Immune-related MiRNA-mRNA Regulation Network in the Livers of DHAV-3-infected Ducklings

Overview

Journal BMC Genomics

Publisher Biomed Central

Specialty Genetics

Date 2020 Feb 6

PMID 32019511

Citations 8

Authors

Fengyao Wu

Fengying Lu

Xin Fan

Jin Chao

Chuanmin Liu

Qunxing Pan

Huawei Sun

Xiaofei Zhang

Affiliations

Soon will be listed here.

Abstract

Background: Duck hepatitis A virus type 3 (DHAV-3) is one of the most harmful pathogens in the duck industry. However, the molecular mechanism underlying DHAV-3 infection in ducklings remains poorly understood. To study the genetic regulatory network for miRNA-mRNA and the signaling pathways involved in DHAV-3 infection in ducklings, we conducted global miRNA and mRNA expression profiling of duckling liver tissues infected with lethal DHAV-3 by high-throughput sequencing.

Results: We found 156 differentially expressed miRNAs (DEMs) and 7717 differentially expressed genes (DEGs) in livers of mock-infected and DHAV-3-infected duckling. A total of 19,606 miRNA-mRNA pairs with negatively correlated expression patterns were identified in miRNA-mRNA networks constructed on the basis of these DEMs and DEGs. Moreover, immune-related pathways, including the cytokine-cytokine receptor interaction, apoptosis, Toll-like receptor, Jak-STAT, and RIG-I-like receptor signaling pathway, were significantly enriched through analyzing functions of mRNAs in the network in response to DHAV-3 infection. Furthermore, apl-miR-32-5p, apl-miR-125-5p, apl-miR-128-3p, apl-miR-460-5p, and novel-m0012-3p were identified as potential regulators in the immune-related signaling pathways during DHAV-3 infection. And some host miRNAs were predicted to target the DHAV-3 genome.

Conclusions: This is the first integrated analysis of miRNA and mRNA in DHAV-3-infected ducklings. The results indicated the important roles of miRNAs in regulating immune response genes and revealed the immune related miRNA-mRNA regulation network in the DHAV-3-infected duckling liver. These findings increase our knowledge of the roles of miRNAs and their target genes in DHAV-3 replication and pathogenesis. They also aid in the understanding of host-virus interactions.

Citing Articles

Integrated analysis of miRNA and mRNA expression profiles in the bursa of Fabricius of specific pathogen-free chickens infected with avian reticuloendotheliosis virus strain SNV.

Zhao Y, Zhang Q, Wang M, Wu B, Zhao S, Wei X Poult Sci. 2025; 104(3):104847.

PMID: 39874788 PMC: 11810829. DOI: 10.1016/j.psj.2025.104847.

Single-cell RNA sequencing reveals intrahepatic signature related to pathobiology of duck hepatitis A virus type 3 (DHAV-3) infection.

Zhang Y, Ding D, Li S, Pan Q, Ru J, Zhao H Poult Sci. 2025; 104(2):104798.

PMID: 39799860 PMC: 11770546. DOI: 10.1016/j.psj.2025.104798.

Genomic Landscape and Regulation of RNA Editing in Pekin Ducks Susceptible to Duck Hepatitis A Virus Genotype 3 Infection.

Zhao H, Wu Z, Wang Z, Ru J, Wang S, Li Y Int J Mol Sci. 2024; 25(19).

PMID: 39408741 PMC: 11476845. DOI: 10.3390/ijms251910413.

Interleukin-2 enhancer binding factor 2 negatively regulates the replication of duck hepatitis A virus type 1 by disrupting the RNA-dependent RNA polymerase activity of 3D polymerase.

An H, Yu X, Li J, Shi F, Liu Y, Shu M Vet Res. 2024; 55(1):40.

PMID: 38532469 PMC: 10967090. DOI: 10.1186/s13567-024-01294-x.

Molecular Detection and Genetic Characterization of Vertically Transmitted Viruses in Ducks.

Wang X, Yu H, Zhang W, Fu L, Wang Y Animals (Basel). 2024; 14(1).

PMID: 38200736 PMC: 10777988. DOI: 10.3390/ani14010006.

References

Cui M, Jia R, Huang J, Wu X, Hu Z, Zhang X . Analysis of the microRNA expression profiles in DEF cells infected with duck Tembusu virus. Infect Genet Evol. 2018; 63:126-134. DOI: 10.1016/j.meegid.2018.05.020. View

Li J, Bi Y, Chen C, Yang L, Ding C, Liu W . Genetic characterization of Duck Hepatitis A Viruses isolated in China. Virus Res. 2013; 178(2):211-6. DOI: 10.1016/j.virusres.2013.10.007. View

Papadopoulou A, Dooley J, Linterman M, Pierson W, Ucar O, Kyewski B . The thymic epithelial microRNA network elevates the threshold for infection-associated thymic involution via miR-29a mediated suppression of the IFN-α receptor. Nat Immunol. 2011; 13(2):181-7. PMC: 3647613. DOI: 10.1038/ni.2193. View

Agarwal V, Bell G, Nam J, Bartel D . Predicting effective microRNA target sites in mammalian mRNAs. Elife. 2015; 4. PMC: 4532895. DOI: 10.7554/eLife.05005. View

Feng N, Zhou Z, Li Y, Zhao L, Xue Z, Lu R . Enterovirus 71-induced has-miR-21 contributes to evasion of host immune system by targeting MyD88 and IRAK1. Virus Res. 2017; 237:27-36. DOI: 10.1016/j.virusres.2017.05.008. View

Zhang X, Cao C, Liu Y, Qi H, Zhang W, Hao C . Comparative liver transcriptome analysis in ducklings infected with duck hepatitis A virus 3 (DHAV-3) at 12 and 48 hours post-infection through RNA-seq. Vet Res. 2018; 49(1):52. PMC: 6011267. DOI: 10.1186/s13567-018-0545-7. View

Trobaugh D, Gardner C, Sun C, Haddow A, Wang E, Chapnik E . RNA viruses can hijack vertebrate microRNAs to suppress innate immunity. Nature. 2013; 506(7487):245-8. PMC: 4349380. DOI: 10.1038/nature12869. View

Rehmsmeier M, Steffen P, Hochsmann M, Giegerich R . Fast and effective prediction of microRNA/target duplexes. RNA. 2004; 10(10):1507-17. PMC: 1370637. DOI: 10.1261/rna.5248604. View

Hazra B, Kumawat K, Basu A . The host microRNA miR-301a blocks the IRF1-mediated neuronal innate immune response to Japanese encephalitis virus infection. Sci Signal. 2017; 10(466):eaaf5185. DOI: 10.1126/scisignal.aaf5185. View

10.

Bernier A, Sagan S . The Diverse Roles of microRNAs at the Host⁻Virus Interface. Viruses. 2018; 10(8). PMC: 6116274. DOI: 10.3390/v10080440. View

11.

Zhang X, Cao C, Qu Z, Zhang W, Liu Y, Qi H . Pathogenicity of duck hepatitis A virus type 3 and innate immune responses of the ducklings to virulent DHAV-3. Mol Immunol. 2018; 95:30-38. DOI: 10.1016/j.molimm.2018.01.007. View

12.

Yao Y, Nair V . Role of virus-encoded microRNAs in Avian viral diseases. Viruses. 2014; 6(3):1379-94. PMC: 3970156. DOI: 10.3390/v6031379. View

13.

Takaoka A, Hayakawa S, Yanai H, Stoiber D, Negishi H, Kikuchi H . Integration of interferon-alpha/beta signalling to p53 responses in tumour suppression and antiviral defence. Nature. 2003; 424(6948):516-23. DOI: 10.1038/nature01850. View

14.

Piedade D, Azevedo-Pereira J . The Role of microRNAs in the Pathogenesis of Herpesvirus Infection. Viruses. 2016; 8(6). PMC: 4926176. DOI: 10.3390/v8060156. View

15.

Doherty D . Immunity, tolerance and autoimmunity in the liver: A comprehensive review. J Autoimmun. 2015; 66:60-75. DOI: 10.1016/j.jaut.2015.08.020. View

16.

Langmead B, Trapnell C, Pop M, Salzberg S . Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 2009; 10(3):R25. PMC: 2690996. DOI: 10.1186/gb-2009-10-3-r25. View

17.

Samir M, Vaas L, Pessler F . MicroRNAs in the Host Response to Viral Infections of Veterinary Importance. Front Vet Sci. 2016; 3:86. PMC: 5065965. DOI: 10.3389/fvets.2016.00086. View

18.

Slonchak A, Shannon R, Pali G, Khromykh A . Human MicroRNA miR-532-5p Exhibits Antiviral Activity against West Nile Virus via Suppression of Host Genes SESTD1 and TAB3 Required for Virus Replication. J Virol. 2015; 90(5):2388-402. PMC: 4810706. DOI: 10.1128/JVI.02608-15. View

19.

Chen K, Liu J, Cao X . Regulation of type I interferon signaling in immunity and inflammation: A comprehensive review. J Autoimmun. 2017; 83:1-11. DOI: 10.1016/j.jaut.2017.03.008. View

20.

Dang L, Teng M, Li H, Ma S, Lu Q, Hao H . Marek's disease virus type 1 encoded analog of miR-155 promotes proliferation of chicken embryo fibroblast and DF-1 cells by targeting hnRNPAB. Vet Microbiol. 2017; 207:210-218. DOI: 10.1016/j.vetmic.2017.06.015. View