The heterogeneous HIV expressing reservoir: dynamics, persistence mechanisms, tissue distribution, and contribution to rebound

摘要：虽然潜伏的和完整的艾滋病毒宿主构成了治愈的理论障碍，但它也是至关重要的 了解体内那些被重新激活和/或表达艾滋病毒的细胞，这些细胞有助于免疫激活 并可能在ART中断后更有可能启动反弹。然而，之前对该问题的研究 “转录活性储存库”还不能完全描述这些细胞的异质性。 根据它们是否转录不完整或完整并拼接的艾滋病毒RNA而有所不同，无论是艾滋病毒RNA 是从有缺陷的或完整的前病毒转录而来的，以及它是否被翻译成HIV蛋白。本期P01聚焦 根据新的假设，表达不同类型HIV RNA和/或蛋白质的细胞亚群将不同 关于它们的频率、存活率或清除率、对免疫激活的贡献、细胞基因表达、 不同组织之间的差异、反弹潜力和对旨在治愈艾滋病毒的新疗法的敏感性。为了测试 在这些假设下，P01中的三个协同项目将采用一系列新的和尖端的 可以根据HIV RNA的处理能力、存在或 没有缺失或超突变，翻译成HIV蛋白，以及人类转录组/蛋白质组。 项目1将测量艾滋病毒转录的区块变化以及有缺陷或完整的艾滋病毒RNA和 在急性或慢性感染期间启动抗逆转录病毒治疗的精英控制员和个人的血液中蛋白质随时间的变化 (目标1)，确定它们与免疫反应和免疫激活/炎症的关系(目标2)； 确定宿主细胞基因的差异表达与这些细胞表达HIV和 在血液和淋巴结中存活(目标3)。在项目2中，我们将测量完好/有缺陷的总负担 体内不同器官和组织的前病毒和完整/缺陷艾滋病毒RNA(目标1)， 确定在不同组织中表达不同类型艾滋病毒RNA转录物的细胞的频率和表型 (目标2)，并确定艾滋病毒负担和残余转录活性对宿主细胞因子的原位影响 在组织驻留的淋巴和髓样细胞中(目标3)。项目3将确定哪些艾滋病毒宿主-- 表达细胞(以及完整的和可诱导的储存库)和宿主因素最能预测反弹的时间 在急性感染与慢性感染期间启动抗逆转录病毒治疗的个体(目标1)，定义反弹的特征 病毒和治疗中断期间最早可检测到的感染细胞(目标2)，并评估 对这些艾滋病毒宿主采取基于免疫的治疗干预措施(目标3)。为了实现这些目标，生物信息学 核心将帮助分析转录、蛋白质组和高维数据，而管理核心将帮助分析 促进科学交流和协作，协调资源分配，跟踪和评估 进步。这些研究的发现将产生关于艾滋病毒感染细胞的丰富的新知识， 有助于ART的免疫激活和ART中断后的病毒学反弹，这可能导致新的 旨在治愈或减少艾滋病毒相关免疫激活和器官损害的方法。

Abstract: While the latent and intact HIV reservoirs pose theoretical barriers to cure, it is also critical to understand those cells that are reactivated and/or express HIV in vivo, which contribute to immune activation and may have more potential to initiate rebound after ART interruption. However, prior studies of the “transcriptionally active reservoir” have not been able to fully characterize the heterogeneity of these cells, which vary in terms of whether they transcribe incomplete or completed and spliced HIV RNA, whether the HIV RNA is transcribed from defective or intact proviruses, and whether it is translated into HIV protein. This P01 focuses on the novel hypothesis that subsets of cells expressing different types of HIV RNA and/or protein will differ in terms of their frequency, survival or clearance rate, contribution to immune activation, cellular gene expression, differences across tissues, rebound potential, and susceptibility to new therapies aimed at HIV cure. To test these hypotheses, the three synergistic projects in this P01 will employ an array of new and cutting-edge technologies that can distinguish HIV-expressing cells based on the processivity of the HIV RNA, presence or absence of deletions or hypermutations, translation into HIV protein, and human transcriptome/proteome. Project #1 will measure the changes in blocks to HIV transcription and levels of defective or intact HIV RNA and protein over time in the blood of elite controllers and individuals who initiate ART during acute or chronic infection (aim 1), determine how they relate to immune responses and immune activation/inflammation (aim 2), and determine how differential expression of host cell genes relates to the ability of these cells to express HIV and survive in blood and lymph nodes (aim 3). In Project #2, we will measure the total burden of intact/defective proviruses and intact/defective HIV RNA across the full spectrum of different organs and tissues in vivo (aim 1), define the frequencies and phenotypes of cells expressing different types of HIV RNA transcripts across tissues (aim 2), and determine the in situ impact of HIV burden and residual transcriptional activity on host cell factors in tissue-resident lymphoid and myeloid cells (aim 3). Project #3 will determine which reservoirs of HIV- expressing cells (as well as the intact and inducible reservoir) and host factors best predict the timing of rebound in individuals who initiated ART during acute vs. chronic infection (aim 1), define the features of the rebounding virus and earliest detectable infected cells during treatment interruption (aim 2), and assess the effects of immune-based cure interventions on these HIV reservoirs (aim 3). To achieve these goals, the Bioinformatics Core will help analyze transcriptomic, proteomic, and high dimensional data, while the Administrative Core will facilitate scientific crosstalk and collaboration, coordinate allocation of resources, and track and evaluate progress. Findings from these studies will generate a wealth of new knowledge about the HIV-infected cells that contribute to immune activation on ART and virologic rebound after ART interruption, which may lead to new approaches aimed at HIV cure or reducing HIV-associated immune activation and organ damage.