Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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ADAM-28: A potential oncogene involved in asbestos-related lung adenocarcinomas

ABSTRACT: To identify gene expression biomarkers associated with asbestos-related lung adenocarcinoma, we analyzed primary tumour gene expression for a total of 36 primary lung adenocarcinomas on 22,323 element microarrays, comparing 12 patients with lung asbestos body counts above levels associated with urban dwelling (ARLC-AC: asbestos-related lung cancer-adenocarcinoma) with 24 patients with no asbestos bodies (NARLC-AC: non-asbestos related lung cancer-adenocarcinoma). To identify gene expression biomarkers associated with asbestos-related lung tumorigenicity, we performed gene expression array analysis on tumours of 36 patients with primary lung adenocarcinoma, comparing twelve patients with lung asbestos body counts above levels associated with urban dwelling (ARLC-AC: asbestos-related lung cancer-adenocarcinoma) with twenty-four patients with no asbestos bodies (NARLC-AC: non-asbestos related lung cancer-adenocarcinoma). Synthesis of the labelled first strand cDNA was conducted using Amersham CyScribe Post-Labelling kit with starting material of 20 ug of total RNA. The amino-allyl labeled dNTP mix was added to the reaction to generate amino-allyl labelled second strand cDNA. Following the hydrolysis reaction, single-stranded cDNA probes were purified using Amersham GFX columns. Dye coupling reactions were performed by mixing the cDNA samples with Amersham Cy3 (reference) or Cy5 (tumour) and incubating in the dark. The reactions were purified with Amersham GFX columns to remove the unincorporated/quenched dyes. After the purification samples were combined for hybridization, the labeled cDNAs were co-hybridized to 22K oligo microarrays. Slides were scanned on GMS418 confocal scanner (Agilent). Genes differentially expressed between ARLC-AC and NARLC-AC were identified on fold change and P-value, and then prioritised using gene ontology.

ORGANISM(S): Homo sapiens

SUBMITTER: Jill Larsen

PROVIDER: E-GEOD-20875 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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ADAM28: a potential oncogene involved in asbestos-related lung adenocarcinomas.

Wright Casey M CM Larsen Jill E JE Hayward Nicholas K NK Martins Maria U MU Tan Maxine E ME Davidson Morgan R MR Savarimuthu Santiyagu M SM McLachlan Rebecca E RE Passmore Linda H LH Windsor Morgan N MN Clarke Belinda E BE Duhig Edwina E EE Yang Ian A IA Bowman Rayleen V RV Fong Kwun M KM

Genes, chromosomes & cancer 20100801 8

Asbestos-related lung cancer accounts for 4-12% of all lung cancers worldwide. Since putative mechanisms of carcinogenesis differ between asbestos and tobacco induced lung cancers, tumors induced by the two agents may be genetically distinct. To identify gene expression biomarkers associated with asbestos-related lung tumorigenicity we performed gene expression array analysis on tumors of 36 patients with primary lung adenocarcinoma, comparing 12 patients with lung asbestos body counts above lev ...[more]

PMID: 20544843

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Project description:This series repressents the data set from the paper "Expression microarray analysis and oligo array CGH of aquired gemcitabine resistance in mouse colon reveals selection for chromosomal aberrations". Biological material: One solid mouse tumor "Colon 26A" was routinely maintained by successive transplantation. A subset of mice with this tumor was treated at the maximum tolerable dosage of Gemcitabine and successively transplanted 5 times and similarly treated. The last passage was completly resistant and designated, "Colon 26G". Expression array: Total RNA was isolated from frozen mouse tumors using Tryzol. Single stranded cDNA was synthetized from 30 mg of total RNA by reverse transcription using aminoallyl labeled dUTP (Ambion). Labelling was performed according to the aminoallyl labeling protocol. Briefly, cDNA was incubated at room temperature for 1 h with fluorolink monofunctional cy5 or cy3 (Amersham) followed by 15 min 4 M hydroxylamine treatment. Uncoupled dyes were removed using Qiaquick PCR purification columns (Qiagen) and mixed with 12 mg poly(dA) (Amersham), 60 mg yeast tRNA (Sigma) and 24 mg Cot-1 DNA (Invitroen). The probe was dissolved in 127 ml hybridization mixture containing 46% formamide, 9.5% dextran sulfate, 2x SSC and 0.2% SDS. The probe was heated to 70Â°C for 10 min and annealed at 37Â°C for 1 h. Slides were hybridized for 14 h at 37Â°C over-night (HyArray 12â¢, Perkin Elmer). After hybridization the slides were washed in the HybArray 12â¢ with 50% formamide, 2x SSC, pH 7 at 35Â°C for 15 min, followed b PI buffer (0.1 M sodium phosphate, 0.1% Igepal Ca630, pH 8) at room temperature and 3 washes of 0.2x SSC, 0.1x SSC and 0.01x SSC at room temperature followed by centrifugation. Arrays were scanned using a laser scanner (ScanArray Express, Perkin Elmer) and analysed using ImaGene version 5.6. Cy5 cy3 ratios are calculating by taking the log2 of the signal mean of each spot minus the median background mean of all spots on the array. This is followed by a standard normalization for spot intensity and calculation of the ratios.

Dataset Information

ADAM-28: A potential oncogene involved in asbestos-related lung adenocarcinomas

Publications

ADAM28: a potential oncogene involved in asbestos-related lung adenocarcinomas.

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