EZH2 inhibition in glioblastoma stem cells increases the expression of neuronal genes and the neuronal developmental regulators ZIC2, ZNF423 and MAFB

Glioblastoma multiforme (GBM) is an aggressive brain cancer with a very poor prognosis. It has been shown that GBM stem cells within a GBM tumour have increased resistance to standard therapies, so new approaches are needed to increase the range of treatment options available. Here we use two GBM stem cell lines, representing the classical/pro-neural and mesenchymal GBM subtypes, to investigate the effects of three different EZH2 inhibitors on GBM stem cell survival and gene expression: EPZ6438, GSK343 and UNC1999. EZH2 is the catalytic component of the PRC2 chromatin repressor complex, which represses transcription through methylation of histone H3 at lysine 27. Both cell lines showed significantly reduced colony formation after 48-hour exposure to the inhibitors, indicating they were sensitive to all three EZH2 inhibitors. RNA-seq analysis revealed that all three EZH2 inhibitors led to increased expression of genes related to neurogenesis and/or neuronal structure in both GBM stem cell lines. Chromatin immunoprecipitation (ChIP-Seq) was used to identify potential direct targets of the histone methylation activity of EZH2 that might be driving the increase in neuronal gene expression. Three genes were identified as candidate regulatory targets common to both cell lines: MAFB, ZIC2 and ZNF423. These transcription factors all have known roles in regulating neurogenesis, brain development and/or neuronal function. Through analysis of three different EZH2 inhibitors and two GBM stem cell lines, this study demonstrates a common underlying mechanism for how inhibition of EZH2 activity reduces GBM stem cell proliferation and survival.