Hepatoblastoma as a model to study the interplay between gene expression, miRNA expression and DNA methylation in development-related tumors. Free

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Hepatoblastoma (HB) is a pediatric liver tumor that displays different degrees of tumor cell differentiation evoking fetal liver stages. This tumor could therefore originate from immature liver precursor cells. Our recent data on gene expression profiles of 30 HB cases further enforced the notion that tumor components recapitulate various steps of the liver maturation process. To get a comprehensive view of the development-related nature of HB and of the mechanisms underlying HB pathogenesis, we combined gene expression profiling with analysis of genetic alterations by array CGH and epigenetic events such as DNA methylation and miRNA expression. Moreover, the combination of these molecular approaches could provide a more refined tumor classification with respect to clinical data. To this aim, 400 miRNA and 12,000 human promoter probeset-containing microarrays were assayed with tumor samples previously characterized by Affymetrix and CGH arrays, and the results were crossed with the gene expression data and clinical annotations. We found a strong correlation between deregulated expression of several development-related miRNAs and tumor differentiation stage. By contrast, DNA methylation seemed to be commonly altered in all tumors, correlating with tumor growth and invasiveness. Particularly, we identified altered methylation of genes involved in liver-specific pathways, and in pathways related to cell migration and tumor growth, like cell adhesion, cytoskeletal remodeling, and growth factor response. We also observed differential methylation of genes involved in different tumor-related processes, including DNA repair, cell-cycle check-points, proliferation and apoptosis. Comparison of the different approaches revealed that gene expression profiles and miRNA expression yielded similar patterns of tumor classification, based on cell differentiation stage and prognosis. By contrast, methylation profiling provided rather a tumor cell signature, with selective association with tumor growth and size. Altogether, these data point to crucial and complementary roles of miRNA expression and DNA methylation in HB genesis, progression and outcome. Integrated analysis of miRNA expression, DNA methylation and transcriptome could contribute to unveil the molecular basis of HB pathogenesis.