Profiling of Gene Expression in Rat Liver and Rat Primary Cultured Hepatocytes Treated With Peroxisome Proliferators

Abstract

-The Toxicogenomics project has been constructing a large-scale database of about 150 compounds exposed to rat (single dose, 3, 6, 9, 24 hrs and repeated dose for 3, 7, 14 28 days with 3 dose levels) and rat hepatocytes (2, 8, 24 hr with 3 concentrations) and data of transcriptome in liver using GeneChip, and the related toxicological measures are being accumulated. In the present study, the data of three ligands of peroxisome proliferator activated receptor α (PPARα), i.e., clofibrate, WY-14643 and gemfibrozil in our database were analyzed. Many of the β-oxidation-related genes were commonly induced in vivo and in vitro, whereas expression changes in genes related to cell proliferation, apoptosis, were detected in vivo (single and repeated dose) but not in vitro. Changes in those related to the immune response, coagulation and the stress response were also detectable exclusively in vivo. Using the genes mobilized in two or three PPARα agonists, hierarchical clustering was performed on 32 compounds stored in our database. In the profiling of an in vivo single dose, benzbromarone and aspirin were located in the same cluster of the three PPARα agonists. The clustering of in vitro data revealed that benzbromarone, three NSAIDs (aspirin, indomethacin and diclofenac sodium) and valproic acid belonged to the same cluster of PPARα agonists, supporting the reports that benzbromarone,valproic acid and some NSAIDs were reported to be PPARα agonists. Using the genes commonly up-regulated both in vivo and in vitro, principal component analysis was performed in 32 compounds, and principal component 1 was found to be the convenient parameter to extract PPARα agonist-like compounds from the database.

Peroxisome Proliferator-activated Receptor (PPAR) Gene Profiling Uncovers Insulin-like Growth Factor-1 as a PPARα Target Gene in Cardioprotection

“…Microarray profiling and genome wide identification of PPREs by stimulation with isoform-selective synthetic ligands have suggested the existence of a considerable number of PPAR-regulated genes, which have not previously been described as PPAR target genes (32,33). Although useful, selective activation of PPAR isoforms by their synthetic ligands is seriously hampered by their overlapping specificity (34).…”

Transcriptome analyses demonstrate that Peroxisome Proliferator-Activated Receptor α (PPARα) activity of an ultraviolet absorber, 2-(2’-hydroxy-3’,5’-di-tert-butylphenyl)benzotriazole, as possible mechanism of their toxicity and the gender differences

“…We focused on 41 genes previously reported to have been altered by representative PPARα ligands in common both in vivo and in vitro (Tamura et al, 2006). Almost of these 41 genes are known as PPAR target genes and including genes have peroxisome proliferator response element (PPRE) on the promoter region, such as Cyp4a1 (cytochrome P450 a1), Acot2 (Acyl-CoA Thioesterase 2), Ech1(the enoylCoA hydratase) and Acaa1(3-oxoacyl-CoA thiolase).…”

“…Surprisingly, the degree of upregulation equaled or surpassed that in the 100 mg/kg clofibrate representative PPARα ligands. Forty-one genes (probesets) that were affected by representative PPARα ligands both in vitro and in vivo were selected as targets (Tamura et al, 2006). Gene expression data for the PPARα ligands were downloaded from the Open Toxicogenomics Project-Genomics Assisted Toxicity Evaluation system (TG GATEs, http://toxico.nibio.…”

“…Toxicogenomics, is a powerful tool for collecting expression changes of a large number of genes simultaneously and thus it is quite suitable for screening of potential activation of nuclear receptors by compared with reference database. It has been reported that gene expression profiling revealed the specific changes through PPARα in both in vivo and in vitro (Tamura et al, 2006).…”

Evaluation of DNA microarray results in the Toxicogenomics Project (TGP) consortium in Japan

“…The purpose of TGP2 was to identify biomarkers for diagnosing and/or predicting compound toxicity based upon the gene expression data accumulated in TGP1. A number of biomarkers and gene expression profiles indicative of exposure to particular toxic compounds were reported following the TGP1 and TGP2 studies (Kiyosawa et al, 2006;Morishita et al, 2006;Tamura et al, 2006aTamura et al, , 2006bKiyosawa et al, 2007;Omura et al, 2007;Hirode et al, 2008Hirode et al, , 2009aHirode et al, and 2009bUehara et al, 2008aUehara et al, , 2008bUehara et al, and 2008cKondo et al, 2009;Minowa et al, 2012). Prior to use of the gene expression data accumulated during TGP1 in future drug discovery studies, the procedures used to analyze gene expression must be validated and the degree of inter-laboratory variation must be assessed.…”