RNA-seq of tumor residing CD8+ T cells overexpressing Runx3

Tissue-resident memory CD8+ T cells (Trm) are positioned at common sites of pathogen exposure where they elicit rapid and robust protective immune responses1,2. However, the molecular signals controlling Trm differentiation and homeostasis are not fully understood. Here we show that mouse Trm precursor cells represent a unique CD8+ T cell subset that is distinct from the precursors of circulating memory populations at the levels of gene expression and chromatin accessibility. Exploiting computational and functional RNAi in vivo screens, we identified the transcription factor (TF) Runx3 as a key regulator of Trm differentiation and homeostasis. Runx3 was required to establish Trm populations in diverse tissue environments and supported expression of critical tissue-residency genes while suppressing genes associated with tissue egress and recirculation. Analysis of the accessibility of Runx3 target genes in Trm-precursor cells revealed a distinct regulatory role for Runx3 in controlling Trm differentiation despite relatively widespread and uniform expression among all CD8+ T cell subsets. Further, we show that human and murine tumor-infiltrating lymphocytes (TIL) share a core tissue-residency gene-expression signature with Trm. In a mouse model of adoptive T cell therapy for melanoma, Runx3-deficient CD8+ TIL failed to accumulate in tumors, resulting in greater rates of tumor growth and mortality. Conversely, overexpression of Runx3 enhanced TIL abundance, delayed tumor growth, and prolonged survival. In addition to establishing Runx3 as a central regulator of Trm differentiation, these results provide novel insight into the signals that promote T cell residency in tissues, which could be leveraged to enhance vaccine efficacy or adoptive cell therapy treatments that target cancer. 6 samples: 2 Runx3-overexpressing tumor P14 samples, 2 control tumor P14 samples, 2 control spleen samples

组织驻留记忆CD8+ T细胞（Tissue-resident memory CD8+ T cells，Trm）定位于病原体暴露的常见部位，并可在此触发快速且强效的保护性免疫应答1,2。然而，调控Trm分化与稳态的分子信号尚未完全阐明。本研究显示，小鼠Trm前体细胞是一类独特的CD8+ T细胞亚群，在基因表达与染色质可及性层面均与循环记忆群体的前体存在显著差异。通过整合计算分析与体内RNA干扰（RNAi）功能筛选，我们鉴定出转录因子（transcription factor，TF）Runx3是Trm分化与稳态的关键调控因子。Runx3对于在多种组织环境中构建Trm群体不可或缺，其可促进关键组织驻留相关基因的表达，同时抑制与组织迁出及细胞再循环相关的基因。对Trm前体细胞中Runx3靶基因的染色质可及性分析显示，尽管Runx3在所有CD8+ T细胞亚群中表达相对广泛且均匀，但其在调控Trm分化过程中发挥着独特的调控功能。此外，本研究发现人类与小鼠的肿瘤浸润淋巴细胞（tumor-infiltrating lymphocytes，TIL）与Trm共享一套核心的组织驻留基因表达特征。在黑色素瘤过继T细胞治疗的小鼠模型中，Runx3缺陷型CD8+ T细胞无法在肿瘤内聚集，进而导致肿瘤生长加速与死亡率升高。反之，Runx3过表达可提升TIL的丰度，延缓肿瘤生长并延长小鼠存活时长。本研究不仅确立了Runx3作为Trm分化的核心调控因子，还为调控T细胞组织驻留的信号通路提供了全新视角，该发现可用于优化靶向癌症的疫苗效力或过继细胞治疗方案。本数据集共包含6个样本：2个Runx3过表达的肿瘤P14样本、2个对照肿瘤P14样本以及2个对照脾脏样本。