Environmental factors outweigh drug-response factors at early time points in toxicogenomic experiments

抄録

The combination of microarray technology and the use of human hepatocytes for the in vitro prediction of drug toxicity promises to expedite drug discovery while at the same time delivering safer drugs to patients. To explore the suitability of cryopreserved human hepatocytes for toxicogenomic studies we treated hepatocytes from three donors with a range of model compounds and monitored their gene expression profiles using Affymetrix GeneChip technology. Plated hepatocytes were treated with acetaminophen, chlorpromazine, diclofenac, gemfibrozil, isoniazid, nitrosodimethylamine, phenobarbital, tetracycline and DMSO vehicle control. Total RNA was isolated after 1, 4 and 24 h and used to synthesize biotin-labelled cRNA. Labelled cRNA from the three donors was pooled and hybridized to an Affymetrix HG U133A GeneChip. Two replicates for each compound at each time point were performed. Differential expression analysis of the data across all treatments yielded significantly altered gene sets for the three time points studied. Principal component analysis and hierarchical clustering show that after 1 h, samples cluster according to experimental group rather than chemical treatment. Later time points suggest no group dependency as replicate samples cluster together. These results indicate that environmental factors are the prominent cause of gene expression differences at early time points in in vitro studies and as such, early time course data should be treated with caution.