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| Status |
Public on Jun 17, 2008 |
| Title |
Variability in Small Airway Epithelial Gene Expression Among Normal Smokers |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by array
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| Summary |
Despite overwhelming data that cigarette smoking causes chronic obstructive pulmonary disease (COPD), only a minority of chronic smokers are affected, strongly suggesting that genetic factors modify susceptibility to this disease. We hypothesized that there are individual variations in the response to cigarette smoking, with variability among smokers in expression levels of protective / susceptibility genes. Affymetrix arrays and TaqMan PCR were used to assess the variability of gene expression in the small airway epithelium obtained by fiberoptic bronchoscopy of 18 normal non-smokers, 18 normal smokers and 18 smokers with COPD.
We identified 201 probesets representing 150 smoking-responsive genes that were significantly up- or down-regulated, and assessed the coefficient of variation in expression levels among the study population. Variation was a reproducible property of each gene as assessed by different microarray probesets and realtime PCR and was observed in both normal smokers and smokers with COPD. There was greater individual variability in smokers with COPD than in normal smokers. The majority of these highly variable smoking responsive genes were in the functional categories of signal transduction, xenobiotic degradation, metabolism, transport, oxidant-related and transcription. A similar pattern of the same highly variable genes was observed in an independent data set.We propose that there is likely genetic diversity within this subset of genes with highly variable individual to individual responses of the small airway epithelium to smoking, and this subset of genes represent putative candidates for assessment of susceptibility/protection from disease for future gene-based epidemiological studies for the risk of smokers for COPD.
Keywords: disease state analysis
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| Overall design |
Affymetrix arrays and TaqMan PCR were used to assess the variability of gene expression in the small airway epithelium obtained by fiberoptic bronchoscopy of 18 normal non-smokers, 18 normal smokers and 18 smokers with COPD.
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| Contributor(s) |
Ammous Z, Hackett NR, Butler MW, Raman T, Dolgalev I, O'Connor TP, Harvey B, Crystal RG |
| Citation(s) |
18339782 |
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| Submission date |
Jul 20, 2007 |
| Last update date |
Mar 25, 2019 |
| Contact name |
Yael Strulovici-Barel |
| E-mail(s) |
[email protected]
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| Organization name |
Weill Cornell Medical College
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| Department |
Department of Genetic Medicine
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| Lab |
Crystal
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| Street address |
1300 York Avenue
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| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10021 |
| Country |
USA |
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| Platforms (1) |
| GPL570 |
[HG-U133_Plus_2] Affymetrix Human Genome U133 Plus 2.0 Array |
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| Samples (54)
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| GSM101095 |
small airways, non-smoker 001, RMA and MAS |
| GSM101096 |
small airways, non-smoker 004, RMA and MAS |
| GSM101097 |
small airways, non-smoker 002, RMA and MAS |
| GSM101098 |
small airways, non-smoker 003, RMA and MAS |
| GSM101100 |
small airways, non-smoker 006, RMA and MAS |
| GSM101101 |
small airways, non-smoker 021, RMA and MAS |
| GSM101102 |
small airways, non-smoker 019, RMA and MAS |
| GSM101103 |
small airways, non-smoker 014, RMA and MAS |
| GSM101104 |
small airways, non-smoker 008, RMA and MAS |
| GSM101105 |
small airways, non-smoker 015, RMA and MAS |
| GSM101106 |
small airways, non-smoker 005, RMA and MAS |
| GSM101109 |
small airways, smoker 027, RMA and MAS |
| GSM101110 |
small airways, smoker 033, RMA and MAS |
| GSM101111 |
small airways, smoker 001, RMA and MAS |
| GSM101113 |
small airways, smoker 048, RMA and MAS |
| GSM101114 |
small airways, smoker 041, RMA and MAS |
| GSM101115 |
small airways, smoker 044, RMA and MAS |
| GSM101116 |
small airways, smoker 049, RMA and MAS |
| GSM114089 |
small airways, smoker 058, MAS5 |
| GSM114090 |
small airways, smoker 063, MAS5 |
| GSM114092 |
small airways, COPD 008, MAS5 |
| GSM114094 |
small airways, COPD 015, MAS5 |
| GSM114095 |
small airways, COPD 020, MAS5 |
| GSM190151 |
small airways, non-smoker 034 |
| GSM190153 |
Small airways, non-smoker 036 |
| GSM252830 |
small airways, COPD 014 |
| GSM252833 |
small airways, COPD 036 |
| GSM252835 |
small airways, COPD 046 |
| GSM252836 |
small airways, COPD 059 |
| GSM252837 |
small airways, COPD 068 |
| GSM252839 |
small airways, COPD 080 |
| GSM252841 |
small airways, COPD 103 |
| GSM252867 |
small airways, non-smoker 035 |
| GSM252879 |
small airways, smoker 074 |
| GSM252882 |
small airways, smoker 095 |
| GSM252884 |
small airways, smoker 098 |
| GSM252885 |
small airways, smoker 103 |
| GSM254149 |
small airways, non-smoker 045 |
| GSM254150 |
small airways, non-smoker 059 |
| GSM254151 |
small airways, non-smoker 071 |
| GSM254152 |
small airways, non-smoker 078 |
| GSM254157 |
small airways, smoker 112 |
| GSM254158 |
small airways, smoker 114 |
| GSM254159 |
small airways, smoker 119 |
| GSM254160 |
small airways, smoker 152 |
| GSM254161 |
small airways, smoker 169 |
| GSM254163 |
small airways, COPD 024 |
| GSM254169 |
small airways, COPD 093 |
| GSM254171 |
small airways, COPD 108 |
| GSM254172 |
small airways, COPD 110 |
| GSM254173 |
small airways, COPD 114 |
| GSM254174 |
small airways, COPD 119 |
| GSM254175 |
small airways, COPD 122 |
| GSM254176 |
small airways, COPD 134 |
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| Relations |
| BioProject |
PRJNA101689 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE8545_RAW.tar |
1.1 Gb |
(http)(custom) |
TAR (of CEL, CHP) |
| Processed data included within Sample table |
| Processed data provided as supplementary file |
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