Identifying and Targeting 3D Regulatory Nodes that Maintain Glioblastoma Programs

NIH RePORTER · NS · R01 · $675,615 · view on reporter.nih.gov ↗

Abstract

PROJECT SUMMARY Glioblastoma (GBM) is a highly aggressive and incurable brain tumor. The inter-patient and intra-tumoral heterogeneity of GBM, resulting from genetic alterations and epigenetic plasticity, poses a major challenge in its treatment. GBM IDH-wt tumors are composed by different proportions of transcriptionally defined cell states, which although resemble neurodevelopmental cell types, are highly plastic and interconvertible -rather than hierarchic- as we and others have shown. This suggests the presence of a core regulatory logic that enables toggling among different transcriptional states, endowing GBM tumors with increased phenotypic plasticity and fitness. Here, we aim to unravel core regulatory modules that are critical for GBM programs with a particular focus on enhancers, which together with transcription factors govern cell-state specific programs. Enhancer dysregulation by genetic variants and epigenetic mechanisms is increasingly appreciated as a key process in oncogenic transformation and drug resistance. However, dissecting and modulating enhancer function remains very challenging due to the large number of putative enhancers and the complex ways they control their target genes in the context of the three-dimensional (3D) genome. By constructing 3D enhancer-promoter interaction networks in four patient-derived glioma stem-like cells (GSCs) and normal neuronal stem cells -as controls- we have identified a subset of GSC-specific hyperconnected enhancers, which we coin "3D regulatory hubs”. 3D hubs harbor genes with robust and coordinated transcriptional levels that enrich for oncogenic pathways and are associated with worse patient outcomes. Importantly, epigenetic perturbation of a highly-recurrent enhancer hub in GSCs resulted in concordant donwregulation of multiple hub-connected genes, leading into significant shifts in the transcriptional states and altered clonogenic and proliferation capacities. Building on this foundational work, we prop

Key facts

NIH application ID
11317181
Project number
5R01NS136475-03
Recipient
WEILL MEDICAL COLL OF CORNELL UNIV
Principal Investigator
Effie Apostolou; Howard A. Fine; EKTA KHURANA
Activity code
R01
Funding institute
NS
Fiscal year
2026
Award amount
$675,615
Award type
5
Project period
2024-05-01T00:00:00 → 2029-04-30T00:00:00