Transcriptional Control of HIV Latency in Hematopoietic Stem and Progenitor Cells

造血干细胞和祖细胞中 HIV 潜伏期的转录控制

• 批准号: 10325142
• 负责人: Maria Virgilio
• 金额: $ 3.76万
• 依托单位: UNIVERSITY OF MICHIGAN AT ANN ARBOR
• 依托单位国家: 美国
• 财政年份: 2021
• 资助国家: 美国
• 起止时间: 2021-09-01 至 2024-08-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10325142
• 关键词: Affect; Anti-Retroviral Agents; Atlases; Biochemical; Biological Markers; CD4 Positive T Lymphocytes; Cells; Characteristics; Chromatin; Chromatin Structure; Computer Models; Computing Methodologies; DNA; DNA Binding; Data; Defense Mechanisms; Epigenetic Process; Future; Gene Expression; Genes; Genetic Transcription; Genome; Genomics; HIV; Hematopoietic stem cells; Histone Deacetylase; Histone Deacetylase Inhibitor; Immune response; In Vitro; Infection; Interruption; Life; Link; Long Terminal Repeats; Modeling; Molecular Biology Techniques; Nucleic Acid Regulatory Sequences; Patients; Play; Population; Promoter Regions; Proteins; Proviruses; RNA; Reporter; Resistance; Rest; Role; Site; System; T memory cell; T-Lymphocyte; Testing; Transcriptional Regulation; Viral; Viral reservoir; Viremia; Virus; Virus Activation; Virus Latency; Work; XCL1 gene; Zinc Fingers; antiretroviral therapy; chronic infection; differential expression; epigenomics; hematopoietic differentiation; histone methylation; integration site; latent infection; multiple omics; novel; recruit; self-renewal; single-cell RNA sequencing; stem cells; tool; transcription factor; transcriptomics

Abstract HIV establishes a persistent infection despite the host immune response and treatment with antiretroviral therapy (ART). This is due to the establishment of latent infections in a small subset of cells – predominantly resting memory T lymphocytes (TRM), which can survive for decades, and from which virus can rebound with interruption in therapy. In addition to CD4+ T cells, we have demonstrated that HIV can also infect and establish latent infections in CD4+ hematopoietic stem and progenitor cells (HSPCs). HSPCs are extremely long-lived, have the potential for self- renewal, and importantly, contribute to viremia in patients that have maintained ART for many years. In vitro studies of HIV latency demonstrate immediate latency establishment in HSPCs in contrast to a period of weeks required for most T cell latency models. Some of the mechanisms that control latency in CD4+ T cells have been well established and primarily involve epigenetic factors such as histone methylation or lack of recruitment of an activating factor to the 5’ long terminal repeat (LTR). Whether silencing of HIV is established similarly in HSPCs has yet to be determined. Discovering the biochemical factors that control latency reversal as well as markers that identify latently infected cells could facilitate targeting or activation of latently infected cells and elimination of the viral reservoir. Our recent work suggests that the global transcriptomic and epigenetic changes that occur during hematopoietic differentiation affect viral latency and activation. We have found that latency in the most primitive HSPCs is relatively resistant to reversal by histone deacetylase inhibitors. Moreover, we generated intriguing preliminary data suggesting the novel hypothesis that unique stem cell specific mechanisms play important roles in silencing HIV gene expression in HSPCs. To test this hypothesis, we will use a combination of single-cell, biochemical, and molecular biology techniques in addition to computational approaches to better define the characteristics of latently versus actively infected HSPCs with the following aims: (1) determine the transcriptomic and epigenomic landscape of latent versus actively infected HSPCs, and (2) determine the extent to which integration site and local chromatin structure play a role in silencing HIV proviral genomes in HSPCs. Together, these aims will identify DNA and RNA biomarkers of latency, uncover HSPC specific silencing mechanisms and produce an integrated transcriptomic and epigenomic atlas of the HIV reservoir in HSPCs.

摘要 尽管宿主免疫应答和用抗病毒药物治疗， 抗逆转录病毒疗法（ART）。这是由于在一个小的子集建立潜伏感染 细胞-主要是静息记忆T淋巴细胞（TRM），可以存活数十年， 在治疗中断的情况下病毒会反弹。除了CD 4 + T细胞外，我们还有 证明HIV也可以感染并在CD 4+造血干细胞中建立潜伏感染， 和祖细胞（HSPC）。HSPC寿命极长，具有自我调节的潜力， 更新，重要的是，有助于病毒血症的患者，已维持ART的许多 年HIV潜伏期的体外研究表明， 这与大多数T细胞潜伏期模型所需的数周时间形成对比。的一些机制 控制CD 4 + T细胞的潜伏期已经得到很好的建立，主要涉及表观遗传 例如组蛋白甲基化或缺乏激活因子向5'长链的募集等因素， 末端重复序列（LTR）。在HSPC中是否同样建立了HIV沉默还有待进一步研究。 测定发现控制潜伏期逆转的生化因素以及标记物 识别潜伏感染的细胞可以促进靶向或激活潜伏感染的细胞， 和消除病毒储存库。我们最近的工作表明，全球转录组和 造血分化过程中发生的表观遗传变化影响病毒潜伏期， activation.我们已经发现，最原始的HSPC中的延迟相对抵抗 组蛋白去乙酰化酶抑制剂逆转。此外，我们得到了有趣的初步数据， 这表明独特的干细胞特异性机制发挥重要作用的新假设 在HSPCs中沉默HIV基因表达。为了验证这个假设，我们将使用以下组合： 单细胞，生物化学和分子生物学技术，除了计算 更好地定义潜伏性与活动性感染HSPC特征的方法， 以下目的：（1）确定潜在与潜在的转录组和表观基因组景观 活动性感染的HSPC，和（2）确定整合位点和局部染色质 结构在HSPC中HIV前病毒基因组沉默中起作用。这些目标将共同确定 潜伏期的DNA和RNA生物标志物，揭示HSPC特异性沉默机制，并产生 HSPC中HIV储库的整合转录组学和表观基因组图谱。