Abstract 5248: Identification of a chromatin-remodeling peptide in diffuse midline glioma by immunopeptidomics

Abstract The identification of peptides presented by major histocompatibility complex class I (MHC-I) molecules on cancer cells is crucial for developing targeted immunotherapies, particularly for malignancies like pediatric diffuse midline gliomas (DMG), where therapeutic options remain limited. In this study, we applied advanced immunopeptidomics and mass spectrometry techniques to characterize the immunopeptidome of DMG H3K27M-altered. To identify DMG specific peptides, we included comparative studies to the immunepeptidome of adult glioblastoma (GBM). We identified a total of 454 peptides in DMG and U87 (glioblastoma) xenografts pertaining to 229 genes. Among these, 42 peptides were uniquely expressed in DMGs and 11 were shared with U87 xenografts, highlighting distinct antigen presentation profiles between these tumors. Notably, the peptide RSRKESYSVVYYKVLKQVHPD, which stems from the Histone H2B type 1-M (H2B1M) gene, is presented by the MHC-I molecule HLA-B*57:01, and is associated with chromatin remodeling, was enriched in DMG cells compared to GBM, revealing a potential immunotherapeutic target specific to DMG. To explore whether targeted therapies alter the identified immunopeptidome, we utilized MTX-241F, a previously described experimental compound that inhibits key proliferative pathways (EGFR/PI3K) in DMG and GBM. Comparative analysis of MTX-241F-treated DMGs and U87 xenografts revealed both overlapping and unique regulatory patterns of peptides, underscoring the tumor-specific effects of MTX-241F. MTX-241F selectively upregulated peptides in DMG stemming from the NCOA4, VATF and THOC2 genes that are linked to MHC-I presentation. In summary, our findings provide the first evidence of dynamic treatment dependent modulation of antigen presentation in DMGs and offer new insights into the tumor immunopeptidome. The distinct peptide profiles of DMG and U87 and their different responses to MTX-241F suggest potential therapeutic avenues for precision immunotherapy targeting DMG. In addition, the identification of a shared immunopeptidome presents an opportunity to develop a therapeutic for both pediatric and adult glioma. Citation Format: Niloofar Khairkhah, Ali Namvar, Arun Everest-Dass, Seeta Nyayapathy, Richard Jones, Julie M. Rumble, Christopher E. Whitehead, Judith S. Sebolt-Leopold, Stefanie Galban. Identification of a chromatin-remodeling peptide in diffuse midline glioma by immunopeptidomics [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 1 (Regular Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_1):Abstract nr 5248.