Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Transcription profiling of human gastrointestinal stromal tumour is predictive of rapid response to imatinib mesylate

ABSTRACT: Gene expression profiling using oligonucleotide microarrays performed on tumor samples obtained before and after imatinib mesylate (IM) therapy. Rapid responding (to IM) samples were compared to non-responding/stable disease samples as measured by CT scan measurements to identify a gene signature that can predict rapid response to IM. Experiment Overall Design: 54 samples, 29 pre-treatment biopsy samples, 25 post-treatment/post-surgery tumor samples from Gastrointestinal Stromal Tumors

ORGANISM(S): Homo sapiens

SUBMITTER: Michael Ochs

PROVIDER: E-GEOD-15966 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Gene expression signatures and response to imatinib mesylate in gastrointestinal stromal tumor.

Rink Lori L Skorobogatko Yuliya Y Kossenkov Andrew V AV Belinsky Martin G MG Pajak Thomas T Heinrich Michael C MC Blanke Charles D CD von Mehren Margaret M Ochs Michael F MF Eisenberg Burton B Godwin Andrew K AK

Molecular cancer therapeutics 20090811 8

Despite initial efficacy of imatinib mesylate in most gastrointestinal stromal tumor (GIST) patients, many experience primary/secondary drug resistance. Therefore, clinical management of GIST may benefit from further molecular characterization of tumors before and after imatinib mesylate treatment. As part of a recent phase II trial of neoadjuvant/adjuvant imatinib mesylate treatment for advanced primary and recurrent operable GISTs (Radiation Therapy Oncology Group S0132), gene expression profi ...[more]

PMID: 19671739

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Project description:One day-old broilers (Ross/Ross, Longenecker's Hatchery, Elizabethtown, PA) were housed in Petersime starter brooder units and randomly assigned to 4 groups (5 birds/group). Carvacrol (Nature Chemicals, Hamburg, Germany) and cinnamaldehyde (Alys Technologies SA, Bussigny-près-Lausanne, Switzerland) were obtained from the compound obtained from synthesis. Crushed C. annuum fruits (Pushp Brand Spices, Munimji Foods and Spices Pvt. Ltd. Indore, India) were extracted with volatile solvents using the percolation method to obtain oleoresin. Chickens were fed for 7 days beginning from hatch with a standard diet alone (control) or with diets supplemented with carvacrol, cinnamaldehyde, or Capsicum oleoresin.<br> Following euthanization of the birds, intestines were cut longitudinally and washed three times with ice-cold Hanks? balanced salt solution (HBSS) containing 100 U/ml of penicillin and 100 mg/ml of streptomycin (Sigma, St. Louis, MO). The mucosal layer of entire intestine was carefully scraped using a surgical scalpel and intraepithelial lymphocytes (IELs) were isolated by Percoll density gradient centrifugation as previously described (Min et al. 2005). Total RNA was isolated from 5.0 x 107 cells using Trizol (Invitrogen, Carlsbad, CA) and purified using the RNeasy Mini RNA Purification Kit (Qiagen, Valencia, CA). Aminoallyl-labeled RNA from IELs was prepared using the Amino Allyl Message Amp II aRNA Amplification Kit (Ambion, Austin, TX). Two of 20 ?g aliquots of each aminoallyl-RNA sample were fluorescently labeled with AlexaFluor 555 or AlexaFluor 647 (Invitrogen) and labeled RNAs were column-purified using the RNA Amplification Kit (Ambion). RNA concentrations and labeling efficiencies were determined spectrophotometrically.<br> Hybridizations were performed using HybIt hybridization buffer (TeleChem, Sunnyvale, CA) in ArrayIt reaction cassettes at 50°C overnight as described (Kim et al., 2008). After hybridization, the slides were rinsed in 0.5 X SSC, 0.01% SDS at room temperature and washed once for 15 min in 0.2 X SSC, 0.2% SDS at 50°C, 3 times for 1 min in 0.2 X SSC at room temperature, and 3 times for 1 min in distilled water at room temperature. Each sample had a repeated hybridization using the alternate fluorescent dye between the treatment and control.

Dataset Information

Transcription profiling of human gastrointestinal stromal tumour is predictive of rapid response to imatinib mesylate

Publications

Gene expression signatures and response to imatinib mesylate in gastrointestinal stromal tumor.

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