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

项目2：揭示SIV组织库的病毒种群和宿主环境动态

• 批准号: 10460077
• 负责人: Ramon Lorenzo-Redondo
• 金额: $ 21.9万
• 依托单位: NORTHWESTERN UNIVERSITY AT CHICAGO
• 依托单位国家: 美国
• 财政年份: 2022
• 资助国家: 美国
• 起止时间: 2022-07-15 至 2027-04-30
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10460077
• 关键词: Anatomy; Biological Process; Biology; Blood specimen; Cells; Characteristics; Clonal Expansion; Data; Detection; Environment; Evaluation; Event; Future; Gene Expression; Gene Expression Profile; Genetic Transcription; Genome; Genomics; HIV; HIV-1; Immune; Immune response; Individual; Infection; Interruption; Knowledge; Label; Laboratories; Laboratory Finding; Lead; Lymphoid Tissue; Macaca; Macaca mulatta; Methods; Modeling; Mucous Membrane; Nature; Phylogenetic Analysis; Play; Population; Population Characteristics; Population Dynamics; Population Sizes; Positron-Emission Tomography; Process; Production; Property; Research Design; Residual state; Role; SIV; Sampling; Signal Transduction; Site; Source; Surveys; System; Techniques; Tissue Sample; Tissues; Update; Viral; Viral Antigens; Viral Genes; Viral reservoir; Viremia; Virus; Virus Replication; X-Ray Computed Tomography; antiretroviral therapy; base; biological systems; cell type; chronic infection; design; env Gene Products; experimental study; in vivo; insight; mast cell; novel; single cell analysis; spatiotemporal; study characteristics; success; transcriptome sequencing; transcriptomics; viral rebound; virus characteristic; virus envelope; virus host interaction

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.

项目摘要/摘要 尽管组合抗逆转录病毒疗法（CART）取得了显着成功，以控制HIV-1感染，但病毒 储层无限期地持续治疗。这些剩下的病毒种群构成主要伯恩 对于有效的HIV-1治疗，当治疗失败或分析后导致病毒血症的快速反弹 治疗中断（ATI）。不幸的是，我们对HIV-1持久性机制的理解 购物车受到限制，因为病毒式居住者人口大小很小，并且在种类范围内建立 易感时机，无法评估。因此，这些困难，大多数水库研究 不要包括组织样品或研究组织储层的采样非常有限。因此，我们不是 可以正确研究这些病毒群体，其主要特征仍然未知。了解 处理期间这些组织储层的性质和特性是设计成功的HIV-1治疗的关键 战略。由Hope Lab和Villinger博士完成的团队优化并完善了他们的89ZR标签 Fab2探针允许在感染猕猴中表达SIV ENV的细胞体内检测。使用此 方法，他们为识别和下游产生了一个新的基于PET-CT的工作流程 SIV感染的焦点在组织中的表征。此更新的“信标指导系统”完全敏感 在卡车或ATI之后，发现和表征被感染细胞的小焦点非常强大， 在任何可检测的病毒血症之前。这些焦点是极少数的事件，这是理解的关键 迄今为止，仅通过对组织的随机和/或有偏见的调查发现了基本的SIV生物学。在 当前的建议，我们打算使用希望实验室的能力将SIV活跃病毒性位点定位在受感染的猕猴中 并完成我们团队优化的基因组分析工作流程，以执行深入的空间时间 储层病毒种群动态的研究。我们将使用系统发育，进化和植物解剖学 分析研究特征组织储层。我们还将评估生物过程的贡献 例如克隆扩张，残留病毒复制和病毒产生在储层过程中爆发 购物车期间的持久性。此外，我们将分析该特征和转录曲线 使用我们多种完整的基因组技术，将储层带有储层的不同细胞类型。 我们将使用pet-ct引导的rnaseq和pet-ct引导的空间转录组学，来自SIV阳性时机，以及 分离特定类型的感染细胞，使用单细胞分析分析其转录曲线。由于 Hope Lab的发现表明，肥大细胞可能是储层持久性的关键，我们计划专门 研究这些肥大细胞在组织库的病毒种群动力学中的作用。通过此操作 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 在治疗期间，该水库藏有水库，并且是治疗时反弹病毒的初始来源 中断。