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

Abstract

Hepatoblastomas are uncommon embryonal liver tumors accounting for approximately 80% of childhood hepatic cancer. We hypothesized that epigenetic changes, including DNA methylation, could be relevant to hepatoblastoma onset. The methylomes of eight matched hepatoblastomas and non-tumoral liver tissues were characterized, and data were validated in an independent group (11 hepatoblastomas). In comparison to differentiated livers, hepatoblastomas exhibited a widespread and non-stochastic pattern of global low-level hypomethylation. The analysis revealed 1,359 differentially methylated CpG sites (DMSs) between hepatoblastomas and control livers, which are associated with 765 genes. Hypomethylation was detected in hepatoblastomas for ~58% of the DMSs with enrichment at intergenic sites, and most of the hypermethylated CpGs were located in CpG islands. Functional analyses revealed enrichment in signaling pathways involved in metabolism, negative regulation of cell differentiation, liver development, cancer, and Wnt signaling pathway. Strikingly, an important overlap was observed between the 1,359 DMSs and the CpG sites reported to exhibit methylation changes through liver development (p<0.0001), with similar patterns of methylation in both hepatoblastomas and fetal livers compared to adult livers. Overall, 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. This genome-wide methylation dysfunction, taken together with a relatively small number of driver genetic mutations reported for both adult and pediatric liver cancers, shed light on the relevance of epigenetic mechanisms for hepatic tumorigenesis.

Mutational burden of hepatoblastomas: a role for the CX3CL1/CX3CR1 chemokine signaling pathway

“…Remarkably, one of the CEP164-mutated HBs exhibited a complex genome, with several copy number alterations and two large LOH regions. Three genes, which we have previously reported as differentially methylated in HBs [38], were mutated in the present cohort, reinforcing a possible role in HB tumorigenesis: EGFR, LMBRD1, and AHRR. LMBRD1 encodes a lysosomal membrane protein and is associated with a vitamin B12 metabolism disorder [42], and AHRR and EGFR are involved in regulation of cell growth and differentiation.…”

“…Additionally, an integrative analysis based on previous DNA methylation (DNAm) data from the same group of HB samples [38] showed a partial overlap between the set of genes presenting somatic mutations and the set with DNAm changes: EGFR and LMBRD1, hypermethylated, and AHRR, hypomethylated, respectively.…”

“…DNA methylation (DNAm) data at gene bodies and promoters of CX3CL1 and CX3CR1 were recovered for HB samples [38] to correlate with the expression level of these genes (Supplementary Figure 2). A significant DNAm decrease was observed in CX3CL1 promoter in tumors compared to control liver samples (p-adj 0.006), and an inverse correlation between gene expression and DNAm level in the CX3CL1 gene body (Spearman's rho 0.46, P-value 0.02), although the latter presented great inter-tumor heterogeneity.…”

Integrated multiomics analysis of hepatoblastoma unravels its heterogeneity and provides novel druggable targets

“…The genetic hallmark of hepatoblastoma is aberrant activation of Wnt signaling pathway [4][5][6] , and several studies that addressed the genomic profile of hepatoblastoma revealed the high prevalence of Wnt-activating mutations shared by most hepatoblastoma cases [7][8][9][10] . However, genetic determinants of the clinical heterogeneity of this cancer are still unclear.…”

Insights into the Chemical Biology of Childhood Embryonal Solid Tumors by NMR-Based Metabolomics

“…Due to the rarity, genetic predisposing factors for HB are still unrevealed. Additionally, HB presents a relatively stable genome with just few genetic alterations reported recently [55,56]. Clinical trials examining multimodal therapy, which consists of neoadjuvant chemotherapy followed by complete surgical resection and subsequent cycles of chemotherapy, have led to improved outcome for children with HB [57].…”