Understanding PRRSV Infection in Porcine Lung Based on Genome-Wide Transcriptome Response Identified by Deep Sequencing

Abstract

Porcine reproductive and respiratory syndrome (PRRS) has been one of the most economically important diseases affecting swine industry worldwide and causes great economic losses each year. PRRS virus (PRRSV) replicates mainly in porcine alveolar macrophages (PAMs) and dendritic cells (DCs) and develops persistent infections, antibody-dependent enhancement (ADE), interstitial pneumonia and immunosuppression. But the molecular mechanisms of PRRSV infection still are poorly understood. Here we report on the first genome-wide host transcriptional responses to classical North American type PRRSV (N-PRRSV) strain CH 1a infection using Solexa/Illumina's digital gene expression (DGE) system, a tag-based high-throughput transcriptome sequencing method, and analyse systematically the relationship between pulmonary gene expression profiles after N-PRRSV infection and infection pathology. Our results suggest that N-PRRSV appeared to utilize multiple strategies for its replication and spread in infected pigs, including subverting host innate immune response, inducing an anti-apoptotic and anti-inflammatory state as well as developing ADE. Upregulation expression of virus-induced pro-inflammatory cytokines, chemokines, adhesion molecules and inflammatory enzymes and inflammatory cells, antibodies, complement activation were likely to result in the development of inflammatory responses during N-PRRSV infection processes. N-PRRSV-induced immunosuppression might be mediated by apoptosis of infected cells, which caused depletion of immune cells and induced an anti-inflammatory cytokine response in which they were unable to eradicate the primary infection. Our systems analysis will benefit for better understanding the molecular pathogenesis of N-PRRSV infection, developing novel antiviral therapies and identifying genetic components for swine resistance/susceptibility to PRRS.

Antiviral Regulation in Porcine Monocytic Cells at Different Activation States

“…Because of the lack of an effective vaccine, PRRSV has devastated swine herds worldwide for more than 20 years with an estimated loss nearing $800 million annually in the United States (44). Furthermore, this porcine virus evolves rapidly to form novel, highly pathogenic strains, causing new pandemic threats, such as the highly pathogenic PRRSV first seen in China in 2006 (30,44). Activation statuses of monocytic cells regulate inflammation, tissue repair, antimicrobial activity, and T-and B-cell responses (1-5).…”

“…In this case, the differentially expressed genes between two samples were assayed based on an algorithm as described previously (29). Functional classification of genes was conducted through Gene Ontology using the DAVID web tool (29,30,39). This method maps all DEGs to GO terms in the database (http://www.geneontology.org/), calculates gene numbers for every term, and then uses a hypergeometric test to find significantly enriched GO terms in DEGs compared with the genome background.…”

“…The quality of RNA-Seq data was analyzed in terms of the proportion of gene-mapped reads and the saturation/randomness for genome-wide gene coverage using published procedures (29,30,39). Differentially expressed genes (DEGs) (genes with a false discovery rate [FDR] of Յ0.001, a fold change of Ͼ2) were profiled with an edgeR package (39).…”

“…Few studies have focused on the activation status of porcine monocytic cells or how cell activation status modulates antiviral immunity (27,28). Notably, in this study we focused on examining Gene Ontology (GO) analysis based on comparative transcriptomes revealed in macrophages at different activation statuses upon viral infection, rather than a transcriptomic comparison between infected and noninfected tissues/cells, which has been well documented in previous studies (29,30). In this context, we used a multiplex cytokine assay and transcriptomic sequencing (RNA-Seq) analysis to profile gene response pathways in porcine monocytic cells polarized to typical activation statuses and antiviral states.…”

<i>GBP6</i>: differential expression in pulmonary alveolar macrophages under PRRSV infection and association with blood parameters of its missense mutation

“…The spleen is the secondary lymphoid tissue in all vertebrates (Bar-Ephraim and Mebius, 2016), which means that the GBP6 protein probably expressed on the mature B cells, which migrate from the spleen to blood and settle in secondary lymphoid tissues to assist in the immune response (LeBien and Tedder, 2008). PRRSV enters and replicates in macrophages and lymph nodes present in the lung (Xiao et al, 2010), suggesting that expression of GBP6 in the lung was important in the immune surveillance system in the organs of the pig (Beyer et al, 2000).…”