Modern Molecular Profiling Recontextualizes the NRG/RTOG 0539 Trial and Reveals Hidden High-Risk and Radiotherapy Resistant Meningiomas

Background: Meningiomas are the most common primary intracranial tumors and exhibit clinical heterogeneity. Radiotherapy (RT) remains the only adjuvant therapy, but response is variable and biomarkers are limited. NRG/RTOG 0539 is the first prospective phase 2 trial to stratify meningioma patients for adjuvant RT based on clinical risk. Here, we apply modern molecular tools to this cohort and uncover correlates of RT response. Methods: Tumor tissue from 100 RTOG 0539 patients was profiled using DNA methylation arrays, RNA sequencing, and whole-exome sequencing. Recurrence scores, Molecular Groups, gene expression, and copy number alterations were compared across clinical groups and between RT responders and non-responders. Results: Modern grading criteria, including brain invasion, TERT mutation, CDKN2A/B deletion and 1p/1q status, would reclassify 10% of tumors and alter treatment group assignment in 7%. Non-responders to RT had more frequent 1p and 14q loss, and greater copy number burden. Transcriptomic and epigenetic profiling revealed immune-related signatures in responders and cell cycle–related pathways in non-responders, several of which overlapped with targets of vorinostat, a histone deacetylase inhibitor previously validated in aggressive meningioma models. The Proliferative Molecular Group was an independent predictor of post-RT recurrence in multivariable analysis, outperforming WHO grade. Conclusion: Multi-omic analysis of the RTOG 0539 cohort shows that updated WHO grading criteria, incorporating molecular and cytogenetic features, improve risk stratification. However, molecular classification, particularly the Proliferative group, remains an independent and stronger predictor of RT response. These findings support integrating molecular biomarkers alongside modern grading frameworks to guide treatment and trial design in meningioma. Publication History Article published online: 27 February 2026 © 2026. Thieme. All rights reserved. Georg Thieme Verlag KG Oswald-Hesse-Straße 50, 70469 Stuttgart, Germany