Transcriptome profiles of organ tissues from pigs experimentally infected with African swine fever virus in early phase of infection

References

• Dixon LK, Sun H, Roberts HJ. African swine fever. Antiviral Res. 2019;165:34–41. doi:10.1016/j.antiviral.2019.02.018
   PubMed Web of Science ®Google Scholar
• Wang N, Zhao D, Wang J, et al. Inception of memories that guide vocal learning in the songbird. Science 2019;366:83–89. doi:10.1126/science.aaw4226
   PubMed Web of Science ®Google Scholar
• Zhao D, Sun E, Huang L, et al. Highly lethal genotype I and II recombinant African swine fever viruses detected in pigs. Nat Commun. 2023;14:3096. doi:10.1038/s41467-023-38868-w
   PubMed Web of Science ®Google Scholar
• Mai NT, Vu XD, Nguyen TT, et al. Molecular profile of African swine fever virus (ASFV) circulating in Vietnam during 2019-2020 outbreaks. Arch Virol. 2021;166:885–890. doi:10.1007/s00705-020-04936-5
   PubMed Web of Science ®Google Scholar
• Cho KH, Kim HJ, Jang MK, et al. Detection of African swine fever at an abattoir in South Korea, 2020. Vet Sci. 2022;9:150. doi:10.3390/vetsci9040150
   PubMedGoogle Scholar
• Rock DL. Challenges for African swine fever vaccine development—“ … perhaps the end of the beginning.”. Vet Microbiol. 2017;206:52–58. doi:10.1016/j.vetmic.2016.10.003
   PubMed Web of Science ®Google Scholar
• Franzoni G, Graham SP, Sanna G, et al. Interaction of porcine monocyte-derived dendritic cells with African swine fever viruses of diverse virulence. Vet Microbiol. 2018;216:190–197. doi:10.1016/j.vetmic.2018.02.021
   PubMed Web of Science ®Google Scholar
• Dixon LK, Islam M, Nash R, et al. African swine fever virus evasion of host defences. Virus Res. 2019;266:25–33. doi:10.1016/j.virusres.2019.04.002
   PubMed Web of Science ®Google Scholar
• Lv L, Zhang T, Jia H, et al. Temporally integrated transcriptome analysis reveals ASFV pathology and host response dynamics. Front Immunol. 2022;13:995998. doi:10.3389/fimmu.2022.995998
   PubMed Web of Science ®Google Scholar
• Schäfer A, Franzoni G, Netherton CL, et al. Analyses of the impact of immunosuppressive cytokines on porcine macrophage responses and susceptibility to infection to African swine fever viruses. Pathogens 2022;11:166. doi:10.3390/pathogens11020166
   PubMed Web of Science ®Google Scholar
• Salguero FJ, Sánchez-Cordón PJ, Nunez A, et al. Proinflammatory cytokines induce lymphocyte apoptosis in acute African swine fever infection. J Comp Pathol. 2005;132:289–302. doi:10.1016/j.jcpa.2004.11.004
   PubMed Web of Science ®Google Scholar
• Fan W, Cao Y, Jiao P, et al. Synergistic effect of the responses of different tissues against African swine fever virus. Transbound Emerg Dis. 2022;69:204–212. doi:10.1111/tbed.14375
   PubMed Web of Science ®Google Scholar
• Li Z, Chen W, Li X, et al. Transcriptome profiling in swine macrophages infected with African swine fever virus at single-cell resolution. Proc Natl Acad Sci. U.S.A. 2022;119:e2201288119. doi:10.1073/pnas.2201288119
   PubMed Web of Science ®Google Scholar
• Yang B, Shen C, Zhang D, et al. Mechanism of interaction between virus and host is inferred from the changes of gene expression in macrophages infected with African swine fever virus CN/GS/2018 strain. Virol J. 2021;18:170. doi:10.1186/s12985-021-01637-6
   PubMed Web of Science ®Google Scholar
• Zhu JJ, Ramanathan P, Bishop EA, et al. Mechanisms of African swine fever virus pathogenesis and immune evasion inferred from gene expression changes in infected swine macrophages. PLoS One 2019;14:e0221200. doi:10.1371/journal.pone.0221200
   PubMed Web of Science ®Google Scholar
• Cackett G, Portugal R, Matelska D, et al. African swine fever virus and host response: transcriptome profiling of the Georgia 2007/1 strain and porcine macrophages. J Virol. 2022;96:e0193921.
   PubMed Web of Science ®Google Scholar
• Machuka EM, Juma J, Muigai AW, et al. Transcriptome profile of spleen tissues from locally-adapted Kenyan pigs (Sus scrofa) experimentally infected with three varying doses of a highly virulent African swine fever virus genotype IX isolate: Ken12/busia. 1 (ken-1033). BMC Genomics 2022;23:522.
   PubMed Web of Science ®Google Scholar
• Lee HS, Bui VN, Dao DT, et al. Pathogenicity of an African swine fever virus strain isolated in Vietnam and alternative diagnostic specimens for early detection of viral infection. Porcine Health Manag. 2021;7:1–11. doi:10.1186/s40813-020-00179-7
   PubMed Web of Science ®Google Scholar
• Sheet S, Oh YI, Arora D, et al. Insight into the potential candidate genes and signaling pathways involved in lymphoma disease in dogs using a comprehensive whole blood transcriptome analysis. Gene 2022;838:146735. doi:10.1016/j.gene.2022.146735
   PubMed Web of Science ®Google Scholar
• Urbano AC, Ferreira F. African swine fever control and prevention: an update on vaccine development. Emerg Microbes Infect. 2022;11:2021–2033. doi:10.1080/22221751.2022.2108342
   PubMed Web of Science ®Google Scholar
• Chen W, Zhao D, He X, et al. A seven-gene-deleted African swine fever virus is safe and effective as a live attenuated vaccine in pigs. Sci China Life Sci. 2020;63:623–634. doi:10.1007/s11427-020-1657-9
   PubMed Web of Science ®Google Scholar
• Borca MV, Ramirez-Medina E, Silva E, et al. Development of a highly effective African swine fever virus vaccine by deletion of the I177L gene results in sterile immunity against the current epidemic Eurasia strain. J Virol. 2020;94:e02017–e02019.
   PubMed Web of Science ®Google Scholar
• Liu Y, Shen Z, Xie Z, et al. African swine fever virus I73R is a critical virulence-related gene: A potential target for attenuation. Proc Natl Acad Sci. USA. 2023;120: e2210808120. doi:10.1073/pnas.2210808120
   PubMed Web of Science ®Google Scholar
• Gao P, Zhou L, Wu J, et al. Riding apoptotic bodies for cell–cell transmission by African swine fever virus. Proc Natl Acad Sci USA. 2023;120:e2309506120. doi:10.1073/pnas.2309506120
   PubMed Web of Science ®Google Scholar
• Liu Y, Zhang X, Qi W, et al. Prevention and control strategies of African swine fever and progress on pig farm repopulation in China. Viruses. 2021;13:2552. doi:10.3390/v13122552
   PubMed Web of Science ®Google Scholar
• Oh SI, Bui NA, Bui VN, et al. Pathobiological analysis of African swine fever virus contact-exposed pigs and estimation of the basic reproduction number of the virus in Vietnam. Porcine Health Manag. 2023;9:30. doi:10.1186/s40813-023-00330-0
   PubMed Web of Science ®Google Scholar
• Sánchez-Torres C, Gómez-Puertas P, Gomez-del-Moral M, et al. Expression of porcine CD163 on monocytes/macrophages correlates with permissiveness to African swine fever infection. Arch Virol. 2003;148:2307–2323. doi:10.1007/s00705-003-0188-4
   PubMed Web of Science ®Google Scholar
• Wang S, Song R, Wang Z, et al. S100a8/A9 in inflammation. Front. Immunol. 2018;9:1298. doi:10.3389/fimmu.2018.01298
   PubMed Web of Science ®Google Scholar
• Calandra T, Roger T. Macrophage migration inhibitory factor: a regulator of innate immunity. Nat Rev Immunol. 2003;3:791–800. doi:10.1038/nri1200
   PubMed Web of Science ®Google Scholar
• Zhang H, Coblentz C, Watanabe-Smith K, et al. Gain-of-function mutations in granulocyte colony–stimulating factor receptor (CSF3R) reveal distinct mechanisms of CSF3R activation. J Biol Chem. 2018;293:7387–7396. doi:10.1074/jbc.RA118.002417
   PubMed Web of Science ®Google Scholar
• Ma L, Li Q, Cai S, et al. The role of NK cells in fighting the virus infection and sepsis. Int J Med Sci. 2021;18:3236–3248. doi:10.7150/ijms.59898
   PubMed Web of Science ®Google Scholar
• Villani AC, Satija R, Reynolds G, et al. Single-cell RNA-seq reveals new types of human blood dendritic cells, monocytes, and progenitors. Science 2017;356:eaah4573. doi:10.1126/science.aah4573
   PubMed Web of Science ®Google Scholar
• Hamidi T, Cano CE, Grasso D, et al. NUPR1 works against the metabolic stress-induced autophagy-associated cell death in pancreatic cancer cells. Autophagy 2013;9:95–97. doi:10.4161/auto.22258
   PubMed Web of Science ®Google Scholar
• Wang S, Zhang J, Zhang Y, et al. Cytokine storm in domestic pigs induced by infection of virulent African swine fever virus. Front Vet Sci. 2021;7:601641. doi:10.3389/fvets.2020.601641
   PubMed Web of Science ®Google Scholar
• Peperzak V, Veraar EA, Xiao Y, et al. Cd8+ T cells produce the chemokine CXCL10 in response to CD27/CD70 costimulation To promote generation of the CD8+ effector T cell pool. J Immunol. 2013;191:3025–3036. doi:10.4049/jimmunol.1202222
   PubMed Web of Science ®Google Scholar
• Asgari S, Schlapbach LJ, Anchisi S, et al. Severe viral respiratory infections in children with IFIH1 loss-of-function mutations. Proc Natl Acad Sci USA. 2017;114:8342–8347. doi:10.1073/pnas.1704259114
   PubMed Web of Science ®Google Scholar
• Kholod N, Koltsov A, Koltsova G. Analysis of gene expression in monocytes of immunized pigs after infection with homologous or heterologous African swine fever virus. Front Vet Sci. 2022;9:936978. doi:10.3389/fvets.2022.936978
   PubMed Web of Science ®Google Scholar
• Franzoni G, Pedrera M, Sánchez-Cordón PJ. African swine fever virus infection and cytokine response in vivo: an update. Viruses 2023;15:233. doi:10.3390/v15010233
   PubMed Web of Science ®Google Scholar
• Bosch-Camós L, Alonso U, Esteve-Codina A, et al. Cross-protection against African swine fever virus upon intranasal vaccination is associated with an adaptive-innate immune crosstalk. PLoS Pathog. 2022;18:e1010931. doi:10.1371/journal.ppat.1010931
   PubMed Web of Science ®Google Scholar
• Sánchez-Cordón PJ, Jabbar T, Berrezaie M, et al. Evaluation of protection induced by immunisation of domestic pigs with deletion mutant African swine fever virus BeninΔMGF by different doses and routes. Vaccine 2018;36:707–715. doi:10.1016/j.vaccine.2017.12.030
   PubMed Web of Science ®Google Scholar
• Faas M, Ipseiz N, Ackermann J, et al. IL-33-induced metabolic reprogramming controls the differentiation of alternatively activated macrophages and the resolution of inflammation. Immunity 2021;54:2531–2546. doi:10.1016/j.immuni.2021.09.010
   PubMed Web of Science ®Google Scholar
• Radulovic E, Mehinagic K, Wüthrich T, et al. The baseline immunological and hygienic status of pigs impact disease severity of African swine fever. PLoS Pathog. 2022;18:e1010522. doi:10.1371/journal.ppat.1010522
   PubMed Web of Science ®Google Scholar
• Liao W, Lin J-X, Leonard WJ. IL-2 family cytokines: new insights into the complex roles of IL-2 as a broad regulator of T helper cell differentiation. Curr Opin Immunol. 2011;23:598–604. doi:10.1016/j.coi.2011.08.003
   PubMed Web of Science ®Google Scholar
• Silva-Filho J, Caruso-Neves C, Pinheiro A. IL-4: an important cytokine in determining the fate of T cells. Biophys Rev. 2014;6:111–118. doi:10.1007/s12551-013-0133-z
   PubMedGoogle Scholar
• González-Serna D, Ortiz-Fernández L, Vargas S, et al. Association of a rare variant of the TNFSF13B gene with susceptibility to rheumatoid arthritis and systemic lupus erythematosus. Sci Rep. 2018;8:8195. doi:10.1038/s41598-018-26573-4
   PubMed Web of Science ®Google Scholar
• Matesanz-Isabel J, Sintes J, Llinàs L, et al. New B-cell CD molecules. Immunol Lett. 2011;134:104–112. doi:10.1016/j.imlet.2010.09.019
   PubMed Web of Science ®Google Scholar
• Zheng Y, Li S, Li SH, et al. Transcriptome profiling in swine macrophages infected with African Swine Fever Virus (ASFV) uncovers the complex and close relationship with host. Pathogens 2022;11:1411. doi:10.3390/pathogens11121411
   PubMed Web of Science ®Google Scholar
• Sánchez EG, Quintas A, Pérez-Núñez D, et al. African swine fever virus uses macropinocytosis to enter host cells. PLoS Pathog. 2012;8:e1002754.
   PubMed Web of Science ®Google Scholar
• Diehl N, Schaal H., Make yourself at home: viral hijacking of the PI3K/Akt signaling pathway. Viruses 2013;5:3192–3212.
   PubMed Web of Science ®Google Scholar
• De Marchi T, Timmermans AM, Smid M, et al. Annexin-A1 and caldesmon are associated with resistance to tamoxifen in estrogen receptor positive recurrent breast cancer. Oncotarget. 2016;7:3098–3110. doi:10.18632/oncotarget.6521
   PubMedGoogle Scholar
• Chen H, Wang Z, Gao X, et al. ASFV pD345L protein negatively regulates NF-κB signalling by inhibiting IKK kinase activity. Vet Res. 2022;53:32. doi:10.1186/s13567-022-01050-z
   PubMed Web of Science ®Google Scholar
• Gao Q, Yang Y, Feng Y, et al. Effects of the NF-κB signaling pathway inhibitor BAY11-7082 in the replication of ASFV. Viruses 2022;14:297. doi:10.3390/v14020297
   PubMed Web of Science ®Google Scholar
• Gao Q, Yang Y, Feng Y, et al. Aloe-emodin inhibits African swine fever virus replication by promoting apoptosis via regulating NF-κB signaling pathway. Virol J. 2023;20:158. doi:10.1186/s12985-023-02126-8
   PubMed Web of Science ®Google Scholar
• Zhu Z, Mao R, Liu B, et al. Single-cell profiling of African swine fever virus disease in the pig spleen reveals viral and host dynamics. Proc Natl Acad Sci USA. 2024;121:e2312150121. doi:10.1073/pnas.2312150121
   PubMed Web of Science ®Google Scholar
• Kobayashi M, Oshima S, Maeyashiki C, et al. ESCRT-0 dysfunction compromises autophagic degradation of protein aggregates and facilitates ER stress-mediated neurodegeneration via apoptotic and necroptotic pathways. Sci Rep. 2016;6:36780. doi:10.1038/srep24997
   PubMed Web of Science ®Google Scholar
• Wang Q, Li Q, Liu T, et al. Host interaction analysis of PA-N155 and PA-N182 in chicken cells reveals an essential role of UBA52 for replication of H5N1 avian influenza virus. Front Microbiol. 2018;9:936. doi:10.3389/fmicb.2018.00936
   PubMed Web of Science ®Google Scholar
• Barrado-Gil L, Del Puerto A, Galindo I, et al. African swine fever virus ubiquitin-conjugating enzyme is an immunomodulator targeting NF-κB activation. Viruses 2012;13:1160.
   Google Scholar
• Freitas FB, Frouco G, Martins C, et al. African swine fever virus encodes for an E2-ubiquitin conjugating enzyme that is mono- and di-ubiquitinated and required for viral replication cycle. Sci Rep. 2018;8:3471. doi:10.1038/s41598-018-21872-2
   PubMed Web of Science ®Google Scholar