Abstract A047: A conserved enhancer locus in ecDNA and HSRs activates MYC transcription in Group 3 Medulloblastoma

Abstract Extrachromosomal DNA (ecDNA) is an emergent prognostic marker for poor disease outcome in a variety of cancer types, including pediatric medulloblastoma, where MYC is commonly amplified on ecDNA in Group 3 tumors (G3-MB). Tumors with ecDNA have higher recurrence and relapse rates with current therapies, highlighting a need for more targeted therapeutic intervention; however, the underlying mechanisms controlling MYC expression from ecDNA are still poorly understood. A structure-function investigation identified and characterized a conserved enhancer that drives MYC activation specifically in G3-MB with MYC amplified on ecDNA or homogenous staining regions (HSRs). This enhancer, termed ecMYC E1, exhibits enhancer hallmarks of open chromatin and H3K27ac enrichment exclusively in MYC-amplified G3-MB but not in other MYC-dependent cancer cell lines, including those with and without MYC amplification on ecDNA or HSRs. This provides a tumor-specific regulatory mechanism for oncogenic gene transcription. Silencing of the ecMYC E1 enhancer locus significantly reduced MYC transcription acutely, but this reduction in oncogene expression was compensated for by an increase in ecDNA copy number during prolonged enhancer silencing. This compensation was not observed in HSR-driven G3-MB. The increase in ecDNA copy number resulted in tumor cells reverting back to baseline levels of MYC transcription; therefore, ecDNA copy number could be used as a biomarker for therapy evasion or adaptation. Mechanistically, we showed that the transcription factor NeuroD1 and epigenetic regulator BRD4 interact with each other and bind to ecMYC E1 in G3-MB. This study defines a novel mechanism for ecDNA or HSR regulation of amplified MYC gene expression exclusively in G3-MB. Citation Format: Jake D. Friske, Flore Cuisin, Paloma Guernalec, Hayden A. Malone, Stephanie Nance, Declan Bennett, Steven Burden, Ti-Cheng Chang, Hao Shi, Justin S. Williams, Virginia Valentine, Barbara Passaia, Bensheng Ju, Modupeore Adetunji, Paul Geeleher, Brian J. Abraham, Gang Wu, Chunliang Li, Martine F. Roussel. A conserved enhancer locus in ecDNA and HSRs activates MYC transcription in Group 3 Medulloblastoma abstract. In: Proceedings of the AACR Special Conference in Cancer Research: Brain Cancer; 2026 Mar 23-25; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2026;86 (6Suppl): Abstract nr A047.