Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Chronic Hypoxia predicts Poor Prognosis in Hepatocellular Carcinoma


ABSTRACT: Background - Hepatocellular carcinomas (HCCs) are heterogeneous tumors with respect to etiology, cell of origin and biology. The course of the disease is unpredictable and is in part dependent on the tumor microenvironment. One of the microenvironmental factors is hypoxia, which is known to promote aggressiveness in other malignant tumors. We hypothesized that certain regions in HCC exist with chronic hypoxia and a characteristic gene expression pattern. Moreover, during the development of HCC there is an important contribution of this chronic hypoxia on prognosis via this gene expression. Until now, most research has been performed in acute hypoxic models (< 24 hours). Methods – Human hepatoblastoma cells HepG2 were cultured in either normoxic (20% O2) or hypoxic (2% O2) conditions for 72 hrs, the time it takes to adapt to chronic hypoxia. After 3 days the cells were harvested and analyzed by microarray technology. The highly significant differentially expressed genes were selected and used to assess the clinical value of our in vitro chronic hypoxia gene signature in four published patient studies. Three of these independent microarray studies on HCC patients were used as training sets to determine a minimal prognostic gene set and one study was used for validation. Gene expression analysis and correlation with clinical outcome was assessed with the bioinfomatic method of Goeman et al (). Results – In the HepG2 cells, 3592 genes were differentially expressed in cells cultured at 2% oxygen for 72 hrs. Out of these, 265 showed a high significant change (2-fold change and p=0.0001). The level of gene expression after 72 hrs was different from the acute hypoxic response (during the first 24 hours) and represented chronicity. Using computational methods we identified 7 out of the 265 highly significant genes that showed correlation with prognosis in all three different training sets and this was independently validated in a 4th dataset. With our approach we could include the largest number of HCC patients in one single study. Conclusion – We identified a 7-gene signature, which is associated with chronic hypoxia and predicts prognosis in patients with HCC. In the future this signature could be used as a diagnostic tool. In addition, chronic hypoxia gene expression information can be used in the search for new therapeutic targets. Two conditions were compared and each sample has a biological replicate. Samples are hybridized in dye-swap, resulting in 4 hybridizations.

ORGANISM(S): Homo sapiens

SUBMITTER: Joke Allemeersch 

PROVIDER: E-GEOD-15366 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

A seven-gene set associated with chronic hypoxia of prognostic importance in hepatocellular carcinoma.

van Malenstein Hannah H   Gevaert Olivier O   Libbrecht Louis L   Daemen Anneleen A   Allemeersch Joke J   Nevens Frederik F   Van Cutsem Eric E   Cassiman David D   De Moor Bart B   Verslype Chris C   van Pelt Jos J  

Clinical cancer research : an official journal of the American Association for Cancer Research 20100630 16


<h4>Purpose</h4>Hepatocellular carcinomas (HCC) have an unpredictable clinical course, and molecular classification could provide better insights into prognosis and patient-directed therapy. We hypothesized that in HCC, certain microenvironmental regions exist with a characteristic gene expression related to chronic hypoxia which would induce aggressive behavior.<h4>Experimental design</h4>We determined the gene expression pattern for human HepG2 liver cells under chronic hypoxia by microarray a  ...[more]

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