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

项目摘要/摘要 尽管联合抗逆转录病毒疗法(CART)在控制艾滋病毒-1感染方面取得了显著成功，但病毒 在处理的情况下，水库会无限期地持续存在。这些剩余的病毒种群构成了主要的负担 对于有效的HIV-1治疗，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，因为病毒库的种群规模非常小，而且它建立在广泛的品种中 指易受感染的组织，无法评估。因此，大多数油藏研究都存在这些困难 不包括组织样本或研究组织储存库的非常有限的样本。因此，我们不是 能否适当地研究这些病毒种群及其主要特征仍不清楚。了解 治疗过程中这些组织储存库的性质和性质是设计成功治愈HIV-1病毒的关键 策略。由霍普实验室和维林格博士组成的团队已经优化和完善了他们的89Zr标记 Fab2探针，可用于体内检测感染猕猴体内表达SIV env的细胞。使用这个 方法，他们已经生成了一个新的基于PET-CT的工作流程，用于识别和下游 组织中SIV感染源的特征。这个最新的“信标制导系统”非常灵敏。 在CART期间或ATI后早期发现和表征感染细胞的小病灶是极其强大的， 在任何可检测到的病毒血症之前。这些焦点代表了极其罕见的事件，它们是理解 然而，迄今为止，只有通过对组织的随机和/或有偏见的调查才能发现。在 目前的建议，我们打算利用霍普实验室的能力来定位受感染猕猴中SIV活跃的病毒血症部位 和由我们团队优化的互补基因组分析工作流，以执行深入的时空分析 水库病毒种群动态研究。我们将使用系统发育、进化和系统解剖学 分析研究组织油气藏的特征。我们还将评估生物过程的贡献 如克隆扩张、残留病毒复制和病毒在储存过程中的突然产生 在购物车中坚持不懈。此外，我们还将分析该基因的特征和转录特征 利用我们的多重互补基因组技术，我们可以利用不同类型的细胞在组织中储存储存库。 我们将使用PET-CT引导的RNAseq和PET-CT引导的SIV阳性组织的空间转录，以及 分离特定类型的感染细胞，使用单细胞分析来分析它们的转录图谱。由于 希望实验室的发现表明肥大细胞可能是水库持久性的关键，我们计划具体 研究这些肥大细胞在组织储存库的病毒种群动态中的作用。遵循这一点 多维方法，我们将以前所未有的详细定义组织中细胞的主要属性 在治疗过程中存在蓄水池，在治疗过程中是反弹病毒的初始来源 被打断了。

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.