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E-GEOD-33650 - Gene Expression differences in Hepatic Parenchyma and Portal Tracts in Hepatitis C Virus Infected Subjects with High and Low Fibrosis

Status
Released on 13 August 2013, last updated on 21 August 2013
Organism
Homo sapiens
Samples (72)
Array (1)
Protocols (7)
Description
Background & Aims: Chronic hepatitis C virus (HCV) infection is complicated by hepatic fibrosis. Hypothesizing that fibrogenic signals may originate in cells susceptible to HCV infection, gene expression of hepatocytes was analyzed from persons with chronic HCV at different stages of liver fibrosis. Methods: HCV-infected subjects with significant liver fibrosis (Ishak fibrosis ≥3) were matched for age, race, and gender to subjects with minimal fibrosis (Ishak fibrosis 0-1). RNA from portal tracts and hepatic parenchyma was isolated from biopsies by laser capture and transcriptome profiling was performed using hybridization arrays. Results: Portal tracts from both groups were enriched for immune related genes when compared to hepatocytes but high fibrosis subjects showed a loss of this enrichment. Hepatocytes from persons with high fibrosis were depleted for genes involved in small molecule and drug metabolism, especially butyrylcholinesterase (BCHE), a gene involved in the metabolism of drugs of abuse. Differential expression of BCHE was validated in the same tissues using qPCR. Cross-sectional and longitudinal testing in an expanded cohort of HCV-infected individuals showed that serum BCHE activity decreased in advance of progression to fibrosis. Conclusion: Chronic HCV infection is associated with a loss of hepatocyte metabolic function, decreased enrichment of immune-related genes in portal tracts and downregulation of BCHE in hepatocytes. Our results indicate that BCHE may be involved in the progression of fibrosis during HCV infection among injection drug users and may serve as a useful marker for fibrosis progression. Liver tissues were chosen from five subjects with chronic HCV infection and Ishak fibrosis stage 3-5 who had sufficient tissue stored in OCT and no HIV infection. Tissues that were stored in Trizol® or other lysis buffers were excluded to avoid homogenization of transcriptomes between cellular constituents. Five control tissues were selected from persons of the same race and gender with chronic HCV infection estimated to be of similar duration (by age matching) but whose baseline Ishak fibrosis score was 0-1. One high fibrosis case was later excluded because the subject was found to be HBsAg positive, leaving a total of nine subjects.
Experiment type
transcription profiling by array 
Contacts
Supriya Munshaw <smunsha1@jhmi.edu>, Ashwin Balagopal, David L Thomas, Hyon S Hwang, Jacquie Astemborski, Jeffrey Quinn, Kasper D Hansen, Michael Torbenson, Shruti H Mehta, Stuart C Ray
Citation
Laser captured hepatocytes show association of butyrylcholinesterase gene loss and fibrosis progression in hepatitis C-infected drug users. Munshaw S, Hwang HS, Torbenson M, Quinn J, Hansen KD, Astemborski J, Mehta SH, Ray SC, Thomas DL, Balagopal A. , PMID:22331678
MIAME
PlatformsProtocolsVariablesProcessedRaw
Files
Investigation descriptionE-GEOD-33650.idf.txt
Sample and data relationshipE-GEOD-33650.sdrf.txt
Raw data (2)E-GEOD-33650.raw.1.zip, E-GEOD-33650.raw.2.zip
Processed data (1)E-GEOD-33650.processed.1.zip
Additional data (1)E-GEOD-33650.additional.1.zip
Array designA-GEOD-14877.adf.txt
Links