Identification and Characterization of a ceRNA Regulatory Network Involving LINC00482 and PRRC2B in Peripheral Blood Mononuclear Cells: Implications for COPD Pathogenesis and Diagnosis

References

• Chen S, Kuhn M, Prettner K, et al. The global economic burden of chronic obstructive pulmonary disease for 204 countries and territories in 2020–50: a health-augmented macroeconomic modelling study. Lancet Glob Health. 2023;11:e1183–e93. doi:10.1016/S2214-109X(23)00217-6
   PubMed Web of Science ®Google Scholar
• Christenson SA, Smith BM, Bafadhel M, Putcha N. Chronic obstructive pulmonary disease. Lancet. 2022;399:2227–2242. doi:10.1016/S0140-6736(22)00470-6
   PubMed Web of Science ®Google Scholar
• Suissa S, Dell’Aniello S, Ernst P. Long-term natural history of chronic obstructive pulmonary disease: severe exacerbations and mortality. Thorax. 2012;67:957–963. doi:10.1136/thoraxjnl-2011-201518
   PubMed Web of Science ®Google Scholar
• Hurst JR, Donaldson GC, Perera WR, et al. Use of plasma biomarkers at exacerbation of chronic obstructive pulmonary disease. Am J Respir Crit Care Med. 2006;174:867–874. doi:10.1164/rccm.200604-506OC
   PubMed Web of Science ®Google Scholar
• Sivapalan P, Lapperre TS, Janner J, et al. Eosinophil-guided corticosteroid therapy in patients admitted to hospital with COPD exacerbation (CORTICO-COP): a multicentre, randomised, controlled, open-label, non-inferiority trial. Lancet Respir Med. 2019;7:699–709. doi:10.1016/S2213-2600(19)30176-6
   PubMed Web of Science ®Google Scholar
• Nuñez A, Marras V, Harlander M, et al. Association between routine blood biomarkers and clinical phenotypes and exacerbations in chronic obstructive pulmonary disease. Int J Chron Obstruct Pulmon Dis. 2020;15:681–690. doi:10.2147/COPD.S240720
   PubMed Web of Science ®Google Scholar
• Aldonyte R, Jansson L, Piitulainen E, Janciauskiene S. Circulating monocytes from healthy individuals and COPD patients. Respir Res. 2003;4:11. doi:10.1186/1465-9921-4-11
   PubMed Web of Science ®Google Scholar
• Cornwell WD, Kim V, Fan X, et al. Activation and polarization of circulating monocytes in severe chronic obstructive pulmonary disease. BMC Pulm Med. 2018;18:101. doi:10.1186/s12890-018-0664-y
   PubMed Web of Science ®Google Scholar
• Bahr TM, Hughes GJ, Armstrong M, et al. Peripheral blood mononuclear cell gene expression in chronic obstructive pulmonary disease. Am J Respir Cell Mol Biol. 2013;49:316–323. doi:10.1165/rcmb.2012-0230OC
   PubMed Web of Science ®Google Scholar
• Chi Y, Wang D, Wang J, Yu W, Yang J. Long non-coding RNA in the pathogenesis of cancers. Cells. 2019;9:8. doi:10.3390/cells9010008
   PubMedGoogle Scholar
• Salmena L, Poliseno L, Tay Y, Kats L, Pandolfi PP. A ceRNA hypothesis: the Rosetta Stone of a hidden RNA language? Cell. 2011;146:353–358. doi:10.1016/j.cell.2011.07.014
   PubMed Web of Science ®Google Scholar
• Chang L, Xia J. MicroRNA regulatory network analysis using miRNet 2.0. Methods Mol Biol. 2023;2594:185–204.
   PubMedGoogle Scholar
• McGeary SE, Lin KS, Shi CY, et al. The biochemical basis of microRNA targeting efficacy. Science. 2019;2019:366.
   Google Scholar
• Chen Y, Wang X. miRDB: an online database for prediction of functional microRNA targets. Nucleic Acids Res. 2020;48:D127–d31. doi:10.1093/nar/gkz757
   PubMed Web of Science ®Google Scholar
• Volders PJ, Anckaert J, Verheggen K, et al. LNCipedia 5: towards a reference set of human long non-coding RNAs. Nucleic Acids Res. 2019;47:D135–d9. doi:10.1093/nar/gky1031
   PubMed Web of Science ®Google Scholar
• Cao Z, Pan X, Yang Y, Huang Y, Shen HB. The lncLocator: a subcellular localization predictor for long non-coding RNAs based on a stacked ensemble classifier. Bioinformatics. 2018;34:2185–2194. doi:10.1093/bioinformatics/bty085
   PubMed Web of Science ®Google Scholar
• Szklarczyk D, Kirsch R, Koutrouli M, et al. The STRING database in 2023: protein-protein association networks and functional enrichment analyses for any sequenced genome of interest. Nucleic Acids Res. 2023;51:D638–d46. doi:10.1093/nar/gkac1000
   PubMed Web of Science ®Google Scholar
• Chen L, Zhou Y, Li H. LncRNA, miRNA and lncRNA-miRNA interaction in viral infection. Virus Res. 2018;257:25–32. doi:10.1016/j.virusres.2018.08.018
   PubMed Web of Science ®Google Scholar
• Ulitsky I. Interactions between short and long noncoding RNAs. FEBS Lett. 2018;592:2874–2883. doi:10.1002/1873-3468.13085
   PubMed Web of Science ®Google Scholar
• Long Y, Wang X, Youmans DT, Cech TR. How do lncRNAs regulate transcription? Sci Adv. 2017;3:eaao2110. doi:10.1126/sciadv.aao2110
   PubMed Web of Science ®Google Scholar
• Chen Z, Chen X, Lei T, et al. Integrative analysis of NSCLC identifies LINC01234 as an oncogenic lncRNA that interacts with HNRNPA2B1 and regulates miR-106b biogenesis. Mol Ther. 2020;28:1479–1493. doi:10.1016/j.ymthe.2020.03.010
   PubMed Web of Science ®Google Scholar
• Xu J, Xu J, Liu X, Jiang J. The role of lncRNA-mediated ceRNA regulatory networks in pancreatic cancer. Cell Death Discov. 2022;8:287. doi:10.1038/s41420-022-01061-x
   PubMed Web of Science ®Google Scholar
• Wang Y, Chen J, Chen W, et al. LINC00987 ameliorates COPD by regulating LPS-induced cell apoptosis, oxidative stress, inflammation and autophagy through let-7b-5p/SIRT1 axis. Int J Chron Obstruct Pulmon Dis. 2020;15:3213–3225. doi:10.2147/COPD.S276429
   PubMed Web of Science ®Google Scholar
• Qiao X, Hou G, He YL, et al. The novel regulatory role of the lncRNA-miRNA-mRNA axis in chronic inflammatory airway diseases. Front Mol Biosci. 2022;9:927549. doi:10.3389/fmolb.2022.927549
   PubMed Web of Science ®Google Scholar
• Glare EM, Divjak M, Bailey MJ, Walters EH. beta-Actin and GAPDH housekeeping gene expression in asthmatic airways is variable and not suitable for normalising mRNA levels. Thorax. 2002;57:765–770. doi:10.1136/thorax.57.9.765
   PubMed Web of Science ®Google Scholar
• Yang D, Yan Y, Hu F, Wang T. CYP1B1, VEGFA, BCL2, and CDKN1A affect the development of chronic obstructive pulmonary disease. Int J Chron Obstruct Pulmon Dis. 2020;15:167–175. doi:10.2147/COPD.S220675
   PubMed Web of Science ®Google Scholar
• Gao X, Wang X, Jiao N, Chen J, Sun D. Association of VEGFA polymorphisms with chronic obstructive pulmonary disease in Chinese Han and Mongolian populations. Exp Physiol. 2021;106:1839–1848. doi:10.1113/EP089523
   PubMed Web of Science ®Google Scholar
• Hogg JC, Chu F, Utokaparch S, et al. The nature of small-airway obstruction in chronic obstructive pulmonary disease. N Engl J Med. 2004;350:2645–2653. doi:10.1056/NEJMoa032158
   PubMed Web of Science ®Google Scholar
• Liao S, Fang X, Zhou K, et al. LINC00482 sponged miR-2467-3p to promote bone metastasis of prostate cancer through activating Wnt/β-catenin signaling pathway. J Bone Oncol. 2023;41:100494. doi:10.1016/j.jbo.2023.100494
   PubMed Web of Science ®Google Scholar
• Wang Y, Zhang L, Wei N, Sun Y, Pan W, Chen Y. Silencing LINC00482 inhibits tumor-associated inflammation and angiogenesis through down-regulation of MMP-15 via FOXA1 in bladder cancer. Aging. 2021;13(2):2264–2278. doi:10.18632/aging.202247
   Google Scholar
• Xu W, Patel N, Deng Y, Ding S, Wang T, Zhang H. Extracellular vesicle-derived LINC00482 induces microglial M2 polarization to facilitate brain metastasis of NSCLC. Cancer Lett. 2023;561:216146. doi:10.1016/j.canlet.2023.216146
   PubMed Web of Science ®Google Scholar
• Gong X and Huang M. Tumor-suppressive function of lncRNA-MEG3 in glioma cells by regulating miR-6088/SMARCB1 axis. Biomed Res Int. 2020;2020:1–15. doi:10.1155/2020/4309161
   Web of Science ®Google Scholar
• Chen J, Xia Y, Sui X, et al. Steviol, a natural product inhibits proliferation of the gastrointestinal cancer cells intensively. Oncotarget. 2018; 9(41):26299–26308. doi:10.18632/oncotarget.25233
   PubMedGoogle Scholar
• Ishibe Y, Kusaoi M, Murayama G, et al. Changes in the expression of circulating microRnas in systemic lupus erythematosus patient blood plasma after passing through a plasma adsorption membrane. Ther Apher Dial. 2018;22(3):278–289. doi:10.1111/1744-9987.12695
   PubMed Web of Science ®Google Scholar
• Castello A, Fischer B, Eichelbaum K, et al. Insights into RNA biology from an atlas of mammalian mRNA-binding proteins. Cell. 2012;149:1393–1406. doi:10.1016/j.cell.2012.04.031
   PubMed Web of Science ®Google Scholar
• Chowdhury MN, The JH. RGG motif proteins: interactions, functions, and regulations. Wiley Interdiscip Rev RNA. 2023;14:e1748. doi:10.1002/wrna.1748
   PubMed Web of Science ®Google Scholar
• de la Parra C, Ernlund A, Alard A, Ruggles K, Ueberheide B, Schneider RJ. A widespread alternate form of cap-dependent mRNA translation initiation. Nat Commun. 2018;9:3068. doi:10.1038/s41467-018-05539-0
   PubMed Web of Science ®Google Scholar
• Sugiyama H, Takahashi K, Yamamoto T, et al. Nat1 promotes translation of specific proteins that induce differentiation of mouse embryonic stem cells. Proc Natl Acad Sci U S A. 2017;114:340–345. doi:10.1073/pnas.1617234114
   PubMed Web of Science ®Google Scholar
• He S, Yang L, Xiao Z, Tang K, Xu D. Identification of key carcinogenic genes in Wilms’ tumor. Genes Genet Syst. 2021;96:141–149. doi:10.1266/ggs.21-00015
   PubMed Web of Science ®Google Scholar
• Tang Z, Li C, Kang B, Gao G, Li C, Zhang Z. GEPIA: a web server for cancer and normal gene expression profiling and interactive analyses. Nucleic Acids Res. 2017;45:W98–w102. doi:10.1093/nar/gkx247
   PubMed Web of Science ®Google Scholar
• Jiang F, Hedaya OM, Khor E, Wu J, Auguste M, Yao P. RNA binding protein PRRC2B mediates translation of specific mRNAs and regulates cell cycle progression. Nucleic Acids Res. 2023;51:5831–5846. doi:10.1093/nar/gkad322
   PubMed Web of Science ®Google Scholar