TCGA whole-transcriptome sequencing data reveals significantly dysregulated genes and signaling pathways in hepatocellular carcinoma

Abstract

This study systematically evaluates the TCGA whole-transcriptome sequencing data of hepatocellular carcinoma (HCC) by comparing the global gene expression profiles between tumors and their corresponding non-tumorous liver tissue. Based on the differential gene expression analysis, we identified a number of novel dysregulated genes, in addition to those previously reported. Top-listing upregulated (CENPF and FOXM1) and downregulated (CLEC4G, CRHBP, and CLEC1B) genes were successfully validated using qPCR on our cohort of 65 pairs of human HCCs. Further examination for the mechanistic overview by subjecting significantly upregulated and downregulated genes to gene set enrichment analysis showed that different cellular pathways were involved. This study provides useful information on the transcriptomic landscape and molecular mechanism of hepatocarcinogenesis for development of new biomarkers and further in-depth characterization.

Keywords

TCGA / whole-transcriptome sequencing / HCC / liver cancer

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Acknowledgements

The study was supported in part by the SK Yee Medical Research Fund 2011, University Development Fund, and the Small Project Funding (201309176065). IOL Ng is Loke Yew Professor in Pathology.

Daniel Wai-Hung Ho, Alan Ka-Lun Kai, and Irene Oi-Lin Ng declare that they have no conflict of interest. The use of human tissue in this study was approved by the Institutional Review Board of the University of Hong Kong/Hospital Authority Hong Kong West Cluster (UW 09-185).

Electronic Supplementary Material Supplementary material is available in the online version of this article at http://dx.doi.org/10.1007/s11684-015-0408-9 and is accessible for authorized users.

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2014 Higher Education Press and Springer-Verlag Berlin Heidelberg