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Series GSE60753 Query DataSets for GSE60753
Status Public on Sep 16, 2014
Title Epigenetic signatures of alcohol abuse and hepatitis infection during hepatocarcinogenesis
Organism Homo sapiens
Experiment type Methylation profiling by genome tiling array
Summary Hepatocellular carcinoma (HCC) is the second most common cause of cancer deaths worldwide. Altered DNA methylation landscapes are ubiquitous features of cancer. Interpretation of epigenetic aberrations in HCC is confounded by effects of multiple etiologic drivers and underlying cirrhosis in most cases. We globally profiled the DNA methylome of 34 normal livers and 122 primary liver disease tissues arising in the setting of chronic hepatitis B (HBV) or C (HCV) viral infection, alcoholism (EtOH), and other causes to examine how these environmental agents impact DNA methylation in a manner that contributes to liver disease. Our results demonstrate that each etiologic factor leaves unique and overlapping signatures on the DNA methylome. CpGs aberrantly methylated in cirrhosis-HCV and conserved in HCC were enriched for cancer driver genes, suggesting a pathogenic role for HCV-induced methylation changes. Additionally, large genomic regions displaying stepwise hypermethylation or hypomethylation during disease progression were identified. HCC-HCV/EtOH methylomes overlap highly with cryptogenic HCC, suggesting shared epigenetically deregulated pathways for hepatic carcinogenesis. Finally, overlapping methylation abnormalities between primary and cultured tumors unveil highly conserved epigenetic signatures in HCC. Taken together, this study characterizes progressive liver DNA methylome changes under exposure to detrimental environmental agents and illuminates possible biomarkers for early detection of HCC.
Overall design 156 primary tissues and 25 cultured normal and HCC cell lines
Contributor(s) Hlady RA, Tiedemann RL, Puszyk W, Roberts LR, Choi J, Liu C, Robertson KD
Citation(s) 25294808
Submission date Aug 26, 2014
Last update date Mar 22, 2019
Contact name Keith D Robertson
Phone 507-266-4886
Organization name Mayo Clinic
Department Molecular Pharmacology & Experimental Therapeutics
Lab Epigenetic Etiology of Human Disease Laboratory
Street address 200 First Street SW, Stabile 12-70
City Rochester
State/province MN
ZIP/Postal code 55905
Country USA
Platforms (1)
GPL13534 Illumina HumanMethylation450 BeadChip (HumanMethylation450_15017482)
Samples (199)
GSM1487113 Normal-1
GSM1487114 Normal-2
GSM1487115 Normal-3
BioProject PRJNA259521

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
GSE60753_RAW.tar 183.1 Mb (http)(custom) TAR
GSE60753_Unmethylated_and_methylated_signal_intensities.txt.gz 491.3 Mb (ftp)(http) TXT
Processed data included within Sample table

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