Purpose: Glioblastoma (GBM) is a highly aggressive primary brain tumor. A major challenge in GBM treatment is tumor resistance to radiation and chemotherapy. An important hallmark of GBM is the frequent mutation of epigenetic modifiers resulting in alteration of epigenetic signaling pathways. However, the effect of epigenetic signaling on chemotherapy response in GBM remains to be elucidated. SETD2 is a unique histone methyl transferase that facilitates H3K36 tri-methylation. Here, we unveil the role of SETD2 mutations that frequently occur in GBM in tumor resistance to temozolomide chemotherapy.

Method: We have generated CRISPR/Cas9-mediated SETD2-KO GBM cell lines to study the role of SETD2 in temozolomide response. DNA methylome and whole exome sequencing data from the TCGA databank were analyzed to determine the MGMT (methyl-guanine methyl transferase) promotor methylation status and SETD2 mutations, respectively. H3K36me3 and MSH6 levels were determined in GBM patient samples by immunohistochemical staining. SETD2 mutation status was determined in GBM patient samples by targeted sequencing of the SETD2 gene using the Agilent SureSelect Target technique.

Results: Our TCGA database analysis reveals that SETD2 mutations are associated with reduced overall survival in patients with methylated MGMT promotor who received temozolomide suggesting that mutation of SETD2 is a predictive marker for chemotherapy resistance in GBM. Consequently, we demonstrate that loss of SETD2 results in reduced H3K36me3 levels and a profound resistance to temozolomide in GBM cells. MGMT-deficient tumors can acquire chemoresistance due to disrupted mismatch repair (MMR), a DNA repair pathway that plays a critical role in converting primary temozolomide-induced DNA lesions into toxic DNA double-strand breaks. Strikingly, we found that SETD2 loss abrogates the expression of the MMR factor MSH6 indicating that chemoresistance in SETD2-deficient cells is due to disrupted MMR. Accordingly, low H3K36me3 levels in GBM tumor samples correlate with loss of MSH6 expression. Mechanistically, we show that SETD2 regulates MMR by promoting transcription of the MSH6 gene in GBM. Finally, we establish a strategy to re-sensitize SETD2-deficient GBM cells to temozolomide. Epigenetic modifiers have specific antagonists capable of reversing chromatin alterations induced by these modifiers. This provides a unique opportunity to restore chemotherapy response in SETD2-mutant GBM by targeting the antagonists of SETD2. We demonstrate that combined targeting of H3K36me3-specific histone de-methylases KDM4A and NO66 restores H3K36me3 levels along with MSH6 expression and sensitivity to temozolomide in SETD2-deficient GBM cells.

Conclusions: Our findings establish SETD2 mutation as a novel molecular marker predictive of chemotherapy response in GBM and provide a framework for a novel approach to overcome chemotherapy resistance in this malignant brain tumor by targeting a specific epigenetic signaling pathway.

Fig.1: Immunohistochemical staining of H3K36me3 and MSH6 in GBM tumor sections demonstrating that tumor areas with low H3K36me3 expression lack MSH6 expression.

Citation Format: Nishanth Gabriel, Sonika Dahiya, Xiaowei Wang, Michael Goldstein. SetD2 histone methyltransferase mutation status predicts treatment response in glioblastoma: Strategies to overcome chemoresistance [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 1249.