Identification of T Cell Receptors Targeting a Neoantigen Derived from Recurrently Mutated FGFR3

SIMPLE SUMMARY: Neoantigens are considered good targets for immunotherapy due to their tumor specificity. However, because neoantigens are unique in individual cancers, it is challenging to select personalized target neoantigens. In this study, we focused on "shared neoantigens", which are neoantigens derived from mutations observed commonly in a subset of cancer patients. We identified a shared neoantigen derived from FGFR3(Y373C) through bioinformatics and in vitro screening. We identified that TCR-engineered T cells expressing TCRs for FGFR3(Y373C) showed specific reactivity and cytotoxic activity against mutated FGFR3(Y373C). We believe that immunotherapies targeting shared neoantigens would be a good approach for cancer treatment. ABSTRACT: Immunotherapies, including immune checkpoint blockades, play a critically important role in cancer treatments. For immunotherapies, neoantigens, which are generated by somatic mutations in cancer cells, are thought to be good targets due to their tumor specificity. Because neoantigens are unique in individual cancers, it is challenging to develop personalized immunotherapy targeting neoantigens. In this study, we screened "shared neoantigens", which are specific types of neoantigens derived from mutations observed commonly in a subset of cancer patients. Using exome sequencing data in the Cancer Genome Atlas (TCGA), we predicted shared neoantigen peptides and performed in vitro screening of shared neoantigen-reactive CD8(+) T cells using peripheral blood from healthy donors. We examined the functional activity of neoantigen-specific T cell receptors (TCRs) by generating TCR-engineered T cells. Among the predicted shared neoantigens from TCGA data, we found that the mutated FGFR3(Y373C) peptide induced antigen-specific CD8(+) T cells from the donor with HLA-A*02:06 via an ELISPOT assay. Subsequently, we obtained FGFR3(Y373C)-specific CD8(+) T cell clones and identified two different sets of TCRs specifically reactive to FGFR3(Y373C). We found that the TCR-engineered T cells expressing FGFR3(Y373C)-specific TCRs recognized the mutated FGFR3(Y373C) peptide but not the corresponding wild-type peptide. These two FGFR3(Y373C)-specific TCR-engineered T cells showed cytotoxic activity against mutated FGFR3(Y373C)-loaded cells. These results imply the possibility of strategies of immunotherapies targeting shared neoantigens, including cancer vaccines and TCR-engineered T cell therapies.