Identifying New Tumor Suppressor in Liver Cancer Using Unbiased High‐Throughput Approaches

Abstract

PurposeTumor suppressor genes are often epigenetically silenced. This study identified a new tumor suppressor in hepatocellular cancer (HCC) using an unbiased high throughput approach.Methods/ResultsStudies from our laboratory has established nuclear receptor small heterodimer partner SHP as a tumor suppressor. We also established an inhibitory feedback regulatory loop between SHP and DNA methyltransferases (Dnmts). Methylated DNA‐IP‐on‐ChIP (MeDIP) revealed alterations in DNA methylation and RNA‐sequencing (RNA‐seq) revealed changes in gene expression. By integrating both studies using Bioinformatics tools and appropriate validation, we identified the mitochondrial protein pyruvate dehydrogenase kinase 4 (PDK4) as a putative tumor suppressor. PDK4 promoter was hypermethyalted and its expression downregualted in SHP‐/‐ mice. PDK4 was also silenced in human HCC. Treatment of HCC cell lines with the demethylating agent 5'‐aza ‐2'‐deoxycytidine (Aza) or histone deacetylase inhibitor trichostatin (TSA) induced PDK4 expression. The number of foci was decreased and the tumor sizes were reduced in HCC cells that stably overexpressing PDK4, whereas the opposite was found with PDK4 knockdown. PDK4 overexpression sensitized HCC cells to cell death induced by glucose deprivation by reducing the intracellular ATP contents.ConclusionsEpigenetic silencing of PDK4 is associated with the development of HCC.[Grant support] NIH DK080440, VA Merit Award 1I01BX002634.