Abstract
In present investigation, differential expression of transcriptome after classical swine fever (CSF) vaccination has been explored at the cellular level in crossbred and indigenous (desi) piglets. RNA Sequencing by Expectation-Maximization (RSEM) package was used to quantify gene expression from RNA Sequencing data, and differentially expressed genes (DEGs) were identified using EBSeq, DESeq2, and edgeR softwares. After analysis, 5222, 6037, and 6210 common DEGs were identified in indigenous post-vaccinated verses pre-vaccinated, crossbred post-vaccinated verses pre-vaccinated, and post-vaccinated crossbred verses indigenous pigs, respectively. Functional annotation of these DEGs showed enrichment of antigen processing-cross presentation, B cell receptor signaling, T cell receptor signaling, NF-κB signaling, and TNF signaling pathways. The interaction network among the immune genes included more number of genes with greater connectivity in vaccinated crossbred than the indigenous piglets. Higher expression of IRF3, IL1β, TAP1, CSK, SLA2, SLADM, and NF-kB in crossbred piglets in comparison to indigenous explains the better humoral response observed in crossbred piglets. Here, we predicted that the processed CSFV antigen through the T cell receptor signaling cascade triggers the B cell receptor-signaling pathway to finally activate MAPK kinase and NF-κB signaling pathways in B cell. This activation results in expression of genes/transcription factors that lead to B cell ontogeny, auto immunity and immune response through antibody production. Further, immunologically important genes were validated by qRT-PCR.
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Abbreviations
- CSF:
-
Classical swine fever
- MDA:
-
Maternally derived antibodies
- PBMC:
-
Peripheral blood mononuclear cells,
- FCS:
-
Fetal calf serum
- GTF:
-
Gene transfer file
- GO:
-
Gene ontology
- RIN:
-
RNA integrity number
- DEGs:
-
Differentially expressed genes
- cELISA:
-
Competitive enzyme linked immunosorbent assay
- BioGRID:
-
Biological General Repository for Interaction Datasets
- IRF3:
-
Interferon regulatory factor 3
- TAP1:
-
Transport associated protein1
- NF-kB:
-
Nuclear factor kappaB,
- SLA2:
-
Swine leucocyte antigen 2
- IL1β:
-
Interleukin1 β
- RSEM:
-
RNA Seq by expectation maximization
- BCR:
-
B cell receptor
References
Anders S, Huber W (2010) Differential expression analysis for sequence count data. Genome Biol 11:R106
Borca MV, Gudmundsdottir I, Fernández-Sainzb IJ, Holinkab LG, Risatti GR (2008) Patterns of cellular gene expression in swine macrophages infected with highly virulent classical swine fever virus strain Brescia. Virus Res 138:89–96
Cao Z, Guo K, Zheng M, Ning P, Li H, Kang K, Lin Z, Zhang C, Liang W, Zhang Y (2015) A comparison of the impact of Shimen strain and C strain of classical swine fever virus on toll-like receptor expression. J Gen virol. doi:10.1099/vir0000129
Chen H, Li C, Fang M, Zhu M, Li X, Zhou R, Li K, Zhao S (2009) Understanding Haemophilus parasuis infection in porcine spleen through a transcriptomics approach. BMC Genomics 10:64
Chia YL, Ng CH, Lashmit P, Chu KL, Lew QJ, Ho JP, Lim HL, Nissom PM, Stinski MF, Chao SH (2014) Inhibition of human cytomegalovirus replication by overexpression of CREB1. Antivir Res 102:11–22
Conesa A, Madrigal P, Tarazona S, Gomez-Cabrero D, Cervera A, McPherson A, Szcześniak MW, Gaffney DJ, Elo LL, Zhang X, Mortazavi A (2016) A survey of best practices for RNA seq data analysis. Genome Biol 17:181
Davies G, Genini S, Bishop SC, Guiffra E (2009) An assessment of opportunities to dissect host genetic variation in resistance to infectious diseases in livestock. Animal 3(3):415–436
Dev A, Iyer S, Razani B, Cheng G (2011) NF-κB and innate immunity. Curr Top Microbiol Immunol 349:115–143
Dong XY, Liu WJ, Zhao MQ, Wang JY, Pei JJ, Luo YW, Ju CM, Chen JD (2013) Classical swine fever virus triggers RIG-I and MDA5-dependent signaling pathway to IRF-3 and NF-κB activation to promote secretion of interferon and inflammatory cytokines in porcine alveolar macrophages. Virol J 10:286
Feng L, Li XQ, Li XN, Li J, Meng XM, Zhang HY, Liang JJ, Li H, Sun SK, Cai XB, Su LJ, Yin S, Li YS, Luo TR (2012) In vitro infection with classical swine fever virus inhibits the transcription of immune response genes. Virol J 9:175
Flori L, Rogel-Gaillard C, Cochet M, Lemonnier G, Hugot K, Chardon P, Robin S, Lefevre F (2008) Transcriptomic analysis of the dialogue between pseudorabies virus and porcine epithelial cells during infection. BMC Genomics 9:123
Gladue DP, Zhu J, Holinka LG, Fernandez-Sainz I, Carrillo C, Prarat MV, O’Donnell V, Borca MV (2010) Patterns of gene expression in swine macrophages infected with classical swine fever virus detected by microarray. Virus Res 151:10–18
Haller O, Staeheli P, Kochs G (2007) Interferon-induced Mx proteins in antiviral host defense. Biochimie 89:812–818
Langmead B, Trapnell C, Pop M, Salzberg SL (2009) Ultrafast and memory efficient alignment of short DNA sequences to the human genome. Genome Biol 10(3):R25
Leng N, Dawson JA, Thomson JA, Ruotti V, Rissman AI, Smits BMG, Haag JD, Gould MN, Stewart RM, Kendziorski C (2013) EBSeq: an empirical Bayes hierarchical model for inference in RNA-seq experiments. Bioinformatics 29(8):1035–1043
Li J, Yu YJ, Feng L, Cai XB, Tang HB, Sun SK, Zhang HY, Liang JJ, Luo TR (2010) Global transcriptional profiles in peripheral blood mononuclear cell during classical swine fever virus infection. Virus Res 148(1–2):60–70
Li Y, Liu H, Wang P, Wang L, Sun Y, Liu G, Zhang P, Li K, Jiang S, Jiang Y (2016) RNA-Seq analysis reveals genes underlying different disease responses to porcine circovirus type 2 in pigs. PLoS One 11(5):e0155502. doi:10.1371/journal.pone.0155502
Majewska M, Lipka A, Paukszto L, Jastrzebski JP, Myszczynski K, Gowkielewicz M, Jozwik M, Majewski MK (2017) Transcriptome profile of the human placenta. Funct Integr Genomics. doi:10.1007/s10142-017-0555-y
Newton K, Dixit VM (2012) Signaling in innate immunity and inflammation. Cold Spring Harb Perspect Biol 4(3):a006049
O’Brien LM, Margaret GS, Stephen GL, David RM, Sophie JS, Mark SL, Thomas RL, Stuart DP (2014) Vaccination with recombinant adenoviruses expressing Ebola virus glycoprotein elicits protection in the interferon alpha/beta receptor knock-out mouse. JVirol 452–53:324–333
Oliveros, JC (2007) VENNY. An interactive tool for comparing lists with Venn Diagrams. http://bioinfogp.cnb.csic.es/tools/venny/index.html.
Rahman H (2011) Vision 2030- project directorate on animal disease monitoring and surveillance, ICAR Hebbal, Bengaluru. Karnataka 2
Reimand J, Arak T, Vilo J (2011) G:profiler—a web server for functional interpretation of gene lists. Nucleic Acids Res 39:307–315
Risatti GR, Callahan JD, Nelson WM, Borca MV (2003) Rapid detection of classical swine fever virus by a portable real-time reverse transcriptase PCR assay. J Clin Microbiol 41(1):500–505
Robinson MD, Oshlack A (2010) A scaling normalization method for differential expression analysis of RNA-seq data. Genome Biol 11:R25
Sanchez-Cordon PJ, Nunez A, Salguero FJ, Carrasco L, Gomez-Villamandos JC (2005) Evolution of T lymphocytes and cytokine expression in classical swine fever (CSF) virus infection. J Comp Pathol 132:249–260
Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, Amin N, Schwikowski B, Ideker T (2003) Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res 13:2498–2504
Shi FD, Van Kaer L (2006) Reciprocal regulation between natural killer cells and autoreactive T cells. Nat Rev Immunol 6:751–760
Shi H, Zhu J, Luo J, Cao W, Shi H, Yao D, Li J, Sun Y, Xu H, Yu K, Loor JJ (2015) Genes regulating lipid and protein metabolism are highly expressed in mammary gland of lactating dairy goats. Funct Integr Genomics 15:309. doi:10.1007/s10142-014-0420-1
Singh A, Kumar A, Sahoo NR, Upmanyu V, Kumar B, Bhushan B, Sharma D (2016) Association of humoral response to classical swine fever vaccination with single nucleotide polymorphisms of swine leukocyte antigens. J Appl Anim Res 32:187–190
Stark C, Breitkreutz BJ, Chatr-Aryamontri A, Boucher L, Oughtred R, Livstone MS, Nixon J, Van Auken K, Wang X, Shi X, Reguly T, Rust JM, Winter A, Dolinski K, Tyers M (2011) The BioGRID interaction database: 2011 update. Nucleic Acids Res 39:698–704
Summerfield A, Ruggli N (2015) Immune responses against classical swine fever virus: between ignorance and lunacy. Front Vet Sci doi: 103389/fvets201500010
Sun YK, Zhang XM, Du M, Li YX, Pan HB, Yan YL, Yang YA (2014) Atypical classical swine fever infection changes interleukin Gene expression in pigs. Isr J Vet Med 69(4):221–227
Suradhat S, Intrakamhaeng M, Damrongwatanapokin S (2001) The correlation of virus-specific interferon-gamma production and protection against classical swine fever virus infection. Vet Immunol Immunopathol 83:177–189
Suthram S, Shlomi T, Ruppin E, Sharan R, Ideker T (2006) A direct comparison of protein interaction confidence assignment schemes. BMC Bioinformatics 7:360
Tamura T, Nagashima N, Ruggli N, Summerfield A, Kida H, Sakoda Y (2014) Npro of classical swine fever virus contributes to pathogenicity in pigs by preventing type I interferon induction at local replication sites. Vet Res 17:45–47
Van Oirschot JT (2003) Vaccinology of classical swine fever: from lab to field. Vet Microbiol 96:367–384
Vogan K (2013) PIK3CD mutation cause immunodeficiency. Nat. Genetics 45:1417. doi:10.1038/ng.2840
Zaffuto KM, Piccone ME, Burrage TG, Balinsky CA, Risatti GR, Borca MV, Holinka LG, Rock DL, Afonso CL (2007) Classical swine fever virus inhibits nitric oxide production in infected macrophages. J Gen Virol 88:3007–3012
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Authors are thankful to the ICAR-IVRI and CABIN project of IASRI for providing financial assistance.
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Pathak, S.K., Kumar, A., Bhuwana, G. et al. RNA Seq analysis for transcriptome profiling in response to classical swine fever vaccination in indigenous and crossbred pigs. Funct Integr Genomics 17, 607–620 (2017). https://doi.org/10.1007/s10142-017-0558-8
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DOI: https://doi.org/10.1007/s10142-017-0558-8