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Series GSE56044 Query DataSets for GSE56044
Status Public on Oct 05, 2014
Title Genome-wide DNA methylation analysis of lung carcinoma
Organism Homo sapiens
Experiment type Methylation profiling by genome tiling array
Summary Lung cancer is the worldwide leading cause of death from cancer. DNA methylation in gene promoter regions is a major mechanism of gene expression regulation that may promote tumorigenesis. However, whether clinically relevant subgroups based on DNA methylation patterns exist in lung cancer is not well studied.

We performed whole-genome methylation analysis using 450K Illumina BeadArrays on 124 tumors including 83 adenocarcinomas, 23 squamous cell carcinomas, one adenosquamous cancer, five large cell carcinomas, nine large cell neuroendocrine carcinomas (LCNEC), three small cell carcinomas (SCLC) and 12 normal lung tissues. Unsupervised class discovery was performed to identify DNA methylation subgroups with clinicopathological and molecular features. Subgroups were validated in two independent NSCLC cohorts.

Unsupervised analysis identified five DNA methylation subgroups (epitypes). One epitype was distinctly associated with neuroendocrine tumors (LCNEC and SCLC). For adenocarcinoma, in both discovery and validation cohorts, remaining four epitypes were associated with differences in clinicopathological and molecular features, including global hypomethylation, promoter hypermethylation, copy number alterations, expression of proliferation-associated genes, association with unsupervised and supervised gene expression phenotypes, KRAS, TP53, KEAP1, SMARCA4, and STK11 mutations, smoking history, and patient outcome.

Based on a multicohort approach we conducted a comprehensive survey of genome-wide DNA methylation in lung cancer, identifying a distinct neuroendocrine epitype and four adenocarcinoma epitypes associated with molecular and clinicopathological characteristics, and patient outcome. Our results bring further understanding of the epigenetic characteristics and molecular diversity in lung cancer generally and in adenocarcinoma specifically.

Overall design Genome-wide DNA methylation analysis of 124 lung carcinomas and 12 normal lung tissues using Illumina Human Methylation 450K v1.0 Beadchips.
Contributor(s) Karlsson A, Jönsson M, Lauss M, Brunnström H, Jönsson P, Jönsson G, Ringner M, Planck M, Staaf J
Citation(s) 25278450
Submission date Mar 19, 2014
Last update date Mar 22, 2019
Contact name Johan Staaf
Organization name SCIBLU - Swegene Centre for Integrative Biology at Lund University
Street address Medicon Village
City Lund
ZIP/Postal code SE-223 81
Country Sweden
Platforms (1)
GPL13534 Illumina HumanMethylation450 BeadChip (HumanMethylation450_15017482)
Samples (136)
GSM1351866 LU2
GSM1351867 LU14
GSM1351868 LU16
This SubSeries is part of SuperSeries:
GSE60645 Genome-wide DNA methylation and expression analysis of lung carcinoma
BioProject PRJNA242349

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
GSE56044_GEO_Annotations.xls.gz 20.1 Kb (ftp)(http) XLS
GSE56044_RAW.tar 183.1 Mb (http)(custom) TAR
GSE56044_methylation_raw.txt.gz 832.9 Mb (ftp)(http) TXT
Processed data included within Sample table

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