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SAMPLES (42)

mace:id
Technology # Array version
Species
Organ
Tissue
Physiopathology
Type
Name

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User name	Arndt Benecke
Email	arndt@ihes.fr
Phone / Fax number	+33160926665 / +33160926609
Location	Institut des Hautes Etudes Scientifiques (Integrative Biology) - 35, route de Chartres - 91440 Bures sur Yvette, France

Scientific description

A promising treatment for patients with advanced colorectal cancer is preoperative radiochemotherapy. The early side effects of this treatment have been considered to be acceptable. The aim of this study was to identify the effects of preoperative radiochemotherapy (PRT) on gene expression in tumour and normal colon rectal tissue form the same patients, before and after PRT. For that purpose, tissue samples from ten patients with operable rectal adenocarcinomas were collected for use in whole genomeâ€“microarray based gene expression analysis. A factorial experimental design allowed us to look solely at the radiation effect on tumours. This resulted in 4496 differentially expressed genes in tumour tissue with p<0.05. In addition to known markers for radiochemotherapy, a Gene Set Enrichment Analysis (GSEA) showed a significant enrichment in gene sets associated with cell adhesion and leukocyte transendothelial migration (TEM). We conclude that radiochemotherapy has a greater effect in tumour tissue gene expression than normal tissue. Not only is the effect on normal tissue limited compared to tumour, but significantly different gene sets are enriched. The profound change of cell adhesion molecule expression in tumour tissue could either increase the risk of metastasis, or decrease the tumours invasive potential. Further characterization of genes involved in cell adhesion and leukocyte TEM may give new insights into the molecular responses to radiochemotherapy in colorectal cancer.

Technical description

Sample type 	RNA
  	
Source Name 	colon rectum
Organism(s) 	Homo sapiens
Characteristics 	tissue: normal / tumour tissue
treatment: non-irradiated / irrediated
Treatment protocol 	Each patient received 50 Gy (delivered as fractions of 2 Gy 25 times) during 5 weeks. In addition, patients received Capecitabine (XelodaÂ®, Roche) 2500 mg/ml daily during the whole period. Resection of the rectum was performed four to six weeks after preoperative radiation therapy.
Growth protocol 	The patient group for this study consisted of 10 patients with an operable adenocarcinoma of the rectum. Tissue specimens were taken form both normal and tumor tissue of the rectum before and after therapy and were kept in RNA storage buffer (RNA stabilization reagent, Qiagen GMBH, Germany) and stored at -70Â°C prior to downstream analyses.
Extracted molecule 	total RNA
Extraction protocol 	Disruption and homogenization of tissue specimens were performed in lysis buffer using the MagNa Lyser Instrument (Roche Applied Science, Germany) and according to the manufacturerâ€™s protocol. Subsequently, total RNA was isolated with the MagNa Pure Compact Instrument and the MagNa Pure Compact RNA Isolation Kit (Roche Applied Science, Germany) as previously described (Paulssen et al. 2006). RNA was quantified by measuring absorbance at 260 nm, and RNA purity was determined by the ratios OD260nm/280nm and OD230/280nm using the NanoDrop instrument (NanoDropÂ® ND-1000, Wilmington, USA). The RNA integrity was determined by electrophoresis using the BioRad Experion Bioanalyzer (Data not shown). RNA samples with 16S/28S ratios of >1.4 were used for further analysis.
Label 	DIG
Label protocol 	Total RNA samples were processed into digoxigenin (DIG)- labelled cRNA using the Applied Biosystems Chemiluminescent NanoAmp RT-IVT Labeling Kit (Applied Biosystems Inc., USA) and as described in the manufacturer's protocol.
  	
Hybridization protocol 	Ten micrograms of labelled DIG-cRNA was injected into each microarray hybridization chamber, hybridized at 55ï‚°C for 16 hours, and visualized using the Applied Biosystems Chemiluniescence Detection Kit and as decribed bu the manufacturer's protocol.
Scan protocol 	The signals were detected by the Applied Biosystems 1700 Chemiluninescent Microarray Analyzer. The Human Genome Survey Microarray v.2.0 (Applied Biosystems Inc., USA) with 32,878 probes for the interrogation of 29,098 genes was used for microarray analysis.
Description 	colon tumour rep1
Data processing 	The features were extracted from the arrays using the ABI1700 software. Normalization was carried out using quantile normalization (Bolstad et al. 2003). For the purpose of finding differentially expressed genes, we applied an empirical Bayes analysis using the LIMMA package (Smyth 2004), and significance was determined at the 0.05 level corrected for false discovery rate (FDR) using the Benjamini-Hochberg method (Benjamini & Hochberg 1995). Principal component analysis (PCA) and Partial least squares (PLS) and were carried out on the data in order to visualize the data structure and look for potential outlier samples (Gidsehaug et al. 2004).

References

Paulssen RH, Fenton CG, Snipstad K, KjÃ¦ve J, Anderssen E
Submission date 	Apr 22, 2009
Contact name 	Ruth Hracky Paulssen
E-mail(s) 	ruthp@fagmed.uit.no
Phone 	+47 77645480
Fax 	+47 77644650
URL 	http://www.unn.no/labforum
Organization name 	Universitetet i TromsÃ¸
Department 	Institute of Clinical Medicine
Lab 	Molecular Medical Research
Street address 	MH-Bygget Breivika
City 	TromsÃ¸
ZIP/Postal code 	N-9037
Country 	Norway

Pubmed : http://www.ncbi.nlm.nih.gov/pubmed/19969511

This dataset has previously been published on NCBI/GEO with accession no.: GSE15781