title: Optimal sampling of rat liver tissue for toxicogenomic studies.
abstract: Different degrees of a toxic response between and within the various lobes of the liver have been observed in rodents following treatment with acetaminophen. This study was designed to compare 2 sampling methods of the rat liver for gene-expression analysis. Ten male Fischer 344/N rats, 12-14 weeks of age, were treated with vehicle (0.5% aqueous ethyl cellulose) or acetaminophen (APAP, 1500 mg/kg) and sacrificed 24 hours following dose administration. Two representative sections were collected from the left liver lobe, stained with hematoxylin and eosin (H&E), and evaluated independently by 2 pathologists. The central core of the left lobe was cubed and frozen. Five random cubes were conserved, while the remaining left lobe core was pulverized. From each of the 10 animals, 2 random cubes and 2 samples from the homogeneous, pulverized samples were prepared for microarray analysis. Histopathologic evaluation revealed a variable response of centrilobular necrosis within the left lobe. Multiple methods used to analyze the microarray data indicated that sampling technique was not a major contributor to the variability observed in the gene expression data; however, only the powdered samples clustered for all animals, even those with disparate histopathologic results. Additionally, a powdered sample provided the advantages of a homogenous sample pool and the ability to use sample aliquots for other analyses to include proteomics, metabonomics, and other molecular techniques.
authors.affiliation: Laboratory of Experimental Pathology, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina 27709, USA. foley1@niehs.nih.gov
authors.forename: Julie F
authors.initials: JF
authors.lastname: Foley
authors.forename: Jennifer B
authors.initials: JB
authors.lastname: Collins
authors.forename: David M
authors.initials: DM
authors.lastname: Umbach
authors.forename: Sherry
authors.initials: S
authors.lastname: Grissom
authors.forename: Gary A
authors.initials: GA
authors.lastname: Boorman
authors.forename: Alexandra N
authors.initials: AN
authors.lastname: Heinloth
mesh_terms: D000082:Acetaminophen / Q000633:toxicity*; D018712:Analgesics, Non-Narcotic / Q000633:toxicity; D000704:Analysis of Variance; D000818:Animals; D016000:Cluster Analysis; D020869:Gene Expression Profiling; D005786:Gene Expression Regulation / Q000187:drug effects; D008099:Liver / Q000187:drug effects* / Q000473:pathology; D008297:Male; D020411:Oligonucleotide Array Sequence Analysis; D025341:Principal Component Analysis; D051381:Rats; D011916:Rats, Inbred F344; D015203:Reproducibility of Results; D015983:Selection Bias; D013048:Specimen Handling / Q000379:methods*; D043922:Toxicogenetics / Q000379:methods
chemical_list: D018712:Analgesics, Non-Narcotic; D000082:Acetaminophen