Adoptive T cell therapy targeting a widespread inducible product of aberrant mRNA translation

Deregulated protein production by oncogenic pathways fuels tumor development. Consequently, the induction of tryptophan shortage by Indoleamine 2,3-Dioxygenase 1 (IDO1) enzyme, following interferon-gamma (IFNg) secretion by activated T cells, induces tryptophan to phenylalanine (W>F) substitutants1,2. These defective protein products are processed and presented on Human Leukocyte Antigen (HLA) molecules as neoepitopes. Here, we addressed the potential of substitutant neoepitopes to improve cancer immunotherapy. Adoptive cancer immunotherapy is an attractive treatment mode but suffers from the lack of widespread immunogenic targets, as somatic genetic aberrations in cancer are mostly private and counter-selected for strong immunogenicity3,4. Using immunopeptidomics, we identified IFNg-inducible common W>F substitutant neoepitopes presented on HLA-A*24:02, an abundant receptor allele in the Asian population that favors binding to peptides with phenylalanine in their sequence. TMBIM6W>F neoepitope from this list showed the broadest and second-highest expressed host gene in cancer transcriptome datasets. Therefore, we screened T cells and identified one TCR (TCRTMBIM6W>F.1) possessing high affinity and specificity towards TMBIM6W>F/HLA-A*24:02, compared to its wild-type counterpart. We further demonstrate that TCRTMBIM6W>F.1 T cells are reactivated by IFNg-mediated tryptophan-depleted cancer cells, provided they express HLA-A*24:02, TMBIM6, and IDO1, and are proficient in peptide presentation. Finally, in vivo xenograft experiments confirmed the ability of TCRTMBIM6W>F.1 T cells to suppress tumor progression. Thus, substitutant neoepitopes are widespread inducible products of aberrant mRNA translation that provide novel means to overcome current limitations in T-cell transfer therapy.