DNA methylation profiling in human lung tissue identifies genes associated with COPD

References

• Kundaje A, Meuleman W, Ernst J, Bilenky M, Yen A, Heravi-Moussavi A, Kheradpour P, Zhang Z, Wang J, Ziller MJ, et al. Integrative analysis of 111 reference human epigenomes. Nature 2015; 518:317-30; PMID:25693563; http://dx.doi.org/10.1038/nature14248
   PubMed Web of Science ®Google Scholar
• Feinberg AP. Epigenomics reveals a functional genome anatomy and a new approach to common disease. Nat Biotechnol 2010; 28:1049-1052; PMID:20944596; http://dx.doi.org/10.1038/nbt1010-1049
   PubMed Web of Science ®Google Scholar
• Olsson AH, Volkov P, Bacos K, Dayeh T, Hall E, Nilsson EA, Ladenvall C, Rönn T, Ling C. Genome-Wide Associations between Genetic and Epigenetic Variation Influence mRNA Expression and Insulin Secretion in Human Pancreatic Islets. PLoS Genet 2014; 10:e1004735; PMID:25375650; http://dx.doi.org/10.1371/journal.pgen.1004735
   PubMed Web of Science ®Google Scholar
• Shi J, Marconett CN, Duan J, Hyland PL, Li P, Wang Z, Wheeler W, Zhou B, Campan M, Lee DS, et al. Characterizing the genetic basis of methylome diversity in histologically normal human lung tissue. Nat Commun 2014 Feb 27; 5:3365; PMID:24572595; http://dx.doi.org/10.1038/ncomms4365
   PubMed Web of Science ®Google Scholar
• Yoo S, Takikawa S, Geraghty P, Argmann C, Campbell J, Lin L, Huang T, Tu Z, Feronjy R, Spira A, et al. Integrative Analysis of DNA Methylation and Gene Expression Data Identifies EPAS1 as a Key Regulator of COPD. PLoS Genet 2015; 11:e1004898; PMID:25569234; http://dx.doi.org/10.1371/journal.pgen.1004898
   PubMedGoogle Scholar
• Buro-Auriemma LJ, Salit J, Hackett NR, Walters MS, Strulovici-Barel Y, Staudt MR, Fuller J, Mahmoud M, Stevenson CS, Hilton H, et al. Cigarette smoking induces small airway epithelial epigenetic changes with corresponding modulation of gene expression. Hum Mol Genet 2013; 22:4726-38; PMID:23842454; http://dx.doi.org/10.1093/hmg/ddt326
   PubMed Web of Science ®Google Scholar
• Vucic EA, Chari R, Thu KL, Wilson IM, Cotton AM, Kennett JY, Zhang M, Lonergan KM, Steiling K, Brown CJ, 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 2013; 50:912-22; PMID:24298892; http://dx.doi.org/10.1165/rcmb.2013-0304OC
   PubMed Web of Science ®Google Scholar
• Cho MH, Boutaoui N, Klanderman BJ, Sylvia JS, Ziniti JP, Hersh CP, DeMeo DL, Hunninghake GM, Litonjua AA, Sparrow D, et al. Variants in FAM13A are associated with chronic obstructive pulmonary disease. Nat Genet 2010; 42:200-2; PMID:20173748; http://dx.doi.org/10.1038/ng.535
   PubMed Web of Science ®Google Scholar
• Cho MH, Castaldi PJ, Wan ES, Siedlinski M, Hersh CP, Demeo DL, Himes BE, Sylvia JS, Klanderman BJ, Ziniti JP, et al. A genome-wide association study of COPD identifies a susceptibility locus on chromosome 19q13. Hum Mol Genet 2012; 21:947-57; PMID:22080838; http://dx.doi.org/10.1093/hmg/ddr524
   PubMed Web of Science ®Google Scholar
• Pillai SG, Ge D, Zhu G, Kong X, Shianna KV, Need AC, Feng S, Hersh CP, Bakke P, Gulsvik A, et al. A genome-wide association study in chronic obstructive pulmonary disease (COPD): identification of two major susceptibility loci. PLoS Genet 2009; 5:e1000421; PMID:19300482; http://dx.doi.org/10.1371/journal.pgen.1000421
   PubMed Web of Science ®Google Scholar
• Cho MH, McDonald M-LN, Zhou X, Mattheisen M, Castaldi PJ, Hersh CP, Demeo DL, Sylvia JS, Ziniti J, Laird NM, et al. Risk loci for chronic obstructive pulmonary disease: a genome-wide association study and meta-analysis. Lancet Respir Med 2014; 2:214-25; PMID:24621683; http://dx.doi.org/10.1016/S2213-2600(14)70002-5
   PubMed Web of Science ®Google Scholar
• Cho MH, Castaldi PJ, Hersh CP, Hobbs BD, Barr RG, Tal-Singer R, Bakke P, Gulsvik A, San José Estépar R, Van Beek EJR, et al. A Genome-Wide Association Study of Emphysema and Airway Quantitative Imaging Phenotypes. Am J Respir Crit Care Med 2015; 192:559-69; PMID:26030696; http://dx.doi.org/10.1164/rccm.201501-0148OC
   PubMed Web of Science ®Google Scholar
• Bjornsson H. An integrated epigenetic and genetic approach to common human disease. Trends Genet 2004; 20:350-8; PMID:15262407; http://dx.doi.org/10.1016/j.tig.2004.06.009
   PubMed Web of Science ®Google Scholar
• van Eijk KR, de Jong S, Boks MPM, Langeveld T, Colas F, Veldink JH, de Kovel CGF, Janson E, Strengman E, Langfelder P, et al. Genetic analysis of DNA methylation and gene expression levels in whole blood of healthy human subjects. BMC Genomics 2012; 13:636-636; PMID:23157493; http://dx.doi.org/10.1186/1471-2164-13-636
   PubMed Web of Science ®Google Scholar
• Jones PA. Functions of DNA methylation: islands, start sites, gene bodies and beyond. Nat Rev Genet 2012; 13:484-92; PMID:22641018; http://dx.doi.org/10.1038/nrg3230
   PubMed Web of Science ®Google Scholar
• Maeda Y, Hizawa N, Jinushi E, Honda A, Takahashi D, Fukui Y, Konno S, Shimizu T, Shimizu H, Yamaguchi E, et al. Polymorphisms in the Muscarinic Receptor 1 Gene Confer Susceptibility to Asthma in Japanese Subjects. Am J Respir Crit Care Med 2006; 174:1119-24; PMID:16931638; http://dx.doi.org/10.1164/rccm.200601-081OC
   PubMed Web of Science ®Google Scholar
• Lou X-Y, Ma JZ, Payne TJ, Beuten J, Crew KM, Li MD. Gene-based analysis suggests association of the nicotinic acetylcholine receptor β1 subunit (CHRNB1) and M1 muscarinic acetylcholine receptor (CHRM1) with vulnerability for nicotine dependence. Hum Genet 2006; 120:381-9; PMID:16874522; http://dx.doi.org/10.1007/s00439-006-0229-7
   PubMed Web of Science ®Google Scholar
• Cherubini E, Esposito MC, Scozzi D, Terzo F, Osman GA, Mariotta S, Mancini R, Bruno P, Ricci A. Genetic Polymorphism of CHRM2 in COPD: Clinical Significance and Therapeutic Implications. J Cell Physiol 2016 Aug; 231(8):1745-51; Epub 2016 Jan 15. PMID:26633752; http://dx.doi.org/10.1002/jcp.25277
   PubMed Web of Science ®Google Scholar
• Müller MR, Rao A. NFAT, immunity and cancer: a transcription factor comes of age. Nat Rev Immunol 2010; 10:645-56; PMID:20725108; http://dx.doi.org/10.1038/nri2818
   PubMed Web of Science ®Google Scholar
• Dahlin A, Litonjua A, Irvin CG, Peters SP, Lima JJ, Kubo M, Tamari M, Tantisira KG. Genome-wide association study of leukotriene modifier response in asthma. Pharmacogenomics J 2016 Apr; 16(2):151-7; Epub 2015 Jun 2. PMID:26031901; http://dx.doi.org/10.1038/tpj.2015.34
   PubMed Web of Science ®Google Scholar
• Artigas MS, Loth DW, Wain LV, Gharib SA, Obeidat M'en, Tang W, Zhai G, Zhao JH, Smith AV, Huffman JE, et al. Genome-wide association and large-scale follow up identifies 16 new loci influencing lung function. Nat Genet 2011; 43:1082-90; PMID:21946350; http://dx.doi.org/10.1038/ng.941
   PubMed Web of Science ®Google Scholar
• Marinaş AE, Ciurea P, Mărgăritescu C, Cotoi OS. Expression of Epidermal Growth Factor (EGF) and its receptors (EGFR1 and EGFR2) in chronic bronchitis. Rom J Morphol Embryol 2012; 53(4):957-66; PMID:23303019
   PubMed Web of Science ®Google Scholar
• Heijink IH, de Bruin HG, van den Berge M, Bennink LJC, Brandenburg SM, Gosens R, van Oosterhout AJ, Postma DS. Role of aberrant WNT signalling in the airway epithelial response to cigarette smoke in chronic obstructive pulmonary disease. Thorax 2013; 68:709-16; PMID:23370438; http://dx.doi.org/10.1136/thoraxjnl-2012-201667
   PubMed Web of Science ®Google Scholar
• Sharma S, Tantisira K, Carey V, Murphy AJ, Lasky-Su J, Celedón JC, Lazarus R, Klanderman B, Rogers A, Soto-Quirós M, et al. A Role for Wnt Signaling Genes in the Pathogenesis of Impaired Lung Function in Asthma. Am J Respir Crit Care Med 2010; 181:328-36; PMID:19926868; http://dx.doi.org/10.1164/rccm.200907-1009OC
   PubMed Web of Science ®Google Scholar
• Jaffe AE, Murakami P, Lee H, Leek JT, Fallin MD, Feinberg AP, Irizarry RA. Bump hunting to identify differentially methylated regions in epigenetic epidemiology studies. Int J Epidemiol 2012; 41:200-9; PMID:22422453; http://dx.doi.org/10.1093/ije/dyr238
   PubMed Web of Science ®Google Scholar
• Peters TJ, Buckley MJ, Statham AL, Pidsley R, Samaras K, Lord RV, Clark SJ, Molloy PL. De novo identification of differentially methylated regions in the human genome. Epigenetics Chromatin 2015; 8:1-16; PMID:25621012; http://dx.doi.org/10.1186/1756-8935-8-1
   PubMed Web of Science ®Google Scholar
• Lassalle P, Molet S, Janin A, Van der Heyden J, Tavernier J, Fiers W, Devos R, Tonnel A-B. ESM-1 is a novel human endothelial cell-specific molecule expressed in lung and regulated by cytokines. J Biol Chem 1996; 271:20458-20464; PMID:8702785; http://dx.doi.org/10.1074/jbc.271.34.20458
   PubMed Web of Science ®Google Scholar
• Kamada F, Mashimo Y, Inoue H, Shao C, Hirota T, Doi S, Kameda M, Fujiwara H, Fujita K, Enomoto T, et al. The GSTP1 Gene Is a Susceptibility Gene for Childhood Asthma and the GSTM1 Gene Is a Modifier of the GSTP1 Gene. Int Arch Allergy Immunol 2007; 144:275-86; PMID:17643058; http://dx.doi.org/10.1159/000106316
   PubMed Web of Science ®Google Scholar
• Bell JT, Pai Aa, Pickrell JK, Gaffney DJ, Pique-Regi R, Degner JF, Gilad Y, Pritchard JK. DNA methylation patterns associate with genetic and gene expression variation in HapMap cell lines. Genome Biol 2011; 12:R10-R10; PMID:21251332; http://dx.doi.org/10.1186/gb-2011-12-1-r10
   PubMed Web of Science ®Google Scholar
• Ikenouchi J, Umeda M. FRMD4A regulates epithelial polarity by connecting Arf6 activation with the PAR complex. Proc Natl Acad Sci 2010; 107:748-53; PMID:20080746; http://dx.doi.org/10.1073/pnas.0908423107
   PubMed Web of Science ®Google Scholar
• Yoon D, Kim Y-J, Cui W-Y, Van der Vaart A, Cho YS, Lee J-Y, Ma JZ, Payne TJ, Li MD, Park T. Large-scale genome-wide association study of Asian population reveals genetic factors in FRMD4A and other loci influencing smoking initiation and nicotine dependence. Hum Genet 2012; 131:1009-21; PMID:22006218; http://dx.doi.org/10.1007/s00439-011-1102-x
   PubMed Web of Science ®Google Scholar
• Breton CV, Siegmund KD, Joubert BR, Wang X, Qui W, Carey V, Nystad W, Håberg SE, Ober C, Nicolae D, et al. Prenatal Tobacco Smoke Exposure Is Associated with Childhood DNA CpG Methylation. PLoS ONE 2014; 9:e99716; PMID:24964093; http://dx.doi.org/10.1371/journal.pone.0099716
   PubMed Web of Science ®Google Scholar
• Wan ES, Qiu W, Carey VJ, Morrow J, Bacherman H, Foreman MG, Hokanson JE, Bowler RP, Crapo JD, DeMeo DL. Smoking-Associated Site-Specific Differential Methylation in Buccal Mucosa in the COPDGene Study. Am J Respir Cell Mol Biol 2015; 53:246-54; PMID:25517428; http://dx.doi.org/10.1165/rcmb.2014-0103OC
   PubMed Web of Science ®Google Scholar
• Repapi E, Sayers I, Wain LV, Burton PR, Johnson T, Obeidat M'en, Zhao JH, Ramasamy A, Zhai G, Vitart V, et al. Genome-wide association study identifies five loci associated with lung function. Nat Genet 2010; 42:36-44; PMID:20010834; http://dx.doi.org/10.1038/ng.501
   PubMed Web of Science ®Google Scholar
• Hardin M, Zielinski J, Wan ES, Hersh CP, Castaldi PJ, Schwinder E, Hawrylkiewicz I, Sliwinski P, Cho MH, Silverman EK. CHRNA3/5, IREB2, and ADCY2 Are Associated with Severe Chronic Obstructive Pulmonary Disease in Poland. Am J Respir Cell Mol Biol 2012; 47:203-8; PMID:22461431; http://dx.doi.org/10.1165/rcmb.2012-0011OC
   PubMed Web of Science ®Google Scholar
• Bernstein DL, Le Lay JE, Ruano EG, Kaestner KH. TALE-mediated epigenetic suppression of CDKN2A increases replication in human fibroblasts. J Clin Invest 2015; 125:1998-2006; PMID:25866970; http://dx.doi.org/10.1172/JCI77321
   PubMed Web of Science ®Google Scholar
• Nunna S, Reinhardt R, Ragozin S, Jeltsch A. Targeted Methylation of the Epithelial Cell Adhesion Molecule (EpCAM) Promoter to Silence Its Expression in Ovarian Cancer Cells. PLoS ONE 2014; 9:e87703; PMID:24489952; http://dx.doi.org/10.1371/journal.pone.0087703
   PubMed Web of Science ®Google Scholar
• Rivenbark AG, Stolzenburg S, Beltran AS, Yuan X, Rots MG, Strahl BD, Blancafort P. Epigenetic reprogramming of cancer cells via targeted DNA methylation. Epigenetics 2012; 7:350-60; PMID:22419067; http://dx.doi.org/10.4161/epi.19507
   PubMed Web of Science ®Google Scholar
• Vojta A, Dobrinić P, Tadić V, Bočkor L, Korać P, Julg B, Klasić M, Zoldoš V. Repurposing the CRISPR-Cas9 system for targeted DNA methylation. Nucleic Acids Res 2016; 44:5615-28; PMID:26969735; http://dx.doi.org/10.1093/nar/gkw159
   PubMed Web of Science ®Google Scholar
• Vestbo J, Hurd SS, Agustí AG, Jones PW, Vogelmeier C, Anzueto A, Barnes PJ, Fabbri LM, Martinez FJ, Nishimura M, et al. Global strategy for the diagnosis, management, and prevention of chronic obstructive pulmonary disease: GOLD executive summary. Am J Respir Crit Care Med 2013; 187:347-65; PMID:22878278; http://dx.doi.org/10.1164/rccm.201204-0596PP
   PubMed Web of Science ®Google Scholar
• Hansen KD, Ayree M, Irizarry RA. minfi: Analyze Illumina's 450k methylation arrays (v. 1.5.1). 2012; http://bioconductor.org/packages/release/bioc/html/minfi.html
   Google Scholar
• Chen Y, Lemire M, Choufani S, Butcher DT, Grafodatskaya D, Zanke BW, Gallinger S, Hudson TJ, Weksberg R. Discovery of cross-reactive probes and polymorphic CpGs in the Illumina Infinium HumanMethylation450 microarray. Epigenetics 2013; 8:203-9; PMID:23314698; http://dx.doi.org/10.4161/epi.23470
   PubMed Web of Science ®Google Scholar
• Triche TJ, Weisenberger DJ, Van Den Berg D, Laird PW, Siegmund KD. Low-level processing of Illumina Infinium DNA Methylation BeadArrays. Nucleic Acids Res 2013; 41:e90-e90; PMID:23476028; http://dx.doi.org/10.1093/nar/gkt090
   PubMed Web of Science ®Google Scholar
• Teschendorff AE, Marabita F, Lechner M, Bartlett T, Tegner J, Gomez-Cabrero D, Beck S. A beta-mixture quantile normalization method for correcting probe design bias in Illumina Infinium 450 k DNA methylation data. Bioinformatics 2013; 29:189-96; PMID:23175756; http://dx.doi.org/10.1093/bioinformatics/bts680
   PubMed Web of Science ®Google Scholar
• Bibikova M, Barnes B, Tsan C, Ho V, Klotzle B, Le JM, Delano D, Zhang L, Schroth GP, Gunderson KL, et al. High density DNA methylation array with single CpG site resolution. Genomics 2011; 98:288-95; PMID:21839163; http://dx.doi.org/10.1016/j.ygeno.2011.07.007
   PubMed Web of Science ®Google Scholar
• Smyth GK. Limma: linear models for microarray data. In: Gentleman R, Carey V, Dudoit S, Irizarry R, Huber W, editors. Bioinformatics and Computational Biology Solutions Using {R} and Bioconductor. New York: Springer; 2005. page 397-420; http://dx.doi.org/10.1007/0-387-29362-0
   Google Scholar
• Kamburov A, Stelzl U, Lehrach H, Herwig R. The ConsensusPathDB interaction database: 2013 update. Nucleic Acids Res 2013; 41:D793-800; PMID:23143270; http://dx.doi.org/10.1093/nar/gks1055
   PubMed Web of Science ®Google Scholar
• Wang J, Duncan D, Shi Z, Zhang B. WEB-based GEne SeT AnaLysis Toolkit (WebGestalt): update 2013. Nucleic Acids Res 2013; 41:W77-83; PMID:23703215; http://dx.doi.org/10.1093/nar/gkt439
   PubMed Web of Science ®Google Scholar
• Durinck S, Moreau Y, Kasprzyk A, Davis S, De Moor B, Brazma A, Huber W. BioMart and Bioconductor: a powerful link between biological databases and microarray data analysis. Bioinformatics 2005; 21:3439-40; PMID:16082012; http://dx.doi.org/10.1093/bioinformatics/bti525
   PubMed Web of Science ®Google Scholar
• Morrow J, Qiu W, DeMeo DL, Houston I, Pinto-Plata VM, Celli BR, Marchetti N, Criner GJ, Bueno R, Washko GR, et al. Network Analysis of Gene Expression in Severe COPD Lung Tissue Samples [abstract]. Am J Respir Crit Care Med 2015; 191:A1253; (published conference abstract from: A30. BIG DATA: HARVESTING FRUITS FROM COPD AND LUNG CANCER. May 1, 2015, A1253-A1253)
   Google Scholar
• Lin SM, Du P, Huber W, Kibbe WA. Model-based variance-stabilizing transformation for Illumina microarray data. Nucleic Acids Res 2008; 36:e11-e11; PMID:18178591; http://dx.doi.org/10.1093/nar/gkm1075
   PubMed Web of Science ®Google Scholar
• Du P, Kibbe WA, Lin SM. lumi: a pipeline for processing Illumina microarray. Bioinformatics 2008; 24:1547-8; PMID:18467348; http://dx.doi.org/10.1093/bioinformatics/btn224
   PubMed Web of Science ®Google Scholar