Homo sapiens
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA154393 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:This SuperSeries is composed of the following subset Series: GSE32861: Genome-scale analysis of DNA methylation in lung adenocarcinoma and integration with mRNA expression GSE32863: Gene expression analysis of lung adenocarcinoma and matched adjacent non-tumor lung tissue GSE32866: Genome-scale DNA methylation profiling of lung adenocarcinoma: validation using Ontario Tumor Bank samples Refer to individual Series
2012-03-21 | E-GEOD-32867 | biostudies-arrayexpress
Project description:Gene expression analysis of lung adenocarcinoma and adjacent non-tumor tissues
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Project description:DNA methylation analysis of lung adenocarcinoma and adjacent non-tumor tissues
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Project description: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. 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.
2012-03-21 | E-GEOD-32863 | biostudies-arrayexpress
Project description:Expression profiling of 83 matched pairs of lung adenocarcinomas and non-malignant adjacent tissue
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Project description:Gene expression analysis of colorectal tumors and matched adjacent non-tumor colorectal tissues.
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Project description:Gene expression profile of stage I lung adenocarcinoma and matched multi-site non-tumor lung samples
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Project description:41 lung adenocarcinoma from never-smokers hybridized on Illumina SNP arrays on 13 HumanCNV370-Quadv3 chips. High-resolution array comparative genomic hybridization analysis of lung adenocarcinoma in 41 never smokers for identification of new minimal common regions (MCR) of gain or loss. The SNP array analysis validated copy-number aberrations and revealed that RB1 and WRN were altered by recurrent copy-neutral loss of heterozygosity.The present study has uncovered new aberrations containing cancer genes. The oncogene FUS is a candidate gene in the 16p region that is frequently gained in never smokers. Multiple genetic pathways defined by gains of MYC, deletions of RB1 and WRN or gains on 7p and 7q are involved in lung adenocarcinoma in never smokers. A 'Cartes d'Identite des Tumeurs' (CIT) project from the French National League Against Cancer (http://cit.ligue-cancer.net) 41 samples hybridized on Illumina SNP arrays. Submitter : Fabien PETEL petelf@ligue-cancer.net . Project leader : Pr Pierre FOURET pierre.fouret@psl.aphp.fr
2011-07-28 | E-TABM-1169 | biostudies-arrayexpress
Project description:The independent population of lung adenocarcinoma and adjacent non-tumor lung used for verification of the EDRN/Canary Foundation study 28 lung adenocarcinoma and 27 adjacent non-tumor lung fresh frozen tissues were macrodissected, bisulfite treated and analyzed on the Illumina Infinium HumanMethylation27K BeadChip
2012-03-21 | E-GEOD-32866 | biostudies-arrayexpress
Project description:Genome wide gene expression profiling of lung adenocarcinoma and non-tumor adjacent tissues. The Agilent microarray was used to obtain gene expression profiles. Samples included eight lung cancer and adjacent non-tumor tissues excised from a cohort of 8 patients with lung adenocarcinoma.
2017-03-09 | GSE85841 | GEO