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| Status |
Public on Aug 05, 2013 |
| Title |
Cigarette Smoking Induces Small Airway Epithelial Epigenetic Changes with Corresponding Modulation of Gene Expression |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by array
Methylation profiling by genome tiling array
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| Summary |
The small airway epithelium (SAE), the first site of smoking-induced lung pathology, exhibits genome-wide changes in gene expression in response to cigarette smoking. Based on the increasing evidence that the epigenome can respond to external stimuli in a rapid manner, we assessed the SAE of smokers for genome-wide DNA methylation changes compared to nonsmokers, and whether changes in SAE DNA methylation were linked to the transcriptional output of these cells. Using genome-wide methylation analysis of SAE DNA of nonsmokers and smokers, the data identified 204 unique genes differentially methylated in SAE DNA of smokers compared to nonsmokers, with 67% of the regions with differential methylation occurring within 2 kb of the transcriptional start site. Among the genes with differential methylation were those related to metabolism, transcription, signal transduction and transport. For the differentially methylated genes, 34 exhibited a correlation with gene expression, 53% with an inverse correlation of DNA methylation with gene expression and 47% a direct correlation. These observations provide evidence that cigarette smoking alters the DNA methylation patterning of the SAE and that, for some genes, these changes are associated with the smoking-related changes in gene expression.
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| Overall design |
Small airway epithelium DNA was assessed for genome-wide methylation using the microarray-based high resolution HpaII tiny fragment enriched by ligation-mediated PCR (HELP) assay. Small airway epithelium transcriptome was also assessed for healthy nonsmokers (n=16) and healthy smokers (n=20) with Affymetirx HG-U133 Plus 2.0 arrays
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| Contributor(s) |
Buro-Auriemma LJ, Hackett NR, Salit J, Walters MS, Strulovici-Barel Y, Staudt MR, Fuller J, Ho MW, Crystal RG |
| Citation(s) |
23842454 |
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| Submission date |
Dec 20, 2012 |
| Last update date |
Mar 25, 2019 |
| Contact name |
Yael Strulovici-Barel |
| E-mail(s) |
yas2003@med.cornell.edu
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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 (2) |
| GPL570 |
[HG-U133_Plus_2] Affymetrix Human Genome U133 Plus 2.0 Array |
| GPL16419 |
Nimblegen Human HG19_HELP array [100128_HG19_MKF_HELP_ChIP] |
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| Samples (75)
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| Relations |
| BioProject |
PRJNA184587 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE43079_RAW.tar |
1.8 Gb |
(http)(custom) |
TAR (of CEL, CHP, PAIR) |
| Processed data included within Sample table |
| Processed data provided as supplementary file |
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