3D genome of CD8+ T cells reveals IRF8-mediated exhaustion in cancer

CD8+ T cell responses are essential for anti-tumor immunity, but chronic antigen exposure in cancer can lead to T cell exhaustion, marked by high PD-1 expression. Recent studies have identified progenitor-like CD8+ T cells (Tprog cells) within tumor-infiltrating lymphocytes (TILs) that sustain antitumor responses. These cells can differentiate into terminally exhausted cells (Tterm cells), losing their proliferative and effector functions. Immunotherapy aims to enhance CD8+ TILs functionality, promoting their transition from Tprog to Tterm cells. However, the mechanisms behind this exhaustion remain unclear. Single-cell RNA sequencing and ATAC-seq have revealed distinct profiles and chromatin accessibility between progenitor and terminally exhausted states. Histone modifications predict a loss of enhancer-promoter contacts during this transition. Chromatin structure plays a crucial role in T cell differentiation. We constructed a high-resolution 3D genome map of CD8+ T cell subsets and, through multi-omics integration, identified chromatin structure changes linked to T cell exhaustion, including alterations in topologically associating domains (TADs) and chromatin loops, providing new insights into the genetic basis of CD8+ T cell exhaustion in cancer. Hi-C experiment of naïve, effector,memory, progenitor exhausted, terminal exhausted CD8 T cells in E.G7 tumor and LCMV clone 13 models. Hi-C for cotransferred WT and Irf8-/- OT-I TILs from E.G7 tumors

CD8+ T细胞应答 (CD8+ T cell responses) 是抗肿瘤免疫的核心组成部分，但癌症中的慢性抗原暴露可诱导T细胞耗竭 (T cell exhaustion)，该过程以PD-1的高表达为标志性特征。近期研究在肿瘤浸润淋巴细胞（tumor-infiltrating lymphocytes, TILs）中鉴定出祖细胞样CD8+ T细胞（Tprog细胞），这类细胞可维持抗肿瘤免疫应答。此类细胞可进一步分化为终末耗竭型细胞 (terminally exhausted cells，即Tterm细胞)，并逐渐丧失增殖能力与效应功能。免疫治疗的目标在于增强CD8+肿瘤浸润淋巴细胞的功能，促进其从Tprog细胞向Tterm细胞的转化，但该耗竭过程背后的分子机制仍未阐明。单细胞RNA测序与ATAC-seq已揭示祖细胞状态与终末耗竭状态之间存在显著的转录组特征差异与染色质开放性差异。组蛋白修饰提示，在这一分化转化过程中，增强子与启动子的相互连接会出现丢失。染色质结构在T细胞分化过程中发挥关键调控作用。本研究构建了高分辨率的CD8+ T细胞亚群三维基因组图谱，并通过多组学整合分析，鉴定出与T细胞耗竭相关的染色质结构改变，包括拓扑关联结构域 (topologically associating domains, TADs) 与染色质环的异常，为癌症中CD8+ T细胞耗竭的遗传基础提供了全新的研究视角。本研究针对E.G7肿瘤模型与淋巴细胞性脉络丛脑膜炎病毒 (lymphocytic choriomeningitis virus, LCMV) 克隆13模型中的初始型、效应型、记忆型、祖细胞耗竭型及终末耗竭型CD8+ T细胞开展了Hi-C实验；同时对来自E.G7肿瘤的共转染野生型 (wild type, WT) 与Irf8基因敲除 (Irf8-/-) OT-I肿瘤浸润淋巴细胞进行了Hi-C实验