Phenotypic, Functional and Transcriptional Heterogeneity in T Cell Exhaustion

摘要 T细胞耗竭是一种分化状态，其特征是效应功能丧失，并且T细胞功能增强。 抑制性受体如PD-1的表达。虽然病毒特异性CD8 T细胞通常被认为是 作为一个同质的人口，随着时间的推移逐渐变得疲惫不堪，最近的研究显然 证明了CXCR5hi TCF-1hi亚群作为自我更新的祖细胞群体， 上升到更终末耗尽的CXCR510TCF-110亚群。为了更好地剖析"筋疲力尽"的异质性， CD8 T细胞，该实验室将单细胞RNA-seq（scRNA-seq）应用于慢性LCMV感染，并鉴定了 病毒特异性CD8 T细胞的三个主要亚群，其在表型、功能和转录上 与众不同该实验室不仅通过流式细胞术验证了这些T细胞亚群的存在， 细胞计数，更先进的计算分析也进行了进一步预测其核心 转录网络和发展轨迹。总的来说，研究结果表明，TCF-1hi 祖细胞亚群可以产生真正耗尽的PD-1hi亚群或新鉴定的功能效应子 CX3CR1hi亚群。这一发现奠定了坚实的框架，允许测试如何 细胞外信号和内在遗传回路调节这三个亚群的形成和功能。 CD8 T细胞。更重要的是，它提供了前所未有的机会，探索产生的可能性 来自TCF-1hi祖细胞的功能更强的CX3CR1hi细胞，以克服T细胞耗竭。这个概念 这一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，CD4辅助性T细胞，可能通过产生IL-21， TCF-1hi → CX_3CR_1hi跃迁。这导致了一种假设，即炎症细胞因子（如CD4- 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 进一步剖析炎性细胞因子和转录网络如何调节T细胞异质性 疲惫不堪此外，该实验室还提出通过以下方法来重定向CD8 T细胞分化，使其远离"耗竭"。 单独或与PD-1阻断剂组合提供额外的"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 功能性CX3CR1hi效应细胞。总的来说，从这项研究中获得的知识将提供机械 深入了解如何重新定向功能性效应T细胞的形成，同时限制T细胞 用于改善对慢性感染的病毒控制的衰竭。

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.