A Conserved Enhancer Locus in Extrachromosomal DNA and Homogeneously Staining Regions Activates MYC Transcription in...

MYC is amplified on extrachromosomal DNA (ecDNA) or homogeneously staining regions (HSR) in group 3 medulloblastoma (G3-MB), conferring a poor prognosis. A better understanding of the mechanisms underlying MYC expression in ecDNA and HSRs could be leveraged to develop improved treatments for G3-MB. Using a structure-function approach, we identified and characterized an enhancer (ecMYC E1) that drives MYC activation specifically in G3-MB with MYC-amplified ecDNA or HSRs. The ecMYC E1 locus exhibited enhancer hallmarks exclusively in MYC-amplified G3-MB but not in other MYC-dependent cancer cell lines, including those with MYC amplification. Silencing of the ecMYC E1 enhancer significantly reduced MYC transcription, which was compensated for by increases in ecDNA copy number. Neuronal differentiation 1 and bromodomain-containing protein 4 interacted with each other and bound to ecMYC E1, looping the enhancer to the MYC promoter. Together, these findings define a mechanism that regulates amplified MYC gene expression within ecDNA or HSRs specifically in G3-MB.

Combined structural and functional approaches identified a conserved enhancer activating MYC transcription exclusively in MYC-amplified ecDNA- and HSR-positive group 3 medulloblastoma, providing a potential therapeutic target for suppressing MYC.