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Transcriptional profiling of liver biopsies of precancerous viral hepatitis patients

ABSTRACT: This SuperSeries is composed of the SubSeries listed below.

ORGANISM(S): Homo sapiens

PROVIDER: GSE237332 | GEO | 2025/12/15

REPOSITORIES: GEO

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Transcriptional profiling of liver biopsies of precancerous viral hepatitis patients: Validation cohort

Project description:We used RNA-seq to map the transcriptomes of archived formalin-fixed paraffin-embedded (FFPE) liver biopsies from precancerous chronic viral hepatitis patients with known clinical outcome. This Series contains the validation cohort used to validate the predictive transcriptomic signature.

2025-12-02 | GSE237331 | GEO

Transcriptional profiling of liver biopsies of precancerous viral hepatitis patients: Training cohort

Project description:We used RNA-seq to map the transcriptomes of archived formalin-fixed paraffin-embedded (FFPE) liver biopsies from precancerous chronic viral hepatitis patients with known clinical outcome. This Series contains the training cohort used to generate the predictive transcriptomic signature.

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Transcriptional profiling of liver biopsies of precancerous viral hepatitis patients

Project description:Transcriptional profiling of liver biopsies of precancerous viral hepatitis patients

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Transcriptional profiling of liver biopsies of precancerous viral hepatitis patients: Validation cohort

Project description:Transcriptional profiling of liver biopsies of precancerous viral hepatitis patients: Validation cohort

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Transcriptional profiling of liver biopsies of precancerous viral hepatitis patients: Training cohort

Project description:Transcriptional profiling of liver biopsies of precancerous viral hepatitis patients: Training cohort

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microRNA and mRNA expression in human hepatitis C Virus liver biopsies

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series This dataset is part of the TransQST collection.

2010-03-08 | E-GEOD-15387 | biostudies-arrayexpress

Targeted Transcriptional Profiling of Kidney Transplant Biopsies.

Project description:IntroductionStudies are needed to assess the quality of transcriptome analysis in paired human tissue samples preserved by different methods and different gene amplification platforms to enable data comparisons across experimenters.MethodsRNA was extracted from kidney biopsies, either submerged in RNA-stabilizing solution (RSS) or stored in formalin-fixed, paraffin-embedded (FFPE) blocks. RNA quality and integrity were compared. Gene expression of the common rejection module and other immune cell genes were quantified for both tissue preservation methods in the same sample using conventional quantitative polymerase chain reaction (QPCR) by 2 different commercial platforms, (fluidigm [FD]) or barcoded-oligos (nanostring [NS]).ResultsRNA quality was inferior in FFPE tissues. Despite this, gene expression for 19 measured genes on the same sample, stored in FFPE or RSS, were strongly correlated on the FD (r = 0.81) or NS platforms (r = 0.82). For the same samples, interplatform gene expression correlations were excellent (r = 0.80) for RSS and moderate (r = 0.66) for FFPE. Significant differences in gene expression were confirmed on both platforms (FD: P = 1.1E-03; NS: P = 2.5E-04) for biopsy-confirmed acute rejection.ConclusionOur study provided supportive evidence that despite a low RNA quality of archival FFPE kidney transplantation tissue, small quantities of this tissue can be obtained from existing paraffin blocks to provide a viable and rich biospecimen source for focused gene expression assays. In addition, reliable and reproducible gene expression evaluation can be performed on these FFPE tissues using either a QPCR-based or a barcoded-oligo approach, which provides opportunities for collaborative analytics.

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Liver gene expression profiles of interferon therapy in chronic hepatitis B Patients

Project description:This SuperSeries is composed of the SubSeries listed below.

2017-02-09 | GSE66700 | GEO

Real-time quantitative PCR analysis of human liver biopsies and PBMCs from HBV+ patients, HCV+ patients and healthy donors

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

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Gene expression profiling of liver biopsies from 21 chronic hepatitis C patients undergoing antiviral therapy

Project description:Pegylated interferon-α (pegIFN-α) has replaced un-modified recombinant IFN-α for the treatment of chronic viral hepatitis because of its superior anti-viral efficacy that is generally attributed to improved pharmacokinetic properties. However, the pharmacodynamic effects of pegIFN-α in the liver have not been studied. We analyzed pegIFN-α induced signaling and gene regulation in paired liver biopsies obtained before treatment and during the first week after injection of pegIFN-α in 18 patients. Despite sustained high serum concentrations of pegIFN-α over the entire one-week dosing interval, IFN-α signaling through the Jak-STAT pathway occurs only during the first day. PegIFN-α induces hundreds of genes that can be classified into 4 clusters based on different temporal expression profiles. In all clusters, gene transcription is mainly driven by IFN stimulated gene factor 3 (ISGF3). IFN induced secondary transcription factors do not cause additional waves of gene expression. We could not confirm a role of un-phosphorylated STAT1 in prolonging IFN-α induced gene transcription. Collectively, our results reveal that the major effects of pegIFN-α in the liver are caused by an early and transient activation of ISGF3. Prolonging the serum half-life of IFN-α does not necessarily improve its pharmacodynamic properties.

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