Abstract 1266: Mutant IDH1 alters epigenetic regulation to promote stemness in low grade glioma: Deciphering signaling pathways altered by mIDH1 inhibition
Authors: Stephen Carney, Brandon Zhu, Padma Kadiyala, Maria Garcia-Fabiani, Preethi Gorla, Felipe Nunez, Pedro R. Lowenstein, Maria G. Castro
Journal: Cancer Research (2020)

Abstract Greater than 75% of Low Grade Gliomas (LGG) harbor a mutation in isocitrate dehydrogenase 1 (IDH1) and this molecular subgroup also exhibits mutations in TP53 and ATRX. Mutant IDH1 often recurs and presents with a more aggressive phenotype that is refractory to existing therapies. The production of an oncometabolite, 2-hydroxyglutarate by mutant IDH1 (mIDH1) has been shown to induce histone and DNA hypermethylation. Pharmacological inhibition of mIDH1 (AGI-5198) can restore expression of genes involved in neural differentiation. We hypothesize that mIDH1 remodels chromatin to promote a stem cell-like transcriptional state. Recent single cell RNA-seq data from primary mIDH1 astrocytoma and oligodendroglioma has identified an undifferentiated pool of tumor cells with a neural stem/progenitor transcriptional profile. We aim to identify unique regulatory networks in SF10602, a human primary glioma culture derived from a surgical biopsy, which endogenously expresses mIDH1.We treated SF10602 with AGI-5198 every 2 days for 1 week. We observed a global reduction in histone marks: H3K4me3, H3K36me3, and H3K27me3. This reversibility of histone hypermethylation has previously been described in mIDH1 tumor lines treated with mIDH1 inhibitors that block 2HG production. We confirmed that mIDH1 inhibition reduced 2HG levels by collecting condition media and performing liquid chromatography mass spectrometry. We performed a temporal micrococcal nuclease (Mnase) digestion to assess chromatin accessibility and we observed enhanced chromatin condensation following mIDH1 inhibition. To evaluate if the reversion of chromatin organization resulting from mIDH1 inhibition impacts neural differentiation pathways we performed RNA-seq. We identified 496 differentially up-regulated and 893 down-regulated genes (log2&amp;gt;+/-0.6) comparing SF10602 with/out AGI-5198. Following gene set enrichment analysis, we observed upregulation of pathways involved in epigenetic regulation, DNA conformation and neuronal development. Additionally, we observed downregulation of pathways involved in cell polarity and transcription factor activity. In future work, we will perform ChIP-seq to define enhancers and promoters that regulate stem cell-like characteristics. These findings will reveal novel genomic loci unique to mIDH1 glioma. SC is supported by the T32 Cancer Biology Training Grant, the work is supported by grants from NIH/NINDS to MGC and PRL. Citation Format: Stephen Carney, Brandon Zhu, Padma Kadiyala, Maria Garcia-Fabiani, Preethi Gorla, Felipe Nunez, Pedro R. Lowenstein, Maria G. Castro. Mutant IDH1 alters epigenetic regulation to promote stemness in low grade glioma: Deciphering signaling pathways altered by mIDH1 inhibition [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 1266.