Transcriptome analysis of PK-15 cells in innate immune response to porcine deltacoronavirus infection

Autoři: Shan Jiang aff001;  Fuqiang Li aff001;  Xiuli Li aff001;  Lili Wang aff001;  Li Zhang aff001;  Chao Lu aff001;  Li Zheng aff001;  Minghua Yan aff001
Působiště autorů: Tianjin Institute of Animal Husbandry and Veterinary Medicine, Tianjin Academy of Agricultural Sciences, Tianjin, China aff001;  Tianjin Scientific Observation Experiment Station for Veterinary Medicine and Diagnosis Technology, the Ministry of Agriculture of the People`s Republic of China, Tianjin, China aff002
Vyšlo v časopise: PLoS ONE 14(10)
Kategorie: Research Article


Porcine deltacoronavirus (PDCoV) is a newly emerged swine enteropathogenic coronavirus affecting pigs of all ages and causing diarrhea problems. Research findings indicate that PDCoV has evolved strategies to escape innate immune response in host cells, but mechanism of PDCoV in innate immune modulation is not well understood. In this study, we report our findings on identifying the alterations of host cell innate immune response affected by PDCoV infection and exploring the gene expression profiles of PK-15 cells at 0, 24, and 36 h PDCoV post infection by RNA sequencing. A total of 3,762 and 560 differentially expressed genes (DEGs) were screened by comparison of uninfected PK-15 cells and infected PK-15 cells at 24 h post infection (hpi) (INF_24h versus NC), and also comparison of infected PK-15 cells between 24 and 36 hpi (INF_36h versus INF_24h), which included 156 and 23 porcine innate immune-related genes in the DEGs of INF_24h versus NC and INF_36h versus INF_24h, respectively. Gene Ontology function classification and Kyoto Encyclopedia of Genes and Genomes signaling pathway enrichment analysis were performed based on the DEGs that exhibited the same expression tendencies with most of the innate immune-associated genes among these PK-15 cell samples described above. The enrichment results indicated that extensive gene functions and signaling pathways including innate immune-associated functions and pathways were affected by PDCoV infection. Particularly, 4 of 5 innate immune signaling pathways, which were primarily affected by PDCoV, played important roles in I-IFN’s antiviral function in innate immune response. Additionally, 16 of the host cell endogenous miRNAs were predicted as potential contributors to the modulation of innate immune response affected by PDCoV. Our research findings indicated that the innate immune-associated genes and signaling pathways in PK-15 cells could be modified by the infection of PDCoV, which provides a fundamental foundation for further studies to better understand the mechanism of PDCoV infections, so as to effectively control and prevent PDCoV-induced swine diarrheal disease outbreaks.

Klíčová slova:

Gene expression – Immune receptor signaling – Immune response – MicroRNAs – RNA sequencing – Swine – Immune receptors – Host cells


1. Ma Y, Zhang Y, Liang X, Lou F, Oglesbee M, Krakowka S, et al. Origin, evolution, and virulence of porcine deltacoronaviruses in the United States. M Bio. 2015;6(2):e00064–15. doi: 10.1128/mBio.00064-15 25759498

2. Hu H, Jung K, Vlasova AN, Saif LJ. Experimental infection of gnotobiotic pigs with the cell-culture-adapted porcine deltacoronavirus strain OH-FD22. Arch Virol. 2016;161:3421–34. doi: 10.1007/s00705-016-3056-8 27619798

3. Woo PC, Lau SK, Lam CS, Lau CC, Tsang AK, Lau JH, et al. Discovery of seven novel mammalian and avian coronaviruses in the genus deltacoronavirus supports bat coronaviruses as the gene source of alphacoronavirus and betacoronavirus and avian coronaviruses as the gene source of gammacoronavirus and deltacoronavirus. J Virol. 2012;86(7):3995–4008. doi: 10.1128/JVI.06540-11 22278237

4. Wang L, Byrum B, Zhang Y. Detection and genetic characterization of a deltacoronavirus in pigs in the United States, Ohio, USA, 2014. Emerg Infect Dis. 2014;20(7):1227–30. doi: 10.3201/eid2007.140296 24964136

5. Wang L, Byrum B, Zhang Y. Porcine coronavirus HKU15 detected in 9 US states, 2014. Emerg Infect Dis. 2014;20:1594–5. doi: 10.3201/eid2009.140756 25153521

6. Ajayi T, Dara R, Misener M, Pasma T, Moser L, Poljak Z. Herd-level prevalence and incidence of porcine epidemic diarrhoea virus (PEDV) and porcine deltacoronavirus (PDCoV) in swine herds in Ontario, Canada. Transbound Emerg Dis. 2018;65(5):1197–207. doi: 10.1111/tbed.12858 29607611

7. Lee S, Lee C. Complete genome characterization of Korean porcine deltacoronavirus strain KOR/KNU14-04/2014. Genome Announc. 2014;2(6):e01191–214. doi: 10.1128/genomeA.01191-14 25428966

8. Janetanakit T, Lumyai M, Bunpapong N, Boonyapisitsopa S, Chaiyawong S, Nonthabenjawan N, et al. Porcine deltacoronavirus, Thailand, 2015. Emerg Infect Dis. 2016;22(4):757–59. doi: 10.3201/eid2204.151852 26982324

9. Wang YW, Yue H, Fang W, Huang YW. Complete genome sequence of porcine deltacoronavirus strain CH/Sichuan/S27/2012 from mainland China. Genome Announc. 2015;3(5):e00945–15. doi: 10.1128/genomeA.00945-15 26337879

10. Masuda T, Tsuchiaka S, Ashiba T, Yamasato H, Fukunari K, Omatsu T, et al. Development of one-step real-time reverse transcriptase-PCR-based assays for the rapid and simultaneous detection of four viruses causing porcine diarrhea. Jpn J Vet Res. 2016;64(1):5–14. 27348884

11. Thachil A, Gerber PF, Xiao CT, Huang YW, Opriessnig T. Development and application of an ELISA for the detection of porcine deltacoronavirus IgG antibodies. PLoS One. 2015;10(4):e0124363. doi: 10.1371/journal.pone.0124363 25881086

12. Zhang Q, Yoo D. Immune evasion of porcine enteric coronaviruses and viral modulation of antiviral innate signaling. Virus Res. 2016;226:128–41. doi: 10.1016/j.virusres.2016.05.015 27212682

13. Zhang Q, Ma J, Yoo D. Inhibition of NF-κB activity by the porcine epidemic diarrhea virus nonstructural protein 1 for innate immune evasion. Viroloy. 2017;510:111–1126. doi: 10.1016/j.virol.2017.07.009 28715653

14. J Horner SM. Activation and evasion of antiviral innate immunity by hepatitis C virus. Mol Biol. 2014;426(6):1198–209. doi: 10.1016/j.jmb.2013.10.032 24184198

15. Kopecky-Bromberg SA, Martínez-Sobrido L, Frieman M, Baric RA, Palese P. Severe acute respiratory syndrome coronavirus open reading frame (ORF) 3b, ORF 6, and nucleocapsid proteins function as interferon antagonists. J Virol. 2007;81(2):548–57. doi: 10.1128/JVI.01782-06 17108024

16. Hu Y, Li W, Gao T, Cui Y, Jin Y, Li P, et al. The severe acute respiratory syndrome coronavirus nucleocapsid inhibits type I interferon production by interfering with TRIM25-mediated RIG-I ubiquitination. J Virol. 2017;91(8):e02143–16. doi: 10.1128/JVI.02143-16 28148787

17. Ding Z, Fang L, Yuan S, Zhao L, Wang X, Long S, et al. The nucleocapsid proteins of mouse hepatitis virus and severe acute respiratory syndrome coronavirus share the same IFN-β antagonizing mechanism: attenuation of PACT-mediated RIG-I/ MDA5 activation. Oncotarget. 2017;8(30):49655–49670. doi: 10.18632/oncotarget.17912 28591694

18. Yu L, Zhang X, Wu T, Su J, Wang Y, Wang Y, et al. Avian infectious bronchitis virus disrupts the melanoma differentiation associated gene 5 (MDA5) signaling pathway by cleavage of the adaptor protein MAVS. BMC Vet Res. 2017;13(1):332. doi: 10.1186/s12917-017-1253-7 29132350

19. Luo J, Fang L, Dong N, Fang P, Ding Z, Wang D, et al. Porcine deltacoronavirus (PDCoV) infection suppresses RIG-I-mediated interferon-β production. 2016;495:10–7. doi: 10.1016/j.virol.2016.04.025 27152478

20. Zhu X, Wang D, Zhou J, Pan T, Chen J, Yang Y, et al. Porcine deltacoronavirus nsp5 antagonizes type I interferon signaling by cleaving STAT2. J Virol. 2017;91(10):e00003–17. doi: 10.1128/JVI.00003-17 28250121

21. Zhu X, Fang L, Wang D, Yang Y, Chen J, Ye X, et al. Porcine deltacoronavirus nsp5 inhibits interferon-β production through the cleavage of NEMO. Virology. 2017;502:33–38. doi: 10.1016/j.virol.2016.12.005 27984784

22. Fang P, Fang L, Ren J, Hong Y, Liu X, Zhao Y, et al. Porcine deltacoronavirus accessory protein NS6 antagonizes interferon beta production by interfering with the binding of RIG-I/MDA5 to double-stranded RNA. J Virol. 2018;92(15):e00712–18. doi: 10.1128/JVI.00712-18 29769346

23. Huang J, Lang Q, Li X, Xu Z, Zhu L, Zhou Y. MicroRNA Expression Profiles of Porcine Kidney 15 Cell Line Infected with Porcine Epidemic Diahorrea Virus. Chinese Journal of Virology. 2016;32(4):465–71. (in Chinese) 29995369

24. Mallick B, Ghosh Z, Chakrabarti J. MicroRNome analysis unravels the molecular basis of SARS infection in bronchoalveolar stem cells. PLoS One. 2009;4(11):e7837. doi: 10.1371/journal.pone.0007837 19915717

25. Devhare PB, Steele R, Di Bisceglie AM, Kaplan DE, Ray RB. Differential Expression of MicroRNAs in Hepatitis C Virus-Mediated Liver Disease Between African Americans and Caucasians: Implications for Racial Health Disparities. Gene Expr. 2017;17(2):89–98. doi: 10.3727/105221616X693594 27765085

26. Liu X, Zhu L, Liao S, Xu Z, Zhou Y. The porcine microRNA transcriptome response to transmissible gastroenteritis virus infection. PLoS One. 2015;10(3):e0120377. doi: 10.1371/journal.pone.0120377 25781021

27. Zheng H, Xu L, Liu Y, Li C, Zhang L, Wang T, et al. MicroRNA-221-5p Inhibits Porcine Epidemic Diarrhea Virus Replication by Targeting Genomic Viral RNA and Activating the NF-κB Pathway. Int J Mol Sci. 2018;19(11). pii: E3381. doi: 10.3390/ijms19113381 30380612

28. Ma Y, Wang C, Xue M, Fu F, Zhang X, Li L, et al. Coronavirus TGEV evades the type I interferon response through IRE1α-mediated manipulation of the miR-30a-5p/SOCS1/3 Axis. J Virol. 2018;92(22):e00728–18. doi: 10.1128/JVI.00728-18 30185587

29. Bhanja Chowdhury J, Shrivastava S, Steele R, Di Bisceglie AM, Ray R, Ray RB. Hepatitis C virus infection modulates expression of interferon stimulatory gene IFITM1 by upregulating miR-130A. J Virol. 2012;86(18):10221–5. doi: 10.1128/JVI.00882-12 22787204

30. Zheng L, Li XL, Yan MH, Ren WK, Zhang L, Lu C, et al. Isolation, identification and biological characteristics analysis of porcine deltacoronavirus TJ1[J]. China Animal Husbandry & Veterinary Medicine. 2018;45(1):219–224. (in Chinese)

31. Anders S, Huber W. Differential expression analysis for sequence count data. Genome Biol. 2010;11(10):R106. doi: 10.1186/gb-2010-11-10-r106 20979621

32. Trapnell C, Williams BA, Pertea G, Mortazavi A, Kwan G, van Baren MJ, et al. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat Biotechnol. 2010;28(5):511–5. doi: 10.1038/nbt.1621 20436464

33. Thompson HW, Mera R, Prasad C. A description of the appropriate use of student’s t-test. Nutr Neurosci. 1998;1(2):165–72. doi: 10.1080/1028415X.1998.11747226 27406022

34. Mair KH, Sedlak C, Käser T, Pasternak A, Levast B, Gerner W, et al. The porcine innate immune system: An update. Dev Comp Immunol. 2014;45(2):321–43. doi: 10.1016/j.dci.2014.03.022 24709051

35. Zhang H, Liu Q, Su W, Wang J, Sun Y, Zhang J, et al. Genome-wide analysis of differentially expressed genes and the modulation of PEDV infection in Vero E6 cells. Microb Pathog. 2018;117:247–54. doi: 10.1016/j.micpath.2018.02.004 29408315

36. Hu H, Jung K, Vlasova AN, Chepngeno J, Lu Z, Wang Q, et al. Isolation and characterization of porcine deltacoronavirus from pigs with diarrhea in the United States. J Clin Microbiol. 2015;53(5):1537–48. doi: 10.1128/JCM.00031-15 25740769

37. Zhang J, Chen J, Shi D, Shi H, Zhang X, Liu J, et al. Porcine deltacoronavirus enters cells via two pathways: A protease-mediated one at the cell surface and another facilitated by cathepsins in the endosome. Journal of biological chemistry. J Biol Chem. 2019;294(25):9830–9843. doi: 10.1074/jbc.RA119.007779 31068417

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2019 Číslo 10
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