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Series GSE32863 Query DataSets for GSE32863
Status Public on Mar 21, 2012
Title Gene expression analysis of lung adenocarcinoma and matched adjacent non-tumor lung tissue
Organism Homo sapiens
Experiment type Expression profiling by array
Summary Gene expression profiling of 60 lung adenocarcinoma tumors and their matched histologically normal adjacent lung tissue samples were analyzed using Illumina HumanWG-6 v3.0 expression beadchip. We integrated these data with DNA methylation profiles of the same samples to identify potential DNA methylation regulated genes.
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 58 lung adenocarcinoma and 58 adjacent non-tumor lung fresh frozen tissues were macrodissected, and total RNA was isolated to be analyzed using the Illumina HumanWG-6 v3.0 expression beadchip.
 
Contributor(s) Selamat SA, Gazdar AF, Laird-Offringa IA
Citation(s) 22613842
Submission date Oct 11, 2011
Last update date Feb 18, 2019
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)
GPL6884 Illumina HumanWG-6 v3.0 expression beadchip
Samples (116)
GSM813411 Adjacent non-tumor lung tissue 05L12_N (expression)
GSM813412 Lung adenocarcinoma 05L12_T (expression)
GSM813413 Adjacent non-tumor lung tissue 05L13_N (expression)
This SubSeries is part of SuperSeries:
GSE32867 DNA methylation and gene expression in lung adenocarcinoma
Relations
BioProject PRJNA154393

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
GSE32863_RAW.tar 6.3 Mb (http)(custom) TAR
GSE32863_non-normalized.txt.gz 34.8 Mb (ftp)(http) TXT
Processed data included within Sample table

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