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Original Research

Identification of novel candidate genes involved in the progression of emphysema by bioinformatic methods

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Pages 3733-3747 | Published online: 14 Nov 2018

References

  • Global Health Estimates 2016Deaths by Cause, Age, Sex, by Country and by Region, 2000–2016GenevaWorld Health Organization2018
  • HoggJCTimensWThe pathology of chronic obstructive pulmonary diseaseAnnu Rev Pathol2009443545918954287
  • Global Initiative for Chronic Obstructive Pulmonary Disease: Global Strategy for the Diagnosis, Management and Prevention of COPD revised2017 Available from: https://goldcopd.org/gold-2017-global-strategy-diagnosis-management-prevention-copd/Accessed April 4, 2017
  • SubramanianDRGuptaSBurggrafDEmphysema- and airway-dominant COPD phenotypes defined by standardised quantitative computed tomographyEur Respir J20164819210327230444
  • Ziegler-HeitbrockLFrankenbergerMHeimbeckIThe EvA study: aims and strategyEur Respir J201240482382922441733
  • ChungKFAdcockIMMultifaceted mechanisms in COPD: inflammation, immunity, and tissue repair and destructionEur Respir J20083161334135618515558
  • VermylenJHKalhanRRevealing the complexity of chronic obstructive pulmonary diseaseTransl Res2013162420320723932958
  • GharibSAManiconeAMParksWCMatrix metalloproteinases in emphysemaMatrix Biol201873345129406250
  • TuderRMPetracheIPathogenesis of chronic obstructive pulmonary diseaseJ Clin Invest201212282749275522850885
  • LynchDAAl-QaisiMAQuantitative computed tomography in chronic obstructive pulmonary diseaseJ Thorac Imaging201328528429023748651
  • NambuAZachJSchroederJQuantitative computed tomography measurements to evaluate airway disease in chronic obstructive pulmonary disease: relationship to physiological measurements, clinical index and visual assessment of airway diseaseEur J Radiol201685112144215127776670
  • CastaldiPJSan José EstéparRMendozaCSDistinct quantitative computed tomography emphysema patterns are associated with physiology and function in smokersAm J Respir Crit Care Med201318891083109023980521
  • MorrowJDZhouXLaoTFunctional interactors of three genome-wide association study genes are differentially expressed in severe chronic obstructive pulmonary disease lung tissueSci Rep201774423228287180
  • FerrariRLoveringRCHardyJLewisPAManzoniCWeighted protein interaction network analysis of frontotemporal dementiaJ Proteome Res2017162999101328004582
  • LiJZhaoPLiYTianYWangYSystems pharmacology-based dissection of mechanisms of Chinese medicinal formula Bufei Yishen as an effective treatment for chronic obstructive pulmonary diseaseSci Rep201551529026469778
  • ZanzoniASoler-LópezMAloyPA network medicine approach to human diseaseFEBS Lett2009583111759176519269289
  • HuntleyRPSawfordTMutowo-MeullenetPThe GOA database: gene Ontology annotation updates for 2015Nucleic Acids Res201543Database issueD1057D106325378336
  • Huang daWShermanBTLempickiRASystematic and integrative analysis of large gene lists using DAVID bioinformatics resourcesNat Protoc200941445719131956
  • MarciniakSJLomasDAGenetic susceptibilityClin Chest Med2014351293824507835
  • BarnesPJThe cytokine network in chronic obstructive pulmonary diseaseAm J Respir Cell Mol Biol200941663163819717810
  • McguinnessAJSapeyEOxidative stress in COPD: sources, markers, and potential mechanismsJ Clin Med201762E2128212273
  • BrusselleGGJoosGFBrackeKRNew insights into the immunology of chronic obstructive pulmonary diseaseLancet201137897951015102621907865
  • BurgstallerGOehrleBGerckensMThe instructive extracellular matrix of the lung: basic composition and alterations in chronic lung diseaseEur Respir J2017501160180528679607
  • MckusickVAMendelian inheritance in man and its online version, OMIMAm J Hum Genet200780458860417357067
  • BeckerKGBarnesKCBrightTJWangSAThe genetic association databaseNat Genet200436543143215118671
  • SzklarczykDMorrisJHCookHThe STRING database in 2017: quality-controlled protein-protein association networks, made broadly accessibleNucleic Acids Res201745D1D362D36827924014
  • ShannonPMarkielAOzierOCytoscape: a software environment for integrated models of biomolecular interaction networksGenome Res200313112498250414597658
  • KanehisaMFurumichiMTanabeMSatoYMorishimaKKEGG: new perspectives on genomes, pathways, diseases and drugsNucleic Acids Res201745D1D353D36127899662
  • Puig-ButilleJAGimenez-XavierPViscontiAGenomic expression differences between cutaneous cells from red hair color individuals and black hair color individuals based on bioinformatic analysisOncotarget201787115891159928030792
  • MatysVFrickeEGeffersRTRANSFAC: transcriptional regulation, from patterns to profilesNucleic Acids Res200331137437812520026
  • ChuangHYLeeELiuYTLeeDIdekerTNetwork-based classification of breast cancer metastasisMol Syst Biol2007314017940530
  • OnozawaYFujitaYKuwabaraHActivation of T cell death-associated gene 8 regulates the cytokine production of T cells and macrophages in vitroEur J Pharmacol20126831–332533122445881
  • RaduCGNijagalAMcLaughlinJWangLWitteONDifferential proton sensitivity of related G protein-coupled receptors T cell death-associated gene 8 and G2A expressed in immune cellsProc Natl Acad Sci U S A200510251632163715665078
  • XuHChenXHuangJIdentification of GPR65, a novel regulator of matrix metalloproteinases using high through-put screeningBiochem Biophys Res Commun201343619610323707809
  • HuntJFFangKMalikREndogenous airway acidification. Implications for asthma pathophysiologyAm J Respir Crit Care Med20001613 Pt 169469910712309
  • KottyanLCCollierARCaoKHEosinophil viability is increased by acidic pH in a cAMP- and GPR65-dependent mannerBlood2009114132774278219641187
  • PoonAHHousemanEARyanLVariants of asthma and chronic obstructive pulmonary disease genes and lung function decline in agingJ Gerontol A Biol Sci Med Sci201469790791324253534
  • ReiniusLEGrefASääfADNA methylation in the Neuropeptide S Receptor 1 (NPSR1) promoter in relation to asthma and environmental factorsPLoS One201381e5387723372674
  • IlmarinenPJamesAMoilanenEEnhanced expression of neuropeptide S (NPS) receptor in eosinophils from severe asthmatics and subjects with total IgE above 100 IU/mlPeptides20145110010924239856
  • SilvaGESherrillDLGuerraSBarbeeRAAsthma as a risk factor for COPD in a longitudinal studyChest20041261596515249443
  • Vedel-KroghSNielsenSFLangePVestboJNordestgaardBGBlood eosinophils and exacerbations in chronic obstructive pulmonary disease. The Copenhagen General Population StudyAm J Respir Crit Care Med2016193996597426641631
  • TanCSalehiASvenssonSOldeBErlingeDADP receptor P2Y(13) induce apoptosis in pancreatic beta-cellsCell Mol Life Sci201067344545319915796
  • BiverGWangNGartlandARole of the P2Y13 receptor in the differentiation of bone marrow stromal cells into osteoblasts and adipocytesStem Cells201331122747275823629754
  • PolosaRAdenosine-receptor subtypes: their relevance to adenosine-mediated responses in asthma and chronic obstructive pulmonary diseaseEur Respir J200220248849612212985
  • PellegASchulmanESBarnesPJExtracellular adenosine 5′-triphosphate in obstructive airway diseasesChest2016150490891527568579
  • AoshibaKTsujiTYamaguchiKItohMNakamuraHThe danger signal plus DNA damage two-hit hypothesis for chronic inflammation in COPDEur Respir J20134261689169523397294
  • KumarMSeegerWVoswinckelRSenescence-associated secretory phenotype and its possible role in chronic obstructive pulmonary diseaseAm J Respir Cell Mol Biol201451332333325171460
  • CampisiJD’Adda di FagagnaFCellular senescence: when bad things happen to good cellsNat Rev Mol Cell Biol20078972974017667954
  • AbbadieCPluquetOPourtierAEpithelial cell senescence: an adaptive response to pre-carcinogenic stresses?Cell Mol Life Sci201774244471450928707011
  • ItoKBarnesPJCOPD as a disease of accelerated lung agingChest2009135117318019136405
  • VousdenKHPrivesCBlinded by the light: the growing complexity of p53Cell2009137341343119410540
  • MorissetteMCVachon-BeaudoinGParentJChakirJMilotJIncreased p53 level, Bax/Bcl-x(L) ratio, and TRAIL receptor expression in human emphysemaAm J Respir Crit Care Med2008178324024718511705
  • MizunoSIshizakiTKadowakiMp53 Signaling pathway polymorphisms associated with emphysematous changes in patients with COPDChest20171521586928315337
  • KuskoRLBrothersJFTedrowJIntegrated genomics reveals convergent transcriptomic networks underlying chronic obstructive pulmonary disease and idiopathic pulmonary fibrosisAm J Respir Crit Care Med2016194894896027104832
  • TsujiTAoshibaKNagaiAAlveolar cell senescence in patients with pulmonary emphysemaAm J Respir Crit Care Med2006174888689316888288
  • DagouassatMGaglioloJMChruscielSThe cyclooxygenase-2-prostaglandin E2 pathway maintains senescence of chronic obstructive pulmonary disease fibroblastsAm J Respir Crit Care Med2013187770371423328527
  • MercadoNItoKBarnesPJAccelerated ageing of the lung in COPD: new conceptsThorax201570548248925739910
  • ChristensonSABrandsmaCACampbellJDmiR-638 regulates gene expression networks associated with emphysematous lung destructionGenome Med201351211424380442
  • SpiraABeaneJPinto-PlataVGene expression profiling of human lung tissue from smokers with severe emphysemaAm J Respir Cell Mol Biol200431660161015374838
  • FanerRCruzTCasserrasTNetwork analysis of lung transcriptomics reveals a distinct B-cell signature in emphysemaAm J Respir Crit Care Med2016193111242125326735770
  • FrancisSMLarsenJEPaveySJExpression profiling identifies genes involved in emphysema severityRespir Res2009108119723343
  • HartSNTherneauTMZhangYPolandGAKocherJPCalculating sample size estimates for RNA sequencing dataJ Comput Biol2013201297097823961961