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Series GSE103728 Query DataSets for GSE103728
Status Public on Sep 12, 2018
Title High-resolution liver cancer genomic profiling links etiology, epigenetic and mutation signatures [ChIP-Seq]
Organism Homo sapiens
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary Purpose: This study unravel the mechanisms that link viral infection and cancer
Methods:Human HCC cell line and HCC liver FFPE samples from HCC patients from three etiology groups- HBV, HCV infection, or neither were taken to explore their genomic DNA in two aspects: The HCC genomic mutations within the exons of 224 candidate genes, frequently mutated in HCC, using SureSelectâ„¢ Target Enrichment System kit and the transient response of liver cells to HCV infection, in genome wide histone modifications and gene expression, as demonstrated by ChIP-Seq and RNA-Seq.
Results:Mutational signature was explored by high-resolution targeted sequencing that detected low-frequency passenger mutations in 64 HCC samples from three etiology groups – HBV, HCV, or other. We identified novel distinct etiology-dependent regional mutations signatures. To explore the link between genomic signature and genome wide chromatin organization we studied the epigenetic changes occur following HCV infection. We demonstrated that HCV infection induces epigenetic changes that persist as "epigenetic signature" following virus eradication and reprogram host gene expression. High mutation rate associated with HCV etiology correlated with HCV-induced changes in epigenetic markers leading to closed chromatin.
Conclusions:We present a new link between cancer causing mutagenesis, and increase in liver cancer predisposition in chronic HCV-infected individuals. The sequential events begin with HCV-specific epigenetic signature that in turn dictates a unique HCV-specific somatic mutational profile in HCC
 
Overall design Huh-7.5 cells were infected with HCV and ChIP-seq (at least 3 biological replicates were conducted.) and RNA-seq (6 biological replicates ) were done, all compared to non infected cells
 
Contributor(s) Gal-Tanamy M, Haviv I
Citation(s) 30698808
Submission date Sep 12, 2017
Last update date May 15, 2019
Contact name Assam El-Osta
Organization name Baker Heart and Diabetes Institute
Lab Human Epigenetics
Street address 75 Commercial Road
City Melbourne
ZIP/Postal code 3004
Country Australia
 
Platforms (1)
GPL16791 Illumina HiSeq 2500 (Homo sapiens)
Samples (24)
GSM2779861 H3K9Ac ChIP-seq from HCV infected cells repeat 1
GSM2779862 H3K9Ac ChIP- seq from non-infected cells repeat 1
GSM2779863 H3K9Ac ChIP-seq from HCV infected cells repeat 2
This SubSeries is part of SuperSeries:
GSE103730 High-resolution liver cancer genomic profiling links etiology, epigenetic and mutation signatures
Relations
BioProject PRJNA406884
SRA SRP117315

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Supplementary file Size Download File type/resource
GSE103728_K27Me3.txt.gz 100.1 Mb (ftp)(http) TXT
GSE103728_K4Me3.txt.gz 5.6 Mb (ftp)(http) TXT
GSE103728_K9AC.txt.gz 4.4 Mb (ftp)(http) TXT
GSE103728_K9Me3.txt.gz 108.5 Mb (ftp)(http) TXT
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Processed data are available on Series record
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