Phenotypic, Functional and Transcriptional Heterogeneity in T Cell Exhaustion

T 细胞耗竭中的表型、功能和转录异质性

基本信息

批准号：
10311054
负责人：
WEIGUO CUI
金额：
$ 41.25万
依托单位：
VERSITI WISCONSIN, INC.
依托单位国家：
美国
项目类别：
财政年份：
2019
资助国家：
美国
起止时间：
2019-12-16 至 2022-08-26
项目状态：
已结题

来源：
https://reporter.nih.gov/project-details/10311054
关键词：
ATAC-seq Acetylation Adoptive Transfer Affect Antigens Binding Blocking Antibodies CD4 Positive T Lymphocytes CD8-Positive T-Lymphocytes Cell Differentiation process Cells ChIP-seq Chromatin Chronic Computer Analysis Cytokine Signaling Development Effector Cell Enhancers Epigenetic Process Flow Cytometry Genetic Genetic Transcription Goals Heterogeneity Individual Infection Inflammatory Interferons Interleukin-10 Knowledge Lymphocytic choriomeningitis virus Malignant Neoplasms Mediating Modeling Molecular Genetics Names PD-1 blockade Pathway interactions Phenotype Population Process RNA Interference Research Signal Transduction Site Solid Surface T cell differentiation T-Lymphocyte T-Lymphocyte Subsets Testing Therapeutic Time Viral Virus Virus Diseases acute infection antiviral immunity base cancer immunotherapy chronic infection cytokine design effector T cell exhaust exhaustion extracellular gene regulatory network improved insight progenitor programmed cell death protein 1 receptor response self-renewal single-cell RNA sequencing stem cells success synergism

项目摘要

ABSTRACT T cell exhaustion is a differentiation state that is marked by the loss of effector function and increased expression of inhibitory receptors such as PD-1. Although virus-specific CD8 T cells are commonly considered as a homogeneous population that gradually become exhausted over time, recent research has clearly demonstrated that a CXCR5hi TCF-1hi subset is serving as a self-renewing progenitor population that can give rise to a more terminally exhausted CXCR5lo TCF-1lo subset. To better dissect the heterogeneity of “exhausted” CD8 T cells, the lab applied single cell RNA-seq (scRNA-seq) to the chronic LCMV infection and identified three major subsets of virus-specific CD8 T cells that are phenotypically, functionally and transcriptionally distinct. Not only had the lab validated the existence of these subsets of T cells experimentally by flow cytometry, more advanced computational analyses were also performed to further predict their core transcriptional networks and developmental trajectories. Collectively, the findings reveal that a TCF-1hi progenitor subset can give rise to either a truly exhausted PD-1hi subset or a newly identified functional effector population that is named CX3CR1hi subset. This discovery laid a solid framework that allows testing of how extracellular signals and intrinsic genetic circuits regulate the formation and function of these three subsets of CD8 T cells. More importantly, it provides unprecedented opportunities to explore the possibility of generating more functional CX3CR1hi cells from TCF-1hi progenitors to overcome T cell exhaustion. This conceptual breakthrough is obviously applicable to control over chronic viral infection as well as cancer. Intriguingly, the preliminary study has also demonstrated that CD4 helper T cells, possibly through producing IL-21, are critical for TCF-1hi  CX3CR1hi transition. This led to the hypothesis that inflammatory cytokines (such as CD4- derived IL-21) modulate the cellular, functional and transcriptional diversity of virus-specific CD8 T cells during chronic LCMV infection. Blocking antibodies, RNA interference and genetic deletion models will be used to further dissect how inflammatory cytokines and transcriptional networks regulate heterogeneity in T cell exhaustion. Furthermore, the lab proposes to redirect CD8 T cell differentiation away from “exhaustion” by providing additional “CD4 help”, either alone or in combination with PD-1 blockade. The lab will test if providing IL-21 producing CD4 T cells through adoptive transfer could drive TCF-1hi progenitor cell differentiation into functional CX3CR1hi effector cells. Overall, knowledge gained from this research will provide mechanistic insights into how to redirect the formation of functional effector T cells and simultaneously limit T cell exhaustion for improved viral control over chronic infection.

抽象的 T细胞耗尽是一种差异态，以效应子功能损失和增加为标志抑制受体（如PD-1）的表达。尽管通常认为病毒特异性的CD8 T细胞作为一个同质人群，随着时间的流逝逐渐变得精疲力尽，最近的研究显然已经证明CXCR5HI TCF-1HI子集正在用作自我更新的祖先人群上升到更耗尽的CXCR5LO TCF-1LO子集。更好地剖析“疲惫”的异质性 CD8 T细胞，实验室将单细胞RNA-Seq（SCRNA-Seq）应用于慢性LCMV感染并鉴定病毒特异性CD8 T细胞的三个主要子集，它们在功能上和转录上是表型的清楚的。实验室不仅通过流动证实了这些T细胞的这些子集的存在还进行了细胞仪，更先进的计算分析以进一步预测其核心转录网络和发展轨迹。共同发现，发现TCF-1HI 祖细胞子集可以引起真正耗尽的PD-1HI子集或新鉴定的功能效应器命名为CX3CR1HI子集的人群。这一发现奠定了一个可靠的框架，可以测试如何细胞外信号和内在遗传回路调节这三个子集的形成和功能 CD8 T细胞。更重要的是，它提供了前所未有的机会来探索产生的可能性来自TCF-1HI祖细胞的更多功能性CX3CR1HI细胞克服T细胞耗尽。这个概念突破显然适用于控制慢性病毒感染和癌症。有趣的是，初步研究还表明，通过产生IL-21可能的CD4辅助T细胞至关重要对于TCF-1HICX3CR1HI过渡。这导致了炎性细胞因子（例如CD4-）的假设衍生的IL-21）调节病毒特异性CD8 T细胞的细胞，功能和转录多样性慢性LCMV感染。阻断抗体，RNA干扰和遗传缺失模型将用于进一步剖析炎症细胞因子和转录网络如何调节T细胞中异质性精疲力尽。此外，实验室提议将CD8 T细胞重新定向与“精疲力尽”的区分。单独或与PD-1封锁结合使用其他“ CD4帮助”。实验室将测试是否提供通过自适应转移产生CD4 T细胞的IL-21可以将TCF-1HI祖细胞分化驱动到功能性CX3CR1HI效应细胞。总体而言，从这项研究中获得的知识将提供机理深入了解如何重定向功能效应t细胞的形成，而只是限制T细胞精疲力尽，改善对慢性感染的病毒控制。