Comparison of the Transcriptome Response within the Swine Tracheobronchial Lymphnode Following Infection with PRRSV, PCV-2 or IAV-S.

Miller,; Fleming,; Lager,

doi:10.3390/pathogens9020099

Title: Comparison of the Transcriptome Response within the Swine Tracheobronchial Lymphnode Following Infection with PRRSV, PCV-2 or IAV-S.

Journal Article · Wed Feb 05 00:00:00 EST 2020 · Pathogens

DOI:https://doi.org/10.3390/pathogens9020099· OSTI ID:1598054

Miller,; Fleming,; Lager,

Porcine reproductive and respiratory syndrome virus (PRRSV) is a major respiratory pathogen of swine that has become extremely costly to the swine industry worldwide, often causing losses in production and animal life due to their ease of spread. However, the intracellular changes that occur in pigs following viral respiratory infections are still scantily understood for PRRSV, as well as other viral respiratory infections. The aim of this study was to acquire a better understanding of the PRRS disease by comparing gene expression changes that occur in tracheobronchial lymph nodes (TBLN) of pigs infected with either porcine reproductive and respiratory syndrome virus (PRRSV), porcine circovirus type 2 (PCV-2), or swine influenza A virus (IAV-S) infections. The study identified and compared gene expression changes in the TBLN of 80 pigs following infection by PRRSV, PCV-2, IAV-S, or sham inoculation. Total RNA was pooled for each group and time-point (1, 3, 6, and 14 dpi) to make 16 libraries—analyses are by Digital Gene Expression Tag Profiling (DGETP). The data underwent standard filtering to generate a list of sequence tag raw counts that were then analyzed using multidimensional and differential expression statistical tests. The results showed that PRRSV, IAV-S and PCV-2 viral infections followed a clinical course in the pigs typical of experimental infection of young pigs with these viruses. Gene expression results echoed this course, as well as uncovered genes related to intersecting and unique host immune responses to the three viruses. By testing and observing the host response to other respiratory viruses, our study has elucidated similarities and differences that can assist in the development of vaccines and therapeutics that shorten or prevent a chronic PRRSV infection.

View Journal Article

Cite

Export

Save

Sponsoring Organization:: USDOE

Grant/Contract Number:: AC05-06OR23100

OSTI ID:: 1598054

Journal Information:: Pathogens, Journal Name: Pathogens Vol. 9 Journal Issue: 2; ISSN 2076-0817

Publisher:: MDPI AGCopyright Statement

Country of Publication:: Switzerland

Language:: English

Citation Metrics:

Cited by: 5 works

Citation information provided by
Web of Science

References (50)

Neutrophil granules: a library of innate immunity proteins Borregaard, Niels; Sørensen, Ole E.; Theilgaard-Mönch, Kim Trends in Immunology, Vol. 28, Issue 8 https://doi.org/10.1016/j.it.2007.06.002	journal	August 2007
UniProt: the universal protein knowledgebase Nucleic Acids Research, Vol. 45, Issue D1, p. D158-D169 https://doi.org/10.1093/nar/gkw1099	journal	November 2016
In vitro and ex vivo analyses of co-infections with swine influenza and porcine reproductive and respiratory syndrome viruses Dobrescu, I.; Levast, B.; Lai, K. Veterinary Microbiology, Vol. 169, Issue 1-2 https://doi.org/10.1016/j.vetmic.2013.11.037	journal	February 2014
g:Profiler—a web server for functional interpretation of gene lists (2016 update) Reimand, Jüri; Arak, Tambet; Adler, Priit Nucleic Acids Research, Vol. 44, Issue W1 https://doi.org/10.1093/nar/gkw199	journal	April 2016
AmiGO: online access to ontology and annotation data Carbon, Seth; Ireland, Amelia; Mungall, Christopher J. Bioinformatics, Vol. 25, Issue 2 https://doi.org/10.1093/bioinformatics/btn615	journal	November 2008
Mortality in pigs given porcine circovirus type 2 subgroup 1 and 2 viruses derived from DNA clones Lager, K. M.; Gauger, P. C.; Vincent, A. L. Veterinary Record, Vol. 161, Issue 12 https://doi.org/10.1136/vr.161.12.428	journal	September 2007
Transcriptome analysis of subcutaneous adipose tissues in beef cattle using 3′ digital gene expression-tag profiling1 Jin, W.; Olson, E. N.; Moore, S. S. Journal of Animal Science, Vol. 90, Issue 1 https://doi.org/10.2527/jas.2011-4229	journal	January 2012
Importance of TFEB acetylation in control of its transcriptional activity and lysosomal function in response to histone deacetylase inhibitors Zhang, Jianbin; Wang, Jigang; Zhou, Zhihong Autophagy https://doi.org/10.1080/15548627.2018.1447290	journal	July 2018
Genes controlling vaccine responses and disease resistance to respiratory viral pathogens in cattle Glass, Elizabeth J.; Baxter, Rebecca; Leach, Richard J. Veterinary Immunology and Immunopathology, Vol. 148, Issue 1-2 https://doi.org/10.1016/j.vetimm.2011.05.009	journal	July 2012
Whole Transcriptome Profiling of Successful Immune Response to Vibrio Infections in the Oyster Crassostrea gigas by Digital Gene Expression Analysis de Lorgeril, Julien; Zenagui, Reda; Rosa, Rafael D. PLoS ONE, Vol. 6, Issue 8 https://doi.org/10.1371/journal.pone.0023142	journal	August 2011
The Reactome Pathway Knowledgebase Fabregat, Antonio; Jupe, Steven; Matthews, Lisa Nucleic Acids Research, Vol. 46, Issue D1 https://doi.org/10.1093/nar/gkx1132	journal	November 2017
Economic analysis of outbreaks of porcine reproductive and respiratory syndrome virus in nine sow herds Nieuwenhuis, N.; Duinhof, T. F.; van Nes, A. Veterinary Record, Vol. 170, Issue 9 https://doi.org/10.1136/vr.100101	journal	January 2012
The independence of and associations among apoptosis, autophagy, and necrosis Chen, Qi; Kang, Jian; Fu, Caiyun Signal Transduction and Targeted Therapy, Vol. 3, Issue 1 https://doi.org/10.1038/s41392-018-0018-5	journal	July 2018
Induction of interleukin-10 is dependent on p38 mitogen-activated protein kinase pathway in macrophages infected with porcine reproductive and respiratory syndrome virus Hou, Jun; Wang, Lianghai; Quan, Rong Virology Journal, Vol. 9, Issue 1 https://doi.org/10.1186/1743-422X-9-165	journal	January 2012
Porcine reproductive and respiratory syndrome virus triggers mitochondrial fission and mitophagy to attenuate apoptosis Li, Shuaifeng; Wang, Jiaxing; Zhou, Ao Oncotarget, Vol. 7, Issue 35 https://doi.org/10.18632/oncotarget.10817	journal	July 2016
Translational Control of Viral Gene Expression in Eukaryotes Gale, Michael; Tan, Seng-Lai; Katze, Michael G. Microbiology and Molecular Biology Reviews, Vol. 64, Issue 2 https://doi.org/10.1128/MMBR.64.2.239-280.2000	journal	June 2000
The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update Afgan, Enis; Baker, Dannon; van den Beek, Marius Nucleic Acids Research, Vol. 44, Issue W1 https://doi.org/10.1093/nar/gkw343	journal	May 2016
featureCounts: an efficient general purpose program for assigning sequence reads to genomic features Liao, Y.; Smyth, G. K.; Shi, W. Bioinformatics, Vol. 30, Issue 7 https://doi.org/10.1093/bioinformatics/btt656	journal	November 2013
Comparative analysis of signature genes in PRRSV-infected porcine monocyte-derived cells to different stimuli Miller, Laura C.; Fleming, Damarius S.; Li, Xiangdong PLOS ONE, Vol. 12, Issue 7 https://doi.org/10.1371/journal.pone.0181256	journal	July 2017
Small leucine-rich proteoglycans orchestrate receptor crosstalk during inflammation Moreth, Kristin; Iozzo, Renato V.; Schaefer, Liliana Cell Cycle, Vol. 11, Issue 11 https://doi.org/10.4161/cc.20316	journal	June 2012
Porcine circovirus type 2 (PCV2) infections: Clinical signs, pathology and laboratory diagnosis Segalés, Joaquim Virus Research, Vol. 164, Issue 1-2 https://doi.org/10.1016/j.virusres.2011.10.007	journal	March 2012
HERC5 is an IFN-induced HECT-type E3 protein ligase that mediates type I IFN-induced ISGylation of protein targets Wong, J. J. Y.; Pung, Y. F.; Sze, N. S. -K. Proceedings of the National Academy of Sciences, Vol. 103, Issue 28 https://doi.org/10.1073/pnas.0600397103	journal	June 2006
Swine as a Model for Influenza A Virus Infection and Immunity Rajao, D. S.; Vincent, A. L. ILAR Journal, Vol. 56, Issue 1 https://doi.org/10.1093/ilar/ilv002	journal	May 2015
FQC Dashboard: integrates FastQC results into a web-based, interactive, and extensible FASTQ quality control tool Brown, Joseph; Pirrung, Meg; McCue, Lee Ann Bioinformatics, Vol. 33, Issue 19 https://doi.org/10.1093/bioinformatics/btx373	journal	June 2017
Tag-based approaches for transcriptome research and genome annotation Harbers, Matthias; Carninci, Piero Nature Methods, Vol. 2, Issue 7 https://doi.org/10.1038/nmeth768	journal	July 2005
Viral subversion of the host protein synthesis machinery Walsh, Derek; Mohr, Ian Nature Reviews Microbiology, Vol. 9, Issue 12 https://doi.org/10.1038/nrmicro2655	journal	October 2011
Characterization of a newly emerged genetic cluster of H1N1 and H1N2 swine influenza virus in the United States Vincent, Amy L.; Ma, Wenjun; Lager, Kelly M. Virus Genes, Vol. 39, Issue 2 https://doi.org/10.1007/s11262-009-0386-6	journal	July 2009
Digital Gene Expression by Tag Sequencing on the Illumina Genome Analyzer Morrissy, Sorana; Zhao, Yongjun; Delaney, Allen Current Protocols in Human Genetics, Vol. 65, Issue 1 https://doi.org/10.1002/0471142905.hg1111s65	journal	April 2010
Fcγ Receptor Signaling in Phagocytes Joshi, Trupti; Butchar, Jonathan; Tridandapani, Susheela International Journal of Hematology, Vol. 84, Issue 3 https://doi.org/10.1532/IJH97.06140	journal	October 2006
Mycoplasma hyopneumoniae: From disease to vaccine development Simionatto, Simone; Marchioro, Silvana Beutinger; Maes, Dominiek Veterinary Microbiology, Vol. 165, Issue 3-4 https://doi.org/10.1016/j.vetmic.2013.04.019	journal	August 2013
g:Profiler—a web-based toolset for functional profiling of gene lists from large-scale experiments Reimand, Jüri; Kull, Meelis; Peterson, Hedi Nucleic Acids Research, Vol. 35, Issue suppl_2 https://doi.org/10.1093/nar/gkm226	journal	July 2007
A Role for Neutrophils in Viral Respiratory Disease Camp, Jeremy V.; Jonsson, Colleen B. Frontiers in Immunology, Vol. 8 https://doi.org/10.3389/fimmu.2017.00550	journal	May 2017
Spread like a wildfire—The omnipresence of porcine circovirus type 2 (PCV2) and its ever-expanding association with diseases in pigs Meng, Xiang-Jin Virus Research, Vol. 164, Issue 1-2 https://doi.org/10.1016/j.virusres.2011.12.005	journal	March 2012
Gross and Microscopic Lesions in Porcine Fetuses Infected with Porcine Reproductive and Respiratory Syndrome Virus Lager, Kelly M.; Halbur, Patrick G. Journal of Veterinary Diagnostic Investigation, Vol. 8, Issue 3 https://doi.org/10.1177/104063879600800301	journal	July 1996
Pathogenesis of rhinovirus infection Kennedy, Joshua L.; Turner, Ronald B.; Braciale, Thomas Current Opinion in Virology, Vol. 2, Issue 3 https://doi.org/10.1016/j.coviro.2012.03.008	journal	June 2012
Effective control of viral infections by the adaptive immune system requires assistance from innate immunity Barra, Nicole G.; Gillgrass, Amy; Ashkar, Ali A. Expert Review of Vaccines, Vol. 9, Issue 10 https://doi.org/10.1586/erv.10.119	journal	October 2010
Reactome pathway analysis: a high-performance in-memory approach Fabregat, Antonio; Sidiropoulos, Konstantinos; Viteri, Guilherme BMC Bioinformatics, Vol. 18, Issue 1 https://doi.org/10.1186/s12859-017-1559-2	journal	March 2017
Innate pro-inflammatory and adaptive immune cytokines in PBMC of vaccinated and unvaccinated pigs naturally exposed to porcine circovirus type 2 (PCV2) infection vary with the occurrence of the disease and the viral burden Borghetti, Paolo; Morganti, Marina; Saleri, Roberta Veterinary Microbiology, Vol. 163, Issue 1-2 https://doi.org/10.1016/j.vetmic.2012.12.007	journal	April 2013
Gene: a gene-centered information resource at NCBI Brown, Garth R.; Hem, Vichet; Katz, Kenneth S. Nucleic Acids Research, Vol. 43, Issue D1 https://doi.org/10.1093/nar/gku1055	journal	October 2014
Control of adaptive immunity by the innate immune system Iwasaki, Akiko; Medzhitov, Ruslan Nature Immunology, Vol. 16, Issue 4 https://doi.org/10.1038/ni.3123	journal	March 2015
Modification of intracellular membrane structures for virus replication Miller, Sven; Krijnse-Locker, Jacomine Nature Reviews Microbiology, Vol. 6, Issue 5 https://doi.org/10.1038/nrmicro1890	journal	May 2008
Immunopathological effects of porcine circovirus type 2 (PCV2) on swine alveolar macrophages by in vitro inoculation Chang, Hui-Wen; Jeng, Chian-Ren; Lin, Tsang-Long Veterinary Immunology and Immunopathology, Vol. 110, Issue 3-4 https://doi.org/10.1016/j.vetimm.2005.09.016	journal	April 2006
Analysis of the swine tracheobronchial lymph node transcriptomic response to infection with a Chinese highly pathogenic strain of porcine reproductive and respiratory syndrome virus Miller, Laura C.; Fleming, Damarius; Arbogast, Andrew BMC Veterinary Research, Vol. 8, Issue 1 https://doi.org/10.1186/1746-6148-8-208	journal	January 2012
Influenza A Virus Infection in Pigs Attracts Multifunctional and Cross-Reactive T Cells to the Lung Talker, Stephanie C.; Stadler, Maria; Koinig, Hanna C. Journal of Virology, Vol. 90, Issue 20 https://doi.org/10.1128/JVI.01211-16	journal	August 2016
UniProt: a hub for protein information Consortium, UniPot Nucleic Acids Research, Vol. 43, Issue D1, p. D204-D212 https://doi.org/10.1093/nar/gku989	journal	October 2014
Difference in microRNA expression and editing profile of lung tissues from different pig breeds related to immune responses to HP-PRRSV Li, Jia; Chen, Zhisheng; Zhao, Junlong Scientific Reports, Vol. 5, Issue 1 https://doi.org/10.1038/srep09549	journal	April 2015
Lumican affects tumor cell functions, tumor–ECM interactions, angiogenesis and inflammatory response Nikitovic, Dragana; Papoutsidakis, Antonis; Karamanos, Nikos K. Matrix Biology, Vol. 35 https://doi.org/10.1016/j.matbio.2013.09.003	journal	April 2014
N ONCYTOLYTIC C ONTROL OF V IRAL I NFECTIONS BY THE I NNATE AND A DAPTIVE I MMUNE R ESPONSE Guidotti, Luca G.; Chisari, Francis V. Annual Review of Immunology, Vol. 19, Issue 1 https://doi.org/10.1146/annurev.immunol.19.1.65	journal	April 2001
Efficacy of intranasal administration of a truncated NS1 modified live influenza virus vaccine in swine Vincent, Amy L.; Ma, Wenjun; Lager, Kelly M. Vaccine, Vol. 25, Issue 47 https://doi.org/10.1016/j.vaccine.2007.09.019	journal	November 2007
Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2 Love, Michael I.; Huber, Wolfgang; Anders, Simon Genome Biology, Vol. 15, Issue 12 https://doi.org/10.1186/s13059-014-0550-8	journal	December 2014

Similar Records

Increased microbiome diversity at the time of infection is associated with improved growth rates of pigs after co-infection with porcine reproductive and respiratory syndrome virus (PRRSV) and porcine circovirus type 2 (PCV2)

Journal Article · Fri Aug 18 00:00:00 EDT 2017 · Veterinary Microbiology · OSTI ID:1598054

Ober, Rebecca A.; Thissen, James B.; Jaing, Crystal J.; +3 more

Microbiome associations in pigs with the best and worst clinical outcomes following co-infection with porcine reproductive and respiratory syndrome virus (PRRSV) and porcine circovirus type 2 (PCV2)

Journal Article · Thu Mar 10 00:00:00 EST 2016 · Veterinary Microbiology · OSTI ID:1598054

Niederwerder, Megan C.; Jaing, Crystal J.; Thissen, James B.; +3 more

Gut microbiome associations with outcome following co-infection with porcine reproductive and respiratory syndrome virus (PRRSV) and porcine circovirus type 2 (PCV2) in pigs immunized with a PRRS modified live virus vaccine

Journal Article · Tue Feb 16 00:00:00 EST 2021 · Veterinary Microbiology · OSTI ID:1598054

Constance, Laura A.; Thissen, James B.; Jaing, Crystal J.; +5 more

Title: Comparison of the Transcriptome Response within the Swine Tracheobronchial Lymphnode Following Infection with PRRSV, PCV-2 or IAV-S.

Citation Formats

References (50)

Similar Records

Related Subjects