Elite controllers as a model for a cure of HIV-1 infection

精英控制者作为治愈 HIV-1 感染的典范

• 批准号: 10461864
• 负责人: Xu Yu
• 金额: $ 86.56万
• 依托单位: MASSACHUSETTS GENERAL HOSPITAL
• 依托单位国家: 美国
• 财政年份: 2020
• 资助国家: 美国
• 起止时间: 2020-09-23 至 2026-08-31
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10461864
• 关键词: ATAC-seq; Address; Age; Allogeneic Bone Marrow Transplantation; Anti-Retroviral Agents; Behavior; Biological Assay; Blood; CCR5 gene; Cells; Cellular Assay; ChIP-seq; Characteristics; Chromatin; Complex; DNA; DNA Methylation; Data; Disease Outcome; Disease remission; Epigenetic Process; Frequencies; Genetic; Genetic Transcription; Genome; Genomic Segment; Goals; HIV; HIV-1; HLA Class I Genes; Hematopoietic stem cells; Histones; Human; Human Genome; Hypermethylation; Immune; Immune response; Immunologics; Individual; Infection; Intervention; Link; Lymphoid Tissue; Mediating; Methylation; Modeling; Molecular Profiling; Nature; Pathogenicity; Peripheral Blood Mononuclear Cell; Pharmaceutical Preparations; Predisposition; Proviruses; RNA; Reporting; Research; Resistance; Running; Signal Transduction; Site; Stem cell transplant; Stimulus; Structure; Study models; Techniques; Technology; Testing; Time; Tissues; Variant; Viral; Viral Genes; Viral Load result; Viral reservoir; Viremia; Virus; biocomputing; chromosomal location; clinical development; design; experimental study; genome analysis; genome-wide; genomic locus; in vivo; innovation; integration site; interest; longitudinal analysis; next generation sequencing; novel; patient population; permissiveness; promoter

Abstract While a sterilizing cure of HIV-1 infection has been reported in two individuals after a stem cell transplant with CCR5∆32 homozygous cells, a spontaneous functional cure of HIV-1 occurs in 0.3-0.5% of all infected individuals. These individuals, termed elite controllers (EC), maintain undetectable levels of HIV-1 replication in the absence of treatment, despite the repeated isolation of replication-competent virus from viral reservoir cells. These individuals provide living evidence that spontaneous control of HIV-1 infection is possible, and the identification of virological and immunological mechanisms underlying such a remarkable disease outcome holds promise for inducing a functional cure of HIV-1 infection in broader HIV-1 patient populations. Here, we propose the novel hypothesis that undetectable viral loads in EC are related to specific genetic and epigenetic features of proviral HIV-1 DNA in reservoir cells. Based on strong preliminary data, we posit that intact HIV-1 proviruses from EC are preferentially located in non-genic chromosomal regions that do not permit effective viral gene transcription, resulting in a proviral landscape in deep latency and with very limited responsiveness to reactivation stimuli in vivo. In addition, we propose that intact proviruses from EC are also frequently integrated into chromosomal regions that show epigenetic characteristics of repressive chromatin, evidenced by enhanced distance to accessible chromatin and enrichment with inhibitory histone marks and hypermethylated DNA. To investigate this, we plan to longitudinally analyze the frequency and chromosomal location of intact proviruses in blood and lymphoid tissues of EC, using novel experimental and biocomputational analysis approaches (Specific Aim 1). In addition, we will conduct a detailed analysis of epigenetic chromatin features at the integration sites of intact proviruses, using next-generation sequencing assays for genome-wide characterization of chromatin accessibility, RNA transcription, activating and inhibitory histone marks, and DNA methylation (Specific Aim 2). Finally, we will perform functional experiments to evaluate responsiveness to viral reactivation stimuli, using novel single-cell assays to simultaneously characterize proviral sequence, chromosomal integration sites and HIV-1 transcriptional activity of single viral reservoir cells (Specific Aim 3); these highly innovate single-reservoir-cell assays will allow to functionally test the hypothesis that chromosomal locations of intact proviruses in EC maintain a state of deep latency and confer resistance to viral reactivation stimuli. If successful, this project will significantly expand our current understanding of how natural, drug-free control is possible, and be highly informative for inducing natural control in broader patient populations.

摘要 虽然有报道称，两名患者在接受干细胞移植后， CCR 5 - 32纯合子细胞，HIV-1的自发功能性治愈发生在所有感染者的0.3-0.5%中。 个体这些人，被称为精英控制者（EC），保持不可检测的HIV-1复制水平， 尽管从病毒储库细胞中重复分离有复制能力的病毒，但没有处理。 这些人提供了活生生的证据，表明自发控制HIV-1感染是可能的， 确定这种显著疾病结果背后的病毒学和免疫学机制 有望在更广泛的HIV-1患者人群中诱导HIV-1感染的功能性治愈。在此，我们建议 EC中检测不到病毒载量与特定遗传和表观遗传特征有关的新假设 前病毒HIV-1 DNA的储存细胞。基于强有力的初步数据，我们认为完整的HIV-1前病毒 来自EC的基因优先位于不允许有效病毒基因的非基因染色体区域 转录，导致深潜伏期的前病毒景观，并且对 体内激活刺激。此外，我们认为，完整的前病毒从EC也经常整合 进入显示抑制性染色质的表观遗传特征的染色体区域，通过增强的 与可接近的染色质的距离以及抑制性组蛋白标记和高甲基化DNA的富集。到 为了对此进行研究，我们计划纵向分析完整前病毒的频率和染色体位置 在EC的血液和淋巴组织中，使用新的实验和生物计算分析方法， （具体目标1）。此外，我们还将对表观遗传染色质特征进行详细分析， 完整前病毒的整合位点，使用下一代测序分析进行全基因组表征 染色质可及性、RNA转录、激活和抑制组蛋白标记以及DNA甲基化 （具体目标2）。最后，我们将进行功能实验，以评估对病毒再激活的反应性 刺激，使用新的单细胞测定同时表征前病毒序列，染色体 整合位点和HIV-1转录活性的单个病毒储库细胞（具体目标3）;这些高度 创新的单储库细胞测定将允许在功能上测试以下假设： EC中完整前病毒保持深潜伏状态，并赋予对病毒再活化刺激的抗性。如果 该项目取得成功后，将显着扩大我们目前对自然、无药物控制的了解 这是可能的，并且对于在更广泛的患者群体中诱导自然控制具有高度信息性。