Abstract 5798: Characterization of neoantigen peptides reveals key factors for sequence design to achieve immunogenicity

Abstract Immunotherapy has become a powerful approach by utilizing immune systems to combat cancer. Therapeutic cancer neoantigen vaccines targeting tumor-specific antigen (TSA) have demonstrated promising results in several clinical trials, particularly in adjuvant settings. Neoantigens are tumor-specific antigens that are derived primarily from somatic mutations or non-canonical sequences, which can be presented on major histocompatibility complex (MHC) complexes to stimulate T cells. However, selecting mutations and designing neoantigen sequences to achieve high immunogenicity remains challenging. Compared with RNA-based vaccines, the peptides are more difficult to design due to solubility issues. We have analyzed immune response data from an enzyme-linked immunospot (ELISpot) assay collected from patients enrolled in Phase I clinical trial of neoantigen peptide vaccine at Faculty of Medicine, Chulalongkorn University, Thailand. A total of 12 patients with metastatic melanoma and renal cell carcinoma were treated with neoantigen synthetic long peptides, derived from 15-20 patient-specific somatic variants. The patients received neoantigen vaccine alone, intramuscularly administered in 5-7 injections, without combination with immune checkpoint inhibitors. A total of 239 peptides have been tested by ELISpot. We have characterized several contributing factors to immune response. Notably, we found no significant difference in immunogenicity based on peptide solubility, gene expression levels, variant allele frequency, or sites of injection. However, neoantigen peptides derived from indel mutations exhibited slightly stronger immune responses, than those from single nucleotide variants (SNVs) or frameshift variants. In conclusion, we identified some key factors that can assist in the design of neoantigen peptide sequence, and help prioritize neoantigen candidates for cancer treatments. Citation Format: Piriya Wongkongkathep, Worawan Bunrasmee, Jirattha Siriluksana, Korn Chotirosniramit, Pimpayao Sodsai, Nattiya Hirankarn, Trairak Pisitkun. Characterization of neoantigen peptides reveals key factors for sequence design to achieve immunogenicity [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 1 (Regular Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_1):Abstract nr 5798.