DNA methylation landscape of hepatoblastomas reveals arrest at early stages of liver differentiation and cancer-related alterations

Hepatoblastomas carry few genetic alterations, and we hypothesize that epigenetic changes could be relevant to their onset. DNA methylation profile of hepatoblastomas was explored in relation to liver development using the HM450K platform. Seven paired samples of hepatoblastomas and adjacent non-tumoral livers were studied, with biologicaland results validation validated in an independent group (12 hepatoblastomas) that confirmed 1,359 differentiated methylated CpG sites (DMSs) in hepatoblastomas compared to controls, associated with 979 genes. Hepatoblastomas also exhibited a global low-level hypomethylation when compared with differentiated livers, especially at non-repetitive intergenic DNA (~55% of the hypomethylated CpGs); conversely, most of the hypermethylated CpGs were located in CpG islands. Functional analyses revealed an enrichment in signaling pathways involved in metabolism, negative regulation of cell differentiation, liver development, cancer, and the WNT pathway. Strikingly, an important overlap was observed between hepatoblastomas DMSs and the CpG sites reported to exhibit methylation changes through liver development. Genes with differential methylation were related to maintenance of undifferentiated cell state, cell transformation and tumor progression, and the methylation profile of tumors resembled that of fetal livers. Altogether, our results suggest an arrest at early stages of liver cell differentiation, in line with the hypothesis that hepatoblastoma ontogeny involves the disruption of liver development. Bisulphite converted DNA from the 29 samples (19 hepatoblasmas and 10 livers) were hybridised to the Illumina Infinium 450k Human Methylation Beadchips.