Single-Cell Analysis of the HIV/SIV Reservoir

摘要 潜伏感染的CD4+T淋巴细胞中的病毒储存库是实现HIV-1的关键挑战 解药。我们最近报道了广谱中和抗体(BNAb)PGT121的结合 使用TLR7激动剂导致ART停用后病毒反弹的显著延迟或防止 在感染了希沃克病毒的恒河猴身上。然而，病毒库的生物学和异质性，以及 这些免疫治疗策略针对储存库的机制(S)仍有待确定。 我们假设在解剖位置、细胞表型、 宿主转录本和病毒储存库的病毒序列，以及储存库细胞的某些亚群 更容易受到免疫介导的破坏。提高对不同细胞的理解 构成病毒库的亚群对于理解电流的部分疗效是必不可少的。 用于制定改进的下一代艾滋病毒-1治疗战略。在这项提案中，我们将 继续麻省理工学院(MIT)的亚历克斯·K·沙莱克(Alex K.Shalek)之间正在进行的合作 是单细胞基因组图谱方法方面的专家，贝丝以色列女执事医疗中心的丹·H·巴鲁奇 他是在恒河猴和人类身上进行HIV-1治愈研究的专家。这个独一无二的 而协同伙伴关系将最大限度地应用最有洞察力的、最尖端的单细胞组学分析方法 猴子和人类的相关血液和组织标本，加深了对 病毒式蓄水池。 总体而言，我们将利用这些尖端的单细胞组学技术在多个层面上定义， 病毒库的功能异质性和评估电流 免疫治疗干预针对具有复制能力的储藏细胞亚群。是这样的 将利用知识来确定水库亚群对免疫调节的易感性 通过比较不同免疫治疗方案下的储蓄者身份和表型进行破坏，并 改进和开发下一代艾滋病毒-1疗法。为了实现这一目标，我们提出了以下两个具体建议 目标： 目的1：评估ART中病毒库的解剖、细胞、分子和病毒的异质性。 利用单细胞和种群基因组图谱策略抑制恒河猴 目标2：确定当前免疫治疗干预措施针对不同 恒河猴病毒库的亚群

SUMMARY The viral reservoir in latently infected CD4+ T lymphocytes represents the key challenge for achieving an HIV-1 cure. We recently reported that the combination of the broadly neutralizing antibody (bNAb) PGT121 together with a TLR7 agonist resulted in a substantial delay or prevention of viral rebound following ART discontinuation in SHIV-infected rhesus monkeys. However, the biology and heterogeneity of the viral reservoir, as well as the mechanism(s) by which these immunotherapeutic strategies target the reservoir, remain to be determined. We hypothesize that there is substantial heterogeneity in the anatomic locations, cellular phenotypes, host transcriptomes, and viral sequences of the viral reservoir, and that certain subsets of reservoir cells are more susceptible to immune-mediated destruction. An improved understanding of the different cellular subsets that comprise the viral reservoir will be essential for understanding the partial efficacy of current interventions and for developing improved next-generation HIV-1 cure strategies. In this proposal, we will continue an ongoing collaboration between Alex K. Shalek at Massachusetts Institute of Technology (MIT), who is an expert in single-cell genomic profiling approaches, and Dan H. Barouch at Beth Israel Deaconess Medical School (BIDMC), who is an expert in conducting HIV-1 cure studies in rhesus monkeys and humans. This unique and synergistic partnership will apply the most insightful, cutting-edge, single-cell `-omics' assays to the most relevant blood and tissue specimens from both monkeys and humans, leading to a deeper understanding of the viral reservoir. Overall, we will utilize these cutting-edge, single-cell `-omics' technologies to define, at multiple levels, the functional heterogeneity of the viral reservoir and to evaluate the mechanism by which current immunotherapeutic interventions target subsets of replication-competent reservoir cells. Such knowledge will be leveraged to define the susceptibility of reservoir subpopulations to immune-mediated destruction by comparing reservoir identity and phenotype following distinct immunotherapy protocols, and to refine and develop next generation HIV-1 cures. To accomplish this goal, we propose the following two Specific Aims: Aim 1: To evaluate the anatomic, cellular, molecular, and viral heterogeneity of the viral reservoir in ART- suppressed rhesus monkeys using single-cell and population genomic profiling strategies Aim 2: To determine the extent to which current immunotherapeutic interventions target various subpopulations of the viral reservoir in rhesus monkeys