Reactomes of Porcine Alveolar Macrophages Infected with Porcine Reproductive and Respiratory Syndrome Virus

Abstract

Porcine reproductive and respiratory syndrome (PRRS) has devastated pig industries worldwide for many years. It is caused by a small RNA virus (PRRSV), which targets almost exclusively pig monocytes or macrophages. In the present study, five SAGE (serial analysis of gene expression) libraries derived from 0 hour mock-infected and 6, 12, 16 and 24 hours PRRSV-infected porcine alveolar macrophages (PAMs) produced a total 643,255 sequenced tags with 91,807 unique tags. Differentially expressed (DE) tags were then detected using the Bayesian framework followed by gene/mRNA assignment, arbitrary selection and manual annotation, which determined 699 DE genes for reactome analysis. The DAVID, KEGG and REACTOME databases assigned 573 of the DE genes into six biological systems, 60 functional categories and 504 pathways. The six systems are: cellular processes, genetic information processing, environmental information processing, metabolism, organismal systems and human diseases as defined by KEGG with modification. Self-organizing map (SOM) analysis further grouped these 699 DE genes into ten clusters, reflecting their expression trends along these five time points. Based on the number one functional category in each system, cell growth and death, transcription processes, signal transductions, energy metabolism, immune system and infectious diseases formed the major reactomes of PAMs responding to PRRSV infection. Our investigation also focused on dominant pathways that had at least 20 DE genes identified, multi-pathway genes that were involved in 10 or more pathways and exclusively-expressed genes that were included in one system. Overall, our present study reported a large set of DE genes, compiled a comprehensive coverage of pathways, and revealed system-based reactomes of PAMs infected with PRRSV. We believe that our reactome data provides new insight into molecular mechanisms involved in host genetic complexity of antiviral activities against PRRSV and lays a strong foundation for vaccine development to control PRRS incidence in pigs.

RNA-Sequence Analysis of Primary Alveolar Macrophages after In Vitro Infection with Porcine Reproductive and Respiratory Syndrome Virus Strains of Differing Virulence

“…Such studies have shown that the expression levels of MX1 , USP , IFN-β , IL-10 and TNF-α are affected by PRRSV infection [18], [19]. Overall, these analyses suggest that PRRSV subverts host defenses by inhibiting the expression of pro-inflammatory cytokines [20]–[22] and stimulating weak production of IFN-α [reviewed in 23].…”

Regulation and evasion of antiviral immune responses by porcine reproductive and respiratory syndrome virus

“…Since described in USA in 1987, porcine reproductive and respiratory syndrome (PRRS) has now been one of the most important diseases in pigs, leading to significant economic losses in swine industry worldwide (Albina, 1997;Pejsak et al, 1997;Rossow, 1998). In 2005, the annual costs of PRRS for the American swine industry were approximately 560 million dollars (Neumann et al, 2005), and recently, the estimated costs are increased to about $664 million per year in the United States (Jiang et al, 2013). In the past twenty-seven years, PRRS has emerged in almost all of the pig-producing countries (Bilodeau et al, 1991;Cho and Dee, 2006;Kuwahara et al, 1994).…”

Whole transcriptome analysis with sequencing: methods, challenges and potential solutions

“…The long tags or targets certainly make it easier and more accurate to assign them to genes/transcripts. In terms of data amount, a conventional SAGE analysis usually results in less than 20,000 tag reads per library [59]. However, a typical SAG-seq run (DGETP) can now provide many tag reads, ranging from 3 to 30 million reads.…”