Gene expression profile analysis of human hepatocellular carcinoma using SAGE and LongSAGE

Hui Dong,Hongyi Zhang,Guoping Zhao,Weirong Jin,Hongyang Wang,Xijin Ge,Xiaobo Man,Yalin Kong,Yan Shen,Linlei Chen,Liang Tang,Hong Yuan

doi:10.1186/1755-8794-2-5

Abstract

BackgroundHepatocellular carcinoma (HCC) is one of the most common cancers worldwide and the second cancer killer in China. The initiation and malignant transformation of cancer result from accumulation of genetic changes in the sequences or expression level of cancer-related genes. It is of particular importance to determine gene expression profiles of cancers on a global scale. SAGE and LongSAGE have been developed for this purpose.MethodsWe performed SAGE in normal liver and HCC samples as well as the liver cancer cell line HepG2. Meanwhile, the same HCC sample was simultaneously analyzed using LongSAGE. Computational analysis was carried out to identify differentially expressed genes between normal liver and HCC which were further validated by real-time quantitative RT-PCR.ResultsApproximately 50,000 tags were sequenced for each of the four libraries. Analysis of the technical replicates of HCC indicated that excluding the low abundance tags, the reproducibility of SAGE data is high (R = 0.97). Compared with the gene expression profile of normal liver, 224 genes related to biosynthesis, cell proliferation, signal transduction, cellular metabolism and transport were identified to be differentially expressed in HCC. Overexpression of some transcripts selected from SAGE data was validated by real-time quantitative RT-PCR. Interestingly, sarcoglycan-ε (SGCE) and paternally expressed gene (PEG10) which is a pair of close neighboring genes on chromosome 7q21, showed similar enhanced expression patterns in HCC, implicating that a common mechanism of deregulation may be shared by these two genes.ConclusionOur study depicted the expression profile of HCC on a genome-wide scale without the restriction of annotation databases, and provided novel candidate genes that might be related to HCC.

Highlights

Hepatocellular carcinoma (HCC) is one of the most common cancers worldwide and the second cancer killer in China
Summary of Serial Analysis of Gene Expression (SAGE) data A total of 56,984, 63,800 and 47,149 tags were detected from the normal liver, HCC and HepG2 SAGE libraries respectively, and 51,632 tags were obtained from the HCC LongSAGE library
31%~34% of the total tags of each SAGE library were unique, while unique tags accounted for 45% of total tags of the HCC LongSAGE library (Table 2)

Summary

Introduction

Hepatocellular carcinoma (HCC) is one of the most common cancers worldwide and the second cancer killer in China. Mutations of p53, β-catenin and AXIN1 [6,7,8,9,10], activation of oncogenes such as c-myc, c-met, c-jun, N-ras and nuclear factor κB [11,12,13,14,15,16], and upregulation of a set of genes including GPC3, LCN2, and IGFBP-1 were observed in a certain number of HCC cases [17,18,19]. These studies contributed greatly to our understanding of HCC in terms of individual molecules

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