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Series GSE38226 Query DataSets for GSE38226
Status Public on Jun 15, 2012
Title MicroRNA profiling in TGFβ signaling and development of fibrosis.
Organism Homo sapiens
Experiment type Expression profiling by array
Non-coding RNA profiling by array
Summary End stage liver disease due to Hepatitis C Virus (HCV) infection is a major health concern worldwide. Liver fibrosis following chronic HCV infection plays a pivotal role in loss of liver function and end stage liver disease. However the dynamics and molecular events that lead to fibrosis in HCV infection are poorly defined. Therefore, we determined the influence of HCV infection in altering the miRNA expression levels which can modulate immune responses to HCV leading to fibrosis. Analysis of the miRNA expression profiles of HCV infected liver biopsies revealed that 45 miRNAs were differentially expressed in the HCV infected liver when compared to normal livers. In silico target prediction of these differentially expressed miRNAs indicated that their targets include chemokine/cytokine signaling, cell cycle genes and extracellular matrix protein gene expression. Gene expression profiling using whole genome microarray demonstrated that 1320 genes were differentially expressed in chronic HCV liver when compared to normal. These genes could be functionally grouped into those involved in cell cycle regulation, cytokines and chemokines expression, cell adhesion, intracellular signaling and enzymes. Further pathway analysis using GeneGo software identified cell adhesion, cytoskeleton remodeling, cytokine signaling and metabolic pathways as the major pathways activated in chronic HCV. Combinatorial target prediction analysis of miRNA expression along with gene expression analysis indicated that differentially expressed microRNAs in HCV significantly impact transforming growth factor beta (TGF-β) signaling pathway, cell adhesion (integrin expression), chemokine signaling, Notch signaling and cell-cycle( Cyclin D,K) regulation. Overall these results demonstrate that chronic HCV infection induces specific miRNA signatures that will modulate genes involved in the cytoskeletal remodeling and cytokine signaling that can promote the development of fibrosis following HCV infection.
Overall design Liver biopsies from chronic HCV patients and control liver biopsies from normal subjects (donor liver prior to transplantation) were used to analyze the miRNA and gene expression profile. Patients with HBV and/or HIV were excluded from the study.
Contributor(s) Ramachandran S
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Submission date May 24, 2012
Last update date Feb 18, 2019
Contact name Nobish Varghese
Organization name Washington University in St.Louis
Street address 4444 Forest Park Ave.
City StLouis
State/province MO
ZIP/Postal code 63110
Country USA
Platforms (2)
GPL6947 Illumina HumanHT-12 V3.0 expression beadchip
GPL8179 Illumina Human v2 MicroRNA expression beadchip
Samples (44)
GSM937012 liver-Tumor-rep1
GSM937013 liver-HCV-Non Tumor-rep1
GSM937014 liver-Tumor-rep2
BioProject PRJNA168569

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE38226_RAW.tar 6.3 Mb (http)(custom) TAR
GSE38226_non-normalized.txt.gz 6.5 Mb (ftp)(http) TXT
GSE38226_non-normalized_miRNA.txt.gz 133.9 Kb (ftp)(http) TXT
Processed data included within Sample table

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