Advanced Spatial Analysis Core

核心C项目总结 全面了解免疫反应和病毒之间的动态相互作用 SIV攻击后感染组织的空间背景将是剖析导致SIV感染的机制的关键 启动和维持68-1 RhCMV/SIV疫苗介导的SIV复制抑制效果并确定 MHC-E限制性CD8+T细胞的基础，而不是MHC-Ia或MHC-II限制性CD8+T细胞的能力 这种类型的保护。为了捕捉复杂免疫过程的动态广度和本质 在早期原发SIV感染的组织内，并揭示RhCMV/SIV疫苗的作用机制 高级空间分析核心(核心C)将利用一系列新的高维空间方法来 1)阐明病毒的状态，包括受感染细胞的身份、病毒基因和蛋白质的表达；以及 感染细胞转录模式(S.A.1)，以及2)基本免疫细胞特征，包括表型， 亚群、激活/免疫调节状态、细胞因子信号、效应器功能和转录 情况(S.A.2)，将确定已确定的复制停止的病毒学和免疫学(项目1)和 将通过保护性MHC-E限制性CD8+T区分原发性SIV感染的体内免疫拦截 分化诱导非保护性MHC-E-、MHC-Ia-或MHC-II限制性CD8+T细胞 程序化的RhCMV/SIV载体，或MHC-Ia限制的CD8+T细胞反应 加强疫苗(项目2)。核心将询问空间病毒学、表型和转录数据 与SIV传播相关的组织中的单细胞、种群和细胞邻域 Dimension RNAScope/DNA Scope、Panini-Codex空间表型，以及GeoMx DSP和CosMx SMI 空间转录学平台，并将把空间数据集与批量和单细胞转录学数据集联系起来 在匹配的组织(和血液)上，全面定义基因表达特征、网络和 与RhCMV/SIV疫苗介导的SIV相关的免疫应答(但有额外的空间背景) 复制停止。核心D将应用尖端生物信息学方法来模拟功能产出和 告知RhCMV/SIV疫苗计划免疫反应以保护的作用机制 抗SIV感染。C核心由雅各布·埃斯蒂斯博士执导，他将与D核心迈克尔博士密切合作 小盖尔和Ben Bimber，以及与Core A，统计学家Paul Edlefsen博士一起，提供一致的、高质量的 功能多组学数据生成、集成数据分析、生物统计分析和计算 为支持这一科学计划正在进行的高级空间分析而进行的建模。 1

CORE C PROJECT SUMMARY A comprehensive understanding of the dynamic interplay between immune responses and the virus within the spatial context of infected tissues after SIV challenge will be essential to dissect the mechanisms responsible for initiating and maintaining 68-1 RhCMV/SIV vaccine-mediated SIV replication arrest efficacy and to define the basis of the ability of MHC-E-restricted CD8+ T cells, but not MHC-Ia or MHC-II-restricted CD8+ T cells, to mediate this type of protection. In order to capture the dynamic breadth and nature of the complex immunologic processes within tissues in early primary SIV infection and to unravel the mechanisms of RhCMV/SIV vaccine efficacy, the Advanced Spatial Analysis Core (Core C) will utilize a battery of novel high-dimensional spatial approaches to elucidate 1) the state of the virus, including identity of infected cells, viral gene and protein expression, and infected cell transcriptional patterns (S.A.1), and 2) essential immune cell profiles, including phenotypes, subsets, activation/immunoregulatory states, cytokine signaling, effector functions and transcriptomic landscapes (S.A.2) that will define the virology and immunology of established replication arrest (Project 1) and will distinguish the in vivo immune interception of primary SIV infection by protective MHC-E-restricted CD8+ T cells from non-protective MHC-E-, MHC-Ia- or MHC-II-restricted CD8+ T cells elicited by differentially programmed RhCMV/SIV vectors, or MHC-Ia-restricted CD8+ T cell responses elicited by a conventional prime- boost vaccine (Project 2). The Core will interrogate spatial virologic, phenotypic, and transcriptomic data on single-cells, populations, and cell neighborhoods in tissues associated with SIV transmission using high- dimensional RNAscope/DNAscope, PANINI-CODEX spatial phenotyping, and GeoMx DSP and CosMx SMI spatial transcriptomics platforms, and will link spatial data sets with bulk and single-cell transcriptomic data sets on matched tissues (and blood), to comprehensively define gene expression signatures, networks and immunological responses (but with additional spatial context) associated with RhCMV/SIV vaccine-mediated SIV replication arrest. Core D will apply cutting edge bioinformatics approaches to model the functional outputs and inform the mechanisms of action by which RhCMV/SIV vaccination programs the immune response for protection against SIV infection. Core C is directed by Dr. Jacob Estes, who will work closely with Core D, Drs. Michael Gale, Jr. and Ben Bimber, and with Core A, statistician Dr. Paul Edlefsen, to provide consistent, high-quality functional multi-omics data generation, integrated data analysis, biostatistical analyses and computational modeling in support of the advanced spatial analysis being performed for this scientific program. 1