Novel interferon-sensitive genes unveiled by correlation-driven gene selection and systems biology

Sci Rep. 2021 Sep 10;11(1):18043. doi: 10.1038/s41598-021-97258-8.

Abstract

Interferons (IFNs) are key cytokines involved in alerting the immune system to viral infection. After IFN stimulation, cellular transcriptional profile critically changes, leading to the expression of several IFN stimulated genes (ISGs) that exert a wide variety of antiviral activities. Despite many ISGs have been already identified, a comprehensive network of coding and non-coding genes with a central role in IFN-response still needs to be elucidated. We performed a global RNA-Seq transcriptome profile of the HCV permissive human hepatoma cell line Huh7.5 and its parental cell line Huh7, upon IFN treatment, to define a network of genes whose coordinated modulation plays a central role in IFN-response. Our study adds molecular actors, coding and non-coding genes, to the complex molecular network underlying IFN-response and shows how systems biology approaches, such as correlation networks, network's topology and gene ontology analyses can be leveraged to this aim.

MeSH terms

  • Binding Sites
  • Cell Line, Tumor
  • Computational Biology / methods
  • Gene Expression Profiling* / methods
  • Gene Expression Regulation* / drug effects
  • Gene Regulatory Networks
  • Humans
  • Interferon Regulatory Factors / genetics*
  • Interferon Regulatory Factors / metabolism
  • Interferons / metabolism*
  • Interferons / pharmacology
  • Liver Neoplasms
  • Nucleotide Motifs
  • Protein Binding
  • Systems Biology / methods*
  • Transcriptome*

Substances

  • Interferon Regulatory Factors
  • Interferons