MYCN Amplification Promotes Enhancer Invasion in Neuroblastoma Free

High-risk neuroblastoma is characterized by frequent amplification of MYCN, which encodes a master transcription factor that drives tumorigenesis. MYCN amplification is associated with aggressive disease, and MYCN overexpression is sufficient to induce tumorigenesis in mouse models. However, the genome-wide transcriptional functions of MYCN have not been well characterized, prompting Zeid and colleagues to perform kinetic studies of MYCN activation and withdrawal in neuroblastoma. In neuroblastoma cells, MYCN bound with high affinity to canonical E-box binding motifs (CACGTG) at promoters, and deregulated MYCN expression also promoted binding to noncanonical (CANNTG) E-boxes clustered in enhancers, indicating that MYCN deregulation promotes enhancer “invasion.” When MYCN was not present in excess, it bound primarily to canonical promoter E-boxes. The excess MYCN present in neuroblastoma then spread into weaker E-box enhancer sites. MYCN depletion resulted in a global reduction in transcription, with the strongest effect on MYCN target genes with high enhancer occupancy. Tissue-specific expression was observed for the target genes highly occupied by MYCN, and their expression was linked to poor survival in patients with neuroblastoma. MYCN exhibited strong dose-dependent effects on transcription, suggesting that the affinity of underlying promoter and enhancer regions shapes MYCN-dependent transcriptional amplification in neuroblastoma. MYCN shutdown depleted the MYCN distal enhancer gene signature, and induction of MYCN established the promoter gene signatures before the enhancer gene signatures, providing further evidence for MYCN amplification inducing an enhancer invasion to drive neuroblastoma. TWIST1 co-localized with MYCN at enhancers and was required for expression of the MYCN enhancer target genes. Collectively, these findings indicate that MYCN amplification in neuroblastoma can promote a dose-dependent increase in expression of genes with weak MYCN binding sites in their enhancers to promote tumor-specific expression of MYC target genes and suggest that disruption of the MYCN enhancer regulatory axis may represent a therapeutic approach in neuroblastoma.

Zeid R, Lawlor MA, Poon E, Reyes JM, Fulciniti M, Lopez MA, et al. Enhancer invasion shapes MYCN-dependent transcriptional amplification in neuroblastoma. Nat Genet 2018 Jan 29 [Epub ahead of print].

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