Whole transcriptome analysis reveals differential gene expression profile reflecting macrophage polarization in response to influenza A H5N1 virus infection

Na Zhang,J S Malik Peiris,Amy Hin-Yan Tong,Gary D Bader,Suki Man-Yan Lee,Si Lok,Scott Zuyderduyn,Yun-Juan Bao

doi:10.1186/s12920-018-0335-0

Abstract

BackgroundAvian influenza A H5N1 virus can cause lethal disease in humans. The virus can trigger severe pneumonia and lead to acute respiratory distress syndrome. Data from clinical, in vitro and in vivo suggest that virus-induced cytokine dysregulation could be a contributory factor to the pathogenesis of human H5N1 disease. However, the precise mechanism of H5N1 infection eliciting the unique host response are still not well understood.MethodsTo obtain a better understanding of the molecular events at the earliest time points, we used RNA-Seq to quantify and compare the host mRNA and miRNA transcriptomes induced by the highly pathogenic influenza A H5N1 (A/Vietnam/3212/04) or low virulent H1N1 (A/Hong Kong/54/98) viruses in human monocyte-derived macrophages at 1-, 3-, and 6-h post infection.ResultsOur data reveals that two macrophage populations corresponding to M1 (classically activated) and M2 (alternatively activated) macrophage subtypes respond distinctly to H5N1 virus infection when compared to H1N1 virus or mock infection, a distinction that could not be made from previous microarray studies. When this confounding variable is considered in our statistical model, a clear set of dysregulated genes and pathways emerges specifically in H5N1 virus-infected macrophages at 6-h post infection, whilst was not found with H1N1 virus infection. Furthermore, altered expression of genes in these pathways, which have been previously implicated in viral host response, occurs specifically in the M1 subtype. We observe a significant up-regulation of genes in the RIG-I-like receptor signaling pathway. In particular, interferons, and interferon-stimulated genes are broadly affected. The negative regulators of interferon signaling, the suppressors of cytokine signaling, SOCS-1 and SOCS-3, were found to be markedly up-regulated in the initial round of H5N1 virus replication. Elevated levels of these suppressors could lead to the eventual suppression of cellular antiviral genes, contributing to pathophysiology of H5N1 virus infection.ConclusionsOur study provides important mechanistic insights into the understanding of H5N1 viral pathogenesis and the multi-faceted host immune responses. The dysregulated genes could be potential candidates as therapeutic targets for treating H5N1 disease.

Highlights

Avian influenza A H5N1 virus can cause lethal disease in humans
Macrophage heterogeneity and plasticity in response to H1N1 and H5N1 virus infection The mRNAs isolated from primary human macrophages after infection by H5N1, H1N1 viruses, or mock infection at 1, 3, and 6-h post infection were analyzed by RNA sequencing (RNA-Seq)
To assess if up-regulation of suppressors of cytokine signaling (SOCS) at early stages of H5N1 virus infection would correlate with decreased expression of antiviral IFNs later in infection, we extended our investigation to later time points

Summary

Introduction

Avian influenza A H5N1 virus can cause lethal disease in humans. The virus can trigger severe pneumonia and lead to acute respiratory distress syndrome. According to the World Health Organization, there were 856 human reported cases of influenza A H5N1 virus infection resulting in 452 deaths from January 2003 to May 2017; the fatality rate was over 50% Contributory factors such as high viral load in the infected lungs, tropism for the lower respiratory tract as well as dysregulated host response after infection have been proposed to explain the unusual virulence of this virus [1, 2]. We previously reported that H5N1 virus infection triggers high pro-inflammatory cytokine and chemokine expression in primary human macrophages compared to that by seasonal H1N1 virus infection These data suggest that dysregulated host response contributes to the pathogenesis of H5N1 virus infection, the precise mechanisms as well as the host response profile has not been well studied

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