancy; Location; Maintenance; Maps; Measures; Methamphetamine; Nuclear; Nuclear Structure; Pathology; Patients; Pattern; Phase; Play; Population; Positioning Attribute; Process; Property; Provirus Integration; Proviruses; RNA Splicing; Regulatory Element; Resolution; Risk Factors; Role; STAT5B gene; Site; Structure; Substance Use Disorder; Substance abuse problem; T-Lymphocyte; Techniques; Technology; Treatment Protocols; Viral; Viremia; Virus; Virus Latency; antiretroviral therapy; cell type; cellular engineering; chromatin modification; chromosomal location; cohort; combinatorial; disease transmission; drug of abuse; epigenome; gene function; high risk; immune activation; immune function; in vivo; indexing; insight; integration site; methamphetamine use; novel strategies; pandemic disease; promoter; response; single cell analysis; site-specific integration; structural genomics; transcriptome; transcriptome sequencing; vector

PROJECT SUMMARY/ABSTRACT A major challenge in ending the HIV pandemic is the persistence of the latent HIV reservoir that can lead to viremia, disease progression and transmission to new hosts after discontinuation of antiretroviral therapy (ART). Efficient treatment regimens that successfully eliminate cell populations carrying intact proviruses are not available due to the incomplete understanding of the cellular mechanisms that allow the virus to remain quiescent within the host genome. A compounding risk factor in HIV pathology is substance use disorder (SUD) known to contribute to decreased adherence to and delay of viral decay due to ART, and accelerated progression to AIDS. We hypothesize that persistence of HIV reservoirs is encoded in the proviral location within the 3D architecture of the host genome (nucleome), and influenced by SUD-induced changes in epigenetic structures. During the exploratory high-risk R61 phase of this project, we will first identify SUD-related differences in HIV integration site patterns, the epigenome and the nucleome of CD4+ T lymphocytes derived from patient cohorts that differ in their exposure to methamphetamine (meth). In the second aim, we will apply advanced 3D nucleome mapping strategies to define the interdependence of nuclear structure, proviral genomic location, regulatory elements, and transcriptomes in short-term ex vivo cultivated patient-derived cells from both cohorts. In the third aim, we will use gene-editing techniques to precisely define a role for proviral integration sites (identified in aims 1 and 2) in cellular gene activity and HIV persistence, including those related to meth use. In the R33 phase we propose to assess the impact of targeted provirus integration on nucleome architecture and transcriptomes to clearly identify genes essential for establishing the ART-resistant HIV reservoir. In addition, we will pursue a strategy to define chromatin interactions of proviral integrations and host genes in vivo in human CD4+ T cell populations of HIV-infected individuals.

项目概要/摘要 结束艾滋病毒大流行的一个主要挑战是潜在艾滋病毒储存库的持续存在，这可能导致 停止抗逆转录病毒治疗后病毒血症、疾病进展和传播给新宿主 （艺术）。成功消除携带完整原病毒的细胞群的有效治疗方案是 由于对允许病毒保留的细胞机制的不完全了解，无法获得 在宿主基因组内处于静止状态。 HIV 病理学的一个复合危险因素是物质使用障碍 (SUD) 已知有助于降低 ART 的依从性并延迟病毒衰变，并加速 进展为艾滋病。我们假设 HIV 储存库的持久性是在原病毒位置编码的 在宿主基因组（核组）的 3D 结构内，并受到 SUD 诱导的变化的影响 表观遗传结构。 在该项目的探索性高风险 R61 阶段，我们将首先确定 HIV 中与 SUD 相关的差异 患者来源的 CD4+ T 淋巴细胞的整合位点模式、表观基因组和核组 甲基苯丙胺（meth）暴露程度不同的队列。在第二个目标中，我们将应用先进的 3D 核组作图策略定义核结构、原病毒基因组的相互依赖性 短期离体培养的患者来源细胞中的位置、调控元件和转录组 两个队列。在第三个目标中，我们将使用基因编辑技术来精确定义前病毒的作用 细胞基因活性和 HIV 持久性中的整合位点（在目标 1 和 2 中确定），包括那些 与冰毒的使用有关。 在 R33 阶段，我们建议评估靶向原病毒整合对核组架构的影响 和转录组，以清楚地识别建立抗 ART 病毒库所必需的基因。在 此外，我们将采取一种策略来定义原病毒整合和宿主基因的染色质相互作用 HIV 感染者体内的人类 CD4+ T 细胞群。