Effect of eleutheroside B1 on non‑coding RNAs and protein profiles of influenza A virus‑infected A549 cells

Yan,Wen; Chen,Jing; Wei,Zhenquan; Wang,Xiaohu; Zeng,Zhiqi; Tembo,Dumizulu; Wang,Yutao; Wang,Xinhua

doi:10.3892/ijmm.2020.4468

Effect of eleutheroside B1 on non‑coding RNAs and protein profiles of influenza A virus‑infected A549 cells

Authors:
- Wen Yan
- Jing Chen
- Zhenquan Wei
- Xiaohu Wang
- Zhiqi Zeng
- Dumizulu Tembo
- Yutao Wang
- Xinhua Wang
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Affiliations: Institute of Tropical Medicine, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong 510006, P.R. China, Key Laboratory of Livestock Disease Prevention of Guangdong Province, Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong 510640, P.R. China, State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong 510120, P.R. China, Centre of Immunology of Marseille‑Luminy, Aix‑Marseille University, 13009 Marseille, France
Published online on: January 17, 2020 https://doi.org/10.3892/ijmm.2020.4468
Pages: 753-768
Copyright: © Yan et al. This is an open access article distributed under the terms of Creative Commons Attribution License.

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Abstract

Influenza viruses often pose a serious threat to animals and human health. In an attempt to explore the potential of herbal medicine as a treatment for influenza virus infection, eleutheroside B1, a coumarin compound extracted from herba sarcandrae, was identified, which exhibited antiviral and anti‑inflammatory activities against influenza A virus. In this study, high‑throughput RNA sequencing and isobaric tags for relative and absolute quantification (iTRAQ) assays were performed to determine alterations in the non‑coding RNA (ncRNA) transcriptome and proteomics. Bioinformatics and target prediction analyses were used to decipher the potential roles of altered ncRNAs in the function of eleutheroside B1. Furthermore, long ncRNA (lncRNA) and mRNA co‑expressing networks were constructed to analyze the biological functions by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses. The analysis of RNA sequencing data revealed that 5 differentially expressed ncRNAs were upregulated and 3 ncRNAs were downregulated in the A549 cells infected with A/PR8/34/H1N1, with or without eleutheroside B1 treatment (PR8+eleu and PR8, respectively). Nuclear paraspeckle assembly transcript 1 (NEAT1) was differentially expressed between the PR8 and A549 cell groups. GO and KEGG pathway analyses indicated that eleutheroside B1 took advantage of the host cell biological processes and molecular function for its antiviral and anti‑inflammatory activities, as well as for regulating cytokine‑cytokine receptor interaction in the immune system, consistent with previous findings. The results of the iTRAQ assays indicated that L antigen family member 3 (LAGE3) protein, essential for tRNA processing, tRNA metabolic processes and ncRNA processing, was downregulated in the PR8+eleu compared with the PR8 group. In the present study, these comprehensive, large‑scale data analysis enhanced the understanding of multiple aspects of the transcriptome and proteomics that are involved in the antiviral and anti‑inflammatory activities of eleutheroside B1. These findings demonstrate the potential of eleutheroside B1 for use in the prevention and treatment of influenza A virus‑mediated infections.

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1	Yoon SW, Webby RJ and Webster RG: Evolution and ecology of influenza A viruses. Curr Top Microbiol Immunol. 385:359–375. 2014.PubMed/NCBI
2	Amarelle L, Lecuona E and Sznajder JI: Anti-influenza treatment: Drugs currently used and under development. Arch Bronconeumol. 53:19–26. 2017.In English, Spanish. View Article : Google Scholar
3	Takamatsu K, Marumo S, Fukui M and Hata A: Safety and efficacy of anti-influenza drugs, intravenous peramivir against influenza virus infection in elderly patients with underlying disease. J Microbiol Immunol Infect. 50:541–544. 2017. View Article : Google Scholar : PubMed/NCBI
4	Moss RB, Davey RT, Steigbigel RT and Fang F: Targeting pandemic influenza: A primer on influenza antivirals and drug resistance. J Antimicrob Chemother. 65:1086–1093. 2010. View Article : Google Scholar : PubMed/NCBI
5	Oh DY, Panozzo J, Vitesnik S, Farrukee R, Piedrafita D, Mosse J and Hurt AC: Selection of multi-drug resistant influenza A and B viruses under zanamivir pressure and their replication fitness in ferrets. Antivir Ther. 23:295–306. 2018. View Article : Google Scholar
6	Deyde VM, Xu X, Bright RA, Shaw M, Smith CB, Zhang Y, Shu Y, Gubareva LV, Cox NJ and Klimov AI: Surveillance of resistance to adamantanes among influenza A(H3N2) and A(H1N1) viruses isolated worldwide. J Infect Dis. 196:249–257. 2007. View Article : Google Scholar : PubMed/NCBI
7	Yen HL, McKimm-Breschkin JL, Choy KT, Wong DD, Cheung PP, Zhou J, Ng IH, Zhu H, Webby RJ, Guan Y, et al: Resistance to neuraminidase inhibitors conferred by an R292K mutation in a human influenza virus H7N9 isolate can be masked by a mixed R/K viral population. mBio. 4:pii: e00396-13. 2013. View Article : Google Scholar : PubMed/NCBI
8	Gurib-Fakim A: Medicinal plants: Traditions of yesterday and drugs of tomorrow. Mol Aspects Med. 27:1–93. 2006. View Article : Google Scholar
9	Pan SY, Zhou SF, Gao SH, Yu ZL, Zhang SF, Tang MK, Sun JN, Ma DL, Han YF, Fong WF and Ko KM: New perspectives on how to discover drugs from herbal medicines: CAM's outstanding contribution to modern therapeutics. Evid Based Complement Alternat Med. 2013:6273752013. View Article : Google Scholar : PubMed/NCBI
10	Wang L, Zhang RM, Liu GY, Wei BL, Wang Y, Cai HY, Li FS, Xu YL, Zheng SP and Wang G: Chinese herbs in treatment of influenza: A randomized, double-blind, placebo-controlled trial. Respir Med. 104:1362–1369. 2010. View Article : Google Scholar : PubMed/NCBI
11	Lin TJ, Lin CF, Chiu CH, Lee MC and Horng JT: Inhibition of endosomal fusion activity of influenza virus by Rheum tanguticum (da-huang). Sci Rep. 6:277682016. View Article : Google Scholar : PubMed/NCBI
12	Wu W, Li R, Li X, He J, Jiang S, Liu S and Yang J: Quercetin as an antiviral agent inhibits influenza a virus (IAV) entry. Viruses. 8:pii: E6. 2015. View Article : Google Scholar : PubMed/NCBI
13	Wang Y, Yan W, Chen Q, Huang W, Yang Z, Li X and Wang X: Inhibition viral RNP and anti-inflammatory activity of coumarins against influenza virus. Biomed Pharmacother. 87:583–588. 2017. View Article : Google Scholar : PubMed/NCBI
14	Harrow J, Frankish A, Gonzalez JM, Tapanari E, Diekhans M, Kokocinski F, Aken BL, Barrell D, Zadissa A, Searle S, et al: GENCODE: The reference human genome annotation for the ENCODE project. Genome Res. 22:1760–1774. 2012. View Article : Google Scholar : PubMed/NCBI
15	He JH, Han ZP and Li YG: Association between long non-coding RNA and human rare diseases (Review). Biomed Rep. 2:19–23. 2014. View Article : Google Scholar : PubMed/NCBI
16	Li W, Li N, Shi K and Chen Q: Systematic review and meta-analysis of the utility of long non-coding RNA GAS5 as a diagnostic and prognostic cancer biomarker. Oncotarget. 8:66414–66425. 2017.PubMed/NCBI
17	Shin SY, Jeong JS, Lim JY, Kim T, Park JH, Kim JK and Shin C: Transcriptomic analyses of rice (Oryza sativa) genes and non-coding RNAs under nitrogen starvation using multiple omics technologies. BMC Genomics. 19:5322018. View Article : Google Scholar : PubMed/NCBI
18	Xie H, Ma B, Gao Q, Zhan H, Liu Y, Chen Z, Ye S, Li J, Yao L and Huang W: Long non-coding RNA CRNDE in cancer prognosis: Review and meta-analysis. Clin Chim Acta. 485:262–271. 2018. View Article : Google Scholar : PubMed/NCBI
19	Ng SS, Li OT, Cheung TK, Malik Peiris JS and Poon LL: Heterologous influenza vRNA segments with identical non-coding sequences stimulate viral RNA replication in trans. Virol J. 5:22008. View Article : Google Scholar : PubMed/NCBI
20	Winterling C, Koch M, Koeppel M, Garcia-Alcalde F, Karlas A and Meyer TF: Evidence for a crucial role of a host non-coding RNA in influenza A virus replication. RNA Biol. 11:66–75. 2014. View Article : Google Scholar : PubMed/NCBI
21	Li F, Chen Y, Zhang Z, Ouyang J, Wang Y, Yan R, Huang S, Gao GF, Guo G and Chen JL: Robust expression of vault RNAs induced by influenza A virus plays a critical role in suppression of PKR-mediated innate immunity. Nucleic Acids Res. 43:10321–10337. 2015.PubMed/NCBI
22	Ma Y, Ouyang J, Wei J, Maarouf M and Chen JL: Involvement of host non-coding RNAs in the pathogenesis of the influenza virus. Int J Mol Sci. 18:pii: E39. 2016. View Article : Google Scholar
23	Valadkhan S and Plasek LM: Long non-coding RNA-mediated regulation of the interferon response: A new perspective on a familiar theme. Pathog Immun. 3:126–148. 2018. View Article : Google Scholar : PubMed/NCBI
24	Li Y, Zhang J, Huo C, Ding N, Li J, Xiao J, Lin X, Cai B, Zhang Y and Xu J: Dynamic organization of lncRNA and circular RNA regulators collectively controlled cardiac differentiation in humans. EBioMedicine. 24:137–146. 2017. View Article : Google Scholar : PubMed/NCBI
25	Okholm TLH, Nielsen MM, Hamilton MP, Christensen LL, Vang S, Hedegaard J, Hansen TB, Kjems J, Dyrskjøt L and Pedersen JS: Circular RNA expression is abundant and correlated to aggressiveness in early-stage bladder cancer. NPJ Genom Med. 2:362017. View Article : Google Scholar : PubMed/NCBI
26	Chen YG, Kim MV, Chen X, Batista PJ, Aoyama S, Wilusz JE, Iwasaki A and Chang HY: Sensing self and foreign circular RNAs by intron identity. Mol Cell. 67:228–238.e5. 2017. View Article : Google Scholar : PubMed/NCBI
27	Li X, Liu CX, Xue W, Zhang Y, Jiang S, Yin QF, Wei J, Yao RW, Yang L and Chen LL: Coordinated circRNA biogenesis and function with NF90/NF110 in viral infection. Mol Cell. 67:214–227.e7. 2017. View Article : Google Scholar : PubMed/NCBI
28	Brahmachari G: Discovery and development of antidiabetic agents from natural products. 1st edition. Waltham MA: Elsevier Inc; 2016
29	Luo R and Zhao H: Protein quantitation using iTRAQ: Review on the sources of variations and analysis of nonrandom missingness. Stat Interface. 5:99–107. 2012. View Article : Google Scholar : PubMed/NCBI
30	Smith SB, Dampier W, Tozeren A, Brown JR and Magid-Slav M: Identification of common biological pathways and drug targets across multiple respiratory viruses based on human host gene expression analysis. PLoS One. 7:e331742012. View Article : Google Scholar : PubMed/NCBI
31	Zhou B, Li J, Liang X, Yang Z and Jiang Z: Transcriptome profiling of influenza A virus-infected lung epithelial (A549) cells with lariciresinol-4-β-D-glucopyranoside treatment. PLoS One. 12:e01730582017. View Article : Google Scholar
32	Li X, Zhang Y, Zeng X, Yang L and Deng Y: Chemical profiling of bioactive constituents in Sarcandra glabra and its preparations using ultra-high-pressure liquid chromatography coupled with LTQ Orbitrap mass spectrometry. Rapid Commun Mass Spectrom. 25:2439–2447. 2011. View Article : Google Scholar : PubMed/NCBI
33	Schroeder A, Mueller O, Stocker S, Salowsky R, Leiber M, Gassmann M, Lightfoot S, Menzel W, Granzow M and Ragg T: The RIN: An RNA integrity number for assigning integrity values to RNA measurements. BMC Mol Biol. 7:32006. View Article : Google Scholar : PubMed/NCBI
34	Han Li C and Chen Y: Small and long non-coding RNAs: Novel targets in perspective cancer therapy. Curr Genomics. 16:319–326. 2015. View Article : Google Scholar
35	Kang YJ, Yang DC, Kong L, Hou M, Meng YQ, Wei L and Gao G: CPC2: A fast and accurate coding potential calculator based on sequence intrinsic features. Nucleic Acids Res. 45(W1): W12–W16. 2017. View Article : Google Scholar : PubMed/NCBI
36	Qu Z and Adelson DL: Bovine ncRNAs are abundant, primarily intergenic, conserved and associated with regulatory genes. PLoS One. 7:e426382012. View Article : Google Scholar : PubMed/NCBI
37	Qu Z and Adelson DL: Identification and comparative analysis of ncRNAs in human, mouse and zebrafish indicate a conserved role in regulation of genes expressed in brain. PLoS One. 7:e522752012. View Article : Google Scholar
38	Liu YC, Li JR, Sun CH, Andrews E, Chao RF, Lin FM, Weng SL, Hsu SD, Huang CC, Cheng C, et al: CircNet: A database of circular RNAs derived from transcriptome sequencing data. Nucleic Acids Res. 44(D1): D209–D215. 2016. View Article : Google Scholar :
39	Livak KJ and Schmittgen TD: Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) method. Methods. 25:402–408. 2001. View Article : Google Scholar
40	Li JH, Liu S, Zhou H, Qu LH and Yang JH: starBase v2.0: Decoding miRNA-ceRNA, miRNA-ncRNA and protein-RNA interaction networks from large-scale CLIP-Seq data. Nucleic Acids Res. 42(Database Issue): D92–D97. 2014. View Article : Google Scholar
41	Rinn JL: lncRNAs: Linking RNA to chromatin. Cold Spring Harb Perspect Biol. 6:pii: a018614. 2014. View Article : Google Scholar : PubMed/NCBI
42	Hu J, Gao Z, Wang X, Gu M, Liang Y, Liu X, Hu S, Liu H, Liu W, Chen S, et al: iTRAQ-based quantitative proteomics reveals important host factors involved in the high pathogenicity of the H5N1 avian influenza virus in mice. Med Microbiol Immunol. 206:125–147. 2017. View Article : Google Scholar
43	Xiao YL, Kash JC, Beres SB, Sheng ZM, Musser JM and Taubenberger JK: High-throughput RNA sequencing of a formalin-fixed, paraffin-embedded autopsy lung tissue sample from the 1918 influenza pandemic. J Pathol. 229:535–545. 2013. View Article : Google Scholar :
44	Imamura K, Imamachi N, Akizuki G, Kumakura M, Kawaguchi A, Nagata K, Kato A, Kawaguchi Y, Sato H, Yoneda M, et al: Long noncoding RNA NEAT1-dependent SFPQ relocation from promoter region to paraspeckle mediates IL8 expression upon immune stimuli. Mol Cell. 53:393–406. 2014. View Article : Google Scholar : PubMed/NCBI
45	Mao YS, Zhang B and Spector DL: Biogenesis and function of nuclear bodies. Trends Genet. 27:295–306. 2011. View Article : Google Scholar : PubMed/NCBI
46	Yan W, Zheng C, He J, Zhang W, Huang XA, Li X, Wang Y and Wang X: Eleutheroside B1 mediates its anti-influenza activity through POLR2A and N-glycosylation. Int J Mol Med. 42:2776–2792. 2018.PubMed/NCBI
47	Hirose T, Virnicchi G, Tanigawa A, Naganuma T, Li R, Kimura H, Yokoi T, Nakagawa S, Bénard M, Fox AH and Pierron G: NEAT1 long noncoding RNA regulates transcription via protein sequestration within subnuclear bodies. Mol Biol Cell. 25:169–183. 2014. View Article : Google Scholar :
48	Landeras-Bueno S, Jorba N, Pérez-Cidoncha M and Ortin J: The splicing factor proline-glutamine rich (SFPQ/PSF) is involved in influenza virus transcription. PLoS Pathog. 7:e10023972011. View Article : Google Scholar : PubMed/NCBI
49	Samji T: Influenza A: Understanding the viral life cycle. Yale J Biol Med. 82:153–159. 2009.PubMed/NCBI
50	Li C, Bankhead A III, Eisfeld AJ, Hatta Y, Jeng S, Chang JH, Aicher LD, Proll S, Ellis AL, Law GL, et al: Host regulatory network response to infection with highly pathogenic H5N1 avian influenza virus. J Virol. 85:10955–10967. 2011. View Article : Google Scholar : PubMed/NCBI
51	Luo M: Influenza virus entry. Adv Exp Med Biol. 726:201–221. 2012. View Article : Google Scholar : PubMed/NCBI
52	Rudnicka A and Yamauchi Y: Ubiquitin in influenza virus entry and innate immunity. Viruses. 8:pii: E293. 2016. View Article : Google Scholar : PubMed/NCBI
53	Schreiber G and Walter MR: Cytokine-receptor interactions as drug targets. Curr Opin Chem Biol. 14:511–519. 2010. View Article : Google Scholar : PubMed/NCBI
54	Spangler JB, Moraga I, Mendoza JL and Garcia KC: Insights into cytokine-receptor interactions from cytokine engineering. Annu Rev Immunol. 33:139–167. 2015. View Article : Google Scholar
55	Long M, Wang Y, Chen D, Wang Y, Wang R, Gong D, He H, Rock DL, Hao W and Luo S: Identification of host cellular proteins LAGE3 and IGFBP6 that interact with orf virus protein ORFV024. Gene. 661:60–67. 2018. View Article : Google Scholar : PubMed/NCBI
56	Wan LC, Maisonneuve P, Szilard RK, Lambert JP, Ng TF, Manczyk N, Huang H, Laister R, Caudy AA, Gingras AC, et al: Proteomic analysis of the human KEOPS complex identifies C14ORF142 as a core subunit homologous to yeast Gon7. Nucleic Acids Res. 45:805–817. 2017. View Article : Google Scholar :
57	Rojas-Benitez D, Ibar C and Glavic Á: The Drosophila EKC/KEOPS complex: Roles in protein synthesis homeostasis and animal growth. Fly (Austin). 7:168–172. 2013. View Article : Google Scholar
58	Petrushenko ZM, Budkevich TV, Shalak VF, Negrutskii BS and El'skaya AV: Novel complexes of mammalian translation elongation factor eEF1A.GDP with uncharged tRNA and aminoacyl-tRNA synthetase. Implications for tRNA channeling. Eur J Biochem. 269:4811–4818. 2002. View Article : Google Scholar : PubMed/NCBI
59	Stapulionis R and Deutscher MP: A channeled tRNA cycle during mammalian protein synthesis. Proc Natl Acad Sci USA. 92:7158–7161. 1995. View Article : Google Scholar : PubMed/NCBI
60	Pavon-Eternod M, David A, Dittmar K, Berglund P, Pan T and Bennink JR: Vaccinia and influenza A viruses select rather than adjust tRNAs to optimize translation. Nucleic Acids Res. 41:1914–1921. 2013. View Article : Google Scholar :
61	Landeras-Bueno S and Ortin J: Regulation of influenza virus infection by long non-coding RNAs. Virus Res. 212:78–84. 2016. View Article : Google Scholar
62	Barriocanal M, Carnero E, Segura V and Fortes P: Long non-coding RNA BST2/BISPR is induced by IFN and regulates the expression of the antiviral factor tetherin. Front Immunol. 5:6552015. View Article : Google Scholar : PubMed/NCBI
63	D'Orso I and Frankel AD: RNA-mediated displacement of an inhibitory snRNP complex activates transcription elongation. Nat Struct Mol Biol. 17:815–821. 2010. View Article : Google Scholar : PubMed/NCBI
64	Gupta RA, Shah N, Wang KC, Kim J, Horlings HM, Wong DJ, Tsai MC, Hung T, Argani P, Rinn JL, et al: Long non-coding RNA HOTAIR reprograms chromatin state to promote cancer metastasis. Nature. 464:1071–1076. 2010. View Article : Google Scholar : PubMed/NCBI
65	Kambara H, Niazi F, Kostadinova L, Moonka DK, Siegel CT, Post AB, Carnero E, Barriocanal M, Fortes P, Anthony DD and Valadkhan S: Negative regulation of the interferon response by an interferon-induced long non-coding RNA. Nucleic Acids Res. 42:10668–10680. 2014. View Article : Google Scholar : PubMed/NCBI
66	Mariner PD, Walters RD, Espinoza CA, Drullinger LF, Wagner SD, Kugel JF and Goodrich JA: Human Alu RNA is a modular transacting repressor of mRNA transcription during heat shock. Mol Cell. 29:499–509. 2008. View Article : Google Scholar : PubMed/NCBI