MRNA expression in human hepatitis c virus (HCV) liver biopsy samples
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE15331 | GEO | 2010/03/08
SECONDARY ACCESSION(S): PRJNA123229
REPOSITORIES: GEO
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Project description:In order to infer the inverse expression relationships between microRNAs and mRNAs during HCV infection, we profiled both microRNA and mRNA expressions in HCV positive (HCV+) and HCV negative (HCV-) human liver biopsy tissue samples. This series includes all microRNA profiles.
2010-03-08 | GSE15288 | GEO
Project description:In order to infer the inverse expression relationships between microRNAs and mRNAs during HCV infection, we profiled both microRNA and mRNA expressions in HCV positive (HCV+) and HCV negative (HCV-) human liver biopsy tissue samples. This series includes all microRNA profiles. This series includes microRNA profiles of 36 samples, 24 HCV positives and 12 HCV negatives.
2010-05-06 | E-GEOD-15288 | biostudies-arrayexpress
Project description:Hepatic complications of HCV infection, including fibrosis and cirrhosis are accelerated in HIV-infected individuals. Although liver biopsy remains the gold standard for staging HCV-associated liver disease, this test can result in serious complications and is subject to sampling error. These challenges have prompted a search for non-invasive methods for liver fibrosis staging. To this end, we compared serum proteome profiles at different stages of fibrosis in HIV/HCV co- and HCV mono-infected patients using SELDI-TOF MS.
2018-04-09 | PXD009007 | Pride
Project description:Transcriptional profiling of chimp 190 liver biopsy comparing baseline sample with biopsy taken different days after innoculation with HCV Keywords: Genetic modification
2008-04-10 | GSE11104 | GEO
Project description:Hepatitis C virus uniquely requires the liver specific microRNA-122 for replication, yet global effects on endogenous miRNA targets during infection are unexplored. Here, high-throughput sequencing and crosslinking immunoprecipitation (HITS-CLIP) experiments of human Argonaute (Ago) during HCV infection showed robust Ago binding on the HCV 5’UTR, at known and predicted miR-122 sites. On the human transcriptome, we observed reduced Ago binding and functional mRNA de-repression of miR-122 targets during virus infection. This miR-122 “sponge” effect could be relieved and redirected to miR-15 targets by swapping the miRNA tropism of the virus. Single-cell expression data from reporters containing miR-122 sites showed significant de-repression during HCV infection depending on expression level and number of sites. We describe a quantitative mathematical model of HCV induced miR-122 sequestration and propose that such miR-122 inhibition by HCV RNA may result in global de-repression of host miR-122 targets, providing an environment fertile for the long-term oncogenic potential of HCV.
2015-01-06 | GSE64675 | GEO
Project description:Hepatitis C virus uniquely requires the liver specific microRNA-122 for replication, yet global effects on endogenous miRNA targets during infection are unexplored. Here, high-throughput sequencing and crosslinking immunoprecipitation (HITS-CLIP) experiments of human Argonaute (Ago) during HCV infection showed robust Ago binding on the HCV 5’UTR, at known and predicted miR-122 sites. On the human transcriptome, we observed reduced Ago binding and functional mRNA de-repression of miR-122 targets during virus infection. This miR-122 “sponge” effect could be relieved and redirected to miR-15 targets by swapping the miRNA tropism of the virus. Single-cell expression data from reporters containing miR-122 sites showed significant de-repression during HCV infection depending on expression level and number of sites. We describe a quantitative mathematical model of HCV induced miR-122 sequestration and propose that such miR-122 inhibition by HCV RNA may result in global de-repression of host miR-122 targets, providing an environment fertile for the long-term oncogenic potential of HCV. AGO HITS-CLIP libraries were generated from mock or J6/JFH1 Clone2 infected Huh7.5 cells. Cells were infected at an MOI of 1-2 and harvested 72hours post-infection for CLIP. Libraries were generated with a 4nt index read, a common priming sequence, followed by a 5nt degenerate barcode terminiating in a G. Files have been demultiplexed such that the 5nt degenerate barcode has been appended as the first 5 nucleotides of the read.
2015-01-06 | E-GEOD-64675 | biostudies-arrayexpress
Project description:Introduction: Mechanisms that contribute to the pathogenesis of liver damage caused by hepatitis C virus (HCV) are not fully understood. Our previous work on liver biopsies from chronic HCV patients has shown modulation of the expression of certain cell cycle proteins indicating HCV-induced modifications of cell cycle events. We therefore hypothesize that HCV infection disrupts normal regulation of cell cycle that contributes to disease progression. Objective: To identify molecular disruptions during the course of HCV-associated disease progression, using liver biopsy specimens of chronic hepatitis C patients. Methods: Liver biopsy samples classified on histological basis as early (fibrosis stage 0-1) or advanced (fibrosis stage 3-4) disease stage were studied using oligonucleotide array ( HG U133 Plus 2.0, Affymetrix GeneChip™ System). For comparison, liver specimens from patients with non-viral hepatitis were also analyzed by microarray. Expression data was analyzed using Genespring (GX 7.2) and Ingenuity Pathway analysis (3.0). The differential expression of selected cell cycle genes (cyclin D2, KPNA2, HERC5 and Bcl-2) identified after microarray analysis was confirmed by quantitative real-time RT-PCR. Results: Microarray analysis revealed two-fold or greater transcriptional change in 792 genes of the total 38,500 known human genes in HCV-advance disease stage (HCV-A) as compared to HCV-early disease stage (HCV-E). Most of the genes have a defined role in immune response, extracellular matrix and cell cycle and apoptosis. Keywords: HCV-advance disease state
2007-11-01 | GSE7741 | GEO
Project description:Transcriptional profiling of HCV core transgenic mice liver comparing nontransgenic mice liver or HCV core transgenic mice liver with various core expression levels.
2013-12-31 | GSE16403 | GEO
Project description:Transcriptional profiling of chimp 190 liver biopsy comparing baseline sample with biopsy taken different days after innoculation with HCV Two-condition experiment, baseline vs. infected at weeks 19, 20, 21 and 32 post infection: One replicate per array.
2008-04-10 | E-GEOD-11104 | biostudies-arrayexpress
Project description:In this study, we evaluated transcriptional responses in circulating leukocytes to assess for biomarkers of adverse outcomes in transplant patients after transplantation from a HCV-infected donor. We enrolled renal transplant recipients with and without HCV and performed RNA sequencing on serial samples. CMV DNAemia and allograft rejection outcomes were measured. Regularized logistic regression was utilized to develop gene expression classifiers predictive of clinical outcomes.
2023-02-08 | GSE213705 | GEO