TRANSCRIPTOME 2002: From Functional Genomics to Systems Biology
March 10-13, 2002
Seattle, Washington, USA


From Human Tissue Samples to Transcriptome Analysis : How to Obtain High Quality RNA

Virginie Copois1, Frédéric Bibeau2, Patrick Chalbos2, Sandrine Imbeaud3, Carmella Cappellano4, Marc Ychou2, Charles Auffray3, Emmanuel Conseiller4, Bernard Pau1, Maguy Del Rio1, 1Institut de Biotechnologie et Pharmacologie, Montpellier, FRANCE;  2CRLCC Val D'Aurelle, Centre Paul Lamarque, Montpellier, FRANCE; 3Genexpress, FRANCE; 4Aventis Pharma, Oncology Genomics, Vitry sur Seine, FRANCE

Chemotherapeutic drug resistance is a major clinical problem and a frequent cause of treatment failure. The aim of our work is to identify cellular targets responsible for the resistance to anti-cancer drugs used in colorectal cancer treatment. For the analysis of gene expression profiles of patients suffering from colorectal carcinoma by microarray technology, we had to obtain high quality RNA from the tumor tissue samples. Indeed, the quality of data from microarrays is strongly related to the quality of the extracted RNA. We analyzed the importance of several factors susceptible to influence the integrity of RNA within the tissues. Among those, ischemia appeared to be of critical importance. We recorded the time between surgical extirpation of human tissues and storage of 84 samples from colorectal adenocarcinoma or liver metastasis. Total RNA was extracted from those samples and controlled on RNA 6000 LabChips® demonstrating that RNA was damaged after 30 min of ischemia. Furthermore, we showed that other factors like necrosis might be involved in the degradation of RNA pointing out that macroscopic and microscopic controls of the lesion by a pathologist is essential. A strictly protocoled monitoring of samples allowed us to obtain high quality RNA for transcriptome exploration as confirmed by different analyses.

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