Analysis of LncRNA, MiRNA, and MRNA Expression Profiling in Type I IFN and Type II IFN Overexpressed in Porcine Alveolar Macrophages

Overview

Journal Int J Genomics

Publisher Wiley

Date 2021 Jul 5

PMID 34222462

Citations 5

Authors

Congcong Li

Haoyuan Han

Xiuling Li

Jiao Wu

Xinfeng Li

Hui Niu

Wantao Li

Affiliations

Soon will be listed here.

Abstract

Current data is scarce regarding the function of noncoding RNAs (ncRNAs) such as microRNAs (miRNAs) and long noncoding RNAs (lncRNAs) in the interferon- (IFN-) mediated immune response. This is a comprehensive study that analyzes the lncRNA and miRNA expression profiles of the type I IFN and type II IFN in porcine alveolar macrophages using RNA sequencing. There was a total of 152 overexpressed differentially expressed (DE) lncRNAs and 21 DE miRNAs across type I IFN and type II IFN in porcine alveolar macrophages. Subsequent lncRNA-miRNA-mRNA network construction revealed the involvement of 36 DE lncRNAs and 12 DE miRNAs. LncRNAs such as the XLOC_211306, XLOC_100516, XLOC_00695, XLOC_149196, and XLOC_014459 were expressed at a higher degree in the type I IFN group, while XLOC_222640, XLOC_047290, XLOC_147777, XLOC_162298, XLOC_220210, and XLOC_165237 were expressed at a higher degree in the type II IFN group. These lncRNAs were found to act as "sponges" for miRNAs such as miR-34a, miR-328, miR-885-3p, miR-149, miR-30c-3p, miR-30b-5p, miR-708-5p, miR-193a-5p, miR-365-5p, and miR-7. Their target genes FADS2, RPS6KA1, PIM1, and NOD1 were found to be associated with several immune-related signaling pathways including the NOD-like receptor, Jak-STAT, mTOR, and PPAR signaling pathways. These experiments provide a comprehensive profile of overexpressed noncoding RNAs in porcine alveolar macrophages, providing new insights regarding the IFN-mediated immune response.

Citing Articles

The emerging roles of long non-coding RNA in host immune response and intracellular bacterial infections.

Arunima A, van Schaik E, Samuel J Front Cell Infect Microbiol. 2023; 13:1160198.

PMID: 37153158 PMC: 10160451. DOI: 10.3389/fcimb.2023.1160198.

Comparative transcriptomics reveals small RNA composition and differential microRNA responses underlying interferon-mediated antiviral regulation in porcine alveolar macrophages.

Li J, Sang E, Adeyemi O, Miller L, Sang Y Front Immunol. 2022; 13:1016268.

PMID: 36389683 PMC: 9651005. DOI: 10.3389/fimmu.2022.1016268.

Differential MicroRNA Expression in Porcine Endometrium Related to Spontaneous Embryo Loss during Early Pregnancy.

Gu S, Zang X, Jiang L, Gu T, Meng F, Huang S Int J Mol Sci. 2022; 23(15).

PMID: 35897733 PMC: 9331794. DOI: 10.3390/ijms23158157.

Insight into mechanisms of pig lncRNA FUT3-AS1 regulating E. coli F18-bacterial diarrhea.

Wu Z, Fan H, Jin J, Gao S, Huang R, Wu S PLoS Pathog. 2022; 18(6):e1010584.

PMID: 35696408 PMC: 9191744. DOI: 10.1371/journal.ppat.1010584.

MicroRNA Alterations Induced in Human Skin by Diesel Fumes, Ozone, and UV Radiation.

Valacchi G, Pambianchi E, Coco S, Pulliero A, Izzotti A J Pers Med. 2022; 12(2).

PMID: 35207665 PMC: 8880698. DOI: 10.3390/jpm12020176.

References

Zhao L, Xia M, Wang K, Lai C, Fan H, Gu H . A Long Non-coding RNA IVRPIE Promotes Host Antiviral Immune Responses Through Regulating Interferon β1 and ISG Expression. Front Microbiol. 2020; 11:260. PMC: 7044153. DOI: 10.3389/fmicb.2020.00260. View

Fish E, Platanias L . Interferon receptor signaling in malignancy: a network of cellular pathways defining biological outcomes. Mol Cancer Res. 2014; 12(12):1691-703. PMC: 4272667. DOI: 10.1158/1541-7786.MCR-14-0450. View

Wang L, Zhou L, Hu D, Ge X, Guo X, Yang H . Porcine reproductive and respiratory syndrome virus suppresses post-transcriptionally the protein expression of IFN-β by upregulating cellular microRNAs in porcine alveolar macrophages . Exp Ther Med. 2018; 15(1):115-126. PMC: 5769220. DOI: 10.3892/etm.2017.5397. View

Kong L, Zhang Y, Ye Z, Liu X, Zhao S, Wei L . CPC: assess the protein-coding potential of transcripts using sequence features and support vector machine. Nucleic Acids Res. 2007; 35(Web Server issue):W345-9. PMC: 1933232. DOI: 10.1093/nar/gkm391. View

Stark G, Kerr I, Williams B, Silverman R, Schreiber R . How cells respond to interferons. Annu Rev Biochem. 1998; 67:227-64. DOI: 10.1146/annurev.biochem.67.1.227. View

Li Y, Sassano A, Majchrzak B, Deb D, Levy D, Gaestel M . Role of p38alpha Map kinase in Type I interferon signaling. J Biol Chem. 2003; 279(2):970-9. DOI: 10.1074/jbc.M309927200. View

Kozomara A, Birgaoanu M, Griffiths-Jones S . miRBase: from microRNA sequences to function. Nucleic Acids Res. 2018; 47(D1):D155-D162. PMC: 6323917. DOI: 10.1093/nar/gky1141. View

Zhang X, Chapat C, Wang P, Choi J, Li Q, Luo J . microRNA-induced translational control of antiviral immunity by the cap-binding protein 4EHP. Mol Cell. 2021; 81(6):1187-1199.e5. DOI: 10.1016/j.molcel.2021.01.030. View

Liu X, Huang J, Yang S, Zhao Y, Xiang A, Cao J . Whole blood transcriptome comparison of pigs with extreme production of in vivo dsRNA-induced serum IFN-a. Dev Comp Immunol. 2013; 44(1):35-43. DOI: 10.1016/j.dci.2013.11.008. View

10.

Matikainen S, Sareneva T, Ronni T, Lehtonen A, Koskinen P, Julkunen I . Interferon-alpha activates multiple STAT proteins and upregulates proliferation-associated IL-2Ralpha, c-myc, and pim-1 genes in human T cells. Blood. 1999; 93(6):1980-91. View

11.

Yip-Schneider M, Horie M, Broxmeyer H . Transcriptional induction of pim-1 protein kinase gene expression by interferon gamma and posttranscriptional effects on costimulation with steel factor. Blood. 1995; 85(12):3494-502. View

12.

Fang L, Gao Y, Liu X, Bai J, Jiang P, Wang X . Long non-coding RNA LNC_000641 regulates pseudorabies virus replication. Vet Res. 2021; 52(1):52. PMC: 7992786. DOI: 10.1186/s13567-021-00922-0. View

13.

Ma F, Xu S, Liu X, Zhang Q, Xu X, Liu M . The microRNA miR-29 controls innate and adaptive immune responses to intracellular bacterial infection by targeting interferon-γ. Nat Immunol. 2011; 12(9):861-9. DOI: 10.1038/ni.2073. View

14.

Xu H, Jiang Y, Xu X, Su X, Liu Y, Ma Y . Inducible degradation of lncRNA Sros1 promotes IFN-γ-mediated activation of innate immune responses by stabilizing Stat1 mRNA. Nat Immunol. 2019; 20(12):1621-1630. DOI: 10.1038/s41590-019-0542-7. View

15.

Ouyang J, Zhu X, Chen Y, Wei H, Chen Q, Chi X . NRAV, a long noncoding RNA, modulates antiviral responses through suppression of interferon-stimulated gene transcription. Cell Host Microbe. 2014; 16(5):616-26. PMC: 7104942. DOI: 10.1016/j.chom.2014.10.001. View

16.

Cassatella M, Gasperini S, Calzetti F, Bertagnin A, Luster A, McDonald P . Regulated production of the interferon-gamma-inducible protein-10 (IP-10) chemokine by human neutrophils. Eur J Immunol. 1997; 27(1):111-5. DOI: 10.1002/eji.1830270117. View

17.

Petermann F, Pekowska A, Johnson C, Jankovic D, Shih H, Jiang K . The Magnitude of IFN-γ Responses Is Fine-Tuned by DNA Architecture and the Non-coding Transcript of Ifng-as1. Mol Cell. 2019; 75(6):1229-1242.e5. PMC: 6754279. DOI: 10.1016/j.molcel.2019.06.025. View

18.

Maarouf M, Chen B, Chen Y, Wang X, Rai K, Zhao Z . Identification of lncRNA-155 encoded by MIR155HG as a novel regulator of innate immunity against influenza A virus infection. Cell Microbiol. 2019; 21(8):e13036. DOI: 10.1111/cmi.13036. View

19.

Harada H, Taniguchi T, Tanaka N . The role of interferon regulatory factors in the interferon system and cell growth control. Biochimie. 1998; 80(8-9):641-50. DOI: 10.1016/s0300-9084(99)80017-0. View

20.

Huang X, Xu Y, Lin Q, Guo W, Zhao D, Wang C . Determination of antiviral action of long non-coding RNA loc107051710 during infectious bursal disease virus infection due to enhancement of interferon production. Virulence. 2019; 11(1):68-79. PMC: 6961729. DOI: 10.1080/21505594.2019.1707957. View