Analysis of differentially expressed genes in hepatocellular carcinoma using cDNA arrays

Abstract

Hepatocellular carcinoma (HCC) is characterized by multiple somatic mutations, including DNA rearrangements, that affect many cell-growth regulatory pathways. Many genes differentially expressed in HCC have been reported previously, but the patterns of expression varied significantly between patients who bore different risk factors for HCC. To identify genes whose differential expression could serve as a "signature" for diagnosis and prognosis of HCC, we performed analyses of differentially expressed genes in three cases of HCC with different risk factors using the Atlas Human Cancer cDNA Expression Arrays. Among all 597 genes present on the array, only three were found to be coordinately differentially expressed in all three HCC cases, in agreement with published data. These three genes, Cu/Zn superoxide dismutase, osteonectin/secreted protein acidic and rich in cysteine, and matrix metalloproteinase 14, could serve as candidates for the HCC "signature." Ten genes were found to be coordinately differentially expressed in only two of three tested HCC cases. On the other hand, many genes that had been reported previously as differentially expressed in HCC failed to show the described pattern of expression in this group. The results of this study confirm the great variability in gene-expression patterns in HCC and establish the utility of the array technology for identifying both the HCC signature genes and individual gene-expression patterns for purposes of patient-oriented therapy.

Heterogeneous nuclear ribonucleoprotein A2/B1 in association with hTERT is a potential biomarker for hepatocellular carcinoma

“…Among these 24 proteins, eight were found to be up‐regulated in HCC tissue compared with cirrhotic liver tissue, while 16 proteins were found to be down‐regulated (Table ). Of the 24 proteins, nine were already known as HCC‐related proteins. To identify a new prognostic biomarker related to hTERT, we decided to focus on hnRNP A2/B1, which has been reported as a prognostic biomarker for lung cancer and gastric cancer.…”

“…Further analysis of the fractionated lysates of 350 kDa by LC‐MS/MS revealed that 24 proteins were differentially expressed in HCC tissue when compared with nontumor tissue. In addition, 9 of the 24 proteins were already known as HCC‐related proteins. We therefore focused on hnRNP A2/B1, one of the most abundant and important nuclear RNA‐binding proteins involved in packaging nascent mRNA, alternative splicing and cytoplasmic RNA trafficking, translation, and stabilization.…”

Differential gene expression in distinct virologic types of hepatocellular carcinoma: association with liver cirrhosis

“…Understanding the effects of LC on hepatocarcinogenesis will help us to provide patients suffering from chronic HBV or HCV infections with suitable therapy. DNA microarray studies have detected specific gene-expression patterns associated with HCC (Lau et al, 2000;Okabe et al, 2001;Xu L et al, 2001;Xu XR et al, 2001;Shirota et al, 2001;Delpuech et al, 2002;Goldenberg et al, 2002;Iizuka et al, 2002b). Only one report described on LC-related gene-expression pattern in HCC, but this report did not address the effects of distinct virological backgrounds (Delpuech et al, 2002).…”

Functional characterization of hepatoma‐specific stem cell antigen‐2

“…A number of the overexpressed hepatoma genes have been previously reported [26][27][28][29]. However, the function of Sca-2 in tumor cells has not been characterized.…”