Genome-wide analysis of DNA methylation in neuroblastoma cell lines identifies MEGF10 as a novel epigenetically repressed tumour suppressor gene.
ABSTRACT: Background: Neuroblastoma is a childhood cancer in which many children still have poor outcomes, emphasising the need to better understand its pathogenesis. Despite recent genome-wide mutation analyses, most neuroblastomas do not contain recognisable driver mutations, suggesting that epigenetic changes could underlie many cases. Methods: To discover genes that become epigenetically deregulated during neuroblastoma tumorigenesis, we compared neuroblastomas to their neural crest precursor cells, using genome-wide DNA methylation analysis; probing CpG island promoter microarrays with methyl CpG-immunoprecipitated DNA. Results: We identified 93 genes that were significantly differently methylated between neuroblastoma cell lines and neural crest cells, of which 26 (28%) were hypermethylated and 67 (72%) were hypomethylated. Concentrating on hypermethylated genes to identify candidate tumour suppressor loci, we found the cell engulfment and adhesion factor gene MEGF10 to be epigenetically repressed by DNA hypermethylation or by H3K27/K9 methylation in neuroblastoma cell lines. MEGF10 showed significantly down-regulated expression in neuroblastoma tumour samples; furthermore patients with the lowest-expressing tumours had reduced relapse-free survival. Knock-down of MEGF10 expression in neuroblastoma cell lines promoted cell growth. Conclusion: Our results suggest that MEGF10 is a clinically relevant, epigenetically-deregulated neuroblastoma tumour suppressor. Overall design: Comparison of DNA methylation in human neural crest cells with four human neuroblastoma cell lines.
INSTRUMENT(S): NimbleGen Human DNA Methylation 385K Promoter Plus CpG Island Array [2006-11-02_HG18_CpG_Promo]