Identification of Hub Genes Associated with COPD Through Integrated Bioinformatics Analysis

References

• Labaki WW, Rosenberg SR. Chronic obstructive pulmonary disease. Ann Intern Med. 2020;173(3):ITC17–ITC32. doi:10.7326/AITC202008040
   PubMed Web of Science ®Google Scholar
• Soriano JB, Abajobir AA, Abate KH; GBD 2015 Chronic Respiratory Disease Collaborators. Global, regional, and national deaths, prevalence, disability-adjusted life years, and years lived with disability for chronic obstructive pulmonary disease and asthma, 1990–2015: a systematic analysis for the Global Burden of Disease Study. Lancet Resp Med. 2017;5(9):691–706. doi:10.1016/S2213-2600(17)30293-X
   PubMed Web of Science ®Google Scholar
• Blanco I, Diego I, Bueno P, Casas-Maldonado F, Miravitlles M. Geographic distribution of COPD prevalence in the world displayed by geographic information system maps. Eur Respir J. 2019;54(1):1900610. doi:10.1183/13993003.00610-2019
   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
• Løkke A, Lange P, Scharling H, Fabricius P, Vestbo J. Developing COPD: a 25 year follow up study of the general population. Thorax. 2006;61(11):935–939. doi:10.1136/thx.2006.062802
   PubMed Web of Science ®Google Scholar
• Mannino DM, Buist AS. Global burden of COPD: risk factors, prevalence, and future trends. Lancet. 2007;370(9589):765–773. doi:10.1016/S0140-6736(07)61380-4
   PubMed Web of Science ®Google Scholar
• Lin YZ, Zhong XN, Chen X, Liang Y, Zhang H, Zhu DL. Roundabout signaling pathway involved in the pathogenesis of COPD by integrative bioinformatics analysis. Int J Chron Obstruct Pulmon Dis. 2019;18(14):2145–2162. doi:10.2147/COPD.S216050
   Web of Science ®Google Scholar
• Huang X, Li Y, Guo X, et al. Identification of differentially expressed genes and signaling pathways in chronic obstructive pulmonary disease via bioinformatic analysis. FEBS Open Bio. 2019;9(11):1880–1899. doi:10.1002/2211-5463.12719
   PubMed Web of Science ®Google Scholar
• Spira A, Beane J, Pinto-Plata V, et al. Gene expression profiling of human lung tissue from smokers with severe emphysema. Am J Respir Cell Mol Biol. 2004;31(6):601–610. doi:10.1165/rcmb.2004-0273OC
   PubMed Web of Science ®Google Scholar
• Morrow JD, Zhou X, Lao T, et al. Functional interactors of three genome-wide association study genes are differentially expressed in severe chronic obstructive pulmonary disease lung tissue. Sci Rep. 2017;7(1):44232. doi:10.1038/srep44232
   PubMed Web of Science ®Google Scholar
• Chin CH, Chen SH, Wu HH, Ho CW, Ko MT, Lin CY. cytoHubba: identifying hub objects and sub-networks from complex interactome. BMC Syst Biol. 2014;8 Suppl 4(Suppl4):S11. doi:10.1186/1752-0509-8-S4-S11
   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
• Yip AM, Horvath S. Gene network interconnectedness and the generalized topological overlap measure. BMC Bioinform. 2007;8(1):22. doi:10.1186/1471-2105-8-22
   PubMed Web of Science ®Google Scholar
• Kuang L-J, Deng -T-T, Wang Q, et al. Dendritic cells induce Tc1 cell differentiation via the CD40/CD40L pathway in mice after exposure to cigarette smoke. Am J Physiol Lung Cell Mol Physiol. 2016;311(3):L581–L589. doi:10.1152/ajplung.00002.2016
   PubMed Web of Science ®Google Scholar
• Mirza S, Clay RD, Koslow MA, Scanlon PD. COPD guidelines: a review of the 2018 GOLD report. Mayo Clin Proc. 2018;93(10):1488–1502. doi:10.1016/j.mayocp.2018.05.026
   PubMed Web of Science ®Google Scholar
• Kong Y, Feng ZC, Zhang YL, et al. Identification of immune-related genes contributing to the development of glioblastoma using weighted gene co-expression network analysis. Front Immunol. 2020;11(11):1281. doi:10.3389/fimmu.2020.01281
   PubMed Web of Science ®Google Scholar
• Morris MR, Ricketts C, Gentle D, et al. Identification of candidate tumour suppressor genes frequently methylated in renal cell carcinoma. Oncogene. 2010;29(14):2104–2117. doi:10.1038/onc.2009.493
   PubMed Web of Science ®Google Scholar
• Li X, Zhou F, Jiang C, et al. Identification of a DNA methylome profile of esophageal squamous cell carcinoma and potential plasma epigenetic biomarkers for early diagnosis. PLoS One. 2014;9(7):e103162. doi:10.1371/journal.pone.0103162
   PubMed Web of Science ®Google Scholar
• Guay SP, Brisson D, Mathieu P, Bossé Y, Gaudet D, Bouchard L. A study in familial hypercholesterolemia suggests reduced methylomic plasticity in men with coronary artery disease. Epigenomics. 2015;7(1):17–34. doi:10.2217/epi.14.64
   PubMed Web of Science ®Google Scholar
• Duan J, Martinez M, Sanders AR, et al. Polymorphisms in the trace amine receptor 4 (TRAR4) gene on chromosome 6q23.2 are associated with susceptibility to schizophrenia. Am J Hum Genet. 2004;75(4):624–638. doi:10.1086/424887
   PubMed Web of Science ®Google Scholar
• Xin X, Mains RE, Eipper BA. Monooxygenase X, a member of the copper-dependent monooxygenase family localized to the endoplasmic reticulum. J Biol Chem. 2004;279(46):48159–48167. doi:10.1074/jbc.M407486200
   PubMed Web of Science ®Google Scholar
• Tsuneoka Y, Tsukahara S, Yoshida S, et al. Moxd1 is a marker for sexual dimorphism in the medial preoptic area, bed nucleus of the stria terminalis and medial amygdala. Front Neuroanat. 2017;11:26. doi:10.3389/fnana.2017.00026
   PubMed Web of Science ®Google Scholar
• Han X, He J, Wang Z, Bai Z, Wang W, Li X. Monooxygenase DBH like 1 (MOXD1) knockdown suppresses the proliferation and xenograft tumor growth of osteosarcoma cells via inducing apoptosis. Panminerva Med. 2019;30. doi:10.23736/s0031-0808.19.03717-0
   Google Scholar
• Tei S, Ishii HT, Mitsuhashi H, Ishiura S. Antisense oligonucleotide-mediated exon skipping of CHRNA1 pre-mRNA as potential therapy for congenital myasthenic syndromes. Biochem Biophys Res Commun. 2015;461(3):481–486. doi:10.1016/j.bbrc.2015.04.035
   PubMed Web of Science ®Google Scholar
• Shamseldin HE, Swaid A, Alkuraya FS. Lifting the lid on unborn lethal Mendelian phenotypes through exome sequencing. Genet Med. 2013;15(4):307–309.
   PubMed Web of Science ®Google Scholar
• Fisher AG, Seaborne RA, Hughes TM, et al. Transcriptomic and epigenetic regulation of disuse atrophy and the return to activity in skeletal muscle. FASEB J. 2017;31(12):5268–5282. doi:10.1096/fj.201700089RR
   PubMed Web of Science ®Google Scholar
• Zhang G, Thomas AL, Marshall AL, et al. Nicotinic acetylcholine receptor α1 promotes calpain-1 activation and macrophage inflammation in hypercholesterolemic nephropathy. Lab Invest. 2011;91(1):106–123. doi:10.1038/labinvest.2010.135
   PubMed Web of Science ®Google Scholar
• Posey KL, Coustry F, Hecht JT. Cartilage oligomeric matrix protein: cOMPopathies and beyond. Matrix Biol. 2018;71–72:161–173. doi:10.1016/j.matbio.2018.02.023
   PubMed Web of Science ®Google Scholar
• Huang Y, Xia J, Zheng J, et al. Deficiency of cartilage oligomeric matrix protein causes dilated cardiomyopathy. Basic Res Cardiol. 2013;108(5):374. doi:10.1007/s00395-013-0374-9
   PubMed Web of Science ®Google Scholar
• Vuga LJ, Milosevic J, Pandit K, et al. Cartilage oligomeric matrix protein in idiopathic pulmonary fibrosis. PLoS One. 2013;8(12):e83120. doi:10.1371/journal.pone.0083120
   PubMed Web of Science ®Google Scholar
• Magdaleno F, Arriazu E, Ruiz de Galarreta M, et al. Cartilage oligomeric matrix protein participates in the pathogenesis of liver fibrosis. J Hepatol. 2016;65(5):963–971. doi:10.1016/j.jhep.2016.06.003
   PubMed Web of Science ®Google Scholar
• Liu TT, Liu XS, Zhang M, et al. Cartilage oligomeric matrix protein is a prognostic factor and biomarker of colon cancer and promotes cell proliferation by activating the Akt pathway. J Cancer Res Clin Oncol. 2018;144(6):1049–1063. doi:10.1007/s00432-018-2626-4
   PubMed Web of Science ®Google Scholar
• Li Q, Wang C, Wang Y, et al. HSCs-derived COMP drives hepatocellular carcinoma progression by activating MEK/ERK and PI3K/AKT signaling pathways. J Exp Clin Cancer Res. 2018;37(1):231. doi:10.1186/s13046-018-0908-y
   PubMed Web of Science ®Google Scholar
• Laudon J, Whittaker JL, Ren G, Jaremko JL, Emery CA, Krawetz RJ. Serum cartilage oligomeric matrix protein (COMP) expression in individuals who sustained a youth sport-related intra-articular knee injury 3–10 years previously and uninjured matched controls. Osteoarthritis Cartilage. 2019;27(2):286–293. doi:10.1016/j.joca.2018.09.011
   PubMed Web of Science ®Google Scholar
• Bao Y, Wang L, Shi L, et al. Transcriptome profiling revealed multiple genes and ECM-receptor interaction pathways that may be associated with breast cancer. Cell Mol Biol Lett. 2019;24(1):38. doi:10.1186/s11658-019-0162-0
   PubMed Web of Science ®Google Scholar
• Zou S, Li J, Yan J, Xu J, Lin M, Cao D. Distribution of serum Thrombospondin-2, a novel tumor marker, in general population and cancer patients in China. Clin Chim Acta. 2021;518:123–127. doi:10.1016/j.cca.2021.03.022
   PubMed Web of Science ®Google Scholar
• Weng TY, Wang CY, Hung YH, Chen WC, Chen YL, Lai MD. Differential expression pattern of THBS1 and THBS2 in lung cancer: clinical outcome and a systematic-analysis of microarray databases. PLoS One. 2016;11(8):e0161007. doi:10.1371/journal.pone.0161007
   PubMed Web of Science ®Google Scholar
• Eiro N, Carrión JF, Cid S, et al. Toll-like receptor 4 and matrix metalloproteases 11 and 13 as predictors of tumor recurrence and survival in stage II colorectal cancer. Pathol Oncol Res. 2019;25(4):1589–1597. doi:10.1007/s12253-019-00611-6
   PubMed Web of Science ®Google Scholar
• Yang H, Jiang P, Liu D, et al. Matrix metalloproteinase 11 is a potential therapeutic target in lung adenocarcinoma. Mol Ther Oncolytics. 2019;14:82–93. doi:10.1016/j.omto.2019.03.012
   PubMed Web of Science ®Google Scholar
• De Pasquale V, Pavone LM. Heparan sulfate proteoglycan signaling in tumor microenvironment. Int J Mol Sci. 2020;21(18):6588. doi:10.3390/ijms21186588
   PubMed Web of Science ®Google Scholar
• Brandsma CA, Van den Berge M, Hackett TL, Brusselle G, Timens W. Recent advances in chronic obstructive pulmonary disease pathogenesis: from disease mechanisms to precision medicine. J Pathol. 2020;250(5):624–635. doi:10.1002/path.5364
   PubMed Web of Science ®Google Scholar
• Uddin MN, Li M, Wang X. Identification of transcriptional signatures of colon tumor stroma by a meta-analysis. J Oncol. 2019;2(2019):8752862.
   Google Scholar
• Yang YW, Jablons DM, Lemjabbar-Alaoui H. Extracellular sulfatases as potential blood-based biomarkers for early detection of lung cancer. Exp Lung Res. 2021;47(6):261–279. doi:10.1080/01902148.2021.1885525
   PubMed Web of Science ®Google Scholar
• Zhou Q, Jiang Y, Yin W, Wang Y, Lu J. Single-nucleotide polymorphism in microRNA-binding site of SULF1 target gene as a protective factor against the susceptibility to breast cancer: a case-control study. Onco Targets Ther. 2016;9:2749–2757. doi:10.2147/OTT.S102433
   PubMed Web of Science ®Google Scholar
• Sahota AP, Dhoot GK. A novel SULF1 splice variant inhibits Wnt signalling but enhances angiogenesis by opposing SULF1 activity. Exp Cell Res. 2009;315(16):2752–2764. doi:10.1016/j.yexcr.2009.06.029
   PubMed Web of Science ®Google Scholar
• Brunner C, Laumen H, Nielsen PJ, Kraut N, Wirth T. Expression of the aldehyde dehydrogenase 2-like gene is controlled by BOB.1/OBF.1 in B lymphocytes. J Biol Chem. 2003;278(46):45231–45239. doi:10.1074/jbc.M302539200
   PubMed Web of Science ®Google Scholar
• Teitell MA. OCA-B regulation of B-cell development and function. Trends Immunol. 2003;24(10):546–553. doi:10.1016/j.it.2003.08.002
   PubMed Web of Science ®Google Scholar
• Zhou H, Brekman A, Zuo WL, et al. POU2AF1 functions in the human airway epithelium to regulate expression of host defense genes. J Immunol. 2016;196(7):3159–3167. doi:10.4049/jimmunol.1502400
   PubMed Web of Science ®Google Scholar
• Schiraldi M, Raucci A, Muñoz LM, et al. HMGB1 promotes recruitment of inflammatory cells to damaged tissues by forming a complex with CXCL12 and signaling via CXCR4. J Exp Med. 2012;209(3):551–563. doi:10.1084/jem.20111739
   PubMed Web of Science ®Google Scholar
• Campana L, Bosurgi L, Bianchi ME, Manfredi AA, Rovere-Querini P. Requirement of HMGB1 for stromal cell-derived factor-1/CXCL12-dependent migration of macrophages and dendritic cells. J Leukoc Biol. 2009;86(3):609–615. doi:10.1189/jlb.0908576
   PubMed Web of Science ®Google Scholar
• Hao W, Li M, Pang Y, Du W, Huang X. Increased chemokines levels in patients with chronic obstructive pulmonary disease: correlation with quantitative computed tomography metrics. Br J Radiol. 2021;94(1118):20201030. doi:10.1259/bjr.20201030
   PubMed Web of Science ®Google Scholar
• Isles HM, Herman KD, Robertson AL, et al. The CXCL12/CXCR4 signaling axis retains neutrophils at inflammatory sites in Zebrafish. Front Immunol. 2019;10:1784. doi:10.3389/fimmu.2019.01784
   PubMed Web of Science ®Google Scholar
• Barwinska D, Oueini H, Poirier C, et al. AMD3100 ameliorates cigarette smoke-induced emphysema-like manifestations in mice. Am J Physiol Lung Cell Mol Physiol. 2018;315(3):L382–L386. doi:10.1152/ajplung.00185.2018
   PubMed Web of Science ®Google Scholar