Comment[ArrayExpressAccession] E-GEOD-19407
Public Release Date 2011-04-20
Investigation Title Smoking-induced Wnt pathway downregulation
Comment[Submitted Name] Smoking-induced Wnt pathway downregulation
Experiment Description The Wnt pathway plays a central role in controlling differentiation of epithelial tissues; when Wnt is on, differentiation is suppressed, but when Wnt is off, differentiation is allowed to proceed. Based on this concept, we hypothesized that expression of key genes in the Wnt pathway are suppressed in the human airway epithelium under the stress of cigarette smoking, a stress associated with dysregulation of the differentiated state of the airway epithelium. For this purpose, HG-U133 Plus 2.0 microarrays were used to assess the expression of Wnt-related genes in the small airway (10th-12th generation) epithelium (SAE) obtained via bronchoscopy and brushing of healthy nonsmokers (n=47), healthy smokers (n=58), and smokers with established COPD (n=22). With expression defined as present in >20% of samples, microarray analysis demonstrated that 35 of 57 known Wnt-related genes are expressed in the adult SAE. Wnt pathway downstream targets β-catenin (p<0.05) and the transcription factor 7-like 1 were down-regulated in healthy smokers, and smokers with COPD, as were a number of Wnt target genes, including VEGFA, CCND1, MMP7, CLDN1, SOX9, RHOU (all p<0.05 compared to healthy nonsmokers). As a mechanism to explain this broad, smoking-induced suppression of the Wnt pathway, we assessed expression of the DKK and SFRP families, extracellular regulators that suppress the Wnt pathway. Among these, secreted frizzled-related protein 2 (SFRP2), was up-regulated 4.3-fold (p<0.0001) in healthy smokers and 4.9-fold (p<0.0001) in COPD smokers, an observation confirmed by TaqMan Real-time PCR. AT the protein levels, Western analysis demonstrated SFRP2 up-regulation, and immunohistochemistry demonstrated that the smoking-induced SFRP2 upregulation occurred in differentiated ciliated cells. Finally, cigarette smoke extract mediated up-regulation of SFRP2 and downregulation of Wnt target genes in airway epithelial cells in vitro. These observations are consistent with the hypothesis that the Wnt pathway plays a role in airway epithelial cell differentiation in the adult human airway epithelium, with smoking associated with down-regulation of Wnt pathway, contributing to the dysregulation of airway epithelial differentiation observed in the smoking-related airway disorders. Affymetrix arrays were used to assess gene expression data of genes in the Wnt pathway in small airway epithelium obtained by fiberoptic bronchoscopy of 47 healthy non-smokers and 58 healthy smokers and 22 smokers with COPD.
Date of Experiment
Term Source Name EFO
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Term Source File http://bar.ebi.ac.uk:8080/trac/browser/branches/curator/ExperimentalFactorOntology/ExFactorInOWL/currentrelease/eforelease/efo.owl
Person Last Name Strulovici-Barel Wang Wang Hassan Strulovici-Barel Hackett Crystal
Person First Name Yael Rui Guoqing Ibrahim Yael Neil Ronald
Person Mid Initials R G
Person Email yas2003@med.cornell.edu
Person Affiliation Weill Cornell Medical College
Person Phone 646-962-5560
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Person Address Department of Genetic Medicine, Weill Cornell Medical College, 1300 York Avenue, New York , NY, USA
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Protocol Name P-GSE19407-3 P-GSE19407-1 P-GSE19407-6 P-GSE19407-4 P-GSE19407-2 P-GSE19407-5 P-GSE19407-13 P-GSE19407-12 P-GSE19407-10 P-GSE19407-16 P-GSE19407-9 P-GSE19407-7 P-GSE19407-8 P-GSE19407-15 P-GSE19407-11 P-GSE19407-14
Protocol Description ID_REF =
VALUE = Signal
ABS_CALL = indicating whether the transcript was present (P), absent (A), or marginal (M)
DETECTION P-VALUE = ID_REF = Probe set ID
VALUE = Signal intensity derived from the CEL files, using RMA method
VALUE_MAS = MAS5-calculated Signal intensity
ABS_CALL = the call in an absolute analysis that indicates if the transcript was present (P), absent (A), marginal (M), or no call (NC)
DETECTION P-VALUE = 'detection p-value', p-value that indicates the significance level of the detection call ID_REF =
VALUE = MAS5-calculated signal intensity
ABS_CALL = indicating whether the transcript was present (P), absent (A), or marginal (M)
DETECTION P-VALUE = p-value that indicates the significance level of the detection call ID_REF =
VALUE = MAS5-calculated signal intensity
ABS_CALL = the call in an absolute analysis that indicates if the transcript was present (P), absent (A), or marginal (M)
DETECTION P-VALUE = 'detection p-value', p-value that indicates the significance level of the detection call ID_REF = Probe set ID
VALUE = MAS5-calculated signal intensity
ABS_CALL = the call in an absolute analysis that indicates if the transcript was present (P), absent (A), or marginal (M)
DETECTION P-VALUE = 'detection p-value', p-value that indicates the significance level of the detection call ID_REF =
VALUE = MAS5-calculated signal intensity
ABS_CALL = indicating whether the transcript was present (P), absent (A), or marginal (M)
DETECTION P-VALUE = GeneChips were scanned using the GeneChip Scanner 3000 7G GeneChips were scanned using the GeneChip Scanner 3000 7G . GeneChips were scanned using the GeneChip Scanner 3000 7G. Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on GeneChip HG-U133 Plus 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 450. Following fragmentation, 15 microg of cRNA were hybridized for 16 hr at 45C on GeneChip HG-U133 Plus 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 450. Trizol extraction and RNAeasy clean-up of total RNA was performed according to the manufacturer's instructions. Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3 microg total RNA (Expression Analysis Technical Manual, 701022 Rev.2, Affymetrix). Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1-2 microg total RNA (Expression Analysis Technical Manual, 701022 Rev.2, Affymetrix). The CEL files were generated using Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.
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Protocol Type bioassay_data_transformation bioassay_data_transformation bioassay_data_transformation bioassay_data_transformation bioassay_data_transformation bioassay_data_transformation image_aquisition image_aquisition image_aquisition hybridization hybridization nucleic_acid_extraction labeling labeling feature_extraction feature_extraction
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Experimental Factor Name AGE SMOKING STATUS ETHNIC GROUP SEX
Experimental Factor Type Age smoking status Ethnic group sex
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Publication Title Down-Regulation of the Canonical Wnt β-Catenin Pathway in the Airway Epithelium of Healthy Smokers and Smokers with COPD.
Publication Author List Wang R, Ahmed J, Wang G, Hassan I, Strulovici-Barel Y, Hackett NR, Crystal RG
PubMed ID 21490961
Publication DOI 10.1371/journal.pone.0014793
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Comment[SecondaryAccession] GSE19407
Comment[GEOLastUpdateDate] 2011-04-20
Comment[AEExperimentType] transcription profiling by array
Comment[GEOReleaseDate] 2011-04-19
Comment[ArrayExpressSubmissionDate] 2009-12-10
SDRF File E-GEOD-19407.sdrf.txt