Human T cell-mediated immunity to viruses in tissues and circulation

项目1：项目总结 要了解人类的抗病毒免疫，需要研究人类免疫的复杂性 反应-对不同群体的个体进行采样，并研究它们发挥作用和 维持在全身的组织部位。T细胞通过其自身的免疫调节抗病毒获得性免疫 淋巴组织中的激活和分化，随后向感染组织部位的迁移，以及它们的 作为病毒特异性记忆T细胞亚群在循环和不同组织部位的长期维持。这个 体内大多数记忆T细胞是非循环的、组织驻留的记忆T(TRM)细胞 它可以调节保护性免疫，就像在小鼠模型中所证明的那样，因此对 了解并瞄准抗病毒免疫。在血液残留的人类中研究TRM是具有挑战性的 最容易取样和研究的地点。十多年前，我的实验室建立了一个人体组织资源 从单个器官捐赠者身上获得多种淋巴和粘膜组织，并优化了对 来自500多名捐赠者的免疫细胞，揭示了精确的组织调节区划和部位特异性 改编。在我们目前的HIPC奖下的研究中，我们确定了T细胞是如何针对无处不在的 病毒在组织中分布和发挥作用，最初关注的是巨细胞病毒(CMV)-后来扩展到 流感特异性免疫，以及最近SARS-CoV-2特异性免疫。我们的结果揭示了病毒的特异性 获得性免疫反应在多个层面上受到控制--由病毒本身控制，包括其致病机制 组织靶点，影响T细胞功能的组织部位，与T细胞相关的年龄 分化和传播，以及特定性别的变异。我们的中心假设是病毒，组织， 年龄和性别对抗病毒T细胞反应的直接、特异和可测量的影响，这些影响共同影响 它的功能和保护功效。在拟议的研究中，我们将应用全系统的方法来 通过综合评估分析人类T细胞反应的复杂性和异质性 他们在血液和组织中的档案。在目标1中，我们将量化病毒类型、组织、年龄、 和性别在抗病毒T细胞表型中的作用，以及了解这些因素如何在预测模型中相互作用 人类T细胞免疫。在目标2中，我们将分析病毒特异的T细胞功能状态和克隆特征 跨越不同的组织部位，以解决病毒特异性T细胞如何整合部位和病毒特异性特征 转化为它们的克隆和功能签名。我们将使用Cite-Seq和 巨细胞病毒、流感和SARS-CoV-2应答株成对T细胞受体克隆序列的测定 病毒表位池刺激后的CD4+和CD8+T细胞。功能性和组织特异性签名 将通过细胞因子分析和免疫分析核心的组织成像进行验证，以识别细胞-细胞 作为组织中病毒特异性T细胞的附加特征的相互作用。总而言之，拟议的研究将 提供跨多个组织和病毒特异性的抗病毒T细胞免疫功能图。

PROJECT 1: PROJECT SUMMARY Understanding anti-viral immunity in humans requires investigating the complexity of the human immune response—sampling diverse groups of individuals, and studying immune responses where they function and are maintained in tissue sites throughout the body. T cells coordinate anti-viral adaptive immunity through their activation and differentiation in lymphoid tissues, subsequent migration to tissue sites of infection, and their long-term maintenance as virus-specific memory T cell subsets in circulation and in diverse tissue sites. The majority of memory T cells throughout the body are non-circulating, tissue-resident memory T (TRM) cells which can mediate protective immunity, as demonstrated in mouse models, and are therefore important for understanding and targeting anti-viral immunity. Studying TRM is challenging in humans where blood remains the most readily sampled and studied site. Over 10 years ago, my laboratory set up a human tissue resource to obtain multiple lymphoid and mucosal tissues from individual organ donors, and have optimized the study of immune cells from over 500 donors, revealing precise tissue-regulated compartmentalization and site-specific adaptations. In our studies under the current HIPC award, we identified how T cells-specific for ubiquitous viruses are distributed and function in tissues, with an initial focus on cytomegalovirus (CMV)--later extended to influenza-specific and more recently to SARS-CoV-2-specific immunity. Our results reveal virus-specific adaptive immune responses are controlled on multiple levels—by the virus itself, including its pathogenesis and tissue targets, the tissue site which influences T cell functionality, age which correlates with T cell differentiation and dissemination, and sex-specific variations. Our central hypothesis is that the virus, tissue, age and sex direct specific and measurable influences on the anti-viral T cell response that together influence its functionality and protective efficacy. In the proposed study, we will apply systems-wide approaches to analyze the complexity and heterogeneity of the human T cell response through a comprehensive assessment of their profiles across blood and tissues. In Aim 1 we will quantify the contribution of virus type, tissue, age, and sex in anti-viral T cell phenotypes, and understanding how these factors interact in predictive models for human T cell immunity. In aim 2, we will analyze virus-specific T cell functional states and clonal signatures across diverse tissue sites to address how virus-specific T cells integrate both site- and virus-specific features into their clonal and functional signatures. We will use combinatorial single cell profiling by CITE-Seq with determination of paired T cell receptor clone sequences of CMV-, influenza-, and SARS-CoV-2-responding CD4+ and CD8+T cells following stimulation with viral epitope pools. Functional and tissue-specific signatures will be validated by cytokine analysis and tissue imaging by the immune assay core, to identify cell-cell interactions as additional features of virus-specific T cells in tissues. Together, the proposed studies will provide a functional map of anti-viral T cell immunity across multiple tissues and virus specificities.