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Transcription profiling of human liver samples from subjects with HCV cirrhosis with and without concomitant HCC

ABSTRACT: In this study, we used the Affymetrix HG-U133A 2.0 GeneChip for deriving a multigenic classifier capable of predicting HCV+cirrhosis with vs without concomitant HCC. We studied gene expression in cirrhotic tissues with (N=16) and without (N=47) HCC. Experiment Overall Design: Liver tissue samples were obtained from patients waiting for liver transplantation. For each sample, RNA was extracted and hybridized to an Affymetrix GeneChip.

ORGANISM(S): Homo sapiens

SUBMITTER:

PROVIDER: S-DIXA-D-1046 | biostudies-other |

REPOSITORIES: biostudies-other

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RMA expression data for liver samples from subjects with HCV cirrhosis with and without concomitant HCC

2009-09-11 | GSE17967 | GEO

RMA expression data for liver samples from subjects with HCV cirrhosis with and without concomitant HCC

Project description:In this study, we used the Affymetrix HG-U133A 2.0 GeneChip for deriving a multigenic classifier capable of predicting HCV+cirrhosis with vs without concomitant HCC. We studied gene expression in cirrhotic tissues with (N=16) and without (N=47) HCC. Keywords: cross-sectional Liver tissue samples were obtained from patients waiting for liver transplantation. For each sample, RNA was extracted and hybridized to an Affymetrix GeneChip. This dataset is part of the TransQST collection.

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Project description:The role of chronic hepatitis C virus (HCV) in the pathogenesis of HCV-associated hepatocellular carcinoma (HCC) is not completely understood, particularly at the molecular level. We studied gene expression in normal, pre-malignant (cirrhosis), and tumor (HCC) liver tissues using Affymetrix GeneChips. Experiment Overall Design: Liver tissue samples were obtained from patients waiting for liver transplantation at one of the GR2HCC Centers. Additionally, normal liver and tumor samples were also obtained from the Liver Tissue Cell Distribution System. For each sample, RNA was extracted and hybridized to an Affymetrix GeneChip.

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Proteomic analysis of HCV cirrhosis and HCV-induced HCC: identifying biomarkers for monitoring HCV-cirrhotic patients awaiting liver transplantation.

Project description:Progression from chronic hepatitis C virus (HCV) infection to cirrhosis and hepatocellular carcinoma (HCC) results in protein changes in the peripheral blood. We evaluated global protein expression in plasma samples of HCV-cirrhotic and HCV-cirrhotic-HCC patients.Plasma samples from 25 HCV-cirrhotic-HCC and 10 HCV-cirrhotic patients were quantitatively evaluated for protein expression. Tryptic peptides were analyzed using Thermo linear ion-trap mass spectrometer (LTQ) coupled with a Surveyor HPLC system (Thermo). SEQUEST and X!Tandem database search algorithms were used for peptide sequence identification. Protein relative quantification was performed using the area under the curve from the select ion chromatogram. A significant fold change between groups was based on controlling the false discovery rate (FDR) at less than 5%.We identified and quantified 2320 proteins from the analysis of the different protein pattern between HCV-cirrhosis and HCV-HCC samples. Gene ontology terms classified the more important biologic process related to these proteins as signal transduction, regulation of transcription DNA-dependent, protein amino acid phosphorylation, cell adhesion, transport, and immune response. Seven proteins showed significant expression changes with a FDR less than 5% between cirrhosis and tumor groups. Moreover, 18 proteins showed significant expression changes (FDR <5%) when plasma samples from HCV-cirrhosis were compared with early HCV-HCC.Differential protein expression was observed between samples from HCV patients with cirrhosis with and without HCC. Also, differences were observed between early and advanced HCV-HCC samples. This study provides important information for discovery of potential biomarkers for early HCC diagnosis in HCV cirrhotic patients.

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Expression data from cirrhosis and HCC tissue samples

Project description: Not available

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Transcription profiling of human liver samples from HCV-induced dysplasia and hepatocellular carcinoma patients, progression study

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Transcription profiling by array of human normal liver, HBV, HCV and haemochromatosis background cirrhotic and hematocellular carcinoma liver samples.

Project description: Not available

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Gene expression profiling of HCV genotype 3a initial liver fibrosis and cirrhosis patients using microarray.

Project description:BACKGROUND: Hepatitis C virus (HCV) causes liver fibrosis that may lead to liver cirrhosis or hepatocellular carcinoma (HCC), and may partially depend on infecting viral genotype. HCV genotype 3a is being more common in Asian population, especially Pakistan; the detail mechanism of infection still needs to be explored. In this study, we investigated and compared the gene expression profile between initial fibrosis stage and cirrhotic 3a genotype patients. METHODS: Gene expression profiling of human liver tissues was performed containing more than 22000 known genes. Using Oparray protocol, preparation and hybridization of slides was carried out and followed by scanning with GeneTAC integrator 4.0 software. Normalization of the data was obtained using MIDAS software and Significant Microarray Analysis (SAM) was performed to obtain differentially expressed candidate genes. RESULTS: Out of 22000 genes studied, 219 differentially regulated genes found with P ? 0.05 between both groups; 107 among those were up-regulated and 112 were down-regulated. These genes were classified into 31 categories according to their biological functions. The main categories included: apoptosis, immune response, cell signaling, kinase activity, lipid metabolism, protein metabolism, protein modulation, metabolism, vision, cell structure, cytoskeleton, nervous system, protein metabolism, protein modulation, signal transduction, transcriptional regulation and transport activity. CONCLUSION: This is the first study on gene expression profiling in patients associated with genotype 3a using microarray analysis. These findings represent a broad portrait of genomic changes in early HCV associated fibrosis and cirrhosis. We hope that identified genes in this study will help in future to act as prognostic and diagnostic markers to differentiate fibrotic patients from cirrhotic ones.

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