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Series GSE32861 Query DataSets for GSE32861
Status Public on Mar 21, 2012
Title Genome-scale analysis of DNA methylation in lung adenocarcinoma and integration with mRNA expression
Organism Homo sapiens
Experiment type Methylation profiling by array
Summary Lung cancer is the leading cause of cancer death worldwide and adenocarcinoma is its most common histological subtype. Clinical and molecular evidence indicates that lung adenocarcinoma is a heterogeneous disease, which has important implications for treatment. Here we performed genome-scale DNA methylation profiling using the Illumina Infinium HumanMethylation27 platform on 59 matched lung adenocarcinoma/non-tumor lung samples, with genome-scale verification on an independent set of tissues. We identified 766 genes showing altered DNA methylation between tumors and non-tumor lung. By integrating DNA methylation and mRNA expression data, we identified 164 hypermethylated genes showing concurrent downregulation, and 57 hypomethylated genes showing increased expression. Integrated pathways analysis indicates that these genes are involved in cell differentiation, epithelial to mesenchymal transition, RAS and WNT signaling pathways and cell cycle regulation, among others. Comparison of DNA methylation profiles between lung adenocarcinomas of current and never-smokers showed modest differences, identifying only LGALS4 as significantly hypermethylated and downregulated in smokers. LGALS4, encoding a galactoside-binding protein involved in cell-cell and cell-matrix interactions, was recently shown to be a tumor-suppressor in colorectal cancer. Unsupervised analysis of the DNA methylation data identified two tumor subgroups, one of which showed increased DNA methylation and was significantly associated with KRAS mutation and to a lesser extent, with smoking. Our analysis lays the groundwork for further molecular studies of lung adenocarcinoma by providing new candidate DNA methylation biomarkers for early detection, identifying novel molecular alterations potentially involved in lung adenocarcinoma development/progression, and describing an epigenetic subgroup of lung adenocarcinoma associated with KRAS mutation.
 
Overall design 59 lung adenocarcinoma and 59 adjacent non-tumor lung tissue were macrodissected, bisulfite treated and analyzed on the Illumina Infinium HumanMethylation27K BeadChip
 
Contributor(s) Selamat SA, Laird-Offringa IA
Citation(s) 22613842
Submission date Oct 11, 2011
Last update date Jan 02, 2015
Contact name Ite Laird-Offringa
E-mail(s) ilaird@usc.edu
Phone (323) 865-0655
Fax (323) 865-0158
Organization name University of Southern California
Department Biochemistry
Lab Ite Laird-Offringa
Street address 1441 Eastlake Avenue, Suite 6420
City Los Angeles
State/province CA
ZIP/Postal code 90089
Country USA
 
Platforms (1)
GPL8490 Illumina HumanMethylation27 BeadChip (HumanMethylation27_270596_v.1.2)
Samples (118)
GSM813174 Adjacent non-tumor lung 05L12_N (methylation)
GSM813175 Lung adenocarcinoma 05L12_T (methylation)
GSM813176 Adjacent non-tumor lung 05L13_N (methylation)
This SubSeries is part of SuperSeries:
GSE32867 DNA methylation and gene expression in lung adenocarcinoma
Relations
BioProject PRJNA154391

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE32861_RAW.tar 5.8 Mb (http)(custom) TAR
GSE32861_signals.txt.gz 16.0 Mb (ftp)(http) TXT
Processed data included within Sample table
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