5-hydroxymethylcytosine deposition mediates Polycomb repressive complex 2 function in MYCN-amplified neuroblastoma

MYCN amplification is a strong predictor of poor prognosis in neuroblastoma, an embryonal malignancy that accounts for 15% of pediatric cancer deaths. Here, we found that MYCN-amplified neuroblastoma tumors had increased 5-hydroxymethylcytosine (5-hmC) deposition on Polycomb repressive complex 2 (PRC2) target genes. 5-hmC and H3K27me3, a catalytic product of PRC2, directly co-localized at the nucleosomal level in MYCN-amplified neuroblastoma. Genes with the co-localization of 5-hmC/H3K27me3 were involved in development-related pathways, transcriptionally repressed in MYCN-amplified neuroblastoma, and more likely to be transcriptionally activated upon PRC2 inhibition. Inhibition of 5-hmC deposition resulted in a loss of H3K27me3 on protein-coding genes, accumulation of 5-methylcytosine to maintain transcriptional repression, and sensitized neuroblastoma to DNA demethylating agents. Low expression of genes marked by 5-hmC/H3K27me3 was associated with poor clinical outcome. Our results suggest that 5-hmC/H3K27me3 co-operate to repress mediators of development, highlighting a link between DNA and chromatin modifications with potential therapeutic implications in MYCN-amplified neuroblastoma.