Identifying Hub Genes and MiRNA-mRNA Regulatory Networks in Mice Infected with H1N1 Influenza Virus

Overview

Journal Dis Markers

Publisher Wiley

Specialty Biochemistry

Date 2023 May 25

PMID 37228892

Authors

Mingyang Li

Qizhi He

Lingli Chen

Affiliations

Soon will be listed here.

Abstract

H1N1 influenza virus is a major factor in seasonal influenza outbreaks. After the body is infected with the influenza virus, the expression of certain mRNAs, including miRNAs, could be affected. However, the association between these mRNAs and miRNAs remains unclear. This study is aimed at identifying differentially expressed genes (DEGs) and miRNAs (DEmiRs) caused by H1N1 influenza virus infection and constructing a miRNA-mRNA regulatory network. Nine GSE datasets were downloaded from the Gene Expression Omnibus database, of which seven were mRNA data and two were miRNA data. The limma package in R language package was used to analyze array data, and edgeR package was used to analyze high-throughput sequencing data. At the same time, the genes related to H1N1 infection were further screened by WGCNA analysis. DEGs were subjected to Gene Ontology and KEGG pathway enrichment analyses by DAVID database, while the STRING database predicted the protein-protein interaction (PPI) network. The correspondence between miRNA and target mRNA was analyzed by the miRWalk database. Cytoscape software was used to output PPI results, identify hub genes, and construct a miRNA-mRNA regulatory network. 114 DEGs and 37 candidate DEmiRs were identified for subsequent analysis. These DEGs were significantly enriched in response to the virus, cytokine activity, and symbiont-containing vacuole membrane. According to KEGG analysis, DEGs were enriched in PD-L1 expression and PD-1 checkpoint pathway. The key point Cd274 (PD-L1) was highly expressed in the H1N1-infected group. Finally, a potential miRNA-mRNA regulatory network (containing 8 candidate DEmiRs and 69 candidate DEGs) and a PPI network were constructed. After that, three hub genes were identified: Ifit3, Stat2, and Irf7. These hub genes and Cd274 were validated by another independent high-throughput dataset and were highly expressed pattern. This study will help researchers gain insights into the intrinsic effects of H1N1 influenza virus infection on the host and suggest a novel association of H1N1 virus with the host immune system.

References

Liu L, Hou J, Xu Y, Qin L, Liu W, Zhang H . PD-L1 upregulation by IFN-α/γ-mediated Stat1 suppresses anti-HBV T cell response. PLoS One. 2020; 15(7):e0228302. PMC: 7337294. DOI: 10.1371/journal.pone.0228302. View

Li Y, Chen X, Gu W, Qian H, Tian Y, Tang J . A meta-analysis of tumor necrosis factor (TNF) gene polymorphism and susceptibility to influenza A (H1N1). Comput Biol Chem. 2020; 89:107385. DOI: 10.1016/j.compbiolchem.2020.107385. View

Shao W, Li X, Goraya M, Wang S, Chen J . Evolution of Influenza A Virus by Mutation and Re-Assortment. Int J Mol Sci. 2017; 18(8). PMC: 5578040. DOI: 10.3390/ijms18081650. View

Pichlmair A, Lassnig C, Eberle C, Gorna M, Baumann C, Burkard T . IFIT1 is an antiviral protein that recognizes 5'-triphosphate RNA. Nat Immunol. 2011; 12(7):624-30. DOI: 10.1038/ni.2048. View

Go J, Belisle S, Tchitchek N, Tumpey T, Ma W, Richt J . 2009 pandemic H1N1 influenza virus elicits similar clinical course but differential host transcriptional response in mouse, macaque, and swine infection models. BMC Genomics. 2012; 13:627. PMC: 3532173. DOI: 10.1186/1471-2164-13-627. View

Cha J, Chan L, Li C, Hsu J, Hung M . Mechanisms Controlling PD-L1 Expression in Cancer. Mol Cell. 2019; 76(3):359-370. PMC: 6981282. DOI: 10.1016/j.molcel.2019.09.030. View

Aghbash P, Eslami N, Shamekh A, Entezari-Maleki T, Baghi H . SARS-CoV-2 infection: The role of PD-1/PD-L1 and CTLA-4 axis. Life Sci. 2021; 270:119124. PMC: 7838580. DOI: 10.1016/j.lfs.2021.119124. View

Sticht C, de la Torre C, Parveen A, Gretz N . miRWalk: An online resource for prediction of microRNA binding sites. PLoS One. 2018; 13(10):e0206239. PMC: 6193719. DOI: 10.1371/journal.pone.0206239. View

Fiers W, De Filette M, Birkett A, Neirynck S, Min Jou W . A "universal" human influenza A vaccine. Virus Res. 2004; 103(1-2):173-6. DOI: 10.1016/j.virusres.2004.02.030. View

10.

Paquette S, Banner D, Zhao Z, Fang Y, Huang S, Leon A . Interleukin-6 is a potential biomarker for severe pandemic H1N1 influenza A infection. PLoS One. 2012; 7(6):e38214. PMC: 3367995. DOI: 10.1371/journal.pone.0038214. View

11.

Yang N, Hong X, Yang P, Ju X, Wang Y, Tang J . The 2009 pandemic A/Wenshan/01/2009 H1N1 induces apoptotic cell death in human airway epithelial cells. J Mol Cell Biol. 2011; 3(4):221-9. DOI: 10.1093/jmcb/mjr017. View

12.

Jia D, Rahbar R, Chan R, Lee S, Chan M, Wang B . Influenza virus non-structural protein 1 (NS1) disrupts interferon signaling. PLoS One. 2010; 5(11):e13927. PMC: 2978095. DOI: 10.1371/journal.pone.0013927. View

13.

Johnson B, VanBlargan L, Xu W, White J, Shan C, Shi P . Human IFIT3 Modulates IFIT1 RNA Binding Specificity and Protein Stability. Immunity. 2018; 48(3):487-499.e5. PMC: 6251713. DOI: 10.1016/j.immuni.2018.01.014. View

14.

Wilk E, Pandey A, Leist S, Hatesuer B, Preusse M, Pommerenke C . RNAseq expression analysis of resistant and susceptible mice after influenza A virus infection identifies novel genes associated with virus replication and important for host resistance to infection. BMC Genomics. 2015; 16:655. PMC: 4557482. DOI: 10.1186/s12864-015-1867-8. View

15.

Feng S, Heath E, Jefferson B, Joslyn C, Kvinge H, Mitchell H . Hypergraph models of biological networks to identify genes critical to pathogenic viral response. BMC Bioinformatics. 2021; 22(1):287. PMC: 8164482. DOI: 10.1186/s12859-021-04197-2. View

16.

Stavast C, Erkeland S . The Non-Canonical Aspects of MicroRNAs: Many Roads to Gene Regulation. Cells. 2019; 8(11). PMC: 6912820. DOI: 10.3390/cells8111465. View

17.

Hagau N, Slavcovici A, Gonganau D, Oltean S, Dirzu D, Brezoszki E . Clinical aspects and cytokine response in severe H1N1 influenza A virus infection. Crit Care. 2010; 14(6):R203. PMC: 3220006. DOI: 10.1186/cc9324. View

18.

Josset L, Belser J, Pantin-Jackwood M, Chang J, Chang S, Belisle S . Implication of inflammatory macrophages, nuclear receptors, and interferon regulatory factors in increased virulence of pandemic 2009 H1N1 influenza A virus after host adaptation. J Virol. 2012; 86(13):7192-206. PMC: 3416346. DOI: 10.1128/JVI.00563-12. View

19.

Saito T, Gale Jr M . Principles of intracellular viral recognition. Curr Opin Immunol. 2006; 19(1):17-23. DOI: 10.1016/j.coi.2006.11.003. View

20.

Johnson W, Li C, Rabinovic A . Adjusting batch effects in microarray expression data using empirical Bayes methods. Biostatistics. 2006; 8(1):118-27. DOI: 10.1093/biostatistics/kxj037. View