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Chen J, Wang W, Li S, Wang Z, Zuo W, Nong T, Li Y, Liu H, Wei P, He X. RNA-seq reveals role of cell-cycle regulating genes in the pathogenicity of a field very virulent infectious bursal disease virus. Front Vet Sci 2024; 11:1334586. [PMID: 38362295 PMCID: PMC10867150 DOI: 10.3389/fvets.2024.1334586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Accepted: 01/10/2024] [Indexed: 02/17/2024] Open
Abstract
Infectious bursal disease virus (IBDV) infection causes highly contagious and immunosuppressive disease in poultry. The thymus, serving as the primary organ for T cell maturation and differentiation, plays an important role in the pathogenicity of IBDV in the infected chickens. However, there are no reports on the molecular pathogenesis of IBDV in the thymus currently. The aim of the study was to elucidate the molecular mechanisms underlying the pathogenicity of a field very virulent (vv) IBDV strain NN1172 in the thymus of SPF chickens using integrative transcriptomic and proteomic analyses. Our results showed that a total of 4,972 Differentially expressed genes (DEGs) in the thymus of NN1172-infected chickens by transcriptomic analysis, with 2,796 up-regulated and 2,176 down-regulated. Meanwhile, the proteomic analysis identified 726 differentially expressed proteins (DEPs) in the infected thymus, with 289 up-regulated and 437 down-regulated. Overall, a total of 359 genes exhibited differentially expression at both mRNA and protein levels, with 134 consistently up-regulated and 198 genes consistently down-regulated, as confirmed through a comparison of the RNA-seq and the proteomic datasets. The gene ontology (GO) analysis unveiled the involvement of both DEGs and DEPs in diverse categories encompassing cellular components, biological processes, and molecular functions in the pathological changes in IBDV-infected thymus. The Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis revealed that the host mainly displayed severely disruption of cell survival/repair, proliferation and metabolism pathway, meanwhile, the infection triggers antiviral immune activation with a potential emphasis on the MDA5 pathway. Network inference analysis identified seven core hub genes, which include CDK1, TYMS, MCM5, KIF11, CCNB2, MAD2L1, and MCM4. These genes are all associated with cell-cycle regulating pathway and are likely key mediators in the pathogenesis induced by NN1172 infection in the thymus. This study discovered dominant pathways and genes which enhanced our understanding of the molecular mechanisms underlying IBDV pathogenesis in the thymus.
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Affiliation(s)
- Jinnan Chen
- Guangxi Key Laboratory for Polysaccharide Materials and Modifications, School of Marine Sciences and Biotechnology, Guangxi Minzu University, Nanning, China
| | - Weiwei Wang
- Institute for Poultry Science and Health, Guangxi University, Nanning, China
| | - Shangquan Li
- Guangxi Key Laboratory for Polysaccharide Materials and Modifications, School of Marine Sciences and Biotechnology, Guangxi Minzu University, Nanning, China
| | - Zhiyuan Wang
- Guangxi Key Laboratory for Polysaccharide Materials and Modifications, School of Marine Sciences and Biotechnology, Guangxi Minzu University, Nanning, China
| | - Wenbo Zuo
- Guangxi Key Laboratory for Polysaccharide Materials and Modifications, School of Marine Sciences and Biotechnology, Guangxi Minzu University, Nanning, China
| | - Tingbin Nong
- Guangxi Key Laboratory for Polysaccharide Materials and Modifications, School of Marine Sciences and Biotechnology, Guangxi Minzu University, Nanning, China
| | - Yihai Li
- Guangxi Key Laboratory for Polysaccharide Materials and Modifications, School of Marine Sciences and Biotechnology, Guangxi Minzu University, Nanning, China
| | - Hongquan Liu
- Guangxi Key Laboratory for Polysaccharide Materials and Modifications, School of Marine Sciences and Biotechnology, Guangxi Minzu University, Nanning, China
| | - Ping Wei
- Institute for Poultry Science and Health, Guangxi University, Nanning, China
| | - Xiumiao He
- Guangxi Key Laboratory for Polysaccharide Materials and Modifications, School of Marine Sciences and Biotechnology, Guangxi Minzu University, Nanning, China
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Wang P, Li Q, Wangjing, Deng Q, Li M, Wei P. Transcription analysis of chicken embryo fibroblast cells infected with the recombinant avian leukosis virus isolate GX14FF03. Arch Virol 2022; 167:2613-2621. [PMID: 36070017 DOI: 10.1007/s00705-022-05597-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 07/28/2022] [Indexed: 12/14/2022]
Abstract
Infection with recombinant avian leukosis virus (ALV) has previously been linked to malignancies and immunosuppression. However, the processes behind the unique pathophysiology of recombinant ALV are poorly understood. In this study, we analyzed gene expression patterns in chicken fibroblast cells (CEFs) infected with the recombinant ALV isolate GX14FF03 and used the RNA-seq technique to perform a complete analysis of the transcribed mRNAs. A total of 907 significant differentially expressed genes (SDEGs) were identified. Among these SDEGs, the most significantly upregulated gene was interleukin 8-like 1 (IL8L1), while the most significantly downregulated gene was fibroblast growth factor 16 (FGF16). The 907 SDGEs were highly enriched (p < 0.05) for 252 Gene Ontology (GO) terms, including 197 BP, 3 CC, and 52 MF. According to KEGG data analysis, SDEGs are implicated in eight significant pathways (p < 0.05). Furthermore, protein-protein interaction (PPI) network analysis revealed that IL8L1 interacts with 17 genes. These findings shed light on the molecular mechanisms involved in recombinant ALV infection by showing the mRNA expression profile in CEFs infected with GX14FF03 virus.
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Affiliation(s)
- Peikun Wang
- Institute of Microbe and Host Health, Linyi University, Linyi, 276000, China.
| | - Qiuhong Li
- Institute for Poultry Science and Health, Guangxi University, Nanning, 530004, China
| | - Wangjing
- Animal Epidemic Disease Anticipatory Control Center, Lanshan District, Linyi, 276000, China
| | - Qiaomu Deng
- Institute for Poultry Science and Health, Guangxi University, Nanning, 530004, China
| | - Min Li
- Institute for Poultry Science and Health, Guangxi University, Nanning, 530004, China
| | - Ping Wei
- Institute for Poultry Science and Health, Guangxi University, Nanning, 530004, China.
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Sarker N, Tarlinton R, Owen H, David Emes R, Seddon J, Simmons G, Meers J. Novel insights into viral infection and oncogenesis from koala retrovirus (KoRV) infection of HEK293T cells. Gene 2020; 733:144366. [PMID: 31972306 DOI: 10.1016/j.gene.2020.144366] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Revised: 11/22/2019] [Accepted: 01/12/2020] [Indexed: 01/11/2023]
Abstract
Koala retrovirus is thought to be an underlying cause of high levels of neoplasia and immunosuppression in koalas. While epidemiology studies suggest a strong link between KoRV and disease it has been difficult to prove causality because of the complex nature of the virus, which exists in both endogenous and exogenous forms. It has been difficult to identify koalas completely free of KoRV, and infection studies in koalas or koala cells are fraught with ethical and technical difficulties, respectively. This study uses KoRV infection of the susceptible human cell line HEK293T and RNAseq to demonstrate gene networks differentially regulated upon KoRV infection. Many of the pathways identified are those associated with viral infection, such as cytokine receptor interactions and interferon signalling pathways, as well as viral oncogenesis pathways. This study provides strong evidence that KoRV does indeed behave similarly to infectious retroviruses in stimulating antiviral and oncogenic cellular responses. In addition, it provides novel insights into KoRV oncogenesis with the identification of a group of histone family genes that are part of several oncogenic pathways as upregulated in KoRV infection.
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Affiliation(s)
- Nishat Sarker
- School of Veterinary Science, The University of Queensland, Australia; Laboratory of Sciences and Services Division, International Centre for Diarrhoeal Disease Research, Bangladesh
| | - Rachael Tarlinton
- School of Veterinary Medicine and Science, University of Nottingham, United Kingdom
| | - Helen Owen
- School of Veterinary Science, The University of Queensland, Australia
| | - Richard David Emes
- School of Veterinary Medicine and Science, University of Nottingham, United Kingdom; Advanced Data Analysis Centre (ADAC), University of Nottingham, United Kingdom
| | - Jennifer Seddon
- School of Veterinary Science, The University of Queensland, Australia
| | - Greg Simmons
- School of Veterinary Science, The University of Queensland, Australia
| | - Joanne Meers
- School of Veterinary Science, The University of Queensland, Australia.
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