Comparison of the Transcriptome Response within the Swine Tracheobronchial Lymphnode Following Infection with PRRSV, PCV-2 or IAV-S.
Abstract
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 followedmore »
- Authors:
- Publication Date:
- Sponsoring Org.:
- USDOE
- OSTI Identifier:
- 1598054
- Grant/Contract Number:
- AC05-06OR23100
- Resource Type:
- Published Article
- Journal Name:
- Pathogens
- Additional Journal Information:
- Journal Name: Pathogens Journal Volume: 9 Journal Issue: 2; Journal ID: ISSN 2076-0817
- Publisher:
- MDPI AG
- Country of Publication:
- Switzerland
- Language:
- English
Citation Formats
Miller,, Fleming,, and Lager,. Comparison of the Transcriptome Response within the Swine Tracheobronchial Lymphnode Following Infection with PRRSV, PCV-2 or IAV-S.. Switzerland: N. p., 2020.
Web. doi:10.3390/pathogens9020099.
Miller,, Fleming,, & Lager,. Comparison of the Transcriptome Response within the Swine Tracheobronchial Lymphnode Following Infection with PRRSV, PCV-2 or IAV-S.. Switzerland. https://doi.org/10.3390/pathogens9020099
Miller,, Fleming,, and Lager,. Wed .
"Comparison of the Transcriptome Response within the Swine Tracheobronchial Lymphnode Following Infection with PRRSV, PCV-2 or IAV-S.". Switzerland. https://doi.org/10.3390/pathogens9020099.
@article{osti_1598054,
title = {Comparison of the Transcriptome Response within the Swine Tracheobronchial Lymphnode Following Infection with PRRSV, PCV-2 or IAV-S.},
author = {Miller, and Fleming, and Lager,},
abstractNote = {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.},
doi = {10.3390/pathogens9020099},
journal = {Pathogens},
number = 2,
volume = 9,
place = {Switzerland},
year = {Wed Feb 05 00:00:00 EST 2020},
month = {Wed Feb 05 00:00:00 EST 2020}
}
https://doi.org/10.3390/pathogens9020099
Web of Science
Works referenced in this record:
Neutrophil granules: a library of innate immunity proteins
journal, August 2007
- Borregaard, Niels; Sørensen, Ole E.; Theilgaard-Mönch, Kim
- Trends in Immunology, Vol. 28, Issue 8
UniProt: the universal protein knowledgebase
journal, November 2016
- :(unav),
- Nucleic Acids Research, Vol. 45, Issue D1, p. D158-D169
In vitro and ex vivo analyses of co-infections with swine influenza and porcine reproductive and respiratory syndrome viruses
journal, February 2014
- Dobrescu, I.; Levast, B.; Lai, K.
- Veterinary Microbiology, Vol. 169, Issue 1-2
g:Profiler—a web server for functional interpretation of gene lists (2016 update)
journal, April 2016
- Reimand, Jüri; Arak, Tambet; Adler, Priit
- Nucleic Acids Research, Vol. 44, Issue W1
AmiGO: online access to ontology and annotation data
journal, November 2008
- Carbon, Seth; Ireland, Amelia; Mungall, Christopher J.
- Bioinformatics, Vol. 25, Issue 2
Mortality in pigs given porcine circovirus type 2 subgroup 1 and 2 viruses derived from DNA clones
journal, September 2007
- Lager, K. M.; Gauger, P. C.; Vincent, A. L.
- Veterinary Record, Vol. 161, Issue 12
Transcriptome analysis of subcutaneous adipose tissues in beef cattle using 3′ digital gene expression-tag profiling1
journal, January 2012
- Jin, W.; Olson, E. N.; Moore, S. S.
- Journal of Animal Science, Vol. 90, Issue 1
Importance of TFEB acetylation in control of its transcriptional activity and lysosomal function in response to histone deacetylase inhibitors
journal, July 2018
- Zhang, Jianbin; Wang, Jigang; Zhou, Zhihong
- Autophagy
Genes controlling vaccine responses and disease resistance to respiratory viral pathogens in cattle
journal, July 2012
- Glass, Elizabeth J.; Baxter, Rebecca; Leach, Richard J.
- Veterinary Immunology and Immunopathology, Vol. 148, Issue 1-2
Whole Transcriptome Profiling of Successful Immune Response to Vibrio Infections in the Oyster Crassostrea gigas by Digital Gene Expression Analysis
journal, August 2011
- de Lorgeril, Julien; Zenagui, Reda; Rosa, Rafael D.
- PLoS ONE, Vol. 6, Issue 8
The Reactome Pathway Knowledgebase
journal, November 2017
- Fabregat, Antonio; Jupe, Steven; Matthews, Lisa
- Nucleic Acids Research, Vol. 46, Issue D1
Economic analysis of outbreaks of porcine reproductive and respiratory syndrome virus in nine sow herds
journal, January 2012
- Nieuwenhuis, N.; Duinhof, T. F.; van Nes, A.
- Veterinary Record, Vol. 170, Issue 9
The independence of and associations among apoptosis, autophagy, and necrosis
journal, July 2018
- Chen, Qi; Kang, Jian; Fu, Caiyun
- Signal Transduction and Targeted Therapy, Vol. 3, Issue 1
Induction of interleukin-10 is dependent on p38 mitogen-activated protein kinase pathway in macrophages infected with porcine reproductive and respiratory syndrome virus
journal, January 2012
- Hou, Jun; Wang, Lianghai; Quan, Rong
- Virology Journal, Vol. 9, Issue 1
Porcine reproductive and respiratory syndrome virus triggers mitochondrial fission and mitophagy to attenuate apoptosis
journal, July 2016
- Li, Shuaifeng; Wang, Jiaxing; Zhou, Ao
- Oncotarget, Vol. 7, Issue 35
Translational Control of Viral Gene Expression in Eukaryotes
journal, June 2000
- Gale, Michael; Tan, Seng-Lai; Katze, Michael G.
- Microbiology and Molecular Biology Reviews, Vol. 64, Issue 2
The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update
journal, May 2016
- Afgan, Enis; Baker, Dannon; van den Beek, Marius
- Nucleic Acids Research, Vol. 44, Issue W1
featureCounts: an efficient general purpose program for assigning sequence reads to genomic features
journal, November 2013
- Liao, Y.; Smyth, G. K.; Shi, W.
- Bioinformatics, Vol. 30, Issue 7
Comparative analysis of signature genes in PRRSV-infected porcine monocyte-derived cells to different stimuli
journal, July 2017
- Miller, Laura C.; Fleming, Damarius S.; Li, Xiangdong
- PLOS ONE, Vol. 12, Issue 7
Small leucine-rich proteoglycans orchestrate receptor crosstalk during inflammation
journal, June 2012
- Moreth, Kristin; Iozzo, Renato V.; Schaefer, Liliana
- Cell Cycle, Vol. 11, Issue 11
Porcine circovirus type 2 (PCV2) infections: Clinical signs, pathology and laboratory diagnosis
journal, March 2012
- Segalés, Joaquim
- Virus Research, Vol. 164, Issue 1-2
HERC5 is an IFN-induced HECT-type E3 protein ligase that mediates type I IFN-induced ISGylation of protein targets
journal, June 2006
- Wong, J. J. Y.; Pung, Y. F.; Sze, N. S. -K.
- Proceedings of the National Academy of Sciences, Vol. 103, Issue 28
Swine as a Model for Influenza A Virus Infection and Immunity
journal, May 2015
- Rajao, D. S.; Vincent, A. L.
- ILAR Journal, Vol. 56, Issue 1
FQC Dashboard: integrates FastQC results into a web-based, interactive, and extensible FASTQ quality control tool
journal, June 2017
- Brown, Joseph; Pirrung, Meg; McCue, Lee Ann
- Bioinformatics, Vol. 33, Issue 19
Tag-based approaches for transcriptome research and genome annotation
journal, July 2005
- Harbers, Matthias; Carninci, Piero
- Nature Methods, Vol. 2, Issue 7
Viral subversion of the host protein synthesis machinery
journal, October 2011
- Walsh, Derek; Mohr, Ian
- Nature Reviews Microbiology, Vol. 9, Issue 12
Characterization of a newly emerged genetic cluster of H1N1 and H1N2 swine influenza virus in the United States
journal, July 2009
- Vincent, Amy L.; Ma, Wenjun; Lager, Kelly M.
- Virus Genes, Vol. 39, Issue 2
Digital Gene Expression by Tag Sequencing on the Illumina Genome Analyzer
journal, April 2010
- Morrissy, Sorana; Zhao, Yongjun; Delaney, Allen
- Current Protocols in Human Genetics, Vol. 65, Issue 1
Fcγ Receptor Signaling in Phagocytes
journal, October 2006
- Joshi, Trupti; Butchar, Jonathan; Tridandapani, Susheela
- International Journal of Hematology, Vol. 84, Issue 3
Mycoplasma hyopneumoniae: From disease to vaccine development
journal, August 2013
- Simionatto, Simone; Marchioro, Silvana Beutinger; Maes, Dominiek
- Veterinary Microbiology, Vol. 165, Issue 3-4
g:Profiler—a web-based toolset for functional profiling of gene lists from large-scale experiments
journal, July 2007
- Reimand, Jüri; Kull, Meelis; Peterson, Hedi
- Nucleic Acids Research, Vol. 35, Issue suppl_2
A Role for Neutrophils in Viral Respiratory Disease
journal, May 2017
- Camp, Jeremy V.; Jonsson, Colleen B.
- Frontiers in Immunology, Vol. 8
Spread like a wildfire—The omnipresence of porcine circovirus type 2 (PCV2) and its ever-expanding association with diseases in pigs
journal, March 2012
- Meng, Xiang-Jin
- Virus Research, Vol. 164, Issue 1-2
Gross and Microscopic Lesions in Porcine Fetuses Infected with Porcine Reproductive and Respiratory Syndrome Virus
journal, July 1996
- Lager, Kelly M.; Halbur, Patrick G.
- Journal of Veterinary Diagnostic Investigation, Vol. 8, Issue 3
Pathogenesis of rhinovirus infection
journal, June 2012
- Kennedy, Joshua L.; Turner, Ronald B.; Braciale, Thomas
- Current Opinion in Virology, Vol. 2, Issue 3
Effective control of viral infections by the adaptive immune system requires assistance from innate immunity
journal, October 2010
- Barra, Nicole G.; Gillgrass, Amy; Ashkar, Ali A.
- Expert Review of Vaccines, Vol. 9, Issue 10
Reactome pathway analysis: a high-performance in-memory approach
journal, March 2017
- Fabregat, Antonio; Sidiropoulos, Konstantinos; Viteri, Guilherme
- BMC Bioinformatics, Vol. 18, Issue 1
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
journal, April 2013
- Borghetti, Paolo; Morganti, Marina; Saleri, Roberta
- Veterinary Microbiology, Vol. 163, Issue 1-2
Gene: a gene-centered information resource at NCBI
journal, October 2014
- Brown, Garth R.; Hem, Vichet; Katz, Kenneth S.
- Nucleic Acids Research, Vol. 43, Issue D1
Control of adaptive immunity by the innate immune system
journal, March 2015
- Iwasaki, Akiko; Medzhitov, Ruslan
- Nature Immunology, Vol. 16, Issue 4
Modification of intracellular membrane structures for virus replication
journal, May 2008
- Miller, Sven; Krijnse-Locker, Jacomine
- Nature Reviews Microbiology, Vol. 6, Issue 5
Immunopathological effects of porcine circovirus type 2 (PCV2) on swine alveolar macrophages by in vitro inoculation
journal, April 2006
- Chang, Hui-Wen; Jeng, Chian-Ren; Lin, Tsang-Long
- Veterinary Immunology and Immunopathology, Vol. 110, Issue 3-4
Analysis of the swine tracheobronchial lymph node transcriptomic response to infection with a Chinese highly pathogenic strain of porcine reproductive and respiratory syndrome virus
journal, January 2012
- Miller, Laura C.; Fleming, Damarius; Arbogast, Andrew
- BMC Veterinary Research, Vol. 8, Issue 1
Influenza A Virus Infection in Pigs Attracts Multifunctional and Cross-Reactive T Cells to the Lung
journal, August 2016
- Talker, Stephanie C.; Stadler, Maria; Koinig, Hanna C.
- Journal of Virology, Vol. 90, Issue 20
UniProt: a hub for protein information
journal, October 2014
- Consortium, UniPot
- Nucleic Acids Research, Vol. 43, Issue D1, p. D204-D212
Difference in microRNA expression and editing profile of lung tissues from different pig breeds related to immune responses to HP-PRRSV
journal, April 2015
- Li, Jia; Chen, Zhisheng; Zhao, Junlong
- Scientific Reports, Vol. 5, Issue 1
Lumican affects tumor cell functions, tumor–ECM interactions, angiogenesis and inflammatory response
journal, April 2014
- Nikitovic, Dragana; Papoutsidakis, Antonis; Karamanos, Nikos K.
- Matrix Biology, Vol. 35
N ONCYTOLYTIC C ONTROL OF V IRAL I NFECTIONS BY THE I NNATE AND A DAPTIVE I MMUNE R ESPONSE
journal, April 2001
- Guidotti, Luca G.; Chisari, Francis V.
- Annual Review of Immunology, Vol. 19, Issue 1
Efficacy of intranasal administration of a truncated NS1 modified live influenza virus vaccine in swine
journal, November 2007
- Vincent, Amy L.; Ma, Wenjun; Lager, Kelly M.
- Vaccine, Vol. 25, Issue 47
Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2
journal, December 2014
- Love, Michael I.; Huber, Wolfgang; Anders, Simon
- Genome Biology, Vol. 15, Issue 12