Virus Dataset Detail

> Detail information for each sample

Dataset Information
Accession GSE126831
Status 2019/4/17
Title A temporal proteogenomic atlas of HCV-host interactions unravels cell circuits driving viral and metabolic liver disease
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary Background and aims: Hepatitis C virus (HCV) infection is a major cause of liver disease including steatosis, fibrosis and liver cancer. Viral cure cannot fully eliminate the risk of disease progression and hepatocellular carcinoma (HCC) in advanced liver disease. The mechanisms for establishment of infection, liver disease progression and hepatocarcinogenesis are only partially understood. To address these questions, we probed the functional proteogenomic architecture of HCV infection within a hepatocyte-model. Methods: Time-resolved HCV infection of hepatocyte-like cells was analyzed by RNA sequencing, proteomics, metabolomics, and leveraged by integrative genomic analyses. Using differential expression, gene set enrichment analyses, and protein-protein interaction mapping we identified pathways relevant for liver disease pathogenesis that we validated in livers of 216 cirrhotic patients with HCV. Results: We uncovered marked changes in the protein expression of gene sets involved in innate immunity, metabolism and hepatocarcinogenesis. In infected cells, HCV enhances glucose metabolism and creates a Warburg-like shift of the lactate flux. HCV infection impaired the formation of peroxisomes -organelles required for long-chain fatty acid oxidation- causing intracellular fatty acid accumulation, which is a hallmark of non-alcoholic fatty liver disease (NAFLD). Ex vivo studies confirmed perturbed peroxisomes and revealed an association of hepatic catalase expression with clinical outcomes and phenotypes in HCV-associated cirrhosis, NAFLD and HCC cohorts. Conclusion: Our integrative analyses uncover how HCV perturbs the hepatocyte cell circuits to drive chronic liver disease and hepatocarcinogenesis. This proteogenomic atlas of HCV infection provides a model for the discovery of novel drivers for viral- and non-viral induced liver disease.
Samples
GSM ID Sample info Characteristics Description
GSM3614863 RNA.mock1.day0 cell line:Huh7.5.1; timecourse day:day 0; hcv infection:no -
GSM3614864 RNA.mock2.day0 cell line:Huh7.5.1; timecourse day:day 0; hcv infection:no -
GSM3614865 RNA.mock3.day0 cell line:Huh7.5.1; timecourse day:day 0; hcv infection:no -
GSM3614866 RNA.mock1.day1 cell line:Huh7.5.1; timecourse day:day 1; hcv infection:no -
GSM3614920 RNA.mock1.day10 cell line:Huh7.5.1; timecourse day:day 10; hcv infection:no -
GSM3614921 RNA.mock2.day10 cell line:Huh7.5.1; timecourse day:day 10; hcv infection:no -
GSM3614922 RNA.mock3.day10 cell line:Huh7.5.1; timecourse day:day 10; hcv infection:no -
GSM3614867 RNA.mock2.day1 cell line:Huh7.5.1; timecourse day:day 1; hcv infection:no -
GSM3614923 RNA.HCV1.day10 cell line:Huh7.5.1; timecourse day:day 10; hcv infection:yes -
GSM3614868 RNA.mock3.day1 cell line:Huh7.5.1; timecourse day:day 1; hcv infection:no -
GSM3614924 RNA.HCV2.day10 cell line:Huh7.5.1; timecourse day:day 10; hcv infection:yes -
GSM3614869 RNA.HCV1.day1 cell line:Huh7.5.1; timecourse day:day 1; hcv infection:yes -
GSM3614925 RNA.HCV3.day10 cell line:Huh7.5.1; timecourse day:day 10; hcv infection:yes -
GSM3614870 RNA.HCV2.day1 cell line:Huh7.5.1; timecourse day:day 1; hcv infection:yes -
GSM3614871 RNA.HCV3.day1 cell line:Huh7.5.1; timecourse day:day 1; hcv infection:yes -
GSM3614872 RNA.mock1.day2 cell line:Huh7.5.1; timecourse day:day 2; hcv infection:no -
GSM3614873 RNA.mock2.day2 cell line:Huh7.5.1; timecourse day:day 2; hcv infection:no -
GSM3614874 RNA.mock3.day2 cell line:Huh7.5.1; timecourse day:day 2; hcv infection:no -
GSM3614875 RNA.HCV1.day2 cell line:Huh7.5.1; timecourse day:day 2; hcv infection:yes -
GSM3614876 RNA.HCV2.day2 cell line:Huh7.5.1; timecourse day:day 2; hcv infection:yes -
GSM3614877 RNA.HCV3.day2 cell line:Huh7.5.1; timecourse day:day 2; hcv infection:yes -
GSM3614878 RNA.mock1.day3 cell line:Huh7.5.1; timecourse day:day 3; hcv infection:no -
GSM3614879 RNA.mock2.day3 cell line:Huh7.5.1; timecourse day:day 3; hcv infection:no -
GSM3614880 RNA.mock3.day3 cell line:Huh7.5.1; timecourse day:day 3; hcv infection:no -
GSM3614881 RNA.HCV1.day3 cell line:Huh7.5.1; timecourse day:day 3; hcv infection:yes -
GSM3614882 RNA.HCV2.day3 cell line:Huh7.5.1; timecourse day:day 3; hcv infection:yes -
GSM3614883 RNA.HCV3.day3 cell line:Huh7.5.1; timecourse day:day 3; hcv infection:yes -
GSM3614884 RNA.mock1.day4 cell line:Huh7.5.1; timecourse day:day 4; hcv infection:no -
GSM3614885 RNA.mock2.day4 cell line:Huh7.5.1; timecourse day:day 4; hcv infection:no -
GSM3614886 RNA.mock3.day4 cell line:Huh7.5.1; timecourse day:day 4; hcv infection:no -
GSM3614887 RNA.HCV1.day4 cell line:Huh7.5.1; timecourse day:day 4; hcv infection:yes -
GSM3614888 RNA.HCV2.day4 cell line:Huh7.5.1; timecourse day:day 4; hcv infection:yes -
GSM3614889 RNA.HCV3.day4 cell line:Huh7.5.1; timecourse day:day 4; hcv infection:yes -
GSM3614890 RNA.mock1.day5 cell line:Huh7.5.1; timecourse day:day 5; hcv infection:no -
GSM3614891 RNA.mock2.day5 cell line:Huh7.5.1; timecourse day:day 5; hcv infection:no -
GSM3614892 RNA.mock3.day5 cell line:Huh7.5.1; timecourse day:day 5; hcv infection:no -
GSM3614893 RNA.HCV1.day5 cell line:Huh7.5.1; timecourse day:day 5; hcv infection:yes -
GSM3614894 RNA.HCV2.day5 cell line:Huh7.5.1; timecourse day:day 5; hcv infection:yes -
GSM3614895 RNA.HCV3.day5 cell line:Huh7.5.1; timecourse day:day 5; hcv infection:yes -
GSM3614896 RNA.mock1.day6 cell line:Huh7.5.1; timecourse day:day 6; hcv infection:no -
GSM3614897 RNA.mock2.day6 cell line:Huh7.5.1; timecourse day:day 6; hcv infection:no -
GSM3614898 RNA.mock3.day6 cell line:Huh7.5.1; timecourse day:day 6; hcv infection:no -
GSM3614899 RNA.HCV1.day6 cell line:Huh7.5.1; timecourse day:day 6; hcv infection:yes -
GSM3614900 RNA.HCV2.day6 cell line:Huh7.5.1; timecourse day:day 6; hcv infection:yes -
GSM3614901 RNA.HCV3.day6 cell line:Huh7.5.1; timecourse day:day 6; hcv infection:yes -
GSM3614902 RNA.mock1.day7 cell line:Huh7.5.1; timecourse day:day 7; hcv infection:no -
GSM3614903 RNA.mock2.day7 cell line:Huh7.5.1; timecourse day:day 7; hcv infection:no -
GSM3614904 RNA.mock3.day7 cell line:Huh7.5.1; timecourse day:day 7; hcv infection:no -
GSM3614905 RNA.HCV1.day7 cell line:Huh7.5.1; timecourse day:day 7; hcv infection:yes -
GSM3614906 RNA.HCV2.day7 cell line:Huh7.5.1; timecourse day:day 7; hcv infection:yes -
GSM3614907 RNA.HCV3.day7 cell line:Huh7.5.1; timecourse day:day 7; hcv infection:yes -
GSM3614908 RNA.mock1.day8 cell line:Huh7.5.1; timecourse day:day 8; hcv infection:no -
GSM3614909 RNA.mock2.day8 cell line:Huh7.5.1; timecourse day:day 8; hcv infection:no -
GSM3614910 RNA.mock3.day8 cell line:Huh7.5.1; timecourse day:day 8; hcv infection:no -
GSM3614911 RNA.HCV1.day8 cell line:Huh7.5.1; timecourse day:day 8; hcv infection:yes -
GSM3614912 RNA.HCV2.day8 cell line:Huh7.5.1; timecourse day:day 8; hcv infection:yes -
GSM3614913 RNA.HCV3.day8 cell line:Huh7.5.1; timecourse day:day 8; hcv infection:yes -
GSM3614914 RNA.mock1.day9 cell line:Huh7.5.1; timecourse day:day 9; hcv infection:no -
GSM3614915 RNA.mock2.day9 cell line:Huh7.5.1; timecourse day:day 9; hcv infection:no -
GSM3614916 RNA.mock3.day9 cell line:Huh7.5.1; timecourse day:day 9; hcv infection:no -
GSM3614917 RNA.HCV1.day9 cell line:Huh7.5.1; timecourse day:day 9; hcv infection:yes -
GSM3614918 RNA.HCV2.day9 cell line:Huh7.5.1; timecourse day:day 9; hcv infection:yes -
GSM3614919 RNA.HCV3.day9 cell line:Huh7.5.1; timecourse day:day 9; hcv infection:yes -
Platform GPL18573  : Illumina NextSeq 500 (Homo sapiens)
Literature 30978357  
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xCell Plot
* p<0.05 ** p<0.01