Effect of Smoking and Its Cessation on the Transcript Profile of Peripheral Monocytes in COPD Patients

References

• Roversi S, Corbetta L, Clini E. GOLD 2017 recommendations for COPD patients: toward a more personalized approach. COPD Res Pract. 2017;3(1):5. doi:10.1186/s40749-017-0024-y
   Google Scholar
• Quaderi SA, Hurst JR. The unmet global burden of COPD. Glob Health Epidemiol Genom. 2018;3:4. doi:10.1017/gheg.2018.1
   PubMed Web of Science ®Google Scholar
• Siafakas NM, Tzortzaki EG. Few smokers develop COPD. Why? Respir Med. 2002;96(8):615–624. doi:10.1053/rmed.2002.1318
   PubMed Web of Science ®Google Scholar
• Matsumura K, Shigeaki I. Novel biomarker genes which distinguish between smokers and chronic obstructive pulmonary disease patients with machine learning approach. BMC Pulm Med. 2020;20:29. doi:10.1186/s12890-020-1062-9
   PubMed Web of Science ®Google Scholar
• Kim V, Criner GJ. Chronic Bronchitis and Chronic Obstructive Pulmonary Disease. Am J Respir Crit Care Med. 2013;187(3):228–237. doi:10.1164/rccm.201210-1843CI
   PubMed Web of Science ®Google Scholar
• Morrow JD, Qiu W, Chhabra D, Rennard SI, Belloni P, Belousov A. Identifying a gene expression signature of frequent COPD exacerbations in peripheral blood using network methods. BMC Med Genomics. 2015;8(1). doi:10.1186/s12920-014-0072-y
   PubMed Web of Science ®Google Scholar
• Ham S, Oh YM, Roh TY. Evaluation and interpretation of transcriptome data underlying heterogeneous chronic obstructive pulmonary disease. Genomics Inform. 2019;17(1):e2. doi:10.5808/GI.2019.17.1.e2
   PubMedGoogle Scholar
• Rovina N, Koutsoukou A, Koulouris NG. Inflammation and Immune Response in COPD: where Do We Stand? Mediators Inflamm. 2013;2:413735.
   Google Scholar
• Barnes PJ. Immunology of asthma and chronic obstructive pulmonary disease. Nat Rev Immunol. 2008;8(3):183–192. doi:10.1038/nri2254
   PubMed Web of Science ®Google Scholar
• Varol C, Yona S, Jung S. Origins and tissue-context-dependent fates of blood monocytes. Immunol Cell Biol. 2009;87(1):30–38. doi:10.1038/icb.2008.90
   PubMed Web of Science ®Google Scholar
• Geissmann F, Manz MG, Jung S, Sieweke MH, Merad M, Ley K. Development of monocytes, macrophages, and dendritic cells. Science. 2010;327(5966):656–661. doi:10.1126/science.1178331
   PubMed Web of Science ®Google Scholar
• Gan WQ, Man SFP, Senthilselvan A, Sin DD. Association between chronic obstructive pulmonary disease and systemic inflammation: a systematic review and a meta-analysis. Thorax. 2004;59(7):574–580. doi:10.1136/thx.2003.019588
   PubMed Web of Science ®Google Scholar
• Karadag F, Karul AB, Cildag O, Yilmaz M, Ozcan H. Biomarkers of systemic inflammation in stable and exacerbation phases of COPD. Lung. 2008;186(6):403–409. doi:10.1007/s00408-008-9106-6
   PubMed Web of Science ®Google Scholar
• Poliska S, Csanky E, Szanto A, et al. Chronic Obstructive Pulmonary Disease-Specific Gene Expression Signatures of Alveolar Macrophages as well as Peripheral Blood Monocytes Overlap and Correlate with Lung Function. Respiration. 2011;81(6):499–510. doi:10.1159/000324297
   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(1):101. doi:10.1186/s12890-018-0664-y
   PubMed Web of Science ®Google Scholar
• Panda SK, Ravindran B. Isolation of Human PBMCs. Bio-Protocol. 2013;3(3):e323. doi:10.21769/BioProtoc.323
   Google Scholar
• Trivedi A, Ghosh D, Guleria R, Mehta N, Talwar A. CD14 positive selection displays an edge in the isolation of macrophages from induced sputum of COPD patients using immunobead technology. Indian J Pharmacol. 2018;62(1):32–40.
   Google Scholar
• Khan MA, Sengupta J, Mittal S, et al. Genome-wide expressions in autologous eutopic and ectopic endometrium of fertile women with endometriosis. Reprod Biol Endocrinol. 2012;10(1):84. doi:10.1186/1477-7827-10-84
   PubMed Web of Science ®Google Scholar
• Bhat MA, Sharma JB, Roy KK, et al. Genomic evidence of Y chromosome microchimerism in the endometrium during endometriosis and in cases of infertility. Reprod Biol Endocrinol. 2019;17(1):22. doi:10.1186/s12958-019-0465-z
   PubMed Web of Science ®Google Scholar
• Casares FM, Simple A. Method for Optimization of Reference Gene Identification and Normalization in DNA Microarray Analysis. Med Sci Monit Basic Res. 2016;22:45–52. doi:10.12659/MSMBR.897644
   PubMedGoogle Scholar
• Yeung KY, Ruzzo WL. Principal component analysis for clustering gene expression data. Bioinformatics. 2001;17(9):763–774. doi:10.1093/bioinformatics/17.9.763
   PubMed Web of Science ®Google Scholar
• Gil-Garcia RJ, Badia-Contelles JM. A General Framework for Agglomerative Hierarchical Clustering Algorithms A Pons-Porrata Pattern Recognition, 2006. ICPR. 2006;1:569–572.
   Google Scholar
• Bustin SA, Benes V, Garson JA, et al. The MIQE Guidelines: minimum Information for Publication of Quantitative Real-Time PCR Experiments. Clin Chem. 2009;55(4):611–622. doi:10.1373/clinchem.2008.112797
   PubMed Web of Science ®Google Scholar
• Pfaffl MW, Horgan GW, Dempfle L. Relative expression software tool (REST) for group-wise comparison and statistical analysis of relative expression results in real-time PCR. Nucleic Acid Res. 2002;30:e36. doi:10.1093/nar/30.9.e36
   PubMed Web of Science ®Google Scholar
• Terzikhan N, Verhamme KMC, Hofman A, et al. Prevalence and incidence of COPD in smokers and non-smokers: the Rotterdam Study. Eur J Epidemiol. 2016;31(8):785–792. doi:10.1007/s10654-016-0132-z
   PubMed Web of Science ®Google Scholar
• Spira A, Beane J, Shah V, Liu G, Schembri F, Yang X. Effects of cigarette smoke on the human airway epithelial cell transcriptome. Proc Natl Acad Sci USA. 2004;101(27):10143–10148. doi:10.1073/pnas.0401422101
   PubMed Web of Science ®Google Scholar
• Bhattacharya S, Tyagi S, Srisuma S, DeMeo DL, Shapiro SD, Bueno R. Peripheral blood gene expression profiles in COPD subjects. J Clin Bioinform. 2011;1(1):12. doi:10.1186/2043-9113-1-12
   PubMedGoogle Scholar
• Sossey-Alaoui K, Pluskota E, Davuluri G, et al. Kindlin-3 enhances breast cancer progression and metastasis by activating Twist-mediated angiogenesis. FASEB J. 2014;28(5):2260–2271. doi:10.1096/fj.13-244004
   PubMed Web of Science ®Google Scholar
• Hackett NR, Heguy A, Harvey B-G, O’Connor TP, Luettich K, Flieder DB. Variability of Antioxidant-Related Gene Expression in the Airway Epithelium of Cigarette Smokers. Am J Respir Cell Mol Biol. 2003;29(3):331–343.
   PubMed Web of Science ®Google Scholar
• Singh D, Fox SM, Tal-Singer R, Plumb J, Bates S, Broad P. Induced sputum genes associated with spirometric and radiological disease severity in COPD ex-smokers. Thorax. 2011;66(6):489–495. doi:10.1136/thx.2010.153767
   PubMed Web of Science ®Google Scholar
• Pierrou S, Broberg P, O’Donnell RA, Pawłowski K, Virtala R, Lindqvist E. Expression of genes involved in oxidative stress responses in airway epithelial cells of smokers with chronic obstructive pulmonary disease. Am J Respir Crit Care Med. 2007;175(6):577–586. doi:10.1164/rccm.200607-931OC
   PubMed Web of Science ®Google Scholar
• Fu XW, Wood K, Spindel ER. Prenatal Nicotine Exposure Increases GABA Signaling and Mucin Expression in Airway Epithelium. Am J Respir Cell Mol Biol. 2011;44(2):222–229. doi:10.1165/rcmb.2010-0109OC
   PubMed Web of Science ®Google Scholar
• Golpon HA, Coldren CD, Zamora MR, Cosgrove GP, Moore MD, Tuder RM.Emphysema lung tissue gene expression profiling. Am J Respir Cell Mol Biol. 2004;31(6):595–600. doi:10.1165/rcmb.2004-0008OC
   PubMed Web of Science ®Google Scholar
• Almansa R, Socias L, Garcia M, et al. Critical COPD respiratory illness is linked to increased transcriptomic activity of neutrophil proteases genes. BMC Res Notes. 2012;5:401. doi:10.1186/1756-0500-5-401
   PubMedGoogle Scholar
• Wang M, Stepaniants S, Boie Y, Mortimer JR, Kennedy B, Elliott M. Gene expression profiling in patients with chronic obstructive pulmonary disease and lung cancer. Am J Respir Crit Care Med. 2008;177(4):402–411. doi:10.1164/rccm.200703-390OC
   PubMed Web of Science ®Google Scholar
• Ning W, Li CJ, Kaminski N, Feghali-Bostwick CA, Alber SM, Di YP. Comprehensive gene expression profiles reveal pathways related to the pathogenesis of chronic obstructive pulmonary disease. Proc Natl Acad Sci USA. 2004;101(41):14895–14900. doi:10.1073/pnas.0401168101
   PubMed Web of Science ®Google Scholar
• Bahr TM, Hughes GJ, Armstrong M, Reisdorph R, Coldren CD, Edwards MG. Peripheral Blood Mononuclear Cell Gene Expression in Chronic Obstructive Pulmonary Disease. Am J Respir Cell Mol Biol. 2013;49(2):316–323. doi:10.1165/rcmb.2012-0230OC
   PubMed Web of Science ®Google Scholar
• Kirkham PA, Barnes PJ. Oxidative stress in COPD. Chest. 2013;144(1):266–273. doi:10.1378/chest.12-2664
   PubMed Web of Science ®Google Scholar
• Coenen MJH, Antonicka H, Ugalde C, et al. Mutant Mitochondrial Elongation Factor G1 and Combined Oxidative Phosphorylation Deficiency. New Engl J Med. 2004;351(20):2080–2086. doi:10.1056/NEJMoa041878
   PubMed Web of Science ®Google Scholar
• Kenmochi N, Suzuki T, Uechi T, et al. The Human Mitochondrial Ribosomal Protein Genes: mapping of 54 Genes to the Chromosomes and Implications for Human Disorders. Genomics. 2001;77(1–2):65–70. doi:10.1006/geno.2001.6622
   PubMed Web of Science ®Google Scholar
• Wiegman CH, Michaeloudes C, Haji G, et al. Oxidative stress-induced mitochondrial dysfunction drives inflammation and airway smooth muscle remodeling in patients with chronic obstructive pulmonary disease. J Allergy Clin Immunol. 2015;136(3):769–780. doi:10.1016/j.jaci.2015.01.046
   PubMed Web of Science ®Google Scholar
• Agustí AGN, Sauleda J, Miralles C, et al. Skeletal muscle apoptosis and weight loss in chronic obstructive pulmonary disease. Am J Respir Crit Care Med. 2002;166(4):485–489. doi:10.1164/rccm.2108013
   PubMed Web of Science ®Google Scholar
• Picard M, Godin R, Sinnreich M, et al. The mitochondrial phenotype of peripheral muscle in chronic obstructive pulmonary disease: disuse or dysfunction? Am J Respir Crit Care Med. 2008;178(10):1040–1047.
   PubMed Web of Science ®Google Scholar
• Guo Y, Gosker HR, Schols AMWJ, et al. Autophagy in locomotor muscles of patients with chronic obstructive pulmonary disease. Am J Respir Crit Care Med. 2013;188(11):1313–1320. doi:10.1164/rccm.201304-0732OC
   PubMed Web of Science ®Google Scholar
• Johnston PA, Grandis JR. STAT3 SIGNALING: anticancer Strategies and Challenges. Mol Interv. 2011;11(1):18–26. doi:10.1124/mi.11.1.4
   PubMedGoogle Scholar
• Katoh Y, Katoh M. Identification and characterization of CDC50A, CDC50B and CDC50C genes in silico. Oncol Rep. 2004;12(4):939–943.
   PubMed Web of Science ®Google Scholar
• Higham A, Lea S, Simpson K, et al. Lipids in the lung: respiratory inflammation in COPD. Eur Respir J. 2012;40(56):385.
   Google Scholar
• Chen M, Pratt CP, Zeeman ME, et al. Identification of PHLPP1 as a tumor suppressor reveals the role of feedback activation in PTEN-mutant prostate cancer progression. Cancer Cell. 2011;20(2):173–186. doi:10.1016/j.ccr.2011.07.013
   PubMed Web of Science ®Google Scholar
• Lai Y, Xu P, Liu J, et al. Decreased expression of the long non-coding RNA MLLT4 antisense RNA 1 is a potential biomarker and an indicator of a poor prognosis for gastric cancer. Oncol Lett. 2017;14(3):2629–2634. doi:10.3892/ol.2017.6478
   PubMed Web of Science ®Google Scholar
• Xu X, Dockery DW, Ware JH, et al. Effects of cigarette smoking on rate of loss of pulmonary function in adults: a longitudinal assessment. Am Rev Respir Dis. 1992;146(51):1345–1348. doi:10.1164/ajrccm/146.5_Pt_1.1345
   PubMed Web of Science ®Google Scholar
• Anthonisen NR, Connett JE, Kiley JP, et al. Effects of smoking intervention and the use of an inhaled anticholinergic bronchodilator on the rate of decline of FEV1. JAMA. 1994;272(19):1497–1505. doi:10.1001/jama.1994.03520190043033
   PubMed Web of Science ®Google Scholar
• Wagena EJ, van der Meer RM, Ostelo RJWG, Jacobs JE, van Schayck CP. The efficacy of smoking cessation strategies in people with chronic obstructive pulmonary disease: results from a systematic review. Respir Med. 2004;98(9):805–815. doi:10.1016/j.rmed.2004.06.001
   PubMed Web of Science ®Google Scholar
• Turato G, Di Stefano A, Maestrelli P, et al. Effect of smoking cessation on airway inflammation in chronic bronchitis. Am J Respir Crit Care Med. 1995;152(41):1262–1267. doi:10.1164/ajrccm.152.4.7551380
   PubMed Web of Science ®Google Scholar
• Jiang M-X, Hong X, Liao -B-B, et al. Expression profiling of TRIM protein family in THP1-derived macrophages following TLR stimulation. Sci Rep. 2017;7(1). doi:10.1038/srep42781
   Web of Science ®Google Scholar
• Fiskerstrand T, H’mida-Ben Brahim D, Johansson S, et al. Mutations in ABHD12 Cause the Neurodegenerative Disease PHARC: an Inborn Error of Endocannabinoid Metabolism. Am J Hum Genet. 2010;87(3):410–417. doi:10.1016/j.ajhg.2010.08.002
   PubMed Web of Science ®Google Scholar
• Barrie N, Manolios N. The endocannabinoid system in pain and inflammation: its relevance to rheumatic disease. Eur J Rheumatol. 2017;4(3):210–218. doi:10.5152/eurjrheum.2017.17025
   PubMed Web of Science ®Google Scholar
• Willemse BWM. Effect of 1-year smoking cessation on airway inflammation in COPD and asymptomatic smokers. Eur Respir J. 2005;26(5):835–845. doi:10.1183/09031936.05.00108904
   PubMed Web of Science ®Google Scholar
• Rutgers SR. Ongoing airway inflammation in patients with COPD who do not currently smoke. Thorax. 2000;55(1):12–18. doi:10.1136/thorax.55.1.12
   PubMed Web of Science ®Google Scholar
• Wanders RJA, Waterham HR. Biochemistry of mammalian peroxisomes revisited. Annu Rev Biochem. 2006;75:295–332. doi:10.1146/annurev.biochem.74.082803.133329
   PubMed Web of Science ®Google Scholar
• Steinberg SJ, Dodt G, Raymond GV, et al. Peroxisome biogenesis disorders. Biochim Biophys Acta. 2006;1763(12):1733–1748. doi:10.1016/j.bbamcr.2006.09.010
   PubMed Web of Science ®Google Scholar
• Schmidt EP, Tuder RM. Role of Apoptosis in Amplifying Inflammatory Responses in Lung Diseases. J Cell Death. 2010;3:JCD.S5375. doi:10.4137/JCD.S5375
   PubMedGoogle Scholar
• Kasahara Y, Tuder RM, Cool CD, et al. Endothelial cell death and decreased expression of vascular endothelial growth factor and vascular endothelial growth factor receptor 2 in emphysema. Am J Respir Crit Care Med. 2001;163:737–744. doi:10.1164/ajrccm.163.3.2002117
   PubMed Web of Science ®Google Scholar
• Plataki M, Tzortzaki E, Rytila P, et al. Apoptotic mechanisms in the pathogenesis of COPD. Int J Chron Obstruct Pulmon Dis. 2006;1(2):161–171. doi:10.2147/copd.2006.1.2.161
   PubMedGoogle Scholar
• Song Q, Chen P, Liu XM. The role of cigarette smoke-induced pulmonary vascular endothelial cell apoptosis in COPD. Respir Res. 2021;22:39. doi:10.1186/s12931-021-01630-1
   PubMed Web of Science ®Google Scholar
• Mathanraj S, Vysak K, Yuvarajan S, Vikram R. Correlation of serum TNF alpha level with severity of chronic obstructive pulmonary disease. Int J Res Med Sci. 2017;5(8):3309–3316. doi:10.18203/2320-6012.ijrms20173020
   Google Scholar
• Montes MM, Torres SH, De SJ, Mata A, Hernández N, Tálamo C. Skeletal muscle inflammation and nitric oxide in patients with COPD. Eur Respir J. 2005;26(3):390–397. doi:10.1183/09031936.05.00107404
   PubMed Web of Science ®Google Scholar
• Pobezinskaya YL, Liu Z. The role of TRADD in death receptor signaling. Cell Cycle. 2012;11(871):10. doi:10.4161/cc.11.5.19300
   Web of Science ®Google Scholar
• Yu X, James S, Felce JH. TNF receptor agonists induce distinct receptor clusters to mediate differential agonistic activity. Commun Biol. 2021;4:772. doi:10.1038/s42003-021-02309-5
   PubMed Web of Science ®Google Scholar