Abstract 1883: Large-scale proteomic analysis of glioblastoma tissues reveals novel molecular insights and potential therapeutic targets

Abstract Introduction: Glioblastoma (GBM), classified as WHO grade 4, is a highly aggressive and incurable brain tumor with limited treatment options. Standard treatment consists of maximum safe surgery followed by concurrent chemo/radiation and adjuvant chemotherapy, the Stupp protocol. Despite extensive molecular characterization through DNA sequencing and RNA expression studies, the complex heterogeneity of GBM has yet to translate into improved standard treatments. A key challenge lies in predicting the impact of genetic and transcriptomic alterations at the protein level. Aim: To identify promising protein biomarkers in GBM and trace these back to DNA and RNA data to determine whether they can be detected at earlier stages. We seek to uncover mechanisms of relapse and identify proteomic alterations that may be therapeutically targeted, integrating our findings with clinical data to discover potential prognostic and predictive biomarkers. Experimental Procedures: We collected tumor tissue from 360 newly diagnosed GBM patients between 2016 and 2023, who provided informed consent for whole-exome/genome and RNA sequencing. In total, 514 protein samples were analyzed, including a subset of 58 samples from primary tumors and their matched first relapse. High-throughput proteomic analysis was performed using an Evosep system coupled with a high-sensitivity Orbitrap Astral mass spectrometer. Concurrently, we are analyzing the corresponding RNA and DNA data and plan to analyze 150 plasma samples from 50 of the included patients. Results: Proteomics analysis of 514 GBM tissue samples identified 12, 446 proteins, establishing this study as one of the most extensive proteomic investigations of GBM to date. Notably, O6-methylguanine-DNA methyltransferase (MGMT) exhibited significant regulation in MGMT-methylated patients. Furthermore, in patients with Neurofibromatosis type 1 (NF1) mutations, NF1 was significantly downregulated. Functional analysis revealed that proteins involved in glycosaminoglycan metabolism were upregulated in patients who responded to the STUPP protocol, suggesting key alterations in extracellular matrix composition and signaling pathways. Hedgehog signaling was markedly downregulated in relapse samples, a finding associated with increased cancer aggressiveness, poor prognosis, and elevated mortality. Additionally, the KRAS oncogenic signaling pathway was downregulated, pointing to potential changes in the tumor microenvironment and growth dynamics in relapsed GBM. Conclusion: Our findings provide new insights into GBM proteomics and highlight potential therapeutic targets that could lead to more effective treatment strategies. By linking proteomic data to genetic and transcriptomic profiles, this study offers a valuable resource for improving patient stratification and developing targeted therapies for GBM. Citation Format: Juanjuan Wang, Simone Maarup, Vincent Fougner, Annelaura B. Nielsen, Ulrik Lassen, Luca Robinson, Frederik O. Bagger, Dorte S. Noeroexe. Large-scale proteomic analysis of glioblastoma tissues reveals novel molecular insights and potential therapeutic targets [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 1883.