Tumor-reactive CD8+ tumor-infiltrating lymphocytes (TILs) represent a subtype of T cells that can recognize and destroy tumor specifically. Understanding the regulatory mechanism of tumor-reactive CD8+ T cells has important therapeutic implications. Yet the DNA methylation status of this T cell subtype has not been elucidated. In this study, we segregate tumor-reactive and bystander CD8+ TILs, as well as naïve and effector memory CD8+ T cell subtypes as controls from colorectal cancer patients, to compare their transcriptome and methylome characteristics. Transcriptome profiling confirms previous conclusions that tumor-reactive TILs have an exhausted tissue-resident memory signature. Whole-genome methylation profiling identifies a distinct methylome pattern of tumor-reactive CD8+ T cells, with tumor-reactive markers CD39 and CD103 being specifically demethylated. In addition, dynamic changes are observed during the transition of naïve T cells into tumor-reactive CD8+ T cells. Transcription factor binding motif enrichment analysis identifies several immune-related transcription factors, including three exhaustion-related genes (NR4A1, BATF, and EGR2) and VDR, which potentially play an important regulatory role in tumor-reactive CD8+ T cells. Our study supports the involvement of DNA methylation in shaping tumor-reactive and bystander CD8+ TILs, and provides a valuable resource for the development of novel DNA methylation markers and future therapeutics.

中文翻译：

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全基因组 DNA 甲基化分析揭示结直肠癌患者肿瘤反应性 CD8+ T 细胞的独特表观遗传特征

肿瘤反应性CD8+肿瘤浸润淋巴细胞（TIL）代表T细胞的一种亚型，可以特异性识别和破坏肿瘤。了解肿瘤反应性 CD8+ T 细胞的调节机制具有重要的治疗意义。然而，这种 T 细胞亚型的 DNA 甲基化状态尚未阐明。在这项研究中，我们从结直肠癌患者中分离出肿瘤反应性和旁观者 CD8+ TIL，以及幼稚和效应记忆 CD8+ T 细胞亚型作为对照，以比较其转录组和甲基化组特征。转录组分析证实了之前的结论，即肿瘤反应性 TIL 具有耗尽的组织驻留记忆特征。全基因组甲基化分析可识别肿瘤反应性 CD8+ T 细胞的独特甲基化模式，其中肿瘤反应性标记物 CD39 和 CD103 被特异性去甲基化。此外，在幼稚 T 细胞转变为肿瘤反应性 CD8+ T 细胞的过程中观察到动态变化。转录因子结合基序富集分析鉴定了几种免疫相关转录因子，包括三个耗竭相关基因（NR4A1、BATF 和 EGR2）和 VDR，它们可能在肿瘤反应性 CD8+ T 细胞中发挥重要的调节作用。我们的研究支持 DNA 甲基化参与形成肿瘤反应性和旁观者 CD8+ TIL，并为开发新型 DNA 甲基化标记物和未来治疗方法提供了宝贵的资源。