Determinants of tumor immune evasion: the role of T cell exposed motif frequency and mutant amino acid exposure

Few neoepitopes detected in tumor biopsies are immunogenic. Tumor-specific T cell responses require both the presentation of an epitope that differs from wildtype and the presence of T cells with neoepitope-cognate receptors. We show that mutations detected in tumor biopsies result in an increased frequency of rare amino acid combinations compared to the human proteome and gastrointestinal microorganisms. Mutations in a large data set of oncogene and tumor suppressor gene products were compared to wildtype, and to the count of corresponding amino acid motifs in the human proteome and gastrointestinal microbiome. Mutant amino acids in T cell exposed positions of potential neoepitopes consistently generated amino acid motifs that are less common in both proteome reference datasets. Approximately 10% of the mutant amino acid motifs are absent from the human proteome. Motif frequency does not change when mutants were positioned in the MHC anchor positions hidden from T cell receptors. Analysis of neoepitopes in GBM and LUSC cases showed less common T cell exposed motifs, and HLA binding preferentially placing mutant amino acids in an anchor position for both MHC I and MHC II. Cross-presentation of mutant exposed neoepitopes by MHC I and MHC II was particularly uncommon. Review of a tumor mutation dataset known to generate T cell responses showed immunogenic epitopes were those with mutant amino acids exposed to the T cell receptor and with exposed pentamer motifs present in the human and microbiome reference databases. The study illustrates a previously unrecognized mechanism of tumor immune evasion, as rare T cell exposed motifs produced by mutation are less likely to have cognate T cells in the T cell repertoire. The complex interactions of HLA genotype, binding positions, and mutation specific changes in T cell exposed motif underscore the necessity of evaluating potential neoepitopes in each individual patient.