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Hepatocellular adenomas (HAs) are tumors that can develop under different conditions, including in patients harboring a germline mutation in <i>HNF1A</i>. However, little is known about the pathogenesis of such disease. This work aims to better define what mechanisms lie under the development of this condition. Six HAs were sampled from the liver of a 17-year-old male affected by diabetes and multiple hepatic adenomatosis harboring the heterozygous pathogenic germline variant c.815G>A, p.(Arg272His) in <i>HNF1A,</i> which has a dominant negative effect. All HAs were molecularly characterized. Four of them were shown to harbor a second somatic <i>HNF1A</i> variant and one had a mutation in the <i>ARID1A</i> gene, while no additional somatic changes were found in the remaining HA and normal parenchyma. A transcriptomic profile of the same HA samples was also performed. <i>HNF1A</i> biallelic mutations were associated with the up-regulation of several pathways including the tricarboxylic acid cycle, the metabolism of fatty acids, and mTOR signaling while angiogenesis, endothelial and vascular proliferation, cell migration/adhesion, and immune response were down-regulated. Contrariwise, in the tumor harboring the <i>ARID1A</i> variant, angiogenesis was up-modulated while fatty acid metabolism was down-modulated. Histological analyses confirmed the molecular data. Independently of the second mutation, energetic processes and cholesterol metabolism were up-modulated, while the immune response was down-modulated. This work provides a complete molecular signature of <i>HNF1A</i>-associated HAs, analyzing the association between specific <i>HNF1A</i> variants and the development of HA while identifying potential new therapeutic targets for non-surgical treatment.