Promoter DNA-methylation in the TH-MYCN neuroblastoma mouse model

High-resolution genome-sequencing efforts have discovered a wealth of mutations in genes encoding epigenetic regulators, providing evidence for their predominant role in cancer development. In a previous study, we identified prognostic methylation biomarkers in neuroblastoma using genome-wide promoter methylation analysis. However, therapeutic targeting of the neuroblastoma epigenome remains poorly explored. Therefore, as a prelude to testing of novel epigenetic drugs, we performed MBD-based genome-wide methylation sequencing to establish the methylation pattern in a series of seven tumors from a MYCN-driven neuroblastoma mouse model.Seven hundred nineteen promoters, representing 516 unique genes, are commonly methylated in all seven mouse tumors. This list of methylated genes mainly consists of protein coding genes and pseudogenes, but also contains long noncoding RNAs, microRNAs and small nucleolar RNAs, of which long noncoding RNAs and microRNAs rank amongst the most extensively methylated genes (on the basis of peak height). Interestingly, the protocadherin alpha and beta clusters, which are methylated in virtually every human neuroblastoma tumor, are fully methylated in all seven mouse tumors, supporting the notion that this model can be applied to study DNA methylation in neuroblastoma. Finally, initial cross-species methylation analysis, suggest several cancer-associated genes as interesting hyper-methylated candidate genes for further study. Together, these data show that the TH-MYCN mouse model is valuable in the study of neuroblastoma epigenetics, and provide the rationale for testing of novel epigenetic drugs.High-resolution genome-sequencing efforts have discovered a wealth of mutations in genes encoding epigenetic regulators, providing evidence for their predominant role in cancer development. In a previous study, we identified prognostic methylation biomarkers in neuroblastoma using genome-wide promoter methylation analysis. However, therapeutic targeting of the neuroblastoma epigenome remains poorly explored. Therefore, as a prelude to testing of novel epigenetic drugs, we performed MBD-based genome-wide methylation sequencing to establish the methylation pattern in a series of seven tumors from a MYCN-driven neuroblastoma mouse model.Seven hundred nineteen promoters, representing 516 unique genes, are commonly methylated in all seven mouse tumors. This list of methylated genes mainly consists of protein coding genes and pseudogenes, but also contains long noncoding RNAs, microRNAs and small nucleolar RNAs, of which long noncoding RNAs and microRNAs rank amongst the most extensively methylated genes (on the basis of peak height). Interestingly, the protocadherin alpha and beta clusters, which are methylated in virtually every human neuroblastoma tumor, are fully methylated in all seven mouse tumors, supporting the notion that this model can be applied to study DNA methylation in neuroblastoma. Finally, initial cross-species methylation analysis, suggest several cancer-associated genes as interesting hyper-methylated candidate genes for further study. Together, these data show that the TH-MYCN mouse model is valuable in the study of neuroblastoma epigenetics, and provide the rationale for testing of novel epigenetic drugs.C