title: Use of toxicogenomics for identifying genetic markers of pulmonary oedema.
abstract: This study was undertaken primarily to identify genetic markers of oedema and inflammation. Mild pulmonary injury was induced following the instillation of the oedema-producing agent, bleomycin (0.5 units). Oedema was then confirmed by conventional toxicology (lavage protein levels, free cell counts and lung/body weight ratios) and histology 3 days post-bleomycin instillation. The expression profile of 1176 mRNA species was determined for bleomycin-exposed lung (Clontech Atlas macroarray, n=9). To obtain pertinent results from these data, it was necessary to develop a simple, effective method for bioinformatic analysis of altered gene expression. Data were log10 transformed followed by global normalisation. Differential gene expression was accepted if: (a) genes were statistically significant (P < or = 0.05) from a two-tailed t test; (b) genes were consistently outside a two standard deviation (SD) range from control levels. A combination of these techniques identified 31 mRNA transcripts (approximately 3%) which were significantly altered in bleomycin treated tissue. Of these genes, 26 were down-regulated whilst only five were up-regulated. Two distinct clusters were identified, with 17 genes classified as encoding hormone receptors, and nine as encoding ion channels. Both these clusters were consistently down-regulated. The magnitude of the changes in gene expression were quantified and confirmed by Q-PCR (n = 6), validating the macroarray data and the bioinformatic analysis employed. In conclusion, this study has developed a suitable macroarray analysis procedure and provides the basis for a better understanding of the gene expression changes occurring during the early phase of drug-induced pulmonary oedema. This work has been presented orally, in part at the British Association for Lung Research Summer Meeting, University of Brighton, 3-5 September, 2003 and in full at the British Toxicology Society Annual Congress, Heriot Watt University, Edinburgh, 21-24 April 2004.
authors.affiliation: Cardiff School of Biosciences, Cardiff University, Museum Avenue, Cardiff, CF10 3US, United Kingdom. balharry@cf.ac.uk
authors.forename: Dominique
authors.initials: D
authors.lastname: Balharry
authors.forename: Victor
authors.initials: V
authors.lastname: Oreffo
authors.forename: Roy
authors.initials: R
authors.lastname: Richards
mesh_terms: D000818:Animals; D001761:Bleomycin / Q000008:administration & dosage / Q000009:adverse effects / Q000493:pharmacokinetics; D001992:Bronchoalveolar Lavage Fluid / Q000737:chemistry / Q000166:cytology; D015536:Down-Regulation; D020869:Gene Expression Profiling / Q000379:methods; D005819:Genetic Markers; D007249:Inflammation / Q000139:chemically induced / Q000175:diagnosis / Q000235:genetics; D018836:Inflammation Mediators; D008168:Lung / Q000187:drug effects / Q000473:pathology; D016676:Macrophages, Alveolar / Q000187:drug effects / Q000473:pathology; D008297:Male; D005810:Multigene Family / Q000187:drug effects / Q000502:physiology; D009929:Organ Size / Q000187:drug effects; D011654:Pulmonary Edema / Q000139:chemically induced / Q000235:genetics* / Q000473:pathology; D051381:Rats; D017207:Rats, Sprague-Dawley; D020133:Reverse Transcriptase Polymerase Chain Reaction / Q000379:methods; D013047:Specific Pathogen-Free Organisms; D013997:Time Factors; D043922:Toxicogenetics / Q000379:methods*; D014158:Transcription, Genetic; D015854:Up-Regulation / Q000187:drug effects / Q000502:physiology; D015430:Weight Gain / Q000187:drug effects
chemical_list: D005819:Genetic Markers; D018836:Inflammation Mediators; D001761:Bleomycin