Epigenetic Induction of Gliomagenesis in Neural Progenitor Cells

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Project Summary Gliomas are incurable brain tumors that can be classified into distinct molecular subtypes. One glioma subtype is characterized by isocitrate dehydrogenase 1 (IDH1) gain-of-function mutations and a CpG hypermethylator profile (G-CIMP) directly caused by mutant IDH1 function. CpG methylation in a gene or promoter suppresses gene expression, hence mutant IDH1 was thought to exert its oncogenic role by silencing tumor suppressor genes. The Bernstein laboratory introduced new data that added CCCTC-binding factor (CTCF) binding sites (insulators) to the list of methylated sites in IDH mutant glioma. CTCF partitions the genome into topologically associated domains (TADs): insulated neighborhoods that allow gene-enhancer interactions inside the same TAD while restricting outside interactions. Insulator methylation disrupts TADs and allows aberrant gene- enhancer interactions to take place, driving gene expression. A recurrent insulator loss was identified in the PDGFRA oncogene locus in IDH mutant glioma, allowing for a distal enhancer to upregulate PDGFRA, driving proliferation in established glioma. It is not known whether this epigenetic mechanism can transform neural progenitor cells (NPCs): the likely glioma cell of origin. Hypothesis: Disruption of the PDGFRA insulator in NPCs is sufficient to drive hyper-proliferation and gliomagenesis. Aim 1: Determine the mechanistic effects of insulator dysfunction on PDGFRA expression in NPCs. Aim 2: Assess the consequence of insulator dysfunction on NPCs in vivo. The proposed studies will explore novel mechanisms by which glioma develops from NPCs and would be the first demonstration of an epigenetic mechanism of tumor initiation. Further, the proposed studies can suggest that treatment with hypomethylating agents (5-azacytidine) may be beneficial for mutant IDH1 glioma. Additionally, the proposed studies will establish a faithful mouse model of glioma allowing for preclinical testing of therapeutics in vivo. Mutations in IDH1, similar to those observed in glioma, can be observed in other tumors suggesting that the findings from the study can be applicable to other tumor types. Training plan and environment: The proposed research will take place in the Bernstein lab at Massachusetts General Hospital (MGH) that has spearheaded major advances in epigenomics research. All the necessary equipment is available either in the Bernstein lab or at research cores located in MGH. With affiliations at Harvard Medical School, the Broad Institute, and MGH, I will have ample opportunities to attend seminars and workshops that will help me shape my career as I progress towards an independent research position. As part of my training plan, I will also mentor students in the lab, present my research both locally and nationally, and apply to transition awards allowing me to pursue an independent career in cancer research.