Quantitative Proteomic Analysis Reveals Different Functional Subtypes among IDH-Wildtype Glioblastoma

Purpose: Proteomics of glioma have not yet provided biomarkers and pathways that would clearly discriminate glioma subgroups. Methods: 82 glioma biopsies were prospectively collected and classified into six subgroups defined by methylomic classification: two low-grade glioma (LGG) and four high-grade glioma (HGG) subgroups. Proteins were extracted and processed for liquid chromatography–mass spectrometry (LC–MS). Differentially expressed proteins (DEPs) between subgroups were annotated, and functional validation was performed using inhibitor response assays in subtype-positive, patient-derived glioblastoma single-cell suspensions. Results: 5057 proteins were quantified for each sample. Tumor grading and IDH mutation status were the strongest discriminators for differential expression patterns. The glioblastoma IDH-wildtype subgroups showed diverse patterns of functions enriched with overexpressed DEPs: translation and cell cycle/telomere regulation in proneural glioblastoma (linked to cell proliferation), actin cytoskeleton, cell adhesion, and apoptosis regulation in classical glioblastoma (migration and invasion), and mitochondrial ATP synthesis in mesenchymal glioblastoma (metabolism). The most overexpressed proteins were correlated with survival and mRNA expression data. In vitro, inhibition of these proteins led to reduced cell viability that differed among subgroups, albeit in a small patient-derived exploratory cohort. Conclusion: This mainly descriptive study on proteomics in glioma provides insights into subgroup metabolism and potential biomarkers for further experimental testing.