Glioma sequencing data
Ontology highlight
ABSTRACT:
PROVIDER: EGAS00001006355 | EGA |
REPOSITORIES: EGA
Similar Datasets
Project description:The discovery of the oncometabolite 2-hydroxyglutarate in isocitrate dehydrogenase 1-mutated (IDH1-mutated) tumor entities affirmed the role of metabolism in cancer. However, large databases with tissue metabolites that are modulated by IDH1 mutation remain an area of development. Here, we present an unprecedented and valuable resource for tissue metabolites in diffuse glioma and their modulations by IDH1 mutation, histology, and tumor treatments in 101 tissue samples from 73 diffuse glioma patients (24 astrocytoma, 17 oligodendroglioma, 32 glioblastoma), investigated by NMR-based metabolomics and supported by RNA-Seq. We discovered comparison-specific metabolites and pathways modulated by IDH1 (IDH1 mutation status cohort) and tumor entity. The Longitudinal investigation cohort provides metabolic profiles of untreated and corresponding treated glioma samples at first progression. Most interestingly, univariate and multivariate cox regressions and Kaplan-Meier analyses revealed that tissue metabolites correlate with progression-free and overall survival. Thus, this study introduces potentially novel candidate prognostic and surrogate metabolite biomarkers for future prospective clinical studies, aiming at further refining patient stratification in diffuse glioma. Furthermore, our data will facilitate the generation of so-far-unanticipated hypotheses for experimental studies to advance our molecular understanding of glioma biology.
2022-09-07 | MTBLS3873 | MetaboLights
Project description:We used MHC-I immunopeptidomics to study how MTX-241F, a selective EGFR/PI3K inhibitor, alters antigen presentation in diffuse midline glioma (H3K27M) and glioblastoma xenografts. MHC-I–bound peptides from vehicle- and drug-treated tumors were profiled by LC–MS/MS to identify tumor- and treatment-specific peptides, including candidate brain-enriched biomarkers and immunotherapy targets.
2026-02-10 | PXD070941 | Pride
Project description:Two studies originating from the same team have previously suggested the existence of tectal glioma (TG) as a distinct pediatric low grade circumscribed astrocytic tumor type enriched in KRAS alterations or KRAS and BRAF concomitant alterations, and characterized by a distinct methylation profile. Although the majority of these tumors display a pilocytic astrocytoma (PA) morphology, the imprecise terminology of “glioma” was preferred by these authors. The inclusion of the entity “tectal glioma with KRAS mutation” in a future WHO classification is still under discussion. In this context, we performed a comprehensive analysis of 35 glial tumors located in the tectum including clinical, radiological, histopathological, and molecular data. The majority of tumors encountered were pilocytic astrocytomas. The other tumor types included gangliogliomas, rosette-forming glioneural tumors and a diffuse midline glioma, H3K27-altered. Surprisingly, none of these tumors showed any mutation in the KRAS gene. MAPK gene alterations were diverse: KIAA1549::BRAF, FGFR1 alterations (fusions and duplications), other RAF fusions, NF1 mutations and BRAF mutations. Furthermore, when we compared the epigenetic profile of our tumors with those available from the study by Liu et al., they clustered close to or alongside them.
2026-08-19 | E-MTAB-17457 | biostudies-arrayexpress
Project description:We report a rare adult case of H3K27-altered diffuse glioma arising in an atypical non-midline location, highlighting the diagnostic challenges posed by its radiological and histopathological resemblance to glioblastoma. The study demonstrates the clinical utility of integrated histopathological, methylation-based, and genomic analyses, including rapid Nanopore methylation profiling, for accurate tumor classification and precision neuro-oncology. These findings are of direct relevance to neuropathologists, molecular pathologists, neurooncologists, and translational neuroscience researchers.
2026-09-02 | GSE338747 | GEO
Project description:Mutations in the gene encoding histone H3, p.K28M(K27M) and p.G35R/V(G34R/V), are the major driver gene mutations in gliomas. H3 p.K28M(K27M) mutations are frequently found in gliomas arising in midline structures, so called H3K27M-diffuse midline glioma (DMG), while H3 p.G35R/V(G34R/V) mutations are frequently found in pediatric hemispheric gliomas, so called H3G34R/V-diffuse hemispheric glioma (DHG). In contrast, hemispheric glioma with H3 p.K28M(K27M) mutation, known as H3K27M-DHG, is a rare entity and its clinical and molecular characteristics remain to be fully elucidated. We describe a 41-year-old female patient with the right parietal lobe tumor. Following a gross total resection, the pathology showed a high-grade astrocytoma. Sanger sequencing revealed an H3K27M mutation and an IDH1/2-wildtype, leading to the integrated diagnosis of H3K27M-DHG. She underwent chemoradiotherapy with temozolomide and suffered recurrences twice until her death 55 months after the initial diagnosis. The deoxyribonucleic acid methylation profiling classified the tumor as DMG, H3K27-altered, suggesting that it molecularly belonged to the variant of DMG despite a non-median location. Next-generation sequencing on the recurrent tumor detected fibroblast growth factor receptor (FGFR)1 mutation, a favorable prognostic factor in H3K27M-DMG. A relatively prolonged survival of our patient suggests that FGFR1 mutations may also contribute to a better prognosis in H3K27M-DHG.
2025-12-31 | GSE286743 | GEO
Project description:Anaplastic ependymoma and H3K27M-mutant diffuse midline glioma were analyzed and compared by scRNA-seq.
2024-02-28 | GSE245674 | GEO
Project description:PDGFRA and H3.3 mutations cooperate in an iPSC-based model of diffuse midline glioma to alter tumor biology.
2026-03-01 | GSE225491 | GEO
Project description:PDGFRA and H3.3 mutations cooperate in an iPSC-based model of diffuse midline glioma to alter tumor biology.
2023-06-14 | GSE225490 | GEO
Project description:Adult diffuse gliomas are the deadliest brain tumours including IDH-wildtype glioblastomas of worst prognosis and diffuse low grade IDH-mutant astrocytomas and oligodendrogliomas. These glial tumours display distinct tumoral cell population defeating current therapies. Our group has previously unveiled the role of NOTCH signalling in glioblastoma cell plasticity and in the conversion of oligodendrocytic-like to astrocytic-like tumoral cells in IDH-mutant low-grade gliomas which escalate inevitably to higher grade malignant gliomas. To gain insight into signalling pathways regulating glioma cell plasticity and malignancy, we focused our work on endothelin signalling including endothelin peptide ligands (ET-1, ET-2, ET-3) binding to G-protein coupled endothelin receptors A and B (EDNRA, EDNRB). Here, using glioma patient samples and glioma patient-derived cell lines, we showed that endothelin reduces glioma cell proliferation while increasing migration initiating a proneural to mesenchymal transition. Mechanistically, EDNRB activation led to IP3-dependent calcium mobilization, apamin-sensitive KCNN2/KCNN3 potassium currents and phosphorylation of ERK1/2 and STAT3 in glioma cells. Finally, we studied endothelin receptor regulation by tumoral microenvironment stimuli highlighting a role for EDNRA induced by NOTCH1 and hypoxia in perivascular hypoxic area in glioblastoma. Altogether, this study demonstrates endothelin signalling as a key player in mesenchymal transformation of diffuse IDH-mutant gliomas and glioblastomas.
2026-03-11 | PXD065902 | Pride
Project description:Neural-tumor interactions drive glioma growth as evidenced in preclinical models, but clinical validation is limited. We present an epigenetically defined neural signature of glioblastoma that independently predicts patients’ survival. We use reference signatures of neural cells to deconvolve tumor DNA and classify samples into low- or high-neural tumors. High-neural glioblastomas exhibit hypomethylated CpG sites and upregulation of genes associated with synaptic integration. Single-cell transcriptomic analysis reveals a high abundance of stem cell-like malignant cells in high-neural glioblastoma, primarily of the neural lineage. These cells are further classified as neural precursor cell-like, astrocyte cell-like, and oligodendrocyte precursor-like, alongside oligodendrocytes and neurons. In line with these findings, high-neural glioblastoma cells engender neuron-to-glioma synapse formation in vitro and in vivo and show an unfavorable survival after xenografting. In patients, a high-neural signature associated with decreased survival. High-neural tumors also exhibit increased functional connectivity in magnetencephalography and resting-state magnet resonance imaging and can be detected via DNA analytes and brain-derived neurotrophic factor in patients’ plasma. The prognostic importance of the neural signature was further validated in patients diagnosed with diffuse midline glioma. Our study presents an epigenetically defined malignant neural signature in high-grade gliomas that is prognostically relevant. High-neural gliomas likely require a maximized surgical resection approach for improved outcomes.
2024-03-20 | GSE240704 | GEO