GSE194052
Genetic and epigenetic mechanisms deregulate the CRL2pVHL complex in hepatocellular carcinoma
Dysregulation of ubiquitin-proteasome pathway genes through copy number alteration, promoter hypomethylation, and miRNA deregulation is involved in cancer development and progression. Further characterizing alterations in these genes may uncover novel drug targets across a range of diseases in which druggable alterations are uncommon, including hepatocellular carcinoma (HCC). We analyzed 377 HCC and 59 adjacent non-malignant liver tissue samples, focusing on alterations to component genes of the widely studied CRL2pVHL complex. Patient outcome was significantly worse when complex components VHL, CUL2, ELOC, or RBX1 were overexpressed in tumours. DNA hypomethylation and copy number increase were correlated with this overexpression, but many tumours had mRNA upregulation that was not explained by either mechanism. To assess the potential role of miRNA downregulation in component gene upregulation, we first acquired a wide-ranging view of the liver miRNA transcriptome by finding all miRNAs that were expressed in fetal liver, HCC, or adjacent non-malignant samples.  Interestingly, we found 66 miRNAs, including 39 previously unannotated miRNAs, that were downregulated in HCC and predicted to target one or more CRL2pVHL components. Several miRNAs, including hsa-miR-101-3p and hsa-miR-139-5p, were negatively correlated with multiple component genes, suggesting that miRNA deregulation may contribute to CRL2pVHL overexpression. Combining miRNA and mRNA expression, DNA copy number, and methylation status into one multidimensional survival analysis, we found a significant association between greater numbers of alterations and poorer overall survival for multiple component genes. While the intricacies of CRL2pVHL complex gene regulation require additional research, it is evident that multiple causes for the deregulation of these genes must be considered in HCC, including non-traditional mechanisms. A better understanding of the CRL2pVHL components and further elucidation of their regulation could expand our understanding of HCC oncogenesis and aid in the development of novel inhibitors. Overall design: Ten fetal liver samples were subjected to miRNA sequencing, in order to quantify their expression of both known and unannotated ('novel') miRNAs.