Transcriptomic Analysis Reveals Crucial Regulatory Roles of Immediate-early Response Genes and Related Signaling Pathways in Coronavirus Infectious Bronchitis Virus Infection

Overview

Journal Virology

Specialty Microbiology

Date 2022 Aug 20

PMID 35987078

Authors

Li Xia Yuan

Bei Yang

To Sing Fung

Rui Ai Chen

Ding Xiang Liu

Affiliations

Soon will be listed here.

Abstract

Coronavirus infection of cells differentially regulates the expression of host genes and their related pathways. In this study, we present the transcriptomic profile of cells infected with gammacoronavirus infectious bronchitis virus (IBV). In IBV-infected human non-small cell lung carcinoma cells (H1299 cells), a total of 1162 differentially expressed genes (DEGs), including 984 upregulated and 178 downregulated genes, was identified. These DEGs were mainly enriched in MAPK and Wnt signaling pathways, and 5 out of the 10 top upregulated genes in all transcripts were immediate-early response genes (IEGs). In addition, the induction of 11 transcripts was validated in IBV-infected H1299 and Vero cells by RT-qPCR. The accuracy, reliability and genericity of the transcriptomic data were demonstrated by functional characterization of these IEGs in cells infected with different coronaviruses in our previous publications. This study provides a reliable transcriptomic profile of host genes and pathways regulated by coronavirus infection.

Citing Articles

Host Immune Response Modulation in Avian Coronavirus Infection: Tracheal Transcriptome Profiling In Vitro and In Vivo.

ODowd K, Isham I, Vatandour S, Boulianne M, Dozois C, Gagnon C Viruses. 2024; 16(4).

PMID: 38675946 PMC: 11053446. DOI: 10.3390/v16040605.

References

Bhattacharyya S, Wu M, Fang F, Tourtellotte W, Feghali-Bostwick C, Varga J . Early growth response transcription factors: key mediators of fibrosis and novel targets for anti-fibrotic therapy. Matrix Biol. 2011; 30(4):235-42. PMC: 3135176. DOI: 10.1016/j.matbio.2011.03.005. View

Sabio G, Davis R . TNF and MAP kinase signalling pathways. Semin Immunol. 2014; 26(3):237-45. PMC: 4099309. DOI: 10.1016/j.smim.2014.02.009. View

Chen H, Huang X, Li H, He S, Ni R, Chen C . Expression of FOXJ1 in hepatocellular carcinoma: correlation with patients' prognosis and tumor cell proliferation. Mol Carcinog. 2012; 52(8):647-59. DOI: 10.1002/mc.21904. View

Wei Z, Guo H, Qin J, Lu S, Liu Q, Zhang X . Pan-senescence transcriptome analysis identified RRAD as a marker and negative regulator of cellular senescence. Free Radic Biol Med. 2018; 130:267-277. DOI: 10.1016/j.freeradbiomed.2018.10.457. View

Li S, Liu S, Chen R, Huang M, Fung T, Liu D . Activation of the MKK3-p38-MK2-ZFP36 Axis by Coronavirus Infection Restricts the Upregulation of AU-Rich Element-Containing Transcripts in Proinflammatory Responses. J Virol. 2022; 96(5):e0208621. PMC: 8906397. DOI: 10.1128/jvi.02086-21. View

Kanehisa M, Araki M, Goto S, Hattori M, Hirakawa M, Itoh M . KEGG for linking genomes to life and the environment. Nucleic Acids Res. 2007; 36(Database issue):D480-4. PMC: 2238879. DOI: 10.1093/nar/gkm882. View

Du L, Nakamura T, Moser B, Russell P . Retention but not recruitment of Crb2 at double-strand breaks requires Rad1 and Rad3 complexes. Mol Cell Biol. 2003; 23(17):6150-8. PMC: 180945. DOI: 10.1128/MCB.23.17.6150-6158.2003. View

Auger-Messier M, Accornero F, Goonasekera S, Bueno O, Lorenz J, van Berlo J . Unrestrained p38 MAPK activation in Dusp1/4 double-null mice induces cardiomyopathy. Circ Res. 2012; 112(1):48-56. PMC: 5929162. DOI: 10.1161/CIRCRESAHA.112.272963. View

Hogan P, Chen L, Nardone J, Rao A . Transcriptional regulation by calcium, calcineurin, and NFAT. Genes Dev. 2003; 17(18):2205-32. DOI: 10.1101/gad.1102703. View

10.

Zhou P, Yang X, Wang X, Hu B, Zhang L, Zhang W . A pneumonia outbreak associated with a new coronavirus of probable bat origin. Nature. 2020; 579(7798):270-273. PMC: 7095418. DOI: 10.1038/s41586-020-2012-7. View

11.

Nakabeppu Y, Nathans D . A naturally occurring truncated form of FosB that inhibits Fos/Jun transcriptional activity. Cell. 1991; 64(4):751-9. DOI: 10.1016/0092-8674(91)90504-r. View

12.

Wang X, Liao Y, Yap P, Png K, Tam J, Liu D . Inhibition of protein kinase R activation and upregulation of GADD34 expression play a synergistic role in facilitating coronavirus replication by maintaining de novo protein synthesis in virus-infected cells. J Virol. 2009; 83(23):12462-72. PMC: 2786722. DOI: 10.1128/JVI.01546-09. View

13.

Dinan A, Keep S, Bickerton E, Britton P, Firth A, Brierley I . Comparative Analysis of Gene Expression in Virulent and Attenuated Strains of Infectious Bronchitis Virus at Subcodon Resolution. J Virol. 2019; 93(18). PMC: 6714804. DOI: 10.1128/JVI.00714-19. View

14.

Yang X, Gao W, Liu H, Li J, Chen D, Yuan F . MicroRNA transcriptome analysis in chicken kidneys in response to differing virulent infectious bronchitis virus infections. Arch Virol. 2017; 162(11):3397-3405. DOI: 10.1007/s00705-017-3502-2. View

15.

Clevers H . Wnt/beta-catenin signaling in development and disease. Cell. 2006; 127(3):469-80. DOI: 10.1016/j.cell.2006.10.018. View

16.

Wang J, Fang S, Xiao H, Chen B, Tam J, Liu D . Interaction of the coronavirus infectious bronchitis virus membrane protein with beta-actin and its implication in virion assembly and budding. PLoS One. 2009; 4(3):e4908. PMC: 2653722. DOI: 10.1371/journal.pone.0004908. View

17.

Safe S, Jin U, Morpurgo B, Abudayyeh A, Singh M, Tjalkens R . Nuclear receptor 4A (NR4A) family - orphans no more. J Steroid Biochem Mol Biol. 2015; 157:48-60. PMC: 4618773. DOI: 10.1016/j.jsbmb.2015.04.016. View

18.

Liu R, van Berlo J, York A, Vagnozzi R, Maillet M, Molkentin J . DUSP8 Regulates Cardiac Ventricular Remodeling by Altering ERK1/2 Signaling. Circ Res. 2016; 119(2):249-60. PMC: 4938738. DOI: 10.1161/CIRCRESAHA.115.308238. View

19.

Sahraeian S, Mohiyuddin M, Sebra R, Tilgner H, Afshar P, Au K . Gaining comprehensive biological insight into the transcriptome by performing a broad-spectrum RNA-seq analysis. Nat Commun. 2017; 8(1):59. PMC: 5498581. DOI: 10.1038/s41467-017-00050-4. View

20.

Sultan M, Schulz M, Richard H, Magen A, Klingenhoff A, Scherf M . A global view of gene activity and alternative splicing by deep sequencing of the human transcriptome. Science. 2008; 321(5891):956-60. DOI: 10.1126/science.1160342. View