Neoantigen polypeptide vaccines induce effective antitumor response in colorectal cancer

Abstract Background: The role of neoantigens in cancer immunotherapy is crucial. However, the effectiveness and safety of personalized neoantigen vaccines in colorectal cancer (CRC), especially in Chinese population, has not been well studied. This paper mainly explores the feasibility and effectiveness of personalized neoantigen vaccines in CRC treatment. Methods: Whole-exome sequencing and transcriptome sequencing were used to identify somatic mutations, RNA expression and human leukocyte antigen (HLA) alleles. Neoantigens were predicted, and the immunogenicity of neoantigen candidates was evaluated by ELISPOT in vitro. To verify the immunogenicity in vivo, neoantigen candidates from HLA-A0201+PW11 were used to immunized female 6-8-week-old HLA-A2.1/Kb-transgenic (Tg) mice. Neoantigen-reactive T cells (NRTs) were induced by immunogenic peptides from autologous HLA-A2.1/Kb to adoptive transfer transgenic mice, and C57BL/6nu/nu mice were used for in vivo antitumor response assays.Results: Compared to medium alone (no peptide) or the unrelated peptide VSV-NP43-69, the neoantigens TSHZ3-L523P, RARA-R83H, TP53-R248W, EYA2-V333I and NRAS-G12D from Patient 4 (PW4); HAVCR2-F39V, SEC11A-R11L, TASP1-P161L, RAP1GAP-S215R, MOSPD1-V63I and NAV2-D1973N from Patient 10 (PW10); and SMPDL3B-T452M, LRFN3-R118Q and ULK1-S248L from Patient 11 (PW11) induced notable peptide-specific T cell responses. The results indicated that about half of the predicted neoantigens for all 3 patients can stimulate T cell responses and antitumor effects in CRC. In addition, predicted neoantigens from PW11 (HLA-A0201) showed promising antitumor efficacy in HLA-A2.1/Kb-Tg mice and tumor-bearing mouse models.Conclusion: With the application of next-generation sequencing (NGS) sequencing of patient specimens, neoantigen prediction and a rapid immunoassay system, an evaluation system utilizing in vitro studies and in vivo transgenic and tumor-bearing mouse models can be used to screen strong immunogenic neoantigens in CRC patients. Accurate identification of neoantigens with strong immunogenicity would promote personalized cancer vaccine development.