Neoantigen Detection in Postoperative Colorectal Cancer Patients by Next-Generation Sequencing and Liquid Chromatography-Mass Spectrometry

Background/Aims: The new antigens are considered to be the best targets for anti-tumor T-cell immunity and individualized cancer immunotherapy strategies. The aim of this study is to explore tumor-specific neoantigen peptides produced by exon mutations of differentially expressed genes in postoperative colorectal cancer and their bioinformatics characteristics. Methods: The whole-genome sequencing of the tumor and paracancerous tissues and human leukocyte antigen class I (HLA-I) alleles of the tumor tissues was first detected by nextgeneration sequencing (NGS), tumor nascent antigen peptides were then predicted and identified according to exon mutations using liquid chromatography-mass spectrometry (LC-MS), and finally the affinity of nascent peptides with respective HLA I was calculate using NETMHC 4.0 Server. Differentially expressed genes producing neoantigens in colorectal cancer tissues were detected and the relationship between these genes and immune cells was screened through TIMER website. The mutation frequency and type of these genes were explored through CBioPortal website. The relationship between these genes and disease-free survival (DFS) and overall survival (OS) in colorectal cancer patients was explored through GEPIA website. Results: A total of 7 tumor-specific neoantigen peptides were identified from 4 patients, of which 3 showed certain affinity with HLA I. Frame-shift deletion, non frame-shift insertion and non frame-shift deletion were three main mutation types of exons. Most of the above-mentioned genes were differentially expressed in colorectal cancer, and some genes tended to express Individually in colorectal cancer. In addition to the type and amount of immune cells infiltrated in the tumor stroma, the expression intensity of these genes was also correlated with DFS and OS of colorectal cancer patients. Conclusion: The above results suggest that the type and number of tumor-specific neoantigens may be related to DFS and OS in postoperative colorectal cancer patients, and help predict the risk of postoperative recurrence, metastasis and prognosis.