Comprehensive Molecular Characterization of Childhood Liver Cancer: Identification of Prognostic Biomarkers PDF Download

Author: Marina Simon Coma
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Languages : en
Pages : 219

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Book Description
Malignant tumors in children and adolescents are one of the leading causes of death from disease in this population despite being rare events. The main liver tumor in children is Hepatoblastoma (HB) representing two thirds of the total while pediatric Hepatocellular Carcinoma (pHCC) is rarer than HB and is usually diagnosed in older patients. Patient survival at 5 years is higher than 75% for HB and less than 30% for pHCC. At molecular level, 2 different subclasses of HBs have been described based on a 16-gene signature, C1 and C2, being the latest more aggressive. Nowadays patient stratification is based only in clinical and pathological parameters. For this reason, the identification of prognostic markers easy to apply at the clinical practice is mandatory in order to better stratify patients and diminish the side effects of chemotherapy treatment, moving towards a more personalized medicine. The proteomic profile of 16HBs and 8 paired normal liver (NL) tissue was obtained by 2 different techniques, two-dimensional gel electrophoresis and label-free LC-MS. The differential expressed proteins were validated by western blot (WB) in the same patients and the final protein signature was validated by immunohistochemistry in additional 144 patients. Furthermore, RNA sequencing and copy number variation analysis were performed in 31 HB samples, 11 patient-derived xenografts (PDXs) and 5 pHCC. Results were validated by Sanger sequencing, droplet digital PCR or real time PCR and correlated with clinical features. Two hundred and thirty proteins were identified as deregulated in aggressive C2 tumors and 8 of them were selected and validated by WB considering also their expression in NL. After WB, 2 proteins were found significantly upregulated in C2 tumors while 1 was downregulated. A score was calculated for each protein and biomarkers 1 and 2 were considered altered when their staining was at least 2-fold higher than the NL while the biomarker 3 was considered as altered when no staining was observed. The 3-protein signature was defined by the number of altered biomarkers in each tumor and was highly correlated with patient survival and complementary to the current clinical stratification. RNA-sequencing data revealed that fusion proteins are rare events in HB as they were found in only 2% of patients. Mutational analysis allowed us to identify mutations in CTNNB1 (30%), NFE2L2 (7%) and EPHB4 (7%). Interestingly we identified a downregulation of the RNA editing which is correlated with patient outcome. The copy number variation analysis showed that gains are more frequent than losses in HB tumors and that PDXs maintain 78% of the aberrations, being a good model for the study of HB. In contrast, pHCC are characterized by more aberrations than HB and mainly losses. Thus, we stablished a molecular classification that includes 3 HB types: stable (no big CNVs), gains-enriched and losses-enriched classes. This classification is correlated with event-free survival, CTNNB1 mutations and the expression of stem cell markers. As a result of this thesis, we stablished a 3-protein signature that could be easily applied at the clinical practice and increased the molecular knowledge of childhood liver tumors.