Treatment with drugs can alter tumour gene expression. We are interested in using DNA array approaches to examine alterations in the pattern of gene expression following chemotherapeutic treatment and have used this technology to analyse gene expression in tumours before and during treatment with DNA-damaging agents or signal-transduction inhibitors (see accompanying abstract by Workman et al.). The aim of this strategy was to profile constitutive gene expression and identify drug-responsive genes that may have potential as surrogate markers for drug action or future targets for drug development. To apply the technology to the clinical situation, tumour biopsies were obtained from patients with inoperable bowel cancer. These patients were enrolled in a clinical study examining the utility of a chemotherapeutic regime to reduce tumour volume sufficiently for surgical resection. This regime consists of a single dose of mitomycin C and a protracted venous infusion (PVI) of 5-fluorouracil (5-FU). On evidence of reduced tumour volume, the patients undergo further treatment and the remaining tumour is removed by surgical resection. Diagnostic tumour biopsies were taken by endoscopy before treatment and subsequent biopsies were taken 6 weeks into the treatment with 5-FU. A small portion of each biopsy was set aside for gene expression analysis. Poly(A)+ mRNA was extracted from the biopsy and radiolabelled by reverse transcription from oligodT primers in the presence of [a33P]dATP. Labelled single-strand cDNA was hybridized to commercially available arrays containing IMAGE/LLNL cDNAs and the data collected by phosphorimaging. Good reproducibility was obtained between experiments and changes in gene expression during treatment were detected. These included increased expression of thymidylate synthetase and uracil DNA glycosylase, consistent with treatment of 5-FU. Additional data profiling constitutive gene expression and expression in response to treatment will be presented.