Genome-wide analysis of antiviral signature genes in porcine macrophages at different activation statuses

PLoS One. 2014 Feb 5;9(2):e87613. doi: 10.1371/journal.pone.0087613. eCollection 2014.

Abstract

Macrophages (MФs) can be polarized to various activation statuses, including classical (M1), alternative (M2), and antiviral states. To study the antiviral activation status of porcine MФs during porcine reproductive and respiratory syndrome virus (PRRSV) infection, we used RNA Sequencing (RNA-Seq) for transcriptomic analysis of differentially expressed genes (DEGs). Sequencing assessment and quality evaluation showed that our RNA-Seq data met the criteria for genome-wide transcriptomic analysis. Comparisons of any two activation statuses revealed more than 20,000 DEGs that were normalized to filter out 153-5,303 significant DEGs [false discovery rate (FDR) ≤0.001, fold change ≥2] in each comparison. The highest 5,303 significant DEGs were found between lipopolysaccharide- (LPS) and interferon (IFN)γ-stimulated M1 cells, whereas only 153 significant DEGs were detected between interleukin (IL)-10-polarized M2 cells and control mock-activated cells. To identify signature genes for antiviral regulation pertaining to each activation status, we identified a set of DEGs that showed significant up-regulation in only one activation state. In addition, pathway analyses defined the top 20-50 significantly regulated pathways at each activation status, and we further analyzed DEGs pertinent to pathways mediated by AMP kinase (AMPK) and epigenetic mechanisms. For the first time in porcine macrophages, our transcriptomic analyses not only compared family-wide differential expression of most known immune genes at different activation statuses, but also revealed transcription evidence of multiple gene families. These findings show that using RNA-Seq transcriptomic analyses in virus-infected and status-synchronized macrophages effectively profiled signature genes and gene response pathways for antiviral regulation, which may provide a framework for optimizing antiviral immunity and immune homeostasis.

Publication types

  • Comparative Study
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Animals
  • Gene Expression Regulation / immunology*
  • Genome-Wide Association Study
  • Macrophage Activation*
  • Macrophages / immunology*
  • Macrophages / metabolism
  • Porcine Reproductive and Respiratory Syndrome / immunology*
  • Porcine Reproductive and Respiratory Syndrome / metabolism
  • Porcine Reproductive and Respiratory Syndrome / pathology
  • Porcine respiratory and reproductive syndrome virus / immunology*
  • Porcine respiratory and reproductive syndrome virus / metabolism*
  • Swine

Grant support

This work was supported in part by USDA NIFA/DHS 2010-39559-21860 and USDA NIFA 2013-67015-21236. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.