Transcriptional Control of HIV Latency in Hematopoietic Stem and Progenitor Cells

摘要 尽管有宿主的免疫反应和治疗，HIV仍会建立持续感染 抗逆转录病毒疗法(ART)。这是由于在一小部分人中建立了潜伏感染。 细胞-主要是静止的记忆T淋巴细胞(TRM)，可以存活数十年，以及 在治疗中断的情况下，病毒可以从中反弹。除了CD4+T细胞，我们还有 证明HIV也可以感染并在CD4+造血干细胞中建立潜伏感染 和祖细胞(HSPC)。HSPC寿命极长，具有自我保护的潜力 更新，更重要的是，有助于维持ART许多年的患者的病毒血症 好几年了。体外HIV潜伏期研究显示HSPC中存在即时潜伏期 相比之下，大多数T细胞潜伏期模型需要几周的时间。其中一些机制 控制CD4+T细胞潜伏期已经得到很好的证实，主要涉及表观遗传学 组蛋白甲基化或激活因子缺乏5‘端募集等因素 终端重复(LTR)。人类免疫缺陷病毒的沉默是否在HSPC中得到类似的建立还有待于 下定决心。发现控制潜伏期逆转的生化因素和标志物 识别潜伏感染细胞可以促进潜伏感染细胞的靶向或激活 并清除病毒库。我们最近的工作表明，全球转录和 在造血分化过程中发生的表观遗传变化会影响病毒潜伏期和 激活。我们发现，在最原始的HSPC中，潜伏期相对抵抗 组蛋白脱乙酰酶抑制剂逆转。此外，我们产生了有趣的初步数据 提出了独特的干细胞特异性机制发挥重要作用的新假说 抑制HSPC中HIV基因的表达。为了检验这一假设，我们将使用以下组合 单细胞、生化和分子生物学技术以及计算 更好地确定潜伏感染与主动感染HSPC特征的方法 以下目标：(1)确定潜伏期和表观基因组的转录和表观基因组图谱 以及(2)确定整合部位和局部染色质的程度 结构在抑制HSPC中的HIV前病毒基因组方面发挥了作用。综合起来，这些目标将确定 潜伏期的DNA和RNA生物标记物，揭示HSPC特异性沉默机制并产生 HSPC中HIV储存库的综合转录和表观基因组图谱。

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.