Integrative Computational Immunology Applied to Identify and Characterize CD8+ T-cell Neoepitopes of Shared KRAS Neoantigen Oncogenic Driver Hotspot Mutations

Abstract

Background: Lung, pancreatic, and colorectal cancers continue to rank among the most lethal malignancies. Despite the availability of advanced treatments, these cancer types demand more effective immunotherapeutic solutions. Neoantigen formation is a common feature of cancer mechanisms, with the Kirsten rat sarcoma viral oncogene homolog (KRAS) being the most frequently mutated oncogene in various cancers. This study employed immunoinformatic tools and databases to identify and analyze potential cytotoxic T-cell neoepitopes derived from KRAS hotspot mutations.

Methods: Experimentally validated neoepitopes were obtained from NEPdb. Key parameters such as IC50 values, differential agretopicity, mutation positions, and immunogenicity of the neoepitopes were determined. Results from this analysis, combined with additional factors recommended in the literature, were used to identify and characterize potential KRAS neoepitopes. Sequences with G12A, G12C, G12D, G12S, G12V, G12R, G13D, and A59T mutations were prepared. IC50 values and differential agretopicity were analyzed using NetMHCPan4.1. The epitopes' safety profiles and population coverage were assessed, and the top recommended neoepitopes were docked to calculate the dissociation constant (KD) and Gibbs free energy of binding (ΔGbind).

Results: Twenty-one candidate KRAS CD8+ neoepitopes were identified. The recommended neoepitopes (KLVVVGAAGV, LVVVGAAGV, LVVVGACGV, KLVVVGADGV, LVVVGADGV, KLVVVGASGV, KLVVVGAV, KLVVVGAVGV, LVVVGAVGV, and VVGAVGVGK) exhibit TCR-facing mutated residues, significant differential agretopicity, and higher binding affinity compared to their wild-type counterparts. Safety and population coverage analyses suggest that these candidate KRAS neoepitopes are unlikely to cause allergy, toxicity, or cross-reactivity, and they demonstrate coverage across a substantial proportion of the population.

Conclusion: This study introduced a preliminary integrative workflow for neoepitope identification. Findings indicate that the 21 candidate KRAS neoepitopes have the potential to be recognized by cytotoxic lymphocytes and trigger immune response. This positions them as promising elements for anti-cancer vaccine formulations, pending successful in vitro, animal, and clinical studies.

Keywords: KRAS; Lung cancer; Pancreatic cancer; colorectal cancer; neoepitope.