Upregulation of EZH2 and E2F1 in combination with NF2 alterations underlies the molecular characteristics of aggressive meningiomas

Coding alterations do not significantly contribute to meningioma aggressiveness, except for rare alterations in CDKN2A and TERT . The aim of this study was to investigate specific molecular pathways as potential therapeutic targets. A discovery cohort comprising 35 meningiomas, including 26 high-grade tumors, was investigated for genetic alterations and gene expression profiles. Among these, 28 tumors were further analyzed using unsupervised hierarchical clustering, gene set enrichment analysis (GSEA), and gene set variation analysis (GSVA). The 28 tumors in the discovery cohort were classified into three clusters (Cluster M: Low, Mid, and High) using hierarchical clustering based on genes differentially expressed across CNS WHO grades. These clusters correlated with overall survival and WHO grade. GSEA comparing the Cluster M subgroups revealed that meningioma aggressiveness increased via the downregulation of immune response-related gene sets (Low → Mid), followed by the upregulation of cell proliferation-related gene sets (Mid → High). These findings were supported by GSVA using Hallmark gene sets enrichment scores and by hierarchical clustering based on copy number losses, with enrichment of the E2F target and MYC target gene sets in the high-grade clusters. The findings were subsequently validated through OncoPrint analyses using a larger, previously published dataset. The OncoPrint analyses demonstrated that the most aggressive type of meningiomas is characterized by the upregulation of EZH2 as well as E2F1, but not MYC, in combination with NF2 alterations. The efficacy of an EZH2 inhibitor was evaluated in multiple meningioma cell lines, and meningioma cell growth was suppressed by an EZH2 inhibitor, with its efficacy possibly correlating with EZH2 expression levels. Meningiomas harboring NF2 alterations exhibit distinct biological behaviors depending on the expression of EZH2 and E2F1, and aggressive meningiomas are characterized by the upregulation of these pathways in combination with NF2 alterations. EZH2 is a promising therapeutic target for high-grade meningiomas.