Project Summary
Glioma is the most common primary brain tumor and represents a disproportionate percentage of cancer fatalities in relation
to its incidence. In the last decade, it has been discovered that nearly all lower grade gliomas harbor a characteristic gain of
function mutation in Isocitrate dehydrogenase I (IDH1) allowing the enzyme to form a novel oncometabolite. These lower
grade gliomas invariably progress to high-grade, aggressive glioblastoma. At neither the low-grade nor high-grade stage are
directed therapies available and current treatment is limited to surgical resection and adjuvant radiation and alkylating
chemotherapeutic agents. Recent efforts have attempted to employ inhibitors of mutant IDH1 to treat these tumors but early
evidence is mixed, indicating that mutant IDH1 induces long-lasting epigenetic changes that do not dissipate upon inhibition
of the oncometabolite’s production. Studying these tumors has proven difficult compared to IDH wildtype glioma as patient
tumors cannot be readily grown in culture. To address this, our group generated a model of low-grade glioma in human
neural stem cells (NSCs) which are strongly implicated as the cell of origin for these tumors. This model, referred to as 3-
Hit NSCs, reaffirmed previous observations that the IDH1 mutant induces a block to neural precursor differentiation.
Strikingly, it revealed that this block to differentiation in NSCs can be completely rescued by restoration of expression of
the transcription factor (sex determining region Y)-box 2 (SOX2). Moreover, this reduction of expression and the associated
differentiation phenotype occurs secondary to profound changes in 3-dimensional chromatin organization around the SOX2
genomic locus. The proposed work in this fellowship will examine how central these changes in chromatin organization are
to the glioma-phenotype in NSCs and will characterize the SOX2 enhancer environment in NSCs to understand its regulation
in glioma initiation. Preliminary data suggests that disruption of the SOX2 TAD by preventing binding of the genome
organizer CTCF mirrors reduction in SOX2 expression seen in 3-Hit NSCs. Additionally, those regions which lose
interaction with the SOX2 promoter in 3-Hit NSCs correlate with regions found to have marks of being active enhancers in
other SOX2 expressing cell types. We hypothesize that CTCF eviction in 3-Hit NSCs results in a loss of SOX2 expression
through a disruption of promoter interactions with previously uncharacterized enhancers in the SOX2 locus. To evaluate
this hypothesis, I will employ complementary and independent approaches that address the involvement of CTCF mediated
chromatin architecture dysfunction in glioma initiation, identify novel SOX2 enhancers in NSCs, examine the activity of
these enhancers in glioma initiation, and dissect the activity of these enhancers in stem cell differentiation. Finally, I will
validate the relevance of these enhancers in glioma by inferring their activity from single cell ATAC-sequencing of surgical
low-grade glioma specimens. Through these approaches, paired with the support of the Placantonakis and Skok labs, I will
characterize the role of chromatin disorganization in glioma initiation and help understand the developmental and oncogenic
regulation of SOX2.