Comprehensive Analysis of a Competing Endogenous RNA Co-Expression Network in Chronic Obstructive Pulmonary Disease

References

• Gonçalves I, Guimarães MJ, van Zeller M, Menezes F, Moita J, Simão P; GI DPOC-Grupo de Interesse na Doença Pulmonar Obstrutiva Crónica. Clinical and molecular markers in COPD. Pulmonology. 2018;24(4):250–259. doi:10.1016/j.pulmoe.2018.02.005
   PubMed Web of Science ®Google Scholar
• Halpin DMG, Criner GJ, Papi A, et al. Global initiative for the diagnosis, management, and prevention of chronic obstructive lung disease. The 2020 GOLD Science Committee Report on COVID-19 and chronic obstructive pulmonary disease. Am J Respir Crit Care Med. 2021;203(1):24–36. doi:10.1164/rccm.202009-3533SO
   PubMed Web of Science ®Google Scholar
• Rabe KF, Watz H. Chronic obstructive pulmonary disease. Lancet. 2017;389(10082):1931–1940. doi:10.1016/S0140-6736(17)31222-9
   PubMed Web of Science ®Google Scholar
• Wang C, Xu J, Yang L, et al.; China Pulmonary Health Study Group. Prevalence and risk factors of chronic obstructive pulmonary disease in China (the China Pulmonary Health [CPH] study): a national cross-sectional study. Lancet. 2018;391(10131):1706–1717. doi:10.1016/S0140-6736(18)30841-9
   PubMed Web of Science ®Google Scholar
• Fan Y, Xu W, Wang Y, Wang Y, Yu S, Ye Q. Association of occupational dust exposure with combined chronic obstructive pulmonary disease and pneumoconiosis: a cross-sectional study in China. BMJ Open. 2020;10(9):e038874. doi:10.1136/bmjopen-2020-038874
   PubMed Web of Science ®Google Scholar
• Fan Y, Ma R, Du X, Chai D, Yang S, Ye Q. Small airway dysfunction in pneumoconiosis: a cross-sectional study. BMC Pulm Med. 2022;22(1):167. doi:10.1186/s12890-022-01929-9
   PubMed Web of Science ®Google Scholar
• Silverman EK. Genetics of COPD. Annu Rev Physiol. 2020;82(1):413–431. doi:10.1146/annurev-physiol-021317-121224
   PubMedGoogle Scholar
• Mattick JS, Makunin IV. Non-coding RNA. Hum Mol Genet. 2006;15(Suppl 1):R17–R29. doi:10.1093/hmg/ddl046
   PubMedGoogle Scholar
• Anastasiadou E, Jacob LS, Slack FJ. Non-coding RNA networks in cancer. Nat Rev Cancer. 2018;18(1):5–18. doi:10.1038/nrc.2017.99
   PubMed Web of Science ®Google Scholar
• Li Y, Yin Z, Fan J, Zhang S, Yang W. The roles of exosomal miRNAs and lncRNAs in lung diseases. Signal Transduct Target Ther. 2019;4(1):47. doi:10.1038/s41392-019-0080-7
   PubMed Web of Science ®Google Scholar
• Thomson DW, Dinger ME. Endogenous microRNA sponges: evidence and controversy. Nat Rev Genet. 2016;17(5):272–283. doi:10.1038/nrg.2016.20
   PubMed Web of Science ®Google Scholar
• Wang Z, Qu S, Zhu J, Chen F, Ma L. Comprehensive analysis of lncRNA-associated competing endogenous RNA network and immune infiltration in idiopathic pulmonary fibrosis. J Thorac Dis. 2020;12(5):1856–1865. doi:10.21037/jtd-19-2842
   PubMed Web of Science ®Google Scholar
• Yan YM, Zheng JN, Wu LW, et al. Prediction of a competing endogenous RNA co-expression network by comprehensive methods in systemic sclerosis-related interstitial lung disease. Front Genet. 2021;12:633059. doi:10.3389/fgene.2021.633059
   PubMed Web of Science ®Google Scholar
• Shen Q, Zheng J, Wang X, Hu W, Jiang Y, Jiang Y. LncRNA SNHG5 regulates cell apoptosis and inflammation by miR-132/PTEN axis in COPD. Biomed Pharmacother. 2020;126:110016. doi:10.1016/j.biopha.2020.110016
   PubMed Web of Science ®Google Scholar
• Liu P, Zhang H, Zeng H, et al. LncRNA CASC2 is involved in the development of chronic obstructive pulmonary disease via targeting miR-18a-5p/IGF1 axis. Ther Adv Respir Dis. 2021;15:17534666211028072. doi:10.1177/17534666211028072
   Web of Science ®Google Scholar
• Feghali-Bostwick CA, Gadgil AS, Otterbein LE, et al. Autoantibodies in patients with chronic obstructive pulmonary disease. Am J Respir Crit Care Med. 2008;177(2):156–163. doi:10.1164/rccm.200701-014OC
   PubMed Web of Science ®Google Scholar
• Laucho-Contreras ME, Polverino F, Gupta K, et al. Protective role for club cell secretory protein-16 (CC16) in the development of COPD. Eur Respir J. 2015;45(6):1544–1556. doi:10.1183/09031936.00134214
   PubMed Web of Science ®Google Scholar
• Hogg JC, Timens W. The pathology of chronic obstructive pulmonary disease. Annu Rev Pathol. 2009;4(1):435–459. doi:10.1146/annurev.pathol.4.110807.092145
   PubMed Web of Science ®Google Scholar
• Li JH, Liu S, Zhou H, Qu LH, Yang JH. StarBase v2.0: decoding miRNA-ceRNA, miRNA-ncRNA and protein-RNA interaction networks from large-scale CLIP-Seq data. Nucleic Acids Res. 2014;42(Database issue):D92–D97. doi:10.1093/nar/gkt1248
   PubMed Web of Science ®Google Scholar
• Karagkouni D, Paraskevopoulou MD, Tastsoglou S, et al. DIANA-LncBase v3: indexing experimentally supported miRNA targets on non-coding transcripts. Nucleic Acids Res. 2020;48(D1):D101–D110. doi:10.1093/nar/gkz1036
   PubMed Web of Science ®Google Scholar
• Wang P, Li X, Gao Y, et al. LncACTdb 2.0: an updated database of experimentally supported ceRNA interactions curated from low- and high-throughput experiments. Nucleic Acids Res. 2019;47(D1):D121–D127. doi:10.1093/nar/gky1144
   PubMed Web of Science ®Google Scholar
• Huang HY, Lin YC, Li J, et al. miRTarBase 2020: updates to the experimentally validated microRNA-target interaction database. Nucleic Acids Res. 2020;48(D1):D148–D154.
   PubMed Web of Science ®Google Scholar
• Langfelder P, Horvath S. WGCNA: an R package for weighted correlation network analysis. BMC Bioinform. 2008;9(1):559. doi:10.1186/1471-2105-9-559
   PubMed Web of Science ®Google Scholar
• Newman AM, Liu CL, Green MR, et al. Robust enumeration of cell subsets from tissue expression profiles. Nat Methods. 2015;12(5):453–457. doi:10.1038/nmeth.3337
   PubMed Web of Science ®Google Scholar
• Han MK, Agusti A, Calverley PM, et al. Chronic obstructive pulmonary disease phenotypes: the future of COPD. Am J Respir Crit Care Med. 2010;182(5):598–604. doi:10.1164/rccm.200912-1843CC
   PubMed Web of Science ®Google Scholar
• Schamberger AC, Mise N, Meiners S, Eickelberg O. Epigenetic mechanisms in COPD: implications for pathogenesis and drug discovery. Expert Opin Drug Discov. 2014;9(6):609–628. doi:10.1517/17460441.2014.913020
   PubMed Web of Science ®Google Scholar
• Wu DD, Song J, Bartel S, Krauss-Etschmann S, Rots MG, Hylkema MN. The potential for targeted rewriting of epigenetic marks in COPD as a new therapeutic approach. Pharmacol Ther. 2018;182:1–14. doi:10.1016/j.pharmthera.2017.08.007
   PubMed Web of Science ®Google Scholar
• Serban KA, Pratte KA, Bowler RP. Protein biomarkers for COPD outcomes. Chest. 2021;159(6):2244–2253. doi:10.1016/j.chest.2021.01.004
   PubMed Web of Science ®Google Scholar
• Li N, Zhan X. Identification of clinical trait-related lncRNA and mRNA biomarkers with weighted gene co-expression network analysis as useful tool for personalized medicine in ovarian cancer. EPMA J. 2019;10(3):273–290. doi:10.1007/s13167-019-00175-0
   PubMed Web of Science ®Google Scholar
• Zeng N, Wang T, Chen M, et al. Cigarette smoke extract alters genome-wide profiles of circular RNAs and mRNAs in primary human small airway epithelial cells. J Cell Mol Med. 2019;23(8):5532–5541. doi:10.1111/jcmm.14436
   PubMed Web of Science ®Google Scholar
• Duan R, Niu H, Yu T, et al. Identification and bioinformatic analysis of circular RNA expression in peripheral blood mononuclear cells from patients with chronic obstructive pulmonary disease. Int J Chron Obstruct Pulmon Dis. 2020;15:1391–1401. doi:10.2147/COPD.S252896
   PubMed Web of Science ®Google Scholar
• Guan Q, Tian Y, Zhang Z, Zhang L, Zhao P, Li J. Identification of potential key genes in the pathogenesis of chronic obstructive pulmonary disease through bioinformatics analysis. Front Genet. 2021;12:754569. doi:10.3389/fgene.2021.754569
   PubMed Web of Science ®Google Scholar
• Rab A, Rowe SM, Raju SV, Bebok Z, Matalon S, Collawn JF. Cigarette smoke and CFTR: implications in the pathogenesis of COPD. Am J Physiol Lung Cell Mol Physiol. 2013;305(8):L530–L541. doi:10.1152/ajplung.00039.2013
   PubMed Web of Science ®Google Scholar
• Acha-Sagredo A, Uko B, Pantazi P, et al. Long non-coding RNA dysregulation is a frequent event in non-small cell lung carcinoma pathogenesis. Br J Cancer. 2020;122(7):1050–1058. doi:10.1038/s41416-020-0742-9
   PubMed Web of Science ®Google Scholar
• Chen H, Lan Z, Li Q, Li Y. Abnormal expression of long noncoding RNA FGD5-AS1 affects the development of periodontitis through regulating miR-142-3p/SOCS6/NF-κB pathway. Artif Cells Nanomed Biotechnol. 2019;47(1):2098–2106. doi:10.1080/21691401.2019.1620256
   PubMed Web of Science ®Google Scholar
• Ye B, Wu ZH, Tsui TY, et al. lncRNA KCNQ1OT1 suppresses the inflammation and proliferation of vascular smooth muscle cells through IκBa in intimal hyperplasia. Mol Ther Nucleic Acids. 2020;20:62–72. doi:10.1016/j.omtn.2020.01.032
   PubMedGoogle Scholar
• Bost C, Arleevskaya MI, Brooks WH, Plaza S, Guery JC, Renaudineau Y. Long non-coding RNA Xist contribution in systemic lupus erythematosus and rheumatoid arthritis. Clin Immunol. 2022;236:108937. doi:10.1016/j.clim.2022.108937
   PubMed Web of Science ®Google Scholar
• Yu B, Qi Y, Li R, Shi Q, Satpathy AT, Chang HY. B cell-specific XIST complex enforces X-inactivation and restrains atypical B cells. Cell. 2021;184(7):1790–1803.e17. doi:10.1016/j.cell.2021.02.015
   PubMed Web of Science ®Google Scholar
• Orr C, Myers R, Li B, et al. Longitudinal analysis of serum microRNAs as predictors of cirrhosis regression during treatment of hepatitis B virus infection. Liver Int. 2020;40(7):1693–1700. doi:10.1111/liv.14474
   PubMed Web of Science ®Google Scholar
• Qi B, Yang C, Zhu Z, Chen H. EZH2-inhibited MicroRNA-454-3p promotes M2 macrophage polarization in glioma. Front Cell Dev Biol. 2020;8:574940. doi:10.3389/fcell.2020.574940
   PubMed Web of Science ®Google Scholar
• Liao L, Yang Q, Li H, Meng R, Li Y. Li Y. miR-454-3p prevents ox-LDL-induced apoptosis in HAECs by targeting TRPC3. Exp Ther Med. 2021;21(4):323. doi:10.3892/etm.2021.9754
   PubMed Web of Science ®Google Scholar
• Zhang L, Qin Y, Wu G, et al. PRRG4 promotes breast cancer metastasis through the recruitment of NEDD4 and downregulation of Robo1. Oncogene. 2020;39(49):7196–7208. doi:10.1038/s41388-020-01494-7
   PubMed Web of Science ®Google Scholar
• Justice ED, Barnum SJ, Kidd T. The WAGR syndrome gene PRRG4 is a functional homologue of the commissureless axon guidance gene. PLoS Genet. 2017;13(8):e1006865. doi:10.1371/journal.pgen.1006865
   PubMed Web of Science ®Google Scholar
• Lin J, Xue Y, Su W, Zhang Z, Wei Q, Huang T. Identification of Dysregulated mechanisms and candidate gene markers in chronic obstructive pulmonary disease. Int J Chron Obstruct Pulmon Dis. 2022;17:475–487. doi:10.2147/COPD.S349694
   PubMed Web of Science ®Google Scholar
• Ghosh B, Chengala PP, Shah S, et al. Cigarette smoke-induced injury induces distinct sex-specific transcriptional signatures in mice tracheal epithelial cells. Am J Physiol Lung Cell Mol Physiol. 2023;325(4):L467–L476. doi:10.1152/ajplung.00104.2023
   PubMed Web of Science ®Google Scholar
• Bu T, Wang LF, Yin YQ. How Do Innate immune cells contribute to airway remodeling in COPD progression? Int J Chron Obstruct Pulmon Dis. 2020;15:107–116. doi:10.2147/COPD.S235054
   PubMed Web of Science ®Google Scholar