Immunogenicity of Neoantigens in Colorectal Cancer: Potential Influence of Tumor Mutation Burden, Stages, and Metastasis

Colorectal cancer (CRC) is a leading cause of cancer-related deaths, often due to liver metastases. Neoantigen-based immunotherapy has shown promise in clinical trials of solid tumors, including CRC. However, the immunogenic factors of neoantigens and their optimal selection in metastatic tumors are not well understood. Therefore, this study aimed to identify the relationship between tumor mutation burden and immunogenicity of neoantigens in CRCs and metastatic CRCs and evaluate the changes in immunogenic neoantigens between the primary and metastatic lesions in metastatic CRCs. Five patients with CRC were analyzed. Neoantigen selection was accomplished by integrating whole-exome sequencing, RNA sequencing, and the prediction of human leukocyte antigen binding affinity. Immunogenicity of the peptide was assessed using enzyme-linked immuno-spot assay for interferon-γ production from CD8+ T cells. The immunogenicity of 72 neoantigen peptides was tested, and resulted in nine (12.5%) peptides showing high immunogenicity. These highly immunogenic neoantigens correlated with high tumor mutation burden and distant metastasis. In metastatic CRC, common neoantigens in primary and metastatic lesions showed low immunogenicity. The neoantigen peptide with the highest immunogenicity was confirmed by both in vitro and in vivo sensitization, and the peptide/T cell receptor complex was detected in the corresponding patient's peripheral blood mononuclear cells. In CRC, highly immunogenic neoantigens may be associated with tumor mutational burden and metastasis, whereas common neoantigens in primary and metastatic lesions may be immunologically suppressed.