Single-Cell Analysis of the HIV/SIV Reservoir

总结 潜伏感染的CD4 + T淋巴细胞中的病毒库是实现HIV-1免疫的关键挑战。 疗方我们最近报道了广泛中和抗体（bNAb）PGT121与抗人前列腺素B1抗体的结合， 与TLR7激动剂的联合治疗导致ART停药后病毒反弹的实质性延迟或预防 在感染了HIV的恒河猴身上。然而，病毒储库的生物学和异质性，以及 这些免疫策略靶向储库的机制仍有待确定。 我们假设，在解剖位置、细胞表型， 宿主转录组和病毒库的病毒序列，以及某些储存细胞亚群 更容易受到免疫介导的破坏。更好地理解不同的细胞 包括病毒库的亚群对于理解当前的抗病毒药物的部分功效是必不可少的。 干预措施和制定改进的下一代HIV-1治疗策略。在本提案中，我们将 继续与Alex K. Shalek在马萨诸塞州理工学院（MIT）， 是单细胞基因组分析方法的专家，而Dan H. Beth Israel Deaconess Medical的照片 他是在恒河猴和人类中进行HIV-1治疗研究的专家。这种独特 和协同合作伙伴关系将应用最有见地，最先进的，单细胞"组学"测定，以最 从猴子和人类的相关血液和组织标本，导致更深入的了解， 病毒库 总的来说，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， 病毒储库的功能异质性，并评估电流 免疫干预靶向有复制能力的储库细胞的亚群。等 知识将被用来定义水库亚群对免疫介导的 通过比较不同免疫治疗方案后的储库身份和表型来破坏，以及 改进和开发下一代HIV-1治疗方法。为实现这一目标，我们提出以下两个具体建议： 目的： 目的1：评估ART中病毒库的解剖、细胞、分子和病毒异质性。 使用单细胞和群体基因组分析策略抑制恒河猴 目标2：确定当前免疫干预措施针对各种疾病的程度。 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