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

异质性 HIV 表达库：动力学、持久性机制、组织分布和对反弹的贡献

• 批准号: 10459929
• 负责人: Steven A Yukl
• 金额: $ 157.84万
• 依托单位: UNIVERSITY OF CALIFORNIA, SAN FRANCISCO
• 依托单位国家: 美国
• 财政年份: 2022
• 资助国家: 美国
• 起止时间: 2022-05-01 至 2027-04-30
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10459929
• 关键词: Acute; Autopsy; Bioinformatics; Biological Assay; Blood; Cell Count; Cells; Clinical; Collaborations; Complex; Custom; DNA; Data; Defect; Drug or chemical Tissue Distribution; Environment; Frequencies; Funding; Gene Expression; Genes; Genetic Transcription; Goals; HIV; Heterogeneity; Human; Immune; Immune response; In Situ; Individual; Infection; Inflammation; Integration Host Factors; Interruption; Intervention; Knowledge; Lead; Life Expectancy; Lymphoid Cell; Measures; Medicine; Metabolic Clearance Rate; Monitor; Myeloid Cells; Organ; Persons; Phenotype; Population Heterogeneity; Predisposition; Production; Program Research Project Grants; Proteins; Proteome; Proteomics; Proviruses; RNA; RNA Splicing; Relapse; Research; Research Personnel; Residual state; Resource Allocation; Resources; Sampling; Sudden Death; Survival Rate; Technology; Testing; Time; Tissues; Transcript; Translating; Translations; Viral; Viral Genes; Virus; acute infection; base; chronic infection; clinical phenotype; cohort; differential expression; experimental study; immune activation; immune clearance; improved; in vivo; lymph nodes; multidimensional data; multidisciplinary; nano-string; novel; novel strategies; novel therapeutics; prevent; programs; single-cell RNA sequencing; synergism; transcriptome; transcriptomics; viral RNA; viral rebound

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.

翻译后摘要：虽然潜在的和完整的艾滋病毒水库构成理论障碍，治愈，这也是至关重要的， 了解那些在体内被重新激活和/或表达HIV的细胞，这些细胞有助于免疫激活 并且可能在ART中断后更有可能引发反弹。然而，先前的研究表明， “转录活性储库”还不能完全表征这些细胞的异质性， 它们是否转录不完整的或完整的和剪接的HIV RNA， 是从有缺陷的还是完整的前病毒转录，以及是否翻译成HIV蛋白。P01聚焦 新的假设是，表达不同类型的HIV RNA和/或蛋白质的细胞亚群在 根据它们的频率、存活或清除率、对免疫激活的贡献、细胞基因表达， 组织间的差异、反弹潜力以及对旨在治愈HIV的新疗法的敏感性。测试 根据这些假设，本P01中的三个协同项目将采用一系列新的尖端技术， 这些技术可以根据HIV RNA的持续合成能力、存在或 缺失或超突变的缺失、翻译成HIV蛋白和人转录组/蛋白质组。 项目#1将测量HIV转录块的变化以及缺陷或完整HIV RNA的水平， 精英控制者和在急性或慢性感染期间启动ART的个体血液中随时间推移的蛋白质 (aim 1），确定它们如何与免疫应答和免疫激活/炎症相关（目的2），以及 确定宿主细胞基因的差异表达如何与这些细胞表达HIV的能力相关， 在血液和淋巴结中存活（目标3）。在项目#2中，我们将测量完整/缺陷的总负担 体内不同器官和组织的全谱前病毒和完整/缺陷HIV RNA（目的1）， 确定不同组织中表达不同类型HIV RNA转录物的细胞的频率和表型 (aim 2），并确定HIV负荷和残余转录活性对宿主细胞因子的原位影响 在组织驻留的淋巴样和髓样细胞中（aim 3）。项目#3将确定哪些艾滋病毒库- 表达细胞（以及完整的和可诱导的储库）和宿主因素最能预测反弹的时间 在急性与慢性感染（目的1）期间开始ART的个体中，定义反弹的特征 病毒和最早可检测到的感染细胞在治疗中断（目的2），并评估的影响， 对这些艾滋病毒宿主采取免疫治疗干预措施（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组学，蛋白质组学和高维数据，而管理核心将 促进科学交流与合作，协调资源配置，跟踪评估 中求进工作总这些研究的发现将产生大量关于HIV感染细胞的新知识， 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HIV或减少HIV相关免疫激活和器官损伤的方法。