BACKGROUND The efficacy of checkpoint blockade immunotherapies in colorectal cancer is currently restricted to a minority of patients diagnosed with mismatch repair-deficient tumors having high mutation burden. However, this observation does not exclude the existence of neoantigen-specific T cells in colorectal cancers with low mutation burden and the exploitation of their anti-cancer potential for immunotherapy. Therefore, we investigated whether autologous neoantigen-specific T cell responses could also be observed in patients diagnosed with mismatch repair-proficient colorectal cancers. METHODS Whole-exome and transcriptome sequencing were performed on cancer and normal tissues from seven colorectal cancer patients diagnosed with mismatch repair-proficient tumors to detect putative neoantigens. Corresponding neo-epitopes were synthesized and tested for recognition by in vitro expanded T cells that were isolated from tumor tissues (tumor-infiltrating lymphocytes) and from peripheral mononuclear blood cells stimulated with tumor material. RESULTS Neoantigen-specific T cell reactivity was detected to several neo-epitopes in the tumor-infiltrating lymphocytes of three patients while their respective cancers expressed 15, 21, and 30 non-synonymous variants. Cell sorting of tumor-infiltrating lymphocytes based on the co-expression of CD39 and CD103 pinpointed the presence of neoantigen-specific T cells in the CD39+CD103+ T cell subset. Strikingly, the tumors containing neoantigen-reactive TIL were classified as consensus molecular subtype 4 (CMS4), which is associated with TGF-β pathway activation and worse clinical outcome. CONCLUSIONS We have detected neoantigen-targeted reactivity by autologous T cells in mismatch repair-proficient colorectal cancers of the CMS4 subtype. These findings warrant the development of specific immunotherapeutic strategies that selectively boost the activity of neoantigen-specific T cells and target the TGF-β pathway to reinforce T cell reactivity in this patient group.

中文翻译：

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共识分子亚型4的低突变负荷大肠癌的新抗原特异性免疫。

背景技术检查点封锁免疫疗法在大肠癌中的功效目前仅限于少数被诊断出具有高突变负担的错配修复缺陷肿瘤的患者。但是，该观察结果并未排除突变负担低的结直肠癌中新抗原特异性T细胞的存在及其对免疫疗法的抗癌潜力的开发。因此，我们调查了在诊断患有错配修复的结直肠癌患者中是否还可以观察到自体新抗原特异性T细胞应答。方法对7名被诊断为错配修复能力强的肿瘤的大肠癌患者的癌组织和正常组织进行全外显子组和转录组测序，以检测推定的新抗原。合成相应的新表位并测试其体外扩增的T细胞（从肿瘤组织（浸润肿瘤的淋巴细胞）和受肿瘤物质刺激的外周单个核血细胞中分离）的识别能力。结果在三名患者的肿瘤浸润淋巴细胞中，对几种新表位检测到新抗原特异性T细胞反应性，而他们各自的癌症则表达了15、21和30个非同义词变体。基于CD39和CD103的共表达，对肿瘤浸润淋巴细胞进行细胞分选，明确了CD39 + CD103 + T细胞亚群中新抗原特异性T细胞的存在。令人惊讶的是，含有新抗原反应性TIL的肿瘤被归类为共有分子亚型4（CMS4），与TGF-β途径激活和较差的临床结局有关。结论我们已经在不匹配修复的CMS4亚型结直肠癌中通过自体T细胞检测了靶向新抗原的反应性。这些发现保证了特异性免疫治疗策略的发展，该策略选择性地增强了新抗原特异性T细胞的活性并靶向TGF-β途径来增强该患者组的T细胞反应性。