Project 2: Revealing Viral Population and Host Environment Dynamics of SIV Tissue Reservoir

项目概要/摘要 尽管联合抗逆转录病毒疗法（cART）在控制HIV-1感染方面取得了显着的成功， 储层在处理下无限期地存在。这些剩余的病毒种群构成了 因为当治疗失败或分析后，它们会导致病毒血症迅速反弹， 治疗中断（ATI）。不幸的是，我们对HIV-1持续存在的机制的理解， cART是有限的，因为病毒储库群体的大小非常小，它是建立在广泛的各种 无法评估的敏感组织因此，大多数油藏研究 不包括组织样本或研究非常有限的组织样本库。所以我们不 目前尚不清楚这些病毒的主要特征。了解 在治疗过程中，这些组织储库的性质和特性是设计成功的HIV-1治疗的关键 战略由Hope实验室和Villinger博士组成的团队已经优化和改进了他们的89 Zr标记 FAB 2探针，其允许在受感染的猕猴中体内检测表达SIV env的细胞。使用此 方法，他们已经产生了一个新的PET-CT为基础的工作流程的识别和下游 组织中SIV感染病灶的表征。这个更新的“信标引导系统”非常敏感 并且在cART期间或ATI后早期发现和表征感染细胞的小病灶是非常有效的， 在检测到病毒血症之前这些病灶代表了极其罕见的事件，这些事件是理解 潜在的SIV生物学，然而，迄今为止，仅通过随机和/或有偏见的组织调查发现。在 目前的建议，我们打算利用希望实验室的能力，定位SIV活跃的病毒血症网站在感染猕猴 和互补的基因组分析工作流程，由我们的团队优化，以执行深入的时空 水库病毒种群动态的研究。我们将使用系统发育，进化和解剖学 分析以研究组织储库的特征。我们还将评估生物过程的贡献 如克隆扩增、残余病毒复制和病毒在储存过程中的爆发 cART期间的持续性。此外，我们将分析的特点和转录谱的 利用我们的多种互补基因组技术， 我们将使用来自SIV阳性组织的PET-CT引导的RNAseq和PET-CT引导的空间转录组学， 分离特定类型感染细胞以使用单细胞分析来分析它们的转录谱。由于 希望实验室的研究结果表明，肥大细胞可能是关键的水库持久性，我们计划具体 研究这些肥大细胞在组织储库的病毒种群动力学中的作用。使用此 通过多维方法，我们将以前所未有的细节定义组织中细胞的主要特性， 在治疗过程中，它们是宿主，并且是治疗时反弹病毒的最初来源。 打断

PROJECT SUMMARY/ABSTRACT Despite the remarkable success of the combination antiretroviral therapy (cART) to control HIV-1 infection, viral reservoirs persist indefinitely under treatment. These remaining viral populations constitute the principal burden for an effective HIV-1 cure, as they lead to a rapid rebound in viremia when treatment fails or after analytic treatment interruption (ATI). Unfortunately, our understanding of the mechanisms of HIV-1 persistence during cART is limited because the viral reservoir population size is very small and it is established within a wide variety of susceptible tissues, inaccessible to evaluation. Hence these difficulties, the majority of the reservoir studies do not include tissue samples or study a very limited sampling of the tissue reservoirs. Therefore, we are not able to properly study these viral populations and their main characteristics remain unknown. Understanding the nature and properties of these tissue reservoirs during treatment is key to design a successful HIV-1 cure strategy. The team comprised by the Hope lab and Dr. Villinger has optimized and refined their 89Zr-labelled FAB2 probe that allows for the in vivo detection of cells expressing SIV env in an infected macaque. Using this approach, they have generated a new PET-CT-based workflow for the identification and downstream characterization of foci of SIV infection in tissues. This updated “beacon-guided system” is exquisitely sensitive and it is extremely powerful to find and characterize small foci of infected cells during cART or early after ATI, prior to any detectable viremia. These foci represent extremely rare events that are key to the understanding of underlying SIV biology and yet, to date, were only found through random and/or biased survey of tissue. In the current proposal, we intend to use the Hope lab ability to localize SIV active viremia sites in infected macaques and complementary genomic analysis workflows optimized by our team, to perform in-depth spatio-temporal studies of the reservoir viral population dynamics. We will use phylogenetic, evolutionary, and phyloanatomy analysis to study the characteristics tissue reservoirs. We will also assess the contribution of biological processes such as clonal expansion, residual viral replication, and viral production bursts in the process of reservoir persistence during cART. Additionally, we will analyze the characteristics and transcriptional profiles of the different cell types that harbor the reservoir in tissues using our multiple complementary genomic techniques. We will use PET-CT-guided RNAseq and PET-CT-guided spatial transcriptomics from SIV positive tissues, and isolate specific types of infected cells to analyze their transcriptional profiles using single-cell analysis. Due to Hope lab’s findings indicating that mast cells could be key in the reservoir persistence, we plan to specifically study the role of these mast cells in the viral population dynamics of the tissue reservoirs. By following this multidimensional approach, we will define with unprecedented detail the main properties of the cells in tissues that harbor the reservoir during treatment and are the initial source of the rebounding virus when treatment is interrupted.