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Series GSE17856 Query DataSets for GSE17856
Status Public on Apr 14, 2010
Title Gene expression in nontumoral liver tissue and recurrence-free survival in hepatitis C virus-positive HCC
Organism Homo sapiens
Experiment type Expression profiling by array
Summary Background/Aims: Recurrence-free survival (RFS) following curative resection of hepatocellular carcinoma (HCC) in subjects with hepatitis C virus (HCV) infection is highly variable. Traditional clinico-pathological endpoints are recognized as weak predictors of RFS. It has been suggested that gene expression profiling of HCC and nontumoral liver tissue may improve prediction of RFS, aid in understanding of the underlying liver disease, and guide individualized therapy. The goal of this study was to create a gene expression predictor of HCC recurrence in subjects with HCV.

Methods: Frozen samples of the tumors and nontumoral liver were obtained from 47 subjects with HCV-associated HCC. Additional nontumoral liver samples were obtained from HCV-free subjects with metastatic liver tumors. Gene expression profiling data was used to determine the molecular signature of HCV-associated HCC and to develop a predictor of RFS.

Results: The molecular profile of the HCV-associated HCC confirmed central roles for MYC and TGF-beta1 in liver tumor development. Gene expression in tumors was found to have poor predictive power with regards to RFS, but analysis of nontumoral tissues yielded a strong predictor for RFS in late-recurring (>1 year) subjects. Importantly, nontumoral tissue-derived gene expression predictor of RFS was highly significant in both univariable and multivariable Cox proportional hazard model analyses.

Conclusions: Microarray analysis of the nontumoral tissues from subjects with HCV-associated HCC delivers novel molecular signatures of RFS, especially among the late-recurrence subjects. The gene expression signature of the predictor gives important insights into the pathobiology of HCC recurrence and used in design of the individualized therapy.
 
Overall design 43 tumor (JT) and 44 non-tumor (JNT) liver tissues surgically resected from patients with HCV-associated hepatocellular carcinoma; 8 non-tumor liver tissues (control samples, JC) surgically resected from HCV- or HBV-free patients with metastatic liver tumor.
Inter-batch normalization was carried out using Distance Weighted Discrimination procedure.

The supplementary file 'GSE17856_Readme.txt' contains a description of the replicates used for normalization. The 'GSE17856_US14702406_2514850*' files are the raw data files for the replicates.
 
Contributor(s) Tsuchiya M, Parker JS, Kono H, Matsuda M, Fujii H, Rusyn I
Citation(s) 20380719
Submission date Aug 27, 2009
Last update date Jul 21, 2023
Contact name Ivan Rusyn
E-mail(s) iir@unc.edu
Phone 919-843-2596
Fax 919-843-2596
URL http://cancer.unc.edu/research/faculty/displayMember.asp?ID=398
Organization name University of North Carolina
Department Gillings School of Global Public Health
Lab Environmental Genomics Lab
Street address 0031 Michael Hooker Research Center
City Chapel Hill
State/province NC
ZIP/Postal code 27599-7431
Country USA
 
Platforms (1)
GPL6480 Agilent-014850 Whole Human Genome Microarray 4x44K G4112F (Probe Name version)
Samples (95)
GSM446157 metastatic liver tumor/non-tumor/control-01
GSM446158 metastatic liver tumor/non-tumor/control-02
GSM446159 metastatic liver tumor/non-tumor/control-03
Relations
Reanalyzed by GSE237977
BioProject PRJNA120097

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
GSE17856_RAW.tar 1.3 Gb (http)(custom) TAR (of TXT)
GSE17856_Readme.txt 5.8 Kb (ftp)(http) TXT
GSE17856_US14702406_251485014865_S01_GE2-v5_91_0806_1_1.txt.gz 14.3 Mb (ftp)(http) TXT
GSE17856_US14702406_251485014870_S01_GE2-v5_91_0806_1_4.txt.gz 14.3 Mb (ftp)(http) TXT
GSE17856_US14702406_251485028288_S01_GE2-v5_91_0806_1_1.txt.gz 14.2 Mb (ftp)(http) TXT
GSE17856_US14702406_251485028293_S01_GE2-v5_91_0806_1_4.txt.gz 14.1 Mb (ftp)(http) TXT
GSE17856_US14702406_251485028315_S01_GE2-v5_91_0806_1_1.txt.gz 14.2 Mb (ftp)(http) TXT
GSE17856_US14702406_251485028319_S01_GE2-v5_91_0806_1_4.txt.gz 14.1 Mb (ftp)(http) TXT
GSE17856_US14702406_251485028392_S01_GE2-v5_91_0806_1_1.txt.gz 14.4 Mb (ftp)(http) TXT
GSE17856_US14702406_251485028396_S01_GE2-v5_91_0806_1_4.txt.gz 14.4 Mb (ftp)(http) TXT
GSE17856_US14702406_251485032834_S01_GE2-v5_91_0806_1_1.txt.gz 14.3 Mb (ftp)(http) TXT
GSE17856_US14702406_251485032844_S01_GE2-v5_91_0806_1_1.txt.gz 14.3 Mb (ftp)(http) TXT
GSE17856_US14702406_251485032848_S01_GE2-v5_91_0806_1_4.txt.gz 14.3 Mb (ftp)(http) TXT
GSE17856_US14702406_251485032849_S01_GE2-v5_91_0806_1_1.txt.gz 14.3 Mb (ftp)(http) TXT
GSE17856_US14702406_251485032878_S01_GE2-v5_91_0806_1_1.txt.gz 14.4 Mb (ftp)(http) TXT
GSE17856_US14702406_251485032882_S01_GE2-v5_91_0806_1_4.txt.gz 14.3 Mb (ftp)(http) TXT
GSE17856_US14702406_251485032937_S01_GE2-v5_91_0806_1_4.txt.gz 14.3 Mb (ftp)(http) TXT
GSE17856_US14702406_251485032941_S01_GE2-v5_91_0806_1_2.txt.gz 14.3 Mb (ftp)(http) TXT
GSE17856_US14702406_251485032942_S01_GE2-v5_91_0806_1_1.txt.gz 14.3 Mb (ftp)(http) TXT
GSE17856_US14702406_251485032946_S01_GE2-v5_91_0806_1_4.txt.gz 14.3 Mb (ftp)(http) TXT
Processed data included within Sample table
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