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.

Rnd3/RhoE Is down-regulated in hepatocellular carcinoma and controls cellular invasion

“…Our reanalysis of five transcriptomic studies revealed an alteration of Rnd3 messenger RNA (mRNA) expression in HCC, compared to nontumor liver tissues,5 with four of five showing a down‐expression16‐19 and a single one, based on only four cases, an overexpression 20. Here, we confirm that Rnd3 is down‐regulated in most human HCC and HCC‐related cell lines, and we provide evidence that Rnd3 down‐regulation increases HCC invasion and thus may favor HCC progression.…”

Detection of the inferred interaction network in hepatocellular carcinoma from EHCO (E ncyclopedia of H epatocellular C arcinoma genes O nline)

“…Among the HCC-related microarray studies, EHCO was further reorganized into five gene sets. Differentially expressed HCC-related gene sets were collected from four major studies, including Chen et al, [1] (referred to as SMD1648), Neo et al, [2] (referred to as GIS), Lee et al, [3] (referred to as Lee_NIH), and Kim et al, [4] (referred to as Kim_NIH), and ten additional reports [5-14], which were manually keyed in and are referred to as TableX_mRNA. The differentially expressed genes collected from these sets ranged from 199 (GIS) to 1,161 (SMD1648).…”

Increased osteonectin expression is associated with malignant transformation and tumor associated fibrosis in the lung

“…These include schwannoma [28], glioma [29], hepatocellular carcinoma [30], melanoma [27,31], transitional cell carcinoma [32], prostatic adenocarcinoma [33,34] and meningioma [35]. ON has been shown to directly affect tumor invasion in in vivo models, including ON-null mice [27,34,36] and has been correlated with tumor prognosis in melanomas and transitional cell carcinoma of the bladder [31,32].…”