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：
10743327
负责人：
WEIGUO CUI
金额：
$ 40万
依托单位：
NORTHWESTERN UNIVERSITY AT CHICAGO
依托单位国家：
美国
项目类别：
财政年份：
2022
资助国家：
美国
起止时间：
2022-11-18 至 2024-11-30
项目状态：
已结题

来源：
https://reporter.nih.gov/project-details/10743327
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 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 Viral Physiology Virus Virus Diseases acute infection antiviral immunity cancer immunotherapy chronic infection cytokine design effector T cell exhaust exhaustion extracellular gene regulatory network improved insight interleukin-21 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 细胞耗竭是一种分化状态，其特征是效应功能丧失和效应功能增强。尽管通常认为病毒特异性 CD8 T 细胞表达抑制性受体，例如 PD-1。作为一个随着时间的推移逐渐变得精疲力尽的同质群体，最近的研究清楚地表明证明 CXCR5hi TCF-1hi 子集作为自我更新的祖细胞群体，可以提供上升到更最终耗尽的 CXCR5lo TCF-1lo 子集，以更好地剖析“耗尽”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 细胞的三个主要亚群，分别在表型、功能和转录上实验室不仅通过流式实验验证了这些 T 细胞亚群的存在。细胞计数术，还进行了更先进的计算分析以进一步预测其核心总的来说，研究结果表明TCF-1hi。祖细胞子集可以产生真正耗尽的 PD-1hi 子集或新识别的功能效应子这一发现奠定了一个坚实的框架，可以测试如何进行。细胞外信号和内在遗传电路调节这三个子集的形成和功能更重要的是，它为探索产生CD8 T细胞的可能性提供了前所未有的机会。来自 TCF-1hi 祖细胞的功能更强的 CX3CR1hi 细胞可克服 T 细胞耗竭这一概念。有趣的是，这一突破显然适用于控制慢性病毒感染和癌症。初步研究还表明，CD4 辅助 T 细胞（可能通过产生 IL-21）至关重要对于 TCF-1hi → CX3CR1hi 转变，这导致了炎症细胞因子（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 感染将被用于阻断抗体、RNA 干扰和基因缺失模型。进一步剖析炎症细胞因子和转录网络如何调节 T 细胞的异质性此外，该实验室建议通过改变 CD8 T 细胞的分化方向，使其远离“疲惫”。单独或与 PD-1 阻断结合提供额外的“CD4 帮助” 实验室将测试是否提供。通过过继转移产生 IL-21 的 CD4 T 细胞可以驱动 TCF-1hi 祖细胞分化为总体而言，从这项研究中获得的知识将提供机制。深入了解如何重新定向功能性效应 T 细胞的形成并同时限制 T 细胞精疲力尽以改善对慢性感染的病毒控制。