ID #762 Therapy-Induced DNA G-Quadruplex Remodeling Promotes Treatment Resistance in Pediatric Medulloblastoma

Abstract

Medulloblastoma (MB), the most common malignant pediatric brain tumor, remains a leading cause of cancer-related mortality in children. Despite aggressive multimodal therapy, survivors frequently experience severe, lifelong neurocognitive, endocrine, and auditory toxicities, and tumor recurrence remains a leading cause of mortality. Relapses are driven by a subset of therapy-tolerant residual tumor cells that survive genotoxic treatment and later re-emerge. However, how MB cells epigenetically adapt to therapeutic stress to survive and recur remains poorly understood.

Here, we identify a novel and unexplored mechanism of therapy resistance in MB centered on therapy-induced formation of non-canonical four-stranded DNA secondary structures known as G-quadruplexes (G4s). Our findings reveal an unrecognized role for G4 structures as dynamic scaffolds that coordinate recruitment of repair protein APE1, thereby facilitating accelerated DNA repair during therapeutic stress. We demonstrate that (i) radiation markedly induces G4 formation in MB cells, and cells subjected to repeated radiation exposure exhibited further accumulation of G4 structures compared with radiation-naïve cells, indicating adaptive remodeling of DNA secondary structure. (ii) MB patient tumors exhibit elevated G4 DNA levels, (iii) APE1 binds G4 structures with high affinity and is constitutively enriched in transcribed gene regions, and (iv) deletion of promoter G4 motif by CRISPR-Cas9 genome editing significantly impairs APE1 recruitment and local DNA repair, providing a mechanistic connection of G4 in DNA repair. Importantly, small-molecule G4 ligands (CX-5461 and TMPyP4) disrupt APE1-G4 interactions, impair DNA damage repair, and sensitize MB cells to radiation in a therapy-adapted MB model.

Collectively, our studies uncovered a novel epigenetic mechanism of therapy resistance in MB and established G4 structures as actionable therapeutic targets. By disrupting a DNA repair scaffolding mechanism rather than core repair enzymes, this strategy offers a rational path to enhance therapeutic efficacy without increasing genotoxic burden.