Identification of molecularly targeted therapy-induced immunopeptidome in diffuse midline glioma (DMG).
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INTRODUCTION: Diffuse midline glioma (DMG) with the H3K27M mutation remains one of the most treatment-resistant pediatric brain tumors, in part due to limited antigen presentation and immune visibility. Exploring how glioma biology and therapeutic interventions influence immune recognition offers new opportunities to identify tumor-specific immune targets. MATERIALS AND METHODS: We performed immunopeptidomics on human cell line derived tumor tissue for DMG and glioblastoma (GBM) and defined how MTX-241F, a selective EGFR/PI3K inhibitor, changes the tumor immunopeptidome. Immunopeptides were isolated from xenografted tumors by capturing MHC-I bound peptides followed by mass spectrometry. Comparative analyses were performed across tumor type (DMG vs. GBM) and treatment condition (vehicle vs. MTX-241F). RESULTS: Immunopeptidomic profiling revealed tumor-specific differences in peptide repertoires between DMG and GBM. GBM tumors exhibited twice as many immunopeptides as DMG, which may be due to the distinct biology of each tumor type or may be indicative of potential HLA allotype composition. We identified highly abundant H2B1K-derived immunopeptides in DMG, suggesting that the H3K27M-driven epitranscriptome may promote turnover of other histones. MTX-241F increased the number of immunopeptides in DMG but reduced them in GBM, indicating a tumor-specific change in the immunopeptidome following EGFR/PI3K inhibition. In addition, we identified brain-enriched, HLA-A*02:01-binding and MTX-241F-exclusive immunopeptides that represent treatment-induced changes and may serve as biomarkers of therapeutic response or potential targets for CAR-T cell-based approaches. DISCUSSION: MTX-241F changes the glioma immunopeptidome, unveiling H2B1K, brain-enriched, and treatment-induced immunopeptides as immunologically visible targets. These findings provide a rationale for integrating molecularly targeted therapy with immunotherapeutic approaches to enhance tumor recognition and treatment efficacy in DMG and GBM.