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Volumn 133, Issue 3, 2014, Pages

Dissecting childhood asthma with nasal transcriptomics distinguishes subphenotypes of disease

Author keywords

asthma; bronchial airway epithelium; Nasal airway epithelium; transcriptome

Indexed keywords

CALCIUM ACTIVATED CHLORIDE CHANNEL; INTERLEUKIN 13; INTERLEUKIN 5; SERINE PROTEINASE INHIBITOR; TRANSCRIPTION FACTOR RUNX2; TRANSCRIPTOME;

EID: 84896701857     PISSN: 00916749     EISSN: 10976825     Source Type: Journal    
DOI: 10.1016/j.jaci.2013.11.025     Document Type: Article
Times cited : (198)

References (62)
  • 1
    • 84896720714 scopus 로고    scopus 로고
    • National health interview survey 2004-2011 editor. Hyattsville (MD): National Center for Health Statistics
    • National health interview survey 2004-2011. In: Prevention CfDCa, editor. Hyattsville (MD): National Center for Health Statistics.
    • Prevention CfDCa
  • 2
    • 35649028488 scopus 로고    scopus 로고
    • Genome-wide profiling identifies epithelial cell genes associated with asthma and with treatment response to corticosteroids
    • P.G. Woodruff, H.A. Boushey, G.M. Dolganov, C.S. Barker, Y.H. Yang, and S. Donnelly et al. Genome-wide profiling identifies epithelial cell genes associated with asthma and with treatment response to corticosteroids Proc Natl Acad Sci U S A 104 2007 15858 15863
    • (2007) Proc Natl Acad Sci U S A , vol.104 , pp. 15858-15863
    • Woodruff, P.G.1    Boushey, H.A.2    Dolganov, G.M.3    Barker, C.S.4    Yang, Y.H.5    Donnelly, S.6
  • 6
    • 33646777094 scopus 로고    scopus 로고
    • The nose revisited: A brief review of the comparative structure, function, and toxicologic pathology of the nasal epithelium
    • J.R. Harkema, S.A. Carey, and J.G. Wagner The nose revisited: a brief review of the comparative structure, function, and toxicologic pathology of the nasal epithelium Toxicol Pathol 34 2006 252 269
    • (2006) Toxicol Pathol , vol.34 , pp. 252-269
    • Harkema, J.R.1    Carey, S.A.2    Wagner, J.G.3
  • 7
    • 46049092364 scopus 로고    scopus 로고
    • Smoking-induced gene expression changes in the bronchial airway are reflected in nasal and buccal epithelium
    • S. Sridhar, F. Schembri, J. Zeskind, V. Shah, A.M. Gustafson, and K. Steiling et al. Smoking-induced gene expression changes in the bronchial airway are reflected in nasal and buccal epithelium BMC Genomics 9 2008 259
    • (2008) BMC Genomics , vol.9 , pp. 259
    • Sridhar, S.1    Schembri, F.2    Zeskind, J.3    Shah, V.4    Gustafson, A.M.5    Steiling, K.6
  • 8
    • 13444280369 scopus 로고    scopus 로고
    • Altered gene expression profiles in nasal respiratory epithelium reflect stable versus acute childhood asthma
    • J.R. Guajardo, K.W. Schleifer, M.O. Daines, R.M. Ruddy, B.J. Aronow, and M. Wills-Karp et al. Altered gene expression profiles in nasal respiratory epithelium reflect stable versus acute childhood asthma J Allergy Clin Immunol 115 2005 243 251
    • (2005) J Allergy Clin Immunol , vol.115 , pp. 243-251
    • Guajardo, J.R.1    Schleifer, K.W.2    Daines, M.O.3    Ruddy, R.M.4    Aronow, B.J.5    Wills-Karp, M.6
  • 10
    • 84884905323 scopus 로고    scopus 로고
    • Factors associated with degree of atopy in Latino children in a nationwide pediatric sample: The Genes-environments and Admixture in Latino Asthmatics (GALA II) study
    • R. Kumar, E.A. Nguyen, L.A. Roth, S.S. Oh, C.R. Gignoux, and S. Huntsman et al. Factors associated with degree of atopy in Latino children in a nationwide pediatric sample: the Genes-environments and Admixture in Latino Asthmatics (GALA II) study J Allergy Clin Immunol 132 2013 896 905.e1
    • (2013) J Allergy Clin Immunol , vol.132
    • Kumar, R.1    Nguyen, E.A.2    Roth, L.A.3    Oh, S.S.4    Gignoux, C.R.5    Huntsman, S.6
  • 13
    • 84876996918 scopus 로고    scopus 로고
    • TopHat2: Accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions
    • D. Kim, G. Pertea, C. Trapnell, H. Pimentel, R. Kelley, and S.L. Salzberg TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions Genome Biol 14 2013 R36
    • (2013) Genome Biol , vol.14 , pp. 36
    • Kim, D.1    Pertea, G.2    Trapnell, C.3    Pimentel, H.4    Kelley, R.5    Salzberg, S.L.6
  • 14
    • 84859885816 scopus 로고    scopus 로고
    • Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks
    • C. Trapnell, A. Roberts, L. Goff, G. Pertea, D. Kim, and D.R. Kelley et al. Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks Nat Protoc 7 2012 562 578
    • (2012) Nat Protoc , vol.7 , pp. 562-578
    • Trapnell, C.1    Roberts, A.2    Goff, L.3    Pertea, G.4    Kim, D.5    Kelley, D.R.6
  • 15
    • 77952123055 scopus 로고    scopus 로고
    • Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation
    • C. Trapnell, B.A. Williams, G. Pertea, A. Mortazavi, G. Kwan, and M.J. van Baren et al. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation Nat Biotechnol 28 2010 511 515
    • (2010) Nat Biotechnol , vol.28 , pp. 511-515
    • Trapnell, C.1    Williams, B.A.2    Pertea, G.3    Mortazavi, A.4    Kwan, G.5    Van Baren, M.J.6
  • 17
    • 84886557480 scopus 로고    scopus 로고
    • Finding consistent patterns: A nonparametric approach for identifying differential expression in RNA-Seq data
    • J. Li, and R. Tibshirani Finding consistent patterns: a nonparametric approach for identifying differential expression in RNA-Seq data Stat Methods Med Res 22 2013 519 536
    • (2013) Stat Methods Med Res , vol.22 , pp. 519-536
    • Li, J.1    Tibshirani, R.2
  • 18
    • 79957822290 scopus 로고    scopus 로고
    • Characterizing the impact of smoking and lung cancer on the airway transcriptome using RNA-Seq
    • J. Beane, J. Vick, F. Schembri, C. Anderlind, A. Gower, and J. Campbell et al. Characterizing the impact of smoking and lung cancer on the airway transcriptome using RNA-Seq Cancer Prev Res (Phila) 4 2011 803 817
    • (2011) Cancer Prev Res (Phila) , vol.4 , pp. 803-817
    • Beane, J.1    Vick, J.2    Schembri, F.3    Anderlind, C.4    Gower, A.5    Campbell, J.6
  • 20
    • 74549125753 scopus 로고    scopus 로고
    • An abundance of ubiquitously expressed genes revealed by tissue transcriptome sequence data
    • D. Ramskold, E.T. Wang, C.B. Burge, and R. Sandberg An abundance of ubiquitously expressed genes revealed by tissue transcriptome sequence data PLoS Comput Biol 5 2009 e1000598
    • (2009) PLoS Comput Biol , vol.5 , pp. 1000598
    • Ramskold, D.1    Wang, E.T.2    Burge, C.B.3    Sandberg, R.4
  • 22
    • 84870549641 scopus 로고    scopus 로고
    • Self-cleavage of human CLCA1 protein by a novel internal metalloprotease domain controls calcium-activated chloride channel activation
    • Z. Yurtsever, M. Sala-Rabanal, D.T. Randolph, S.M. Scheaffer, W.T. Roswit, and Y.G. Alevy et al. Self-cleavage of human CLCA1 protein by a novel internal metalloprotease domain controls calcium-activated chloride channel activation J Biol Chem 287 2012 42138 42149
    • (2012) J Biol Chem , vol.287 , pp. 42138-42149
    • Yurtsever, Z.1    Sala-Rabanal, M.2    Randolph, D.T.3    Scheaffer, S.M.4    Roswit, W.T.5    Alevy, Y.G.6
  • 24
    • 70450213353 scopus 로고    scopus 로고
    • Oncostatin M (OSM) is increased in asthma with incompletely reversible airflow obstruction
    • J.L. Simpson, K.J. Baines, M.J. Boyle, R.J. Scott, and P.G. Gibson Oncostatin M (OSM) is increased in asthma with incompletely reversible airflow obstruction Exp Lung Res 35 2009 781 794
    • (2009) Exp Lung Res , vol.35 , pp. 781-794
    • Simpson, J.L.1    Baines, K.J.2    Boyle, M.J.3    Scott, R.J.4    Gibson, P.G.5
  • 25
  • 26
    • 84876996918 scopus 로고    scopus 로고
    • TopHat2: Accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions
    • D. Kim, G. Pertea, C. Trapnell, H. Pimentel, R. Kelley, and S.L. Salzberg TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions Genome Biol 14 2013 R36
    • (2013) Genome Biol , vol.14 , pp. 36
    • Kim, D.1    Pertea, G.2    Trapnell, C.3    Pimentel, H.4    Kelley, R.5    Salzberg, S.L.6
  • 27
    • 65449136284 scopus 로고    scopus 로고
    • TopHat: Discovering splice junctions with RNA-Seq
    • C. Trapnell, L. Pachter, and S.L. Salzberg TopHat: discovering splice junctions with RNA-Seq Bioinformatics 25 2009 1105 1111
    • (2009) Bioinformatics , vol.25 , pp. 1105-1111
    • Trapnell, C.1    Pachter, L.2    Salzberg, S.L.3
  • 28
    • 84859210032 scopus 로고    scopus 로고
    • Fast gapped-read alignment with Bowtie 2
    • B. Langmead, and S.L. Salzberg Fast gapped-read alignment with Bowtie 2 Nat Methods 9 2012 357 359
    • (2012) Nat Methods , vol.9 , pp. 357-359
    • Langmead, B.1    Salzberg, S.L.2
  • 29
    • 77952123055 scopus 로고    scopus 로고
    • Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation
    • C. Trapnell, B.A. Williams, G. Pertea, A. Mortazavi, G. Kwan, and M.J. van Baren et al. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation Nat Biotechnol 28 2010 511 515
    • (2010) Nat Biotechnol , vol.28 , pp. 511-515
    • Trapnell, C.1    Williams, B.A.2    Pertea, G.3    Mortazavi, A.4    Kwan, G.5    Van Baren, M.J.6
  • 30
    • 84859885816 scopus 로고    scopus 로고
    • Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks
    • C. Trapnell, A. Roberts, L. Goff, G. Pertea, D. Kim, and D.R. Kelley et al. Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks Nat Protoc 7 2012 562 578
    • (2012) Nat Protoc , vol.7 , pp. 562-578
    • Trapnell, C.1    Roberts, A.2    Goff, L.3    Pertea, G.4    Kim, D.5    Kelley, D.R.6
  • 32
    • 79957822290 scopus 로고    scopus 로고
    • Characterizing the impact of smoking and lung cancer on the airway transcriptome using RNA-Seq
    • J. Beane, J. Vick, F. Schembri, C. Anderlind, A. Gower, and J. Campbell et al. Characterizing the impact of smoking and lung cancer on the airway transcriptome using RNA-Seq Cancer Prev Res (Phila) 4 2011 803 817
    • (2011) Cancer Prev Res (Phila) , vol.4 , pp. 803-817
    • Beane, J.1    Vick, J.2    Schembri, F.3    Anderlind, C.4    Gower, A.5    Campbell, J.6
  • 34
    • 74549125753 scopus 로고    scopus 로고
    • An abundance of ubiquitously expressed genes revealed by tissue transcriptome sequence data
    • D. Ramskold, E.T. Wang, C.B. Burge, and R. Sandberg An abundance of ubiquitously expressed genes revealed by tissue transcriptome sequence data PLoS Comput Biol 5 2009 e1000598
    • (2009) PLoS Comput Biol , vol.5 , pp. 1000598
    • Ramskold, D.1    Wang, E.T.2    Burge, C.B.3    Sandberg, R.4
  • 35
    • 35649028488 scopus 로고    scopus 로고
    • Genome-wide profiling identifies epithelial cell genes associated with asthma and with treatment response to corticosteroids
    • P.G. Woodruff, H.A. Boushey, G.M. Dolganov, C.S. Barker, Y.H. Yang, and S. Donnelly et al. Genome-wide profiling identifies epithelial cell genes associated with asthma and with treatment response to corticosteroids Proc Natl Acad Sci U S A 104 2007 15858 15863
    • (2007) Proc Natl Acad Sci U S A , vol.104 , pp. 15858-15863
    • Woodruff, P.G.1    Boushey, H.A.2    Dolganov, G.M.3    Barker, C.S.4    Yang, Y.H.5    Donnelly, S.6
  • 36
    • 84886557480 scopus 로고    scopus 로고
    • Finding consistent patterns: A nonparametric approach for identifying differential expression in RNA-Seq data
    • J. Li, and R. Tibshirani Finding consistent patterns: A nonparametric approach for identifying differential expression in RNA-Seq data Stat Methods Med Res 22 2013 519 536
    • (2013) Stat Methods Med Res , vol.22 , pp. 519-536
    • Li, J.1    Tibshirani, R.2
  • 39
    • 77958471357 scopus 로고    scopus 로고
    • Differential expression analysis for sequence count data
    • S. Anders, and W. Huber Differential expression analysis for sequence count data Genome Biol 11 2010 R106
    • (2010) Genome Biol , vol.11 , pp. 106
    • Anders, S.1    Huber, W.2
  • 41
    • 0345040873 scopus 로고    scopus 로고
    • Classification and regression by random forest
    • A.W. Liaw, and M. Weiner Classification and regression by random forest R News 2/3 2002 18 22
    • (2002) R News , vol.2-3 , pp. 18-22
    • Liaw, A.W.1    Weiner, M.2
  • 42
    • 0345501553 scopus 로고    scopus 로고
    • Impact of genetic polymorphisms of the beta2-adrenergic receptor on albuterol bronchodilator pharmacodynamics
    • J.J. Lima, D.B. Thomason, M.H. Mohamed, L.V. Eberle, T.H. Self, and J.A. Johnson Impact of genetic polymorphisms of the beta2-adrenergic receptor on albuterol bronchodilator pharmacodynamics Clin Pharmacol Ther 65 1999 519 525
    • (1999) Clin Pharmacol Ther , vol.65 , pp. 519-525
    • Lima, J.J.1    Thomason, D.B.2    Mohamed, M.H.3    Eberle, L.V.4    Self, T.H.5    Johnson, J.A.6
  • 43
    • 0031466866 scopus 로고    scopus 로고
    • Association between genetic polymorphisms of the beta2-adrenoceptor and response to albuterol in children with and without a history of wheezing
    • F.D. Martinez, P.E. Graves, M. Baldini, S. Solomon, and R. Erickson Association between genetic polymorphisms of the beta2-adrenoceptor and response to albuterol in children with and without a history of wheezing J Clin Invest 100 1997 3184 3188
    • (1997) J Clin Invest , vol.100 , pp. 3184-3188
    • Martinez, F.D.1    Graves, P.E.2    Baldini, M.3    Solomon, S.4    Erickson, R.5
  • 44
    • 0242719848 scopus 로고    scopus 로고
    • Family-based association analysis of beta2-adrenergic receptor polymorphisms in the childhood asthma management program
    • E.K. Silverman, D.J. Kwiatkowski, J.S. Sylvia, R. Lazarus, J.M. Drazen, and C. Lange et al. Family-based association analysis of beta2-adrenergic receptor polymorphisms in the childhood asthma management program J Allergy Clin Immunol 112 2003 870 876
    • (2003) J Allergy Clin Immunol , vol.112 , pp. 870-876
    • Silverman, E.K.1    Kwiatkowski, D.J.2    Sylvia, J.S.3    Lazarus, R.4    Drazen, J.M.5    Lange, C.6
  • 45
    • 20444500048 scopus 로고    scopus 로고
    • Evaluation of the CD14/-260 polymorphism and house dust endotoxin exposure in the Barbados Asthma Genetics Study
    • A. Zambelli-Weiner, E. Ehrlich, M.L. Stockton, A.V. Grant, S. Zhang, and P.N. Levett et al. Evaluation of the CD14/-260 polymorphism and house dust endotoxin exposure in the Barbados Asthma Genetics Study J Allergy Clin Immunol 115 2005 1203 1209
    • (2005) J Allergy Clin Immunol , vol.115 , pp. 1203-1209
    • Zambelli-Weiner, A.1    Ehrlich, E.2    Stockton, M.L.3    Grant, A.V.4    Zhang, S.5    Levett, P.N.6
  • 47
    • 80052259316 scopus 로고    scopus 로고
    • Meta-analysis of genome-wide association studies of asthma in ethnically diverse North American populations
    • D.G. Torgerson, E.J. Ampleford, G.Y. Chiu, W.J. Gauderman, C.R. Gignoux, and P.E. Graves et al. Meta-analysis of genome-wide association studies of asthma in ethnically diverse North American populations Nat Genet 43 2011 887 892
    • (2011) Nat Genet , vol.43 , pp. 887-892
    • Torgerson, D.G.1    Ampleford, E.J.2    Chiu, G.Y.3    Gauderman, W.J.4    Gignoux, C.R.5    Graves, P.E.6
  • 51
    • 16044371529 scopus 로고    scopus 로고
    • Phenotypic and physiologic characterization of transgenic mice expressing interleukin 4 in the lung: Lymphocytic and eosinophilic inflammation without airway hyperreactivity
    • J.A. Rankin, D.E. Picarella, G.P. Geba, U.A. Temann, B. Prasad, and B. DiCosmo et al. Phenotypic and physiologic characterization of transgenic mice expressing interleukin 4 in the lung: lymphocytic and eosinophilic inflammation without airway hyperreactivity Proc Natl Acad Sci U S A 93 1996 7821 7825
    • (1996) Proc Natl Acad Sci U S A , vol.93 , pp. 7821-7825
    • Rankin, J.A.1    Picarella, D.E.2    Geba, G.P.3    Temann, U.A.4    Prasad, B.5    Dicosmo, B.6
  • 52
    • 0030028768 scopus 로고    scopus 로고
    • Interleukin 5 deficiency abolishes eosinophilia, airways hyperreactivity, and lung damage in a mouse asthma model
    • P.S. Foster, S.P. Hogan, A.J. Ramsay, K.I. Matthaei, and I.G. Young Interleukin 5 deficiency abolishes eosinophilia, airways hyperreactivity, and lung damage in a mouse asthma model J Exp Med 183 1996 195 201
    • (1996) J Exp Med , vol.183 , pp. 195-201
    • Foster, P.S.1    Hogan, S.P.2    Ramsay, A.J.3    Matthaei, K.I.4    Young, I.G.5
  • 53
    • 84874004801 scopus 로고    scopus 로고
    • Integration of mouse and human genome-wide association data identifies KCNIP4 as an asthma gene
    • B.E. Himes, K. Sheppard, A. Berndt, A.S. Leme, R.A. Myers, and C.R. Gignoux et al. Integration of mouse and human genome-wide association data identifies KCNIP4 as an asthma gene PLoS One 8 2013 e56179
    • (2013) PLoS One , vol.8 , pp. 56179
    • Himes, B.E.1    Sheppard, K.2    Berndt, A.3    Leme, A.S.4    Myers, R.A.5    Gignoux, C.R.6
  • 54
    • 84870294531 scopus 로고    scopus 로고
    • Further replication studies of the EVE Consortium meta-analysis identifies 2 asthma risk loci in European Americans
    • R.A. Myers, B.E. Himes, C.R. Gignoux, J.J. Yang, W.J. Gauderman, and C. Rebordosa et al. Further replication studies of the EVE Consortium meta-analysis identifies 2 asthma risk loci in European Americans J Allergy Clin Immunol 130 2012 1294 1301
    • (2012) J Allergy Clin Immunol , vol.130 , pp. 1294-1301
    • Myers, R.A.1    Himes, B.E.2    Gignoux, C.R.3    Yang, J.J.4    Gauderman, W.J.5    Rebordosa, C.6
  • 55
    • 33751082383 scopus 로고    scopus 로고
    • Intrinsic biochemical and functional differences in bronchial epithelial cells of children with asthma
    • A. Kicic, E.N. Sutanto, P.T. Stevens, D.A. Knight, and S.M. Stick Intrinsic biochemical and functional differences in bronchial epithelial cells of children with asthma Am J Respir Crit Care Med 174 2006 1110 1118
    • (2006) Am J Respir Crit Care Med , vol.174 , pp. 1110-1118
    • Kicic, A.1    Sutanto, E.N.2    Stevens, P.T.3    Knight, D.A.4    Stick, S.M.5
  • 57
    • 84896715160 scopus 로고    scopus 로고
    • GWAS and admixture mapping identify different asthma-associated loci in Latinos: The GALA II study
    • [Epub ahead of print]
    • J.M. Galanter, C.R. Gignoux, D.G. Torgerson, L.A. Roth, C. Eng, and S.S. Oh et al. GWAS and admixture mapping identify different asthma-associated loci in Latinos: the GALA II study J Allergy Clin Immunol 2013 [Epub ahead of print]
    • (2013) J Allergy Clin Immunol
    • Galanter, J.M.1    Gignoux, C.R.2    Torgerson, D.G.3    Roth, L.A.4    Eng, C.5    Oh, S.S.6
  • 60
    • 12344279001 scopus 로고    scopus 로고
    • Reduced expression of transforming growth factor beta 1 exacerbates pathology in an experimental asthma model
    • W. Scherf, S. Burdach, and G. Hansen Reduced expression of transforming growth factor beta 1 exacerbates pathology in an experimental asthma model Eur J Immunol 35 2005 198 206
    • (2005) Eur J Immunol , vol.35 , pp. 198-206
    • Scherf, W.1    Burdach, S.2    Hansen, G.3
  • 62
    • 80052273202 scopus 로고    scopus 로고
    • Genome-wide association study identifies three new susceptibility loci for adult asthma in the Japanese population
    • T. Hirota, A. Takahashi, M. Kubo, T. Tsunoda, K. Tomita, and S. Doi et al. Genome-wide association study identifies three new susceptibility loci for adult asthma in the Japanese population Nat Genet 43 2011 893 896
    • (2011) Nat Genet , vol.43 , pp. 893-896
    • Hirota, T.1    Takahashi, A.2    Kubo, M.3    Tsunoda, T.4    Tomita, K.5    Doi, S.6


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