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ORIGINAL RESEARCH

Construction and Analysis of ceRNA Networks Reveal the Key Genes Associated with Bovine Herpesvirus Type 1 Infection

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Pages 5729-5740 | Received 17 May 2023, Accepted 28 Jul 2023, Published online: 31 Aug 2023

References

  • Jones C. Bovine herpesvirus 1 counteracts immune responses and immune-surveillance to enhance pathogenesis and virus transmission. Front Immunol. 2019;10:1008. doi:10.3389/fimmu.2019.01008
  • Queiroz-Castro VLD, da Costa EP, Alves SVP, et al. Bovine herpesvirus 1 can cross the intact zona pellucida of bovine oocytes after artificial infection. PLoS One. 2019;14(7):e0218963. doi:10.1371/journal.pone.0218963
  • Osman RA, Griebel PJ. CD335 (NKp46)+ T-Cell Recruitment to the Bovine Upper Respiratory Tract during a Primary Bovine Herpesvirus-1 Infection. Front Immunol. 2017;8:1393. doi:10.3389/fimmu.2017.01393
  • Pokhriyal M, Ratta B, Yadav BS, et al. Three newly identified Immediate Early Genes of Bovine herpesvirus 1 lack the characteristic Octamer binding motif-1. Sci Rep. 2018;8(1):11441. doi:10.1038/s41598-018-29490-8
  • Tang L, Chen HY, Hao NB, et al. microRNA inhibitors: natural and artificial sequestration of microRNA. Cancer Lett. 2017;139–147. doi:10.1016/j.canlet.2017.05.025
  • Salmena L, Poliseno L, Tay Y, Kats L, Pandolfi PP. A ceRNA hypothesis: the Rosetta Stone of a hidden RNA language? Cell. 2011;146(3):353–358. doi:10.1016/j.cell.2011.07.014
  • Ye W, Lv Q, Wong CK, et al. The effect of central loops in miRNA:MRE duplexes on the efficiency of miRNA-mediated gene regulation. PLoS One. 2008;3(3):e1719. doi:10.1371/journal.pone.0001719
  • Zhao K, Ye Z, Li Y, et al. LncRNA FTX Contributes to the Progression of Colorectal Cancer Through Regulating miR-192-5p/EIF5A2 Axis. Onco Targets Ther. 2020;13:2677–2688. doi:10.2147/OTT.S241011
  • Lu B, Zhu Y, Wu J, et al. LncRNA34977 promotes the proliferation, migration, and invasion and inhibits the apoptosis of canine mammary tumors by regulating the expression of miR-8881/ELAVL4. Funct Integr Genomics. 2023;23(1):31. doi:10.1007/s10142-022-00955-4
  • Luo Y, Wang Q, Teng L, et al. LncRNA DANCR promotes proliferation and metastasis in pancreatic cancer by regulating miRNA-33b. FEBS Open Bio. 2020;10(1):18–27. doi:10.1002/2211-5463.12732
  • Ghosal S, Das S, Sen R, Chakrabarti J. HumanViCe: host ceRNA network in virus infected cells in human. Front Genet. 2014;5:249. doi:10.3389/fgene.2014.00249
  • Rahmani-Kukia N, Abbasi A. New insights on circular RNAs and their potential applications as biomarkers, therapeutic agents, and preventive vaccines in viral infections: with a glance at SARS-CoV-2. Mol Ther Nucleic Acids. 2022;29:705–717. doi:10.1016/j.omtn.2022.08.012
  • Park HJ, Ji P, Kim S, et al. 3’ UTR shortening represses tumor-suppressor genes in trans by disrupting ceRNA crosstalk. Nat Genet. 2018;50(6):783–789. doi:10.1038/s41588-018-0118-8
  • Bai Y, Huang Y, Li Y, et al. The Murine Reg3a Stimulated by Lactobacillus casei Promotes Intestinal Cell Proliferation and Inhibits the Multiplication of Porcine Diarrhea Causative Agent in vitro. Front Microbiol. 2021;12:675263. doi:10.3389/fmicb.2021.675263
  • Chen S, Zhou Y, Chen Y, Gu J. fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics. 2018;34(17):i884–i890. doi:10.1093/bioinformatics/bty560
  • Langmead B, Salzberg SL. Fast gapped-read alignment with Bowtie 2. Nat Methods. 2012;9(4):357–359. doi:10.1038/nmeth.1923
  • Kim D, Langmead B, Salzberg SL. HISAT: a fast spliced aligner with low 360 memory requirements. Nat Methods. 2015;12(4):357–360. doi:10.1038/nmeth.3317
  • Pertea M, Pertea GM, Antonescu CM, Chang TC, Mendell JT, Salzberg SL. StringTie enables improved reconstruction of a transcriptome from RNA-seq reads. Nat Biotechnol. 2015;33(3):290–295. doi:10.1038/nbt.3122.
  • Pertea M, Kim D, Pertea GM, Leek JT, Salzberg SL. Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown. Nat Protoc. 2016;11(9):1650–1667. doi:10.1038/nprot.2016.095
  • Lai Y. Differential expression analysis of Digital Gene Expression data: RNA-tag filtering, comparison of t-type tests and their genome-wide co-expression based adjustments. Int J Bioinform Res Appl. 2010;6(4):353–365. doi:10.1504/IJBRA.2010.035999
  • Fiorito F, Iovane V, Marullo A, Costagliola A, Granato GE, De Martino L. 2,3,7,8-Tetrachlorodibenzo-p-dioxin influences bovine herpesvirus 1 replication through upregulation of SIRT3 and cytoskeletal reorganization. Vet Res Commun. 2017;41(4):299–306. doi:10.1007/s11259-017-9701-1
  • Wu Y, Zhang L, Zhang Y, Zhen Y, Liu S. Bioinformatics analysis to screen for critical genes between survived and non- survived patients with sepsis. Mol Med Rep. 2018;18(4):3737–3743. doi:10.3892/mmr.2018.9408
  • Shannon P, Markiel A, Ozier O, et al. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res. 2003;13(11):2498–2504. doi:10.1101/gr.1239303
  • Tian L, Hu X, He Y, Wu Z, Li D, Zhang H. Construction of lncRNA-miRNA-mRNA networks reveals functional lncRNAs in abdominal aortic aneurysm. Exp Ther Med. 2018;16(5):3978–3986. doi:10.3892/etm.2018.6690
  • Assenov Y, Ramírez F, Schelhorn SE, Lengauer T, Albrecht M. Computing topological parameters of biological networks. Bioinformatics. 2008;24(2):282–284. doi:10.1093/bioinformatics/btm554
  • Zhan S, Dong Y, Zhao W, et al. Genome-wide identification and characterization of long non-coding RNAs in developmental skeletal muscle of fetal goat. BMC Genomics. 2016;17(1):666. doi:10.1186/s12864-016-3009-3
  • Yu G, Wang LG, Han Y, He QY. clusterProfiler: an R package for comparing biological themes among gene clusters. OMICS. 2012;16(5):284–287. doi:10.1089/omi.2011.0118
  • Miller JM. Experimentally induced infectious bovine rhinotracheitis virus infection during early pregnancy: effect on the bovine corpus luteum and conceptus. Am J Vet Res. 1986;47(2):223–228.
  • Roels S, Charlier G, Letellier C, et al. Natural case of bovine herpesvirus 1 meningoencephalitis in an adult cow. Vet Rec. 2000;146(20):586–588. doi:10.1136/vr.146.20.586
  • Singh A, Prasad M, Mishra B, et al. Transcriptome analysis reveals common differential and global gene expression profiles in bluetongue virus serotype 16 (BTV-16) infected peripheral blood mononuclear cells (PBMCs) in sheep and goats. Genom Data. 2016;11:62–72. doi:10.1016/j.gdata.2016.12.001
  • Manjunath S, Kumar GR, Mishra BP, et al. Genomic analysis of host - Peste des petits ruminants vaccine viral transcriptome uncovers transcription factors modulating immune regulatory pathways. Vet Res. 2015;46:15. doi:10.1186/s13567-015-0153-8
  • Li W, Mao L, Shu X, et al. Transcriptome analysis reveals differential immune related genes expression in bovine viral diarrhea virus-2 infected goat peripheral blood mononuclear cells (PBMCs). BMC Genomics. 2019;20(1):516. doi:10.1186/s12864-019-5830-y
  • Qi X, Zhang DH, Wu N, Xiao JH, Wang X, Ma W. ceRNA in cancer: possible functions and clinical implications. J Med Genet. 2015;52(10):710–718. doi:10.1136/jmedgenet-2015-103334
  • Huang J, Li Y, Lu Z, et al. Analysis of functional hub genes identifies CDC45 as an oncogene in non-small cell lung cancer - a short report. Cell Oncol. 2019;42(4):571–578. doi:10.1007/s13402-019-00438-y
  • Song ZY, Chao F, Zhuo Z, Ma Z, Li W, Chen G. Identification of hub genes in prostate cancer using robust rank aggregation and weighted gene co-expression network analysis. Aging. 2019;11(13):4736–4756. doi:10.18632/aging.102087
  • Cao H, Zhang L, Chen H, et al. Hub genes and gene functions associated with postmenopausal osteoporosis predicted by an integrated method. Exp Ther Med. 2019;17(2):1262–1267. doi:10.3892/etm.2018.7095
  • Liu Z, Meng J, Li X, et al. Identification of Hub Genes and Key Pathways Associated with Two Subtypes of Diffuse Large B-Cell Lymphoma Based on Gene Expression Profiling via Integrated Bioinformatics. Biomed Res Int. 2018;2018:3574534. doi:10.1155/2018/3574534
  • Kaczynski J, Cook T, Urrutia R. Sp1- and Krüppel-like transcription factors. Genome Biol. 2003;4(2):206. doi:10.1186/gb-2003-4-2-206
  • DuShane JK, Maginnis MS. Human DNA Virus Exploitation of the MAPK-ERK Cascade. Int J Mol Sci. 2019;20(14):3427. doi:10.3390/ijms20143427
  • Negash AA, Olson RM, Griffin S, Gale M. Modulation of calcium signaling pathway by hepatitis C virus core protein stimulates NLRP3 inflammasome activation. PLoS Pathog. 2019;15(2):e1007593. doi:10.1371/journal.ppat.1007593
  • Planès R, Serrero M, Leghmari K, BenMohamed L, Bahraoui E. HIV-1 Envelope Glycoproteins Induce the Production of TNF-α and IL-10 in Human Monocytes by Activating Calcium Pathway. Sci Rep. 2018;8(1):17215. doi:10.1038/s41598-018-35478-1
  • Li Y, Zheng G, Zhang Y, et al. MicroRNA analysis in mouse neuro-2a cells after pseudorabies virus infection. J Neurovirol. 2017;23(3):430–440. doi:10.1007/s13365-016-0511-y