Snapshot liver transcriptome in hepatocellular carcinoma
Authors: Andreas Teufel, Jens U. Marquardt, Frank Staib, Peter R. Galle
Journal: Journal of Hepatology (2011)

Hepatocellular carcinoma ranks among the most common cancers worldwide. However, besides surgery, therapeutic strategies remain limited and a detailed analysis and characterization of the tumor biology will be essential in order to identify (novel) therapeutic targets [[1]Teufel A. Staib F. Kanzler S. Weinmann A. Schulze-Bergkamen H. Galle P.R. Genetics of hepatocellular carcinoma.World J Gastroenterol. 2007; 13: 2271-2282Crossref PubMed Scopus (113) Google Scholar]. With the development of sorafenib, a first step of successful targeting molecular changes in HCC has been made but many more will have to follow in order to establish a potent arsenal of specific therapeutic options [[2]Worns M.A. Galle P.R. Novel inhibitors in development for hepatocellular carcinoma.Expert Opin Investig Drugs. 2010; 19: 615-629Crossref PubMed Scopus (29) Google Scholar]. Lately, advances in high throughput technologies in biomedical research have led to a dramatic increase in the accessibility of molecular insights at different levels of cancer biology such as genome, epigenome, transcriptome, proteome, and others. Among the diverse biological layers, the transcriptome has been most extensively studied especially due to the successful and broad introduction of the microarray technology. The future prospect of broad disposability of deep sequencing technology will furthermore lead to a more sensitive detection of lowly expressed transcripts and to an increase in the number of newly identified transcripts, but also to increase the discovery and characterization of alternative splicing. A common goal of large scale transcriptome profiling methods is the stratification of patients, eventually leading to personalized prognostic predictions and therapeutic strategies. Also, the observation that diverse etiologies of the mostly underlying liver cirrhosis (alcohol, HBV, HCV a.o.) are represented by different transcriptome profiles may be valuable for the identification of essential tumor targets [[3]Woo H.G. Park E.S. Thorgeirsson S.S. Kim Y.J. Exploring genomic profiles of hepatocellular carcinoma.Mol Carcinog. 2011; 50: 235-243Crossref PubMed Scopus (57) Google Scholar]. In particular, the field of biomarker discovery and development make considerable use of microarray technologies for clinical research [[4]Maass T. Sfakianakis I. Staib F. Krupp M. Galle P.R. Teufel A. Microarray-based gene expression analysis of hepatocellular carcinoma.Curr Genomics. 2010; 11: 261-268Crossref PubMed Scopus (31) Google Scholar]. In breast cancer, this vision was enthusiastically pursued over the past several years resulting in an FDA-approved molecular signature, which may serve as an example [[5]Glas A.M. Floore A. Delahaye L.J. Witteveen A.T. Pover R.C. Bakx N. et al.Converting a breast cancer microarray signature into a high-throughput diagnostic test.BMC Genomics. 2006; 7: 278Crossref PubMed Scopus (405) Google Scholar]. It has repeatedly been reported that transcriptomic changes not necessarily reflect changes in the corresponding proteins. In model organisms, approximately 25% of changes in gene expression are not accompanied by simultaneous changes in protein abundance, particularly of lowly expressed genes [[6]Gygi S.P. Rochon Y. Franza B.R. Aebersold R. Correlation between protein and mRNA abundance in yeast.Mol Cell Biol. 1999; 19: 1720-1730Crossref PubMed Scopus (3193) Google Scholar]. It has also been observed that the transcriptome of hepatocellular carcinoma often includes surgical material, which has not been subjected to laser capture microdissection. The current data on the transcriptome of hepatocellular carcinoma are, therefore, diluted by cells present in the tumor microenvironment. However, a recent publication by Villanueva et al. demonstrated the usefulness of integrating transcriptomic signatures with clinic-pathological data in HCC and in particular demonstrated partial reproducibility in independent data sets [[7]Villanueva A. Hoshida Y. Battiston C. Tovar V. Sia D. Alsinet C. et al.Combining clinical, pathology, and gene expression data to predict recurrence of hepatocellular carcinoma.Gastroenterology. 2011; 140 (e1502): 1501-1512Abstract Full Text Full Text PDF PubMed Scopus (335) Google Scholar]. Multiple biological mechanisms were shown to change gene activity in HCC. Among them are changes in chromosomal structure, genetic polymorphisms, alternative splicing, epigenetic changes (methylation, histone modification, miRNAs), and proteomic changes. Therefore, we present a short graphical snapshot of the liver transcriptome in HCC (Fig. 1). Changes in chromosomal structure have been extensively described. Obviously, lack or duplication of genetic regions and thus of genes physiologically involved in liver homeostasis may result in disturbed gene expression, which potentially favors hepatocarcinogenesis. Several studies reported correlations of single chromosomal gains or losses with clinicopathological features such as tumor differentiation or prognosis (reviewed in [[8]Herath N.I. Leggett B.A. MacDonald G.A. Review of genetic and epigenetic alterations in hepatocarcinogenesis.J Gastroenterol Hepatol. 2006; 21: 15-21Crossref PubMed Scopus (147) Google Scholar]). Furthermore, high density allelotyping using a large number of microsatellite markers combined with gene mutation analysis led to identification of diverse genetic pathways involved in HCC [[9]Wong C.M. Ng I.O. Molecular pathogenesis of hepatocellular carcinoma.Liver Int. 2008; 28: 160-174Crossref PubMed Scopus (143) Google Scholar] (Table 3). DNA methylation in the promoter region of a gene may be linked to altered gene expression. Hypermethylation of tumor-suppressor genes as well as genes involved in cell cycle regulation, apoptosis, DNA repair or cell adhesion, and DNA methylation plays a crucial role in the development of a variety of cancers. Accordingly, hypomethylation and consecutive activation of oncogenes was also recognized to potentially result in cancer development. Over the past several years, multiple genes exhibiting changes in promoter methylation in HCC were identified (Table 4, [[10]Tischoff I. Tannapfe A. DNA methylation in hepatocellular carcinoma.World J Gastroenterol. 2008; 14: 1741-1748Crossref PubMed Scopus (155) Google Scholar]). In hepatocarcinogenesis, changes in DNA methylation must be considered to occur frequently and early. Furthermore, changes in the methylation status may accompany the progression from precancerous lesion to HCC. Finally, some of these changes were even demonstrated in premalignant conditions, such as liver cirrhosis [[10]Tischoff I. Tannapfe A. DNA methylation in hepatocellular carcinoma.World J Gastroenterol. 2008; 14: 1741-1748Crossref PubMed Scopus (155) Google Scholar]. Histone acetylation is dependent on the equilibrium between the activities of histone acetyltransferases and deacetylases (HDAC), linking acetyl groups to lysine tails. Histone hyperacetylation is associated with a less condensed chromatin structure and thus and unfolded, more easily transcribed DNA. In HCC, evidence for efficacy of HDAC inhibitors stems from preclinical and preliminary clinical phase I and II trials. Among the molecular changes induced through changes of histone acetylation were cell cycle related proteins, such as p21waf1 and p27kip1, and cyclin D1. Lee et al. reported that changes in histone modification may be associated with patients prognosis, with higher levels of genes involved in histone modifications in HCC with poor outcome [[11]Lee J.S. Chu I.S. Heo J. Calvisi D.F. Sun Z. Roskams T. et al.Classification and prediction of survival in hepatocellular carcinoma by gene expression profiling.Hepatology. 2004; 40: 667-676Crossref PubMed Scopus (721) Google Scholar]. Thus, the concept of inhibiting histone acetylation will be interesting to follow in the coming years [10Tischoff I. Tannapfe A. DNA methylation in hepatocellular carcinoma.World J Gastroenterol. 2008; 14: 1741-1748Crossref PubMed Scopus (155) Google Scholar, 12Coradini D. Speranza A. Histone deacetylase inhibitors for treatment of hepatocellular carcinoma.Acta Pharmacol Sin. 2005; 26: 1025-1033Crossref PubMed Scopus (43) Google Scholar]. The discovery of microRNAs (miRNAs) introduced an additional layer of complexity to transcriptome regulation. These small RNAs are non-coding but have the capacity to target multiple genes simultaneously. It has been well established that dysregulation of miRNAs is essential for the development of various cancers. Given their broad transcriptome interference, these molecules may represent promising targets for therapeutic intervention. In addition, both single miRNA and small cluster of miRNAs may be of prognostic value in HCC [[13]Law P.T. Wong N. Emerging roles of microRNA in the intracellular signaling networks of hepatocellular carcinoma.J Gastroenterol Hepatol. 2011; 26: 437-449Crossref PubMed Scopus (82) Google Scholar]. Over the past decade, modern molecular biology and the use of high throughput genomics and transcriptomics have identified multiple biological layers involved in transcriptome regulation. Unraveling the tight and complex interactions between diverse molecules, data and involved biological layers in transcriptome of the HCC tissue will certainly result in a much better understanding of the underlying biology. Thus, bringing together the diverse aspects of transcriptomic changes in HCC will lead to a whole new perception of HCC development and subsequently disclose novel strategies for the diagnosis and treatment of HCC.