Identification of Potential Differentially-Methylated/Expressed Genes in Chronic Obstructive Pulmonary Disease

References

• Decramer M, Janssens W, Miravitlles M. Chronic obstructive pulmonary disease. Lancet. 2012;379(9823):1341–1351. DOI:10.1016/S0140-6736(11)60968-9
   PubMed Web of Science ®Google Scholar
• Agusti A, Soriano JB. COPD as a systemic disease. COPD. 2008;5(2):133–138. DOI:10.1080/15412550801941349
   PubMedGoogle Scholar
• Kurimoto E, Miyahara N, Kanehiro A, et al. IL-17A is essential to the development of elastase-induced pulmonary inflammation and emphysema in mice. Respir Res. 2013;14(1):5. DOI:10.1186/1465-9921-14-5
   PubMed Web of Science ®Google Scholar
• Barnes PJ. Inflammatory mechanisms in patients with chronic obstructive pulmonary disease. J Allergy Clin Immunol. 2016;138(1):16–27. DOI:10.1016/j.jaci.2016.05.011
   PubMed Web of Science ®Google Scholar
• Fujii U, Miyahara N, Taniguchi A, et al. IL-23 is essential for the development of elastase-induced pulmonary inflammation and emphysema. Am J Respir Cell Mol Biol. 2016;55(5):697–707. DOI:10.1165/rcmb.2016-0015OC
   PubMed Web of Science ®Google Scholar
• Cosio MG, Saetta M, Agusti A. Immunologic aspects of chronic obstructive pulmonary disease. N Engl J Med. 2009;360(23):2445–2454. DOI:10.1056/NEJMra0804752
   PubMed Web of Science ®Google Scholar
• Núñez B, Sauleda J, Antó JM, PAC-COPD Investigators, et al. Anti-tissue antibodies are related to lung function in chronic obstructive pulmonary disease. Am J Respir Crit Care Med. 2011;183(8):1025–1031. DOI:10.1164/rccm.201001-0029OC
   PubMed Web of Science ®Google Scholar
• Bonarius HP, Brandsma CA, Kerstjens HA, et al. Antinuclear autoantibodies are more prevalent in COPD in association with low body mass index but not with smoking history. Thorax. 2011;66(2):101–107. DOI:10.1136/thx.2009.134171
   PubMed Web of Science ®Google Scholar
• Arnson Y, Shoenfeld Y, Amital H. Effects of tobacco smoke on immunity, inflammation and autoimmunity. J Autoimmun. 2010;34(3):J258–J265. DOI:10.1016/j.jaut.2009.12.003
   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
• Taniguchi A, Miyahara N, Oda N, et al. Protective effects of bisoprolol against acute exacerbation in moderate-to-severe chronic obstructive pulmonary disease. Acta Med Okayama. 2017;71(5):453–457.
   PubMed Web of Science ®Google Scholar
• Oda N, Miyahara N, Ichikawa H, et al. Long-term effects of beta-blocker use on lung function in Japanese patients with chronic obstructive pulmonary disease. Int J Chron Obstruct Pulmon Dis. 2017;12:1119–1124. DOI:10.2147/COPD.S133071
   PubMed Web of Science ®Google Scholar
• Almagro P, Martinez-Camblor P, Soriano JB, et al. Finding the best thresholds of FEV1 and dyspnea to predict 5-year survival in COPD patients: the COCOMICS study. PLoS One. 2014;9(2):e89866. DOI:10.1371/journal.pone.0089866
   PubMed Web of Science ®Google Scholar
• Lowe KE, Regan EA, Anzueto A, et al. COPDGene(®) 2019: redefining the diagnosis of chronic obstructive pulmonary disease. J COPD F. 2019;6(5):384–399. DOI:10.15326/jcopdf.6.5.2019.0149
   PubMedGoogle Scholar
• Rotondo JC, Aquila G, Oton-Gonzalez L, et al. Methylation of SERPINA1 gene promoter may predict chronic obstructive pulmonary disease in patients affected by acute coronary syndrome. Clin Epigenetics. 2021;13(1):79.
   PubMed Web of Science ®Google Scholar
• Qiu W, Baccarelli A, Carey VJ, et al. Variable DNA methylation is associated with chronic obstructive pulmonary disease and lung function. Am J Respir Crit Care Med. 2012;185(4):373–381. DOI:10.1164/rccm.201108-1382OC
   PubMed Web of Science ®Google Scholar
• Vucic EA, Chari R, Thu KL, et al. DNA methylation is globally disrupted and associated with expression changes in chronic obstructive pulmonary disease small airways. Am J Respir Cell Mol Biol. 2014;50(5):912–922. DOI:10.1165/rcmb.2013-0304OC
   PubMed Web of Science ®Google Scholar
• Sundar IK, Yin Q, Baier BS, et al. DNA methylation profiling in peripheral lung tissues of smokers and patients with COPD. Clin Epigenetics. 2017;9:38. DOI:10.1186/s13148-017-0335-5
   PubMed Web of Science ®Google Scholar
• Vicente CT, Revez JA, Ferreira MAR. Lessons from ten years of genome-wide association studies of asthma. Clin Transl Immunol. 2017;6(12):e165. DOI:10.1038/cti.2017.54
   PubMed Web of Science ®Google Scholar
• Zhao W, Yue X, Liu K, et al. The status of pulmonary fibrosis in systemic sclerosis is associated with IRF5, STAT4, IRAK1, and CTGF polymorphisms. Rheumatol Int. 2017;37(8):1303–1310. DOI:10.1007/s00296-017-3722-5
   PubMed Web of Science ®Google Scholar
• Kalathil SG, Lugade AA, Pradhan V, et al. T-regulatory cells and programmed death 1+ T cells contribute to effector T-cell dysfunction in patients with chronic obstructive pulmonary disease. Am J Respir Crit Care Med. 2014;190(1):40–50. DOI:10.1164/rccm.201312-2293OC
   PubMed Web of Science ®Google Scholar
• Grundy S, Plumb J, Lea S, et al. Down regulation of T cell receptor expression in COPD pulmonary CD8 cells. PLoS One. 2013;8(8):e71629. DOI:10.1371/journal.pone.0071629
   PubMed Web of Science ®Google Scholar
• Hurst JR, Vestbo J, Anzueto A, Evaluation of COPD Longitudinally to Identify Predictive Surrogate Endpoints (ECLIPSE) Investigators, et al. Susceptibility to exacerbation in chronic obstructive pulmonary disease. N Engl J Med. 2010;363(12):1128–1138. DOI:10.1056/NEJMoa0909883
   PubMed Web of Science ®Google Scholar
• Li L, Lv J, He Y, et al. Gene network in pulmonary tuberculosis based on bioinformatic analysis. BMC Infect Dis. 2020;20(1):612. DOI:10.1186/s12879-020-05335-6
   PubMed Web of Science ®Google Scholar
• Rogers AV, Adelroth E, Hattotuwa K, et al. Bronchial mucosal dendritic cells in smokers and ex-smokers with COPD: an electron microscopic study. Thorax. 2008;63(2):108–114. DOI:10.1136/thx.2007.078253
   PubMed Web of Science ®Google Scholar
• Liao SX, Ding T, Rao XM, et al. Cigarette smoke affects dendritic cell maturation in the small airways of patients with chronic obstructive pulmonary disease. Mol Med Rep. 2015;11(1):219–225. DOI:10.3892/mmr.2014.2759
   PubMed Web of Science ®Google Scholar
• Shrestha D, Ye GX, Stabley D, et al. Pulmonary immune cell transcriptome changes in double-hit model of BPD induced by chorioamnionitis and postnatal hyperoxia. Pediatr Res. 2021;90(3):565–575. DOI:10.1038/s41390-020-01319-z
   PubMed Web of Science ®Google Scholar
• Zhang J, Liu J, Xu S, et al. Bioinformatics analyses of the pathogenesis and new biomarkers of chronic obstructive pulmonary disease. Medicine (Baltimore). 2021;100(46):e27737. DOI:10.1097/MD.0000000000027737
   PubMed Web of Science ®Google Scholar
• Laulajainen-Hongisto A, Lyly A, Hanif T, et al. Genomics of asthma, allergy and chronic rhinosinusitis: novel concepts and relevance in airway mucosa. Clin Transl Allergy. 2020;10(1):45. DOI:10.1186/s13601-020-00347-6
   PubMed Web of Science ®Google Scholar
• Kreiner E, Waage J, Standl M, et al. Shared genetic variants suggest common pathways in allergy and autoimmune diseases. J Allergy Clin Immunol. 2017;140(3):771–781. DOI:10.1016/j.jaci.2016.10.055
   PubMed Web of Science ®Google Scholar
• Muro S, Tabara Y, Matsumoto H, Nagahama Study Group, et al. Relationship among Chlamydia and Mycoplasma pneumoniae seropositivity, IKZF1 genotype and chronic obstructive pulmonary disease in a general Japanese population: the Nagahama study. Medicine (Baltimore). 2016;95(15):e3371. DOI:10.1097/MD.0000000000003371
   PubMed Web of Science ®Google Scholar
• Lin LT, Richardson CD. The host cell receptors for measles virus and their interaction with the viral hemagglutinin (H) Protein. Viruses. 2016;8(9):250. DOI:10.3390/v8090250
   PubMed Web of Science ®Google Scholar
• Whittle E, Leonard MO, Gant TW, et al. Multi-Method molecular characterisation of human Dust-Mite-associated allergic asthma. Sci Rep. 2019;9(1):8912. DOI:10.1038/s41598-019-45257-1
   PubMedGoogle Scholar
• Ridolo E, Pucciarini F, Nizi MC, et al. Mabs for treating asthma: omalizumab, mepolizumab, reslizumab, benralizumab, dupilumab. Hum Vaccin Immunother. 2020;16(10):2349–2356. DOI:10.1080/21645515.2020.1753440
   PubMed Web of Science ®Google Scholar
• Wu X, Sun X, Chen C, et al. Dynamic gene expressions of peripheral blood mononuclear cells in patients with acute exacerbation of chronic obstructive pulmonary disease: a preliminary study. Crit Care. 2014;18(6):508. DOI:10.1186/s13054-014-0508-y
   PubMed Web of Science ®Google Scholar
• Chesné J, Danger R, Botturi K, COLT Consortium, et al. Systematic analysis of blood cell transcriptome in end-stage chronic respiratory diseases. PLoS One. 2014;9(10):e109291. DOI:10.1371/journal.pone.0109291
   PubMed Web of Science ®Google Scholar
• Sangle NA, Agarwal AM, Smock KJ, et al. Diffuse large B-cell lymphoma with aberrant expression of the T-cell antigens CD2 and CD7. Appl Immunohistochem Mol Morphol. 2011;19(6):579–583. DOI:10.1097/PAI.0b013e318221c672
   PubMedGoogle Scholar
• Schwartz AG. Genetic epidemiology of cigarette smoke-induced lung disease. Proc Am Thorac Soc. 2012;9(2):22–26. DOI:10.1513/pats.201106-037MS
   PubMedGoogle Scholar
• Smith NL, Hankinson J, Simpson A, et al. Reduced expression of TLR3, TLR10 and TREM1 by human macrophages in chronic cavitary pulmonary aspergillosis, and novel associations of VEGFA, DENND1B and PLAT. Clin Microbiol Infect. 2014;20(11):O960–8. DOI:10.1111/1469-0691.12643
   PubMed Web of Science ®Google Scholar
• Raedler D, Ballenberger N, Klucker E, et al. Identification of novel immune phenotypes for allergic and nonallergic childhood asthma. J Allergy Clin Immunol. 2015;135(1):81–91. DOI:10.1016/j.jaci.2014.07.046
   PubMed Web of Science ®Google Scholar
• Buckland KF, Ramaprakash H, Murray LA, et al. Triggering receptor expressed on myeloid cells-1 (TREM-1) modulates immune responses to Aspergillus fumigatus during fungal asthma in mice. Immunol Invest. 2011;40(7-8):692–722. DOI:10.3109/08820139.2011.578270
   PubMed Web of Science ®Google Scholar
• Karlsson T, Glogauer M, Ellen RP, et al. Aquaporin 9 phosphorylation mediates membrane localization and neutrophil polarization. J Leukoc Biol. 2011;90(5):963–973. DOI:10.1189/jlb.0910540
   PubMed Web of Science ®Google Scholar
• Grigoryev DN, Cheranova DI, Chaudhary S, et al. Identification of new biomarkers for acute respiratory distress syndrome by expression-based genome-wide association study. BMC Pulm Med. 2015;15:95. DOI:10.1186/s12890-015-0088-x
   PubMed Web of Science ®Google Scholar
• Maghsoudloo M, Azimzadeh Jamalkandi S, Najafi A, et al. Identification of biomarkers in common chronic lung diseases by co-expression networks and drug-target interactions analysis. Mol Med. 2020;26(1):9.
   PubMed Web of Science ®Google Scholar
• McDonald ML, Cho MH, Sørheim IC, Evaluation of COPD Longitudinally to Identify Predictive Surrogate Endpoints and COPDGene Investigators, et al. Common genetic variants associated with resting oxygenation in chronic obstructive pulmonary disease. Am J Respir Cell Mol Biol. 2014;51(5):678–687. DOI:10.1165/rcmb.2014-0135OC
   PubMed Web of Science ®Google Scholar
• Uehara A, Fujimoto Y, Fukase K, et al. Various human epithelial cells express functional toll-like receptors, NOD1 and NOD2 to produce anti-microbial peptides, but not proinflammatory cytokines. Mol Immunol. 2007;44(12):3100–3111. DOI:10.1016/j.molimm.2007.02.007
   PubMed Web of Science ®Google Scholar
• Adler J, Rangwalla SC, Dwamena BA, et al. The prognostic power of the NOD2 genotype for complicated Crohn’s disease: a meta-analysis. Am J Gastroenterol. 2011;106(4):699–712. DOI:10.1038/ajg.2011.19
   PubMed Web of Science ®Google Scholar
• Kinose D, Ogawa E, Hirota T, et al. A NOD2 gene polymorphism is associated with the prevalence and severity of chronic obstructive pulmonary disease in a Japanese population. Respirology. 2012;17(1):164–171. DOI:10.1111/j.1440-1843.2011.02069.x
   PubMed Web of Science ®Google Scholar
• Kozomara A, Griffiths-Jones S. miRBase: annotating high confidence microRNAs using deep sequencing data. Nucleic Acids Res. 2014;42(Database issue):D68–73. DOI:10.1093/nar/gkt1181
   PubMedGoogle Scholar
• Baines KJ, Fu JJ, McDonald VM, et al. Airway gene expression of IL-1 pathway mediators predicts exacerbation risk in obstructive airway disease. Int J Chron Obstruct Pulmon Dis. 2017;12:541–550. DOI:10.2147/COPD.S119443
   PubMed Web of Science ®Google Scholar
• Faner R, Sobradillo P, Noguera A, et al. The inflammasome pathway in stable COPD and acute exacerbations. ERJ Open Res. 2016;2(3):00002-2016. DOI:10.1183/23120541.00002-2016
   PubMedGoogle Scholar
• Yang Y, Huang L, Tian C, et al. Magnesium isoglycyrrhizinate inhibits airway inflammation in rats with chronic obstructive pulmonary disease. BMC Pulm Med. 2021;21(1):371. DOI:10.1186/s12890-021-01745-7
   PubMed Web of Science ®Google Scholar
• Zhang J, Xu Q, Sun W, et al. New insights into the role of NLRP3 inflammasome in pathogenesis and treatment of chronic obstructive pulmonary disease. JIR. 2021;14:4155–4168. DOI:10.2147/JIR.S324323
   Google Scholar
• Yang W, Ni H, Wang H, et al. NLRP3 inflammasome is essential for the development of chronic obstructive pulmonary disease. Int J Clin Exp Pathol. 2015;8(10):13209–13216.
   PubMed Web of Science ®Google Scholar
• Sun X, Hou T, Cheung E, et al. Anti-inflammatory mechanisms of the novel cytokine interleukin-38 in allergic asthma. Cell Mol Immunol. 2020;17(6):631–646. DOI:10.1038/s41423-019-0300-7
   PubMed Web of Science ®Google Scholar
• Sharma A, Kitsak M, Cho MH, et al. Integration of molecular interactome and targeted interaction analysis to identify a COPD disease network module. Sci Rep. 2018;8(1):14439. DOI:10.1038/s41598-018-32173-z
   PubMed Web of Science ®Google Scholar
• Zheng Y, Zhang M, Qian M, et al. Genetic comparison of mouse lung telocytes with mesenchymal stem cells and fibroblasts. J Cell Mol Med. 2013;17(4):567–577. DOI:10.1111/jcmm.12052
   PubMed Web of Science ®Google Scholar
• Pietrzyk JJ, Kwinta P, Wollen EJ, et al. Gene expression profiling in preterm infants: new aspects of bronchopulmonary dysplasia development. PLoS One. 2013;8(10):e78585. DOI:10.1371/journal.pone.0078585
   PubMed Web of Science ®Google Scholar
• Karatzas E, Bourdakou MM, Kolios G, et al. Drug repurposing in idiopathic pulmonary fibrosis filtered by a bioinformatics-derived composite score. Sci Rep. 2017;7(1):12569. DOI:10.1038/s41598-017-12849-8
   PubMedGoogle Scholar
• Dang X, Qu X, Wang W, et al. Bioinformatic analysis of microRNA and mRNA regulation in peripheral blood mononuclear cells of patients with chronic obstructive pulmonary disease. Respir Res. 2017;18(1):4. DOI:10.1186/s12931-016-0486-5
   PubMed Web of Science ®Google Scholar
• Bi H, Zhou J, Wu D, et al. Microarray analysis of long non-coding RNAs in COPD lung tissue. Inflamm Res. 2015;64(2):119–126. DOI:10.1007/s00011-014-0790-9
   PubMed Web of Science ®Google Scholar
• Teruya H, Tomita M, Senba M, et al. Human T-cell leukemia virus type I infects human lung epithelial cells and induces gene expression of cytokines, chemokines and cell adhesion molecules. Retrovirology. 2008;5(1):86. DOI:10.1186/1742-4690-5-86
   PubMedGoogle Scholar
• Miao R, Dong X, Gong J, et al. Hsa-miR-106b-5p participates in the development of chronic thromboembolic pulmonary hypertension via targeting matrix metalloproteinase 2. Pulm Circ. 2020;10(3):2045894020928300. DOI:10.1177/2045894020928300
   Web of Science ®Google Scholar
• Duffney PF, Embong AK, McGuire CC, et al. Cigarette smoke increases susceptibility to infection in lung epithelial cells by upregulating caveolin-dependent endocytosis. PLoS One. 2020;15(5):e0232102. DOI:10.1371/journal.pone.0232102
   PubMed Web of Science ®Google Scholar
• Halu A, Liu S, Baek SH, et al. Exploring the cross-phenotype network region of disease modules reveals concordant and discordant pathways between chronic obstructive pulmonary disease and idiopathic pulmonary fibrosis. Hum Mol Genet. 2019;28(14):2352–2364. DOI:10.1093/hmg/ddz069
   PubMed Web of Science ®Google Scholar
• Barnes PJ. Kinases as novel therapeutic targets in asthma and chronic obstructive pulmonary disease. Pharmacol Rev. 2016;68(3):788–815. DOI:10.1124/pr.116.012518
   PubMed Web of Science ®Google Scholar