Tissue-resident memory features are linked to the magnitude of cytotoxic T cell responses in human lung cancer [HNSCC]

Therapies that boost the anti-tumor responses of cytotoxic lymphocytes (CTLs) have shown promise in the clinic. However, clinical responses to currently available immunotherapeutic agents vary considerably, for which the molecular basis is unclear. To date, unbiased transcriptomic studies of CTLs in human cancers have been performed in whole tumors or cells obtained from peripheral blood or metastatic sites of heavily pre-treated patients. We performed global transcriptional profiling of CTLs in tumors and adjacent non-tumor tissue from treatment-naïve patients with early stage lung cancer to define the molecular features associated with robustness of anti-tumor immune responses. We observed major differences in the transcriptional program of tumor-infiltrating CTLs that are shared across tumor subtypes. Pathway analysis revealed enrichment of genes in cell cycle, T cell receptor (TCR) activation and co-stimulation pathways, indicating tumor-driven expansion of presumed tumor antigen-specific CTLs. We also observed marked heterogeneity in the expression of molecules associated with TCR activation and immune checkpoints such as 4-1BB, PD1, TIM3, and their expression was positively correlated with the density of tumor-infiltrating CTLs. Interestingly, transcripts linked to tissue-resident memory cells (TRM), such as CD103, were enriched in tumors containing a high density of CTLs, and CTLs from CD103high tumors displayed features of enhanced cytotoxicity, implying better anti-tumor activity. In an independent cohort of 689 lung cancer patients, we confirmed that patients with CD103high (TRM rich) tumors survived significantly longer. In summary, we define the molecular fingerprint of tumor-infiltrating CTLs at the site of primary tumor and identify a number of novel targets that may be important in modulating the magnitude and specificity of anti-tumor immune responses in lung cancer. Overall design: Analysis of purified populations of CD8 T cells (isolated from primary head and neck squamous cancer tumors from patients) at the transcriptomic level by RNA sequencing.

增强细胞毒性淋巴细胞（Cytotoxic Lymphocytes, CTLs）抗肿瘤应答的疗法在临床中已展现出应用潜力。然而，当前已获批的免疫治疗药物的临床应答差异显著，其背后的分子机制尚不明确。迄今为止，针对人类癌症中CTLs的无偏转录组学研究，多是在实体瘤组织，或取自经多线治疗患者的外周血、转移灶细胞中开展。本研究对早期肺癌初治患者的肿瘤组织及癌旁正常组织中的CTLs进行了全局转录组分析，以明确与抗肿瘤免疫应答稳健性相关的分子特征。我们观察到，肿瘤浸润性CTLs的转录程序存在显著差异，且该特征在不同肿瘤亚型中普遍存在。通路分析显示，细胞周期、T细胞受体（T cell receptor, TCR）激活及共刺激通路相关基因呈现富集特征，提示肿瘤驱动了疑似肿瘤抗原特异性CTLs的扩增。我们还观察到，与TCR激活及免疫检查点（如4-1BB、PD1、TIM3）相关的分子表达存在显著异质性，且这些分子的表达水平与肿瘤浸润性CTLs的密度呈正相关。有趣的是，与组织驻留记忆细胞（tissue-resident memory cells, TRM）相关的转录本（如CD103）在CTLs密度较高的肿瘤中呈现富集；且来自CD103高表达肿瘤的CTLs展现出增强的细胞毒性特征，提示其抗肿瘤活性更佳。在一个包含689名肺癌患者的独立队列中，我们证实了携带CD103高表达（TRM富集）肿瘤的患者生存期显著更长。综上，本研究明确了原发性肿瘤部位肿瘤浸润性CTLs的分子特征谱，并鉴定出多个潜在的新型靶点，这些靶点或可用于调节肺癌中抗肿瘤免疫应答的强度与特异性。实验设计：通过RNA测序对从患者原发性头颈部鳞状细胞癌组织中分离得到的纯化CD8+T细胞群体进行转录组水平分析。