Location: Virus and Prion ResearchTitle: Reactomes of porcine alveolar macrophages infected with porcine reproductive and respiratory syndrome virus) Author
|Kehrli Jr, Marcus|
Submitted to: PLoS One
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 2/13/2013
Publication Date: 3/19/2013
Publication URL: http://handle.nal.usda.gov/10113/55959
Citation: Jiang, Z., Zhou, X., Michal, J.J., Wu, X.-L., Zhang, L., Zhang, M., Ding, B., Liu, B., Manoranjan, V.S., Neill, J.D., Harhay, G.P., Kehrli, Jr., M.E., Miller, L.C. 2013. Reactomes of porcine alveolar macrophages infected with porcine reproductive and respiratory syndrome virus. PLoS One. 8(3):e59229. Interpretive Summary: Porcine reproductive and respiratory syndrome virus (PRRSV) causes highly significant losses to the swine industry worldwide. The ability of the virus to persist in its host shows that it has mechanisms to evade host immune responses. This study examined the effect of porcine reproductive and respiratory virus (PRRSV) on how genes are expressed in porcine alveolar macrophages (PAMs). PAMs were chosen for this study because they are the primary targets of infection by PRRSV. Serial Analysis of Gene Expression (SAGE) is a powerful technique that allows a detailed and profound quantitative and qualitative knowledge of gene expression profile, with out previous knowledge of the sequence of analyzed genes. We determined the normal levels that genes are expressed in normal, non-infected PAM and then compared this to the gene expression levels in PRRSV-infected PAM at several times after infection using serial analysis of gene expression (SAGE). Here, we report the reactome dynamics, and identify pathways, that associate with variation in changes in gene expression occurring in the PRRSV-infected PAM in order to reveal the transcriptional events in response to virus replication and host resistance, thus providing new insight into molecular mechanisms involved in host genetic complexity of antiviral activities against PRRSV.
Technical 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.