H3K27M Mutation Modulates the Antigenic Landscape in Diffuse Midline Glioma.
10 affiliations
- 1Centre for Cancer Research, Hudson Institute of Medical Research, Clayton, VIC 3168, Australia.
- 2Department of Medicine, School of Clinical Sciences, Monash University, Clayton, VIC 3168, Australia.
- 3Peter MacCallum Cancer Centre, Melbourne, VIC 3000, Australia.
- 4Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC 3010, Australia.
- 5Monash Proteomics and Metabolomics Platform, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia.
- 6Department of Paediatrics, University Children's Hospital Zurich, 8008 Zurich, Switzerland.
- 7Department of Molecular and Translational Science, School of Medicine, Nursing and Health Sciences, Monash University, Clayton, VIC 3800, Australia.
- 8Department of Paediatrics, Monash University, Clayton, VIC 3168, Australia.
- 9Michael Rice Centre for Hematology and Oncology, Women's and Children's Hospital, South Australia Health and Medical Research Institute, South Australia Immunogenomics Cancer Institute, Adelaide University, Ade-laide, SA 5000, Australia.
- 10Department of Microbiology and Immunology, The University of Melbourne, Parkville, VIC 3010, Australia.
Abstract
Background/objectives
Diffuse midline gliomas (DMGs) are among the most aggressive paediatric brain tumours, with the pathognomonic H3K27M mutation present in over 80% of cases. This mutation drives epigenetic dysregulation and transcriptional reprogramming, yet its impact on the tumour antigenic landscape remains poorly understood. Given the low mutational burden of DMG, an expanded search beyond neoantigens to include epigenetically dysregulated tumour-associated antigens (TAAs) is critical for advancing antigen-specific immunotherapies.Methods
We performed immunopeptidomic analysis of two patient-derived H3K27M-mutant DMG cell lines (SU-DIPG13 and BT245) and their isogenic counterparts in which only the mutant H3F3A allele was disrupted by CRISPR editing (H3K27M-KO), leaving wild-type histone H3.3 intact. High-resolution mass spectrometry and bioinformatics were used to define H3K27M-associated changes in the immunopeptidome, and functional T cell assays with HLA-matched healthy donor PBMCs assessed peptide immunogenicity.Results
H3K27M modulated the tumour antigenic landscape in a model-specific manner. Loss of the mutant allele increased HLA-I expression in SU-DIPG13 but not BT245, while immunopeptidomic profiling revealed distinct shifts in tumour-associated peptide presentation in both models, indicating that HLA-I abundance alone does not explain these changes. We identified six peptides derived from SLITRK2, PRAME, XKR5 and CBX2 that elicited T-cell responses in vitro; T cells raised against five of these preferentially recognised the parental H3K27M-mutant DMG cells. Several prioritised peptides were detected only in parental H3K27M-mutant cells, supporting mutation-associated, antigen-selective differences in peptide presentation and tumour antigenicity.Conclusions
This study shows that H3K27M modulates the antigenic landscape in DMG in a model-dependent, antigen-selective manner, uncovering immunogenic tumour-associated peptides that could serve as targets for precision immunotherapy and establishing a foundation for T cell-based therapies in this otherwise treatment-refractory disease.
Related
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- Cooperativity through Allee Effects drives growth of diffuse midline gliomas impacting the optimal scheduling of therapeutic interventions
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BibTeX
@article{shamekhi2026h3k27m,
title = {{H3K27M Mutation Modulates the Antigenic Landscape in Diffuse Midline Glioma.}},
author = {Tima Shamekhi and Bijun Zeng and Claire Xin Sun and Paul Daniel and Terry C C Lim Kam Sian and Gabriel Goncalves and Grace Huang and Farnaz Fahimi and Nivedhitha Selvakumar and Erwin Tanuwidjaya and Isaac Woodhouse and Bettina Kritzer and Ralf B Schittenhelm and Roberta Mazzieri and Jason E Cain and Javad Nazarian and Jordan R Hansford and Ron Firestein and Riccardo Dolcetti and Pouya Faridi},
journal = {Cancers},
year = {2026},
month = sep,
doi = {10.3390/cancers18193142},
url = {https://europepmc.org/article/MED/42882837},
note = {CC BY},
}
RIS
TY - JOUR
TI - H3K27M Mutation Modulates the Antigenic Landscape in Diffuse Midline Glioma.
AU - Tima Shamekhi
AU - Bijun Zeng
AU - Claire Xin Sun
AU - Paul Daniel
AU - Terry C C Lim Kam Sian
AU - Gabriel Goncalves
AU - Grace Huang
AU - Farnaz Fahimi
AU - Nivedhitha Selvakumar
AU - Erwin Tanuwidjaya
AU - Isaac Woodhouse
AU - Bettina Kritzer
AU - Ralf B Schittenhelm
AU - Roberta Mazzieri
AU - Jason E Cain
AU - Javad Nazarian
AU - Jordan R Hansford
AU - Ron Firestein
AU - Riccardo Dolcetti
AU - Pouya Faridi
PY - 2026
DA - 2026/09/28
JO - Cancers
DO - 10.3390/cancers18193142
UR - https://europepmc.org/article/MED/42882837
AB - Background/objectives Diffuse midline gliomas (DMGs) are among the most aggressive paediatric brain tumours, with the pathognomonic H3K27M mutation present in over 80% of cases. This mutation drives epigenetic dysregulation and transcriptional reprogramming, yet its impact on the tumour antigenic landscape remains poorly understood. Given the low mutational burden of DMG, an expanded search beyond neoantigens to include epigenetically dysregulated tumour-associated antigens (TAAs) is critical for advancing antigen-specific immunotherapies.Methods We performed immunopeptidomic analysis of two patient-derived H3K27M-mutant DMG cell lines (SU-DIPG13 and BT245) and their isogenic counterparts in which only the mutant H3F3A allele was disrupted by CRISPR editing (H3K27M-KO), leaving wild-type histone H3.3 intact. High-resolution mass spectrometry and bioinformatics were used to define H3K27M-associated changes in the immunopeptidome, and functional T cell assays with HLA-matched healthy donor PBMCs assessed peptide immunogenicity.Results H3K27M modulated the tumour antigenic landscape in a model-specific manner. Loss of the mutant allele increased HLA-I expression in SU-DIPG13 but not BT245, while immunopeptidomic profiling revealed distinct shifts in tumour-associated peptide presentation in both models, indicating that HLA-I abundance alone does not explain these changes. We identified six peptides derived from SLITRK2, PRAME, XKR5 and CBX2 that elicited T-cell responses in vitro; T cells raised against five of these preferentially recognised the parental H3K27M-mutant DMG cells. Several prioritised peptides were detected only in parental H3K27M-mutant cells, supporting mutation-associated, antigen-selective differences in peptide presentation and tumour antigenicity.Conclusions This study shows that H3K27M modulates the antigenic landscape in DMG in a model-dependent, antigen-selective manner, uncovering immunogenic tumour-associated peptides that could serve as targets for precision immunotherapy and establishing a foundation for T cell-based therapies in this otherwise treatment-refractory disease.
SN - 2072-6694
ER -