Transcriptome sequencing reveals non-coding RNAs respond to porcine reproductive and respiratory syndrome virus and Haemophilus parasuis co-infection in Kele piglets
2
조회
0
다운로드
1
인용
0
참고문헌
키워드
초록
Co-infection with porcine reproductive and respiratory syndrome virus (PRRSV) and Haemophilus parasuis (HPS) has severely restricted the healthy development of pig breeding. Exploring disease resistance of non-coding RNAs in pigs co-infected with PRRSV and HPS is therefore critical to complement and elucidate the molecular mechanisms of disease resistance in Kele piglets and to innovate the use of local pig germplasm resources in China. RNA-seq of lungs from Kele piglets with single-infection of PRRSV or HPS and co-infection of both pathogens was performed. Two hundred and twenty-five differentially expressed long non-coding RNAs (DElncRNAs) and 30 DEmicroRNAs (DEmiRNAs) were identified and characterized in the PRRSV and HPS co-infection (PRRSV–HPS) group. Compared with the single-infection groups, 146 unique DElncRNAs, 17 unique DEmiRNAs, and 206 target differentially expressed genes (DEGs) were identified in the PRRSV–HPS group. The expression patterns of 20 DEmiRNAs and DElncRNAs confirmed by real-time quantitative polymerase chain reaction (RT-qPCR) were consistent with those determined by high-throughput sequencing. In the PRRSV–HPS group, the target DEGs were enriched in eight immune Gene Ontology terms relating to two unique DEmiRNAs and 16 DElncRNAs, and the unique target DEGs participated the host immune response to pathogens infection by affecting 15 immune-related Kyoto Encyclopedia of Genes and Genomes enrichment pathways. Notably, competitive endogenous RNA (ceRNA) networks of different groups were constructed, and the ssc-miR-671-5p miRNA was validated as a potential regulatory factor to regulate DTX4 and AEBP1 genes to achieve innate antiviral effects and inhibit pulmonary fibrosis by dual-luciferase reporter assays. These results provided insight into further study on the molecular mechanisms of resistance to PRRSV and HPS co-infection in Kele piglets.
Abstract
Co-infection with porcine reproductive and respiratory syndrome virus (PRRSV) and Haemophilus parasuis (HPS) has severely restricted the healthy development of pig breeding. Exploring disease resistance of non-coding RNAs in pigs co-infected with PRRSV and HPS is therefore critical to complement and elucidate the molecular mechanisms of disease resistance in Kele piglets and to innovate the use of local pig germplasm resources in China. RNA-seq of lungs from Kele piglets with single-infection of PRRSV or HPS and co-infection of both pathogens was performed. Two hundred and twenty-five differentially expressed long non-coding RNAs (DElncRNAs) and 30 DEmicroRNAs (DEmiRNAs) were identified and characterized in the PRRSV and HPS co-infection (PRRSV–HPS) group. Compared with the single-infection groups, 146 unique DElncRNAs, 17 unique DEmiRNAs, and 206 target differentially expressed genes (DEGs) were identified in the PRRSV–HPS group. The expression patterns of 20 DEmiRNAs and DElncRNAs confirmed by real-time quantitative polymerase chain reaction (RT-qPCR) were consistent with those determined by high-throughput sequencing. In the PRRSV–HPS group, the target DEGs were enriched in eight immune Gene Ontology terms relating to two unique DEmiRNAs and 16 DElncRNAs, and the unique target DEGs participated the host immune response to pathogens infection by affecting 15 immune-related Kyoto Encyclopedia of Genes and Genomes enrichment pathways. Notably, competitive endogenous RNA (ceRNA) networks of different groups were constructed, and the ssc-miR-671-5p miRNA was validated as a potential regulatory factor to regulate DTX4 and AEBP1 genes to achieve innate antiviral effects and inhibit pulmonary fibrosis by dual-luciferase reporter assays. These results provided insight into further study on the molecular mechanisms of resistance to PRRSV and HPS co-infection in Kele piglets.
참고문헌 (56)
- Cohen LM, "A descriptive study of acute outbreaks of respiratory disease in Norwegian fattening pig herds", Acta Vet Scand, 62, pp.35~ (2020)[DOI]
- Lin WH, "Molecular serotyping of Haemophilus parasuis isolated from diseased pigs and the relationship between serovars and pathological patterns in Taiwan", PeerJ, 6, pp.e6017~ (2018)[DOI]
- Ke H, "Porcine reproductive and respiratory syndrome virus nonstructural protein 1 beta interacts with nucleoporin 62 to promote viral replication and immune evasion", J Virol, 93, pp.e00469-19~ (2019)[DOI]
- Li X, "PK", PD modeling of Ceftiofur Sodium against Haemophilus parasuis infection in pigs, 2019, pp.15, 272~
- Wang J, "Porcine reproductive and respiratory syndrome virus activates lipophagy to facilitate viral replication through downregulation of NDRG1 expression", J Virol, 93, pp.e00526-19~ (2019)[DOI]
- Yue C, "Autophagy is a defense mechanism inhibiting invasion and inflammation during high-virulent Haemophilus parasuis infection in PK-15 cells", Front Cell Infect Microbiol, 9, pp.93~ (2019)[DOI]
- Cheong Y, "Survey of porcine respiratory disease complex-associated pathogens among commercial pig farms in Korea via oral fluid method", J Vet Sci, 18, pp.283~289 (2017)[DOI]
- Sunaga F, "Development of a one-run real-time PCR detection system for pathogens associated with porcine respiratory diseases", J Vet Med Sci, 82, pp.217~223 (2020)[DOI]
- Li J, "Secondary Haemophilus parasuis infection enhances highly pathogenic porcine reproductive and respiratory syndrome virus (HP-PRRSV)infection-mediated inflammatory responses", Vet Microbiol, 204, pp.35~42 (2017)[DOI]
- Kavanová L, "Immune response of porcine alveolar macrophages to a concurrent infection with porcine reproductive and respiratory syndrome virus and Haemophilus parasuis in vitro", Vet Microbiol, 180, pp.28~35 (2015)[DOI]
- Kavanová L, "Concurrent infection of monocyte-derived macrophages with porcine reproductive and respiratory syndrome virus and Haemophilus parasuis : a role of IFNα in pathogenesis of co-infections", Vet Microbiol, 225, pp.64~71 (2018)[DOI]
- Zhang J, "Transcriptome profiling identifies immune response genes against porcine reproductive and respiratory syndrome virus and Haemophilus parasuis co-infection in the lungs of piglets", J Vet Sci, 23, pp.e2~ (2022)[DOI]
- Do DN, "miRNA regulatory functions in farm animal diseases, and biomarker potentials for effective therapies", Int J Mol Sci, 22, pp.3080~ (2021)[DOI]
- Li C, "PCV2 regulates cellular inflammatory responses through dysregulating cellular miRNA-mRNA networks", Viruses, 11, pp.1055~ (2019)[DOI]
- Mucha SG, "Mycoplasma hyopneumoniae J elicits an antioxidant response and decreases the expression of ciliary genes in infected swine epithelial cells", Sci Rep, 10, pp.13707~13729 (2020)[DOI]
- Fu S, "The effect of baicalin on microRNA expression profiles fo long in porcine aortic vascular endothelial cells infected by Haemophilus parasuis", Mol Cell Biochem, 472, pp.45~56 (2020)[DOI]
- Guo L, "The effect of baicalin on the expression profiles of long non-coding RNAs and mRNAs in porcine aortic vascular endothelial cells infected with Haemophilus parasuis", DNA Cell Biol, 39, pp.801~815 (2020)[DOI]
- He J, "Identification of lncRNAs involved in PCV2 infection of PK-15 cells", Pathogens, 9, pp.479~490 (2020)[DOI]
- Wu J, "Genome-wide analysis of long noncoding RNA and mRNA profiles in PRRSV-infected porcine alveolar macrophages", Genomics, 112, pp.1879~1888 (2020)[DOI]
- Zhen Y, "Identification of differentially expressed non-coding RNA in porcine alveolar macrophages from tongcheng and large white pigs responded to PRRSV", Sci Rep, 8, pp.15621~ (2018)[DOI]
- Sen R, "Competing endogenous RNA: the key to posttranscriptional regulation", Sci World J, 2014, pp.896206~ (2014)[DOI]
- Langmead B, "Aligning short sequencing reads with bowtie", Curr Protoc Bioinformatics, 32, pp.1~14 (2010)[DOI]
- Kozomara A, "miRBase : annotating high confidence microRNAs using deep sequencing data", Nucleic Acids Res, 42, pp.D68~D73 (2014)[DOI]
- Friedländer MR, "miRDeep2 accurately identifies known and hundreds of novel microRNA genes in seven animal clades", Nucleic Acids Res, 40, pp.37~52 (2012)[DOI]
- Wen M, "miREvo : an integrative microRNA evolutionary analysis platform for next-generation sequencing experiments", BMC Bioinform, 13, pp.140~ (2012)[DOI]
- Sun L, "Utilizing sequence intrinsic composition to classify protein-coding and long non-coding transcripts", Nucleic Acids Res, 41, pp.e166~ (2013)[DOI]
- Kang YJ, "CPC2 : a fast and accurate coding potential calculator based on sequence intrinsic features", Nucleic Acids Res, 45, pp.W12~W16 (2017)[DOI]
- El-Gebali S, "The Pfam protein families database in 2019", Nucleic Acids Res, 47, pp.D427~D432 (2019)[DOI]
- Lin MF, "PhyloCSF: a comparative genomics method to distinguish protein coding and non-coding regions", Bioinformatics, 27, pp.i275~i282 (2011)[DOI]
- Love MI, "Moderated estimation of fold change and dispersion for RNAseq data with DESeq2", Genome Biol, 15, pp.550~ (2014)[DOI]
- Enright AJ, "MicroRNA targets in Drosophila", Genome Biol, 5, pp.R1~ (2003)[DOI]
- Krüger J, "RNAhybrid: microRNA target prediction easy, fast and flexible", Nucleic Acids Res, 34, pp.W451~W454 (2006)[DOI]
- Wu J, "KOBAS server: a web-based platform for automated annotation and pathway identification", Nucleic Acids Res, 34, pp.W720~W724 (2006)[DOI]
- Bindea G, "ClueGO : a Cytoscape plug-in to decipher functionally grouped gene ontology and pathway annotation networks", Bioinformatics, 25, pp.1091~1093 (2009)[DOI]
- Zhang K, "Global miRNA, lncRNA, and mRNA transcriptome profiling of endometrial epithelial cells reveals genes related to porcine reproductive failure caused by porcine reproductive and respiratory syndrome virus", Front Immunol, 10, pp.1221~ (2019)[DOI]
- Qin S, "miR-21-5p ameliorates hyperoxic acute lung injury and decreases apoptosis of AEC II cells via PTEN", AKT signaling in rats, 2019, pp.20, 4953~4962
- Li Q, "Exosomal miR-21-5p derived from gastric cancer promotes peritoneal metastasis via mesothelial-to-mesenchymal transition", Cell Death Dis, 9, pp.854~ (2018)[DOI]
- Lou J, "MiR-20b inhibits mycobacterium tuberculosis induced inflammation in the lung of mice through targeting NLRP3", Exp Cell Res, 358, pp.120~128 (2017)[DOI]
- Tian Y, "Clinical significance of miRNA-106a in non-small cell lung cancer patients who received cisplatin combined with gemcitabine chemotherapy", Cancer Biol Med, 15, pp.157~164 (2018)[DOI]
- Li Q, "MicroRNA-7-5p induces cell growth inhibition, cell cycle arrest and apoptosis by targeting PAK2 in non-small cell lung cancer", FEBS Open Bio, 9, pp.1983~1993 (2019)[DOI]
- Liang Z, "Integrative analysis of microRNA and mRNA expression profiles in MARC-145 cells infected with PRRSV", Virus Genes, 56, pp.610~620 (2020)[DOI]
- Mody HR, "miR-202diminishes TGFβ receptors and attenuates TGFβ1-induced emt in pancreatic cancer", Mol Cancer Res, 15, pp.1029~1039 (2017)[DOI]
- Chen J, "Effect of miR-202-5p-mediated ATG7 on autophagy and apoptosis of degenerative nucleus pulposus cells", Eur Rev Med Pharmacol Sci, 24, pp.517~525 (2020)[DOI]
- Liu W, "miR-202-5p inhibits RIG-I-dependent innate immune responses to RGNNV infection by targeting TRIM25 to mediate RIG-I ubiquitination", Viruses, 12, pp.261~ (2020)[DOI]
- Yao F, "Hsa‑miR‑371‑5p inhibits human mesangial cell proliferation and promotes apoptosis in lupus nephritis by directly targeting hypoxia‑inducible factor 1α", Mol Med Rep, 14, pp.5693~5698 (2016)[DOI]
- Li N, "Molecular mechanism of miR-204 regulates proliferation, apoptosis and autophagy of cervical cancer cells by targeting ATF2", Artif Cells Nanomed Biotechnol, 47, pp.2529~2535 (2019)[DOI]
- Yan Y, "Construction of a long non-coding RNAassociated ceRNA network reveals potential prognostic lncRNA biomarkers in hepatocellular carcinoma", Pathol Res Pract, 214, pp.2031~2038 (2018)[DOI]
- Yang H, "CD163 knockout pigs are fully resistant to highly pathogenic porcine reproductive and respiratory syndrome virus", Antiviral Res, 151, pp.63~70 (2018)[DOI]
- Odaka C, "Matrix metalloproteinase-9 in macrophages induces thymic neovascularization following thymocyte apoptosis", J Immunol, 174, pp.846~853 (2005)[DOI]
- Zhang J, "Influenza A virus M1 blocks the classical complement pathway through interacting with C1qA", J Gen Virol, 90, pp.2751~2758 (2009)[DOI]
- Luo J, "Transcriptome analysis reveals an activation of major histocompatibility complex 1 and 2 pathways in chicken trachea immunized with infectious laryngotracheitis virus vaccine", Poult Sci, 93, pp.848~855 (2014)[DOI]
- Li N, "IL21 and IL21R polymorphisms and their interactive effects on serum IL-21 and IgE levels in patients with chronic hepatitis B virus infection", Hum Immunol, 74, pp.567~573 (2013)[DOI]
- Liu J, "AEBP1 promotes epithelial-mesenchymal transition of gastric cancer cells by activating the NF-κB pathway and predicts poor outcome of the patients", Sci Rep, 8, pp.11955~ (2018)[DOI]
- Gerhard GS, "AEBP1 expression increases with severity of fibrosis in NASH and is regulated by glucose, palmitate, and miR-372-3p", PLOS ONE, 14, pp.e0219764~ (2019)[DOI]
- Cui J, "NLRP4 negatively regulates type I interferon signaling by targeting the kinase TBK1 for degradation via the ubiquitin ligase DTX4", Nat Immunol, 13, pp.387~395 (2012)[DOI]
- Oulidi A, "TRPV2mediates adrenomedullin stimulation of prostate and urothelial cancer cell adhesion, migration and invasion", PLOS ONE, 8, pp.e64885~ (2013)[DOI]
