Immunopeptidomic analyses of colorectal cancers with and without microsatellite instability

Colorectal cancer is the second leading cause of cancer death worldwide, and the incidence of this disease is expected to increase as global socioeconomic changes occur. Immune checkpoint inhibition therapy is effective in treating a minority of colorectal cancer tumors; however, microsatellite stable tumors do not respond well to this treatment. Emerging cancer immunotherapeutic strategies aim to activate a cytotoxic T cell response against tumor-specific antigens, presented exclusively at the cell surface of cancer cells. These antigens are rare and are most effectively identified with a mass spectrometry-based approach, which allows the direct sampling and sequencing of these peptides. While the few tumor-specific antigens identified to date are derived from coding regions of the genome, recent findings indicate that a large proportion of tumor-specific antigens originate from allegedly noncoding regions. Here, we employed a novel proteogenomic approach to identify tumor antigens in a collection of colorectal cancer-derived cell lines and biopsy samples consisting of matched tumor and normal adjacent tissue. The generation of personalized cancer databases paired with mass spectrometry analyses permitted the identification of more than 30 000 unique MHC I-associated peptides. We identified 19 tumor-specific antigens in both microsatellite stable and unstable tumors, over two-thirds of which were derived from non-coding regions. Many of these peptides were derived from source genes known to be involved in colorectal cancer progression, suggesting that antigens from these genes could have therapeutic potential in a wide range of tumors. These findings could benefit the development of T cell-based vaccines, in which T cells are primed against these antigens to target and eradicate tumors. Such a vaccine could be used in tandem with existing immune checkpoint inhibition therapies, to bridge the gap in treatment efficacy across subtypes of colorectal cancer with varying prognoses. Data are available via ProteomeXchange with identifier PXD028309. Overall design: RNA-seq

结直肠癌（Colorectal cancer）是全球范围内第二大癌症致死病因，随着全球社会经济结构变迁，该病的发病率预计将持续攀升。免疫检查点抑制疗法（immune checkpoint inhibition therapy）对少数结直肠癌肿瘤具有治疗效果，但微卫星稳定（microsatellite stable）肿瘤对此疗法响应不佳。新兴癌症免疫治疗策略旨在激活针对肿瘤特异性抗原的细胞毒性T细胞应答，这类抗原仅表达于癌细胞的细胞表面。此类抗原极为罕见，唯有基于质谱（mass spectrometry）的检测方法可实现最有效的鉴定，该技术能够直接对这些肽段进行采样与测序。尽管目前已发现的少量肿瘤特异性抗原均源自基因组的编码区域，但最新研究表明，绝大多数肿瘤特异性抗原实则来自此前被认定为非编码的基因组区域。本研究采用一种新型蛋白基因组学（proteogenomic）方法，对一批结直肠癌来源的细胞系及配对肿瘤与癌旁正常组织的活检样本开展了肿瘤抗原鉴定工作。通过构建个性化癌症数据库并结合质谱分析，我们共鉴定出超过30000种独特的MHC I类相关肽段。在微卫星稳定与微卫星不稳定两类肿瘤中，我们共识别出19种肿瘤特异性抗原，其中超过三分之二源自非编码区域。这些肽段中有许多来自已知参与结直肠癌进展的源基因，提示这些基因编码的抗原在多种肿瘤中均具备治疗潜力。本研究成果可为基于T细胞的疫苗开发提供助力，这类疫苗可通过预先致敏T细胞识别上述抗原，从而实现对肿瘤的靶向清除与根除。该疫苗可与现有免疫检查点抑制疗法联合使用，以填补不同预后结直肠癌亚型在治疗疗效上的差距。相关数据已通过ProteomeXchange数据库公开，标识符为PXD028309。整体实验设计：RNA测序（RNA-seq）