Human anti-viral immune responses in tissues and circulation

节目概要 人类对病毒和其他病原体的免疫反应的研究必然集中在采样上 然而，先天性和适应性免疫反应是在外周血中启动、发挥作用和维持的。 不同的组织部位先天性细胞，包括组织巨噬细胞和树突状细胞（DC）， 关键入口点的病原体（例如，肺、肠）不出现在循环中。类似地，T细胞浸润 感染部位，并可以持续作为非循环组织驻留记忆T细胞，这提供了保护性 现场回应。目前，我们对组织定位的先天性和适应性免疫应答的理解是 基于小鼠模型，我们缺乏关于先天和适应性细胞如何组织的基本知识， 并在人体组织中发挥作用这项研究计划在人类免疫的总体目标是获得在- 组织中的人类先天性和适应性免疫细胞如何应对病毒感染的深度概况，重点是 关于全球普遍存在的疱疹病毒--巨细胞病毒（CMV）。CMV建立了终身持久性， 多个位点，对衰老和免疫力有广泛的影响，并可在免疫抑制期间重新激活。 移植和癌症，造成严重的疾病和死亡率。拟议的研究计划，包括 三个项目，五个核心，将获得人类免疫细胞参与控制的深入概况， 使用我们独特的组织资源（淋巴、粘膜和外周组织）， 从个体器官捐献者获得，与来自活性组群的血液反应相比， 感染项目1（PL：Farber）将研究器官供体组织和循环中T细胞对CMV的反应 和移植患者;项目2（PI：B. Reizis）将研究不同部位的DC亚群在功能上如何 对来自两种组织和移植患者队列的CMV和CMV感染的细胞的应答;以及项目3（PI： M. Merad）将通过TLR激动剂和免疫抑制剂来分析组织中的巨噬细胞及其对先天刺激的反应， CMV感染对巨噬细胞功能的影响。行政核心将协调组织 和财务方面的计划，临床核心将提供所有样本，包括组织从器官 捐赠者和血液样本从移植队列的三个项目。转录组学（RNAseq）和 单细胞核心（核心A）将在群体和单细胞水平上提供高通量RNA测序， 和使用飞行时间流式细胞术（CyTOF）的多维蛋白质组分析。病毒检测核心 (Core B）将测量不同组织部位中的CMV持续性，以剖析病毒持续性如何影响 组织免疫反应。数据管理和分析核心（DMAC）将存储、管理和分析所有 从项目和核心的数据输出，应用生物信息学分析转录组和蛋白质组 数据，生成模型来整合数据集，并将原始数据提交到公共数据库，如ImmPort 和NCBI。该计划的结果将确定组织特异性控制人类免疫的特征， 用于促进疫苗和免疫疗法中的原位保护性免疫的应答。

Program Summary Studies of human immune responses to viruses and other pathogens have focused, by necessity, on sampling of peripheral blood; however, innate and adaptive immune responses are initiated, function and maintained in diverse tissue sites. Innate cells, including tissue macrophages and dendritic cells (DC) that encounter pathogens at key entry points (e.g., lungs, intestines) do not appear in circulation. Similarly T cells infiltrate infection sites and can persist as non-circulating tissue-resident memory T cells, which provide protective responses in situ. At present, our understanding of tissue-localized innate and adaptive immune responses is based on mouse models, and we lack fundamental knowledge on how innate and adaptive cells are organized and function in human tissues. The overall goal of this research program in human immunity is to obtain in- depth profiles of how human innate and adaptive immune cells in tissues respond to viral infection, with a focus on the globally pervasive herpesvirus, Cytomegalovirus (CMV). CMV establishes lifelong persistence in multiple sites, has broad effects on aging and immunity, and can be reactivated during immunosuppression in transplantation and cancer, causing serious disease and mortality. The proposed research program, consisting of three projects, and five cores, will obtain in-depth profiles of human immune cells involved in controlling CMV in human tissue sites using our unique tissue resource where lymphoid, mucosal and peripheral tissue are obtained from individual organ donors, compared to blood responses from living cohorts with active infection. Project 1 (PL: Farber) will study T cell responses to CMV in tissues and circulation from organ donors and transplant patients; Project 2 (PI: B. Reizis) will study how DC subsets in different sites functionally respond to CMV and CMV-infected cells from both tissues and cohorts of transplant patients; and Project 3 (PI: M. Merad) will profile macrophages in tissues and their responses to innate stimuli through TLR agonists and CMV, and effect of CMV infection on macrophage function. The administrative core will coordinate organization and financial aspects of the program, the Clinical Core will provide all samples including tissues from organ donors and blood samples from transplant cohorts to the three projects. The Transcriptomics (RNAseq) and single cell core (Core A) will provide high throughput RNA sequencing on the population and single cell level, and multidimensional proteome profiling using cytometry by time-of-flight (CyTOF). The Viral assays core (Core B) will measure CMV persistence in different tissue sites to dissect how virus persistence impacts tissues immune responses. The data management and analysis core (DMAC) will store, curate and analyze all data outputs from the projects and cores, apply bioinformatics for analysis of transcriptomic and proteomic data, generate models to integrate the datasets, and submit raw data to public databases such as ImmPort and NCBI. The results from this program will identify signatures for tissue-specific control of human immune responses for promoting in situ protective immunity in vaccines and immunotherapies.