Accession	GSE103728
Status	2018/9/12
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 SureSelect™ 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
Samples	GSM ID Sample info Characteristics Description GSM2779861 H3K9Ac ChIP-seq from HCV infected cells repeat 1 tissue: liver;cell type: Huh-7.5;chip antibody: ChIPAb Acetyl-Histone H3 (Lys-9) Purified 17-658 (Millipore) - GSM2779862 H3K9Ac ChIP- seq from non-infected cells repeat 1 tissue: liver;cell type: Huh-7.5;chip antibody: ChIPAb Acetyl-Histone H3 (Lys-9) Purified 17-658 (Millipore) - GSM2779863 H3K9Ac ChIP-seq from HCV infected cells repeat 2 tissue: liver;cell type: Huh-7.5;chip antibody: ChIPAb Acetyl-Histone H3 (Lys-9) Purified 17-658 (Millipore) - GSM2779864 H3K9Ac ChIP- seq from non-infected cells repeat 2 tissue: liver;cell type: Huh-7.5;chip antibody: ChIPAb Acetyl-Histone H3 (Lys-9) Purified 17-658 (Millipore) - GSM2779865 H3K9Ac ChIP-seq from HCV infected cells repeat 3 tissue: liver;cell type: Huh-7.5;chip antibody: ChIPAb Acetyl-Histone H3 (Lys-9) Purified 17-658 (Millipore) - GSM2779866 H3K9Ac ChIP- seq from non-infected cells repeat 3 tissue: liver;cell type: Huh-7.5;chip antibody: ChIPAb Acetyl-Histone H3 (Lys-9) Purified 17-658 (Millipore) - GSM2779867 H3K4Me3 ChIP-seq from HCV infected cells repeat 1 tissue: liver;cell type: Huh-7.5;chip antibody: ChIPAb Trimethyl-Histone H3 (Lys-4) 17-614 (Millipore) - GSM2779868 H3K4Me3 ChIP- seq from non-infected cells repeat 1 tissue: liver;cell type: Huh-7.5;chip antibody: ChIPAb Trimethyl-Histone H3 (Lys-4) 17-614 (Millipore) - GSM2779869 H3K4Me3 ChIP-seq from HCV infected cells repeat 2 tissue: liver;cell type: Huh-7.5;chip antibody: ChIPAb Trimethyl-Histone H3 (Lys-4) 17-614 (Millipore) - GSM2779870 H3K4Me3 ChIP- seq from non-infected cells repeat 2 tissue: liver;cell type: Huh-7.5;chip antibody: ChIPAb Trimethyl-Histone H3 (Lys-4) 17-614 (Millipore) - GSM2779871 H3K4Me3 ChIP-seq from HCV infected cells repeat 3 tissue: liver;cell type: Huh-7.5;chip antibody: ChIPAb Trimethyl-Histone H3 (Lys-4) 17-614 (Millipore) - GSM2779872 H3K4Me3 ChIP- seq from non-infected cells repeat 3 tissue: liver;cell type: Huh-7.5;chip antibody: ChIPAb Trimethyl-Histone H3 (Lys-4) 17-614 (Millipore) - GSM2779873 H3K9Me3 ChIP-seq from HCV infected cells repeat 1 tissue: liver;cell type: Huh-7.5;chip antibody: ChIPAb Trimethyl-Histone H3 (Lys-9) Purified 17-10242 (Millipore) - GSM2779874 H3K9Me3 ChIP- seq from non-infected cells repeat 1 tissue: liver;cell type: Huh-7.5;chip antibody: ChIPAb Trimethyl-Histone H3 (Lys-9) Purified 17-10242 (Millipore) - GSM2779875 H3K9Me3 ChIP-seq from HCV infected cells repeat 2 tissue: liver;cell type: Huh-7.5;chip antibody: ChIPAb Trimethyl-Histone H3 (Lys-9) Purified 17-10242 (Millipore) - GSM2779876 H3K9Me3 ChIP- seq from non-infected cells repeat 2 tissue: liver;cell type: Huh-7.5;chip antibody: ChIPAb Trimethyl-Histone H3 (Lys-9) Purified 17-10242 (Millipore) - GSM2779877 H3K9Me3 ChIP-seq from HCV infected cells repeat 3 tissue: liver;cell type: Huh-7.5;chip antibody: ChIPAb Trimethyl-Histone H3 (Lys-9) Purified 17-10242 (Millipore) - GSM2779878 H3K9Me3 ChIP- seq from non-infected cells repeat 3 tissue: liver;cell type: Huh-7.5;chip antibody: ChIPAb Trimethyl-Histone H3 (Lys-9) Purified 17-10242 (Millipore) - GSM2779879 H3K27Me3 ChIP-seq from HCV infected cells rapeat 1 tissue: liver;cell type: Huh-7.5;chip antibody: ChIPAb Trimethyl-Histone H3 (Lys-27) 07-449 (Millipore) - GSM2779880 H3K27Me3 ChIP- seq from non-infected cells rapeat 1 tissue: liver;cell type: Huh-7.5;chip antibody: ChIPAb Trimethyl-Histone H3 (Lys-27) 07-449 (Millipore) - GSM2779881 H3K27Me3 ChIP-seq from HCV infected cells rapeat 2 tissue: liver;cell type: Huh-7.5;chip antibody: ChIPAb Trimethyl-Histone H3 (Lys-27) 07-449 (Millipore) - GSM2779882 H3K27Me3 ChIP- seq from non-infected cells rapeat 2 tissue: liver;cell type: Huh-7.5;chip antibody: ChIPAb Trimethyl-Histone H3 (Lys-27) 07-449 (Millipore) - GSM2779883 H3K27Me3 ChIP-seq from HCV infected cells rapeat 3 tissue: liver;cell type: Huh-7.5;chip antibody: ChIPAb Trimethyl-Histone H3 (Lys-27) 07-449 (Millipore) - GSM2779884 H3K27Me3 ChIP- seq from non-infected cells rapeat 3 tissue: liver;cell type: Huh-7.5;chip antibody: ChIPAb Trimethyl-Histone H3 (Lys-27) 07-449 (Millipore) -
Platform	GPL16791  : Illumina HiSeq 2500 (Homo sapiens)
Literature	30698808
Download	Download Genome Binding/Occupancy Profiling Analysis Data