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High-throughput Quantitative Real-time RT-PCR Assay for Determining Expression Profiles of Types I and III Interferon Subtypes
10:00

High-throughput Quantitative Real-time RT-PCR Assay for Determining Expression Profiles of Types I and III Interferon Subtypes

Published on: March 24, 2015

Gene expression profiling of the cellular transcriptional network regulated by alpha/beta interferon and its partial

Gary K Geiss1, Victoria S Carter, Yupeng He

  • 1Department of Microbiology, School of Medicine, University of Washington, Seattle 98195, USA.

Journal of Virology
|May 14, 2003
PubMed

Insights

Alpha/beta interferons (IFN-alpha/beta) are crucial for antiviral responses but many hepatitis C virus (HCV) strains resist treatment. This study reveals HCV nonstructural 5A protein interferes with IFN-stimulated gene expression, potentially explaining treatment resistance.

Area of Science:

  • Immunology
  • Virology
  • Molecular Biology

Background:

  • Alpha/beta interferons (IFN-alpha/beta) are key cytokines for antiviral and antiproliferative responses, clinically used for chronic hepatitis C virus (HCV) infection.
  • Many HCV isolates exhibit resistance to IFN therapy, a phenomenon not fully understood at the molecular level.

Purpose of the Study:

  • To investigate the global gene expression changes induced by IFN treatment across different human cell types.
  • To identify IFN-stimulated response elements (ISREs) involved in IFN-regulated gene expression.
  • To determine if HCV proteins, specifically NS5A, or replicons interfere with the cellular IFN response and contribute to treatment resistance.

Main Methods:

  • Global gene expression analysis using microarrays in response to IFN treatment in HeLa cells, liver cell lines, and primary fetal hepatocytes.
  • Identification and characterization of IFN-stimulated response elements (ISREs) in the genomic DNA upstream of IFN-stimulated genes.
  • Assessment of HCV NS5A protein and HCV subgenomic replicon effects on IFN-mediated gene induction in IFN-treated cells.

Main Results:

  • IFN treatment consistently induced 50 genes across all tested cell types and an additional 60 genes in a cell type-specific manner.
  • Novel putative ISREs were identified upstream of IFN-stimulated genes.
  • HCV NS5A protein partially inhibited the IFN-induced expression of 14 IFN-stimulated genes, likely by repressing ISRE-mediated transcription.
  • An HCV subgenomic replicon showed minimal impact on IFN-regulated gene expression.

Conclusions:

  • The cellular response to IFN involves a complex network of both conserved and cell type-specific gene induction.
  • HCV NS5A protein can disrupt the IFN signaling pathway by interfering with ISRE-mediated transcription, offering a potential mechanism for IFN resistance in HCV infection.
  • Comparing results from multiple model systems, such as cell lines expressing viral proteins versus those containing replicons, is crucial for understanding complex host-pathogen interactions like IFN resistance.

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