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

Coding variations do not significantly contribute to tumor aggressiveness in meningiomas 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 of 35 meningiomas, including 26 high-grade tumors, was investigated for genetic alterations and gene expression profiling, and analyzed by unsupervised hierarchical clustering, gene set enrichment analysis (GSEA) and gene set variation analysis (GSVA). The results were validated by OncoPrint analyses in a larger dataset published previously. The efficacy of an EZH2 inhibitor was evaluated in multiple meningioma cell lines. Tumors in the discovery cohort were classified into three clusters (Cluster M: Low, Mid, High) using hierarchical clustering based on genes differentially expressed across CNS WHO grades. These clusters correlated with overall survival and WHO grade. GSEA between the subgroups of Cluster M demonstrated that meningiomas gain aggressiveness through the downregulation of gene sets associated with the immune response (Low→Mid), and subsequently by the upregulation of those associated with cell cycle and cell proliferation (Mid→High). These results were corroborated by GSVA based on the enrichment score of the Hallmark gene sets as well as hierarchical clustering based on copy number losses, with enrichment of the E2F target and MYC target gene sets in high-grade clusters. OncoPrint analyses in the published dataset showed that the most aggressive type of meningiomas is characterized by upregulation of EZH2 as well as E2F1, but not MYC, in combination with NF2 alterations. Meningioma cell growth was suppressed by an EZH2 inhibitor with possible correlation with EZH2 expression. Meningiomas with 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 pivotal therapeutic target for high-grade meningiomas.