Reactomes of Porcine Alveolar Macrophages Infected with Porcine Reproductive and Respiratory Syndrome Virus
Identifieur interne : 000A84 ( Main/Exploration ); précédent : 000A83; suivant : 000A85Reactomes of Porcine Alveolar Macrophages Infected with Porcine Reproductive and Respiratory Syndrome Virus
Auteurs : Zhihua Jiang [États-Unis] ; Xiang Zhou [États-Unis] ; Jennifer J. Michal [États-Unis] ; Xiao-Lin Wu [États-Unis] ; Lifan Zhang [États-Unis] ; Ming Zhang [États-Unis] ; Bo Ding [États-Unis] ; Bang Liu [République populaire de Chine] ; Valipuram S. Manoranjan [États-Unis] ; John D. Neill [États-Unis] ; Gregory P. Harhay [États-Unis] ; Marcus E. Kehrli [États-Unis] ; Laura C. Miller [États-Unis]Source :
- PLoS ONE [ 1932-6203 ] ; 2013.
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.
Url:
DOI: 10.1371/journal.pone.0059229
PubMed: 23527143
PubMed Central: 3602036
Affiliations:
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Michal</name><affiliation wicri:level="2"><nlm:aff id="aff1"><addr-line>Department of Animal Sciences, Washington State University, Pullman, Washington, United States of America</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Animal Sciences, Washington State University, Pullman, Washington</wicri:regionArea><placeName><region type="state">Washington (État)</region></placeName></affiliation></author><author><name sortKey="Wu, Xiao Lin" sort="Wu, Xiao Lin" uniqKey="Wu X" first="Xiao-Lin" last="Wu">Xiao-Lin Wu</name><affiliation wicri:level="2"><nlm:aff id="aff2"><addr-line>Department of Dairy Science, University of Wisconsin-Madison, Madison, Wisconsin, United States of America</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Dairy Science, University of Wisconsin-Madison, Madison, Wisconsin</wicri:regionArea><placeName><region type="state">Wisconsin</region></placeName></affiliation></author><author><name sortKey="Zhang, Lifan" sort="Zhang, Lifan" uniqKey="Zhang L" first="Lifan" last="Zhang">Lifan Zhang</name><affiliation wicri:level="2"><nlm:aff id="aff1"><addr-line>Department of Animal Sciences, Washington State University, Pullman, Washington, United States of America</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Animal Sciences, Washington State University, Pullman, Washington</wicri:regionArea><placeName><region type="state">Washington (État)</region></placeName></affiliation></author><author><name sortKey="Zhang, Ming" sort="Zhang, Ming" uniqKey="Zhang M" first="Ming" last="Zhang">Ming Zhang</name><affiliation wicri:level="2"><nlm:aff id="aff1"><addr-line>Department of Animal Sciences, Washington State University, Pullman, Washington, United States of America</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Animal Sciences, Washington State University, Pullman, Washington</wicri:regionArea><placeName><region type="state">Washington (État)</region></placeName></affiliation></author><author><name sortKey="Ding, Bo" sort="Ding, Bo" uniqKey="Ding B" first="Bo" last="Ding">Bo Ding</name><affiliation wicri:level="2"><nlm:aff id="aff1"><addr-line>Department of Animal Sciences, Washington State University, Pullman, Washington, United States of America</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Animal Sciences, Washington State University, Pullman, Washington</wicri:regionArea><placeName><region type="state">Washington (État)</region></placeName></affiliation></author><author><name sortKey="Liu, Bang" sort="Liu, Bang" uniqKey="Liu B" first="Bang" last="Liu">Bang Liu</name><affiliation wicri:level="1"><nlm:aff id="aff3"><addr-line>College of Animal Science and Technology, Huazhong Agricultural University, Hubei, China</addr-line></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>College of Animal Science and Technology, Huazhong Agricultural University, Hubei</wicri:regionArea><wicri:noRegion>Hubei</wicri:noRegion></affiliation></author><author><name sortKey="Manoranjan, Valipuram S" sort="Manoranjan, Valipuram S" uniqKey="Manoranjan V" first="Valipuram S." last="Manoranjan">Valipuram S. Manoranjan</name><affiliation wicri:level="2"><nlm:aff id="aff4"><addr-line>Department of Mathematics, Washington State University, Pullman, Washington, United States of America</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Mathematics, Washington State University, Pullman, Washington</wicri:regionArea><placeName><region type="state">Washington (État)</region></placeName></affiliation></author><author><name sortKey="Neill, John D" sort="Neill, John D" uniqKey="Neill J" first="John D." last="Neill">John D. Neill</name><affiliation wicri:level="2"><nlm:aff id="aff5"><addr-line>Ruminant Diseases and Immunology Research Unit, United States Department of Agriculture, Agricultural Research Service, National Animal Disease Center, Ames, Iowa, United States of America</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Ruminant Diseases and Immunology Research Unit, United States Department of Agriculture, Agricultural Research Service, National Animal Disease Center, Ames, Iowa</wicri:regionArea><placeName><region type="state">Iowa</region></placeName></affiliation></author><author><name sortKey="Harhay, Gregory P" sort="Harhay, Gregory P" uniqKey="Harhay G" first="Gregory P." last="Harhay">Gregory P. Harhay</name><affiliation wicri:level="2"><nlm:aff id="aff6"><addr-line>Animal Health Research Unit, United States Meat Animal Research Center, United States Department of Agriculture, Agricultural Research Service, Clay Center, Nebraska, United States of America</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Animal Health Research Unit, United States Meat Animal Research Center, United States Department of Agriculture, Agricultural Research Service, Clay Center, Nebraska</wicri:regionArea><placeName><region type="state">Nebraska</region></placeName></affiliation></author><author><name sortKey="Kehrli, Marcus E" sort="Kehrli, Marcus E" uniqKey="Kehrli M" first="Marcus E." last="Kehrli">Marcus E. Kehrli</name><affiliation wicri:level="2"><nlm:aff id="aff7"><addr-line>Virus and Prion Research Unit, National Animal Disease Center, United States Department of Agriculture, Agricultural Research Service, Ames, Iowa, United States of America</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Virus and Prion Research Unit, National Animal Disease Center, United States Department of Agriculture, Agricultural Research Service, Ames, Iowa</wicri:regionArea><placeName><region type="state">Iowa</region></placeName></affiliation></author><author><name sortKey="Miller, Laura C" sort="Miller, Laura C" uniqKey="Miller L" first="Laura C." last="Miller">Laura C. Miller</name><affiliation wicri:level="2"><nlm:aff id="aff7"><addr-line>Virus and Prion Research Unit, National Animal Disease Center, United States Department of Agriculture, Agricultural Research Service, Ames, Iowa, United States of America</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Virus and Prion Research Unit, National Animal Disease Center, United States Department of Agriculture, Agricultural Research Service, Ames, Iowa</wicri:regionArea><placeName><region type="state">Iowa</region></placeName></affiliation></author></analytic><series><title level="j">PLoS ONE</title><idno type="eISSN">1932-6203</idno><imprint><date when="2013">2013</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>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.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Goyal, Sm" uniqKey="Goyal S">SM Goyal</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Rossow, Kd" uniqKey="Rossow K">KD Rossow</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Albina, E" uniqKey="Albina E">E Albina</name></author><author><name sortKey="Madec, F" uniqKey="Madec F">F Madec</name></author><author><name sortKey="Cariolet, R" uniqKey="Cariolet R">R Cariolet</name></author><author><name sortKey="Torrison, J" uniqKey="Torrison J">J Torrison</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Park, Bk" uniqKey="Park B">BK 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sort="Jiang, Zhihua" uniqKey="Jiang Z" first="Zhihua" last="Jiang">Zhihua Jiang</name></region><name sortKey="Ding, Bo" sort="Ding, Bo" uniqKey="Ding B" first="Bo" last="Ding">Bo Ding</name><name sortKey="Harhay, Gregory P" sort="Harhay, Gregory P" uniqKey="Harhay G" first="Gregory P." last="Harhay">Gregory P. Harhay</name><name sortKey="Kehrli, Marcus E" sort="Kehrli, Marcus E" uniqKey="Kehrli M" first="Marcus E." last="Kehrli">Marcus E. Kehrli</name><name sortKey="Manoranjan, Valipuram S" sort="Manoranjan, Valipuram S" uniqKey="Manoranjan V" first="Valipuram S." last="Manoranjan">Valipuram S. Manoranjan</name><name sortKey="Michal, Jennifer J" sort="Michal, Jennifer J" uniqKey="Michal J" first="Jennifer J." last="Michal">Jennifer J. Michal</name><name sortKey="Miller, Laura C" sort="Miller, Laura C" uniqKey="Miller L" first="Laura C." last="Miller">Laura C. Miller</name><name sortKey="Neill, John D" sort="Neill, John D" uniqKey="Neill J" first="John D." last="Neill">John D. Neill</name><name sortKey="Wu, Xiao Lin" sort="Wu, Xiao Lin" uniqKey="Wu X" first="Xiao-Lin" last="Wu">Xiao-Lin Wu</name><name sortKey="Zhang, Lifan" sort="Zhang, Lifan" uniqKey="Zhang L" first="Lifan" last="Zhang">Lifan Zhang</name><name sortKey="Zhang, Ming" sort="Zhang, Ming" uniqKey="Zhang M" first="Ming" last="Zhang">Ming Zhang</name><name sortKey="Zhou, Xiang" sort="Zhou, Xiang" uniqKey="Zhou X" first="Xiang" last="Zhou">Xiang Zhou</name></country><country name="République populaire de Chine"><noRegion><name sortKey="Liu, Bang" sort="Liu, Bang" uniqKey="Liu B" first="Bang" last="Liu">Bang Liu</name></noRegion></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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