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Corton JC, Ledbetter V, Cohen SM, Atlas E, Yauk CL, Liu J. A transcriptomic biomarker predictive of cell proliferation for use in adverse outcome pathway-informed testing and assessment. Toxicol Sci 2024; 201:174-189. [PMID: 39137154 DOI: 10.1093/toxsci/kfae102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/15/2024] Open
Abstract
High-throughput transcriptomics (HTTr) is increasingly being used to identify molecular targets of chemicals that can be linked to adverse outcomes. Cell proliferation (CP) is an important key event in chemical carcinogenesis. Here, we describe the construction and characterization of a gene expression biomarker that is predictive of the CP status in human and rodent tissues. The biomarker was constructed from 30 genes known to be increased in expression in prostate cancers relative to surrounding tissues and in cycling human MCF-7 cells after estrogen receptor (ER) agonist exposure. Using a large compendium of gene expression profiles to test utility, the biomarker could identify increases in CP in (i) 308 out of 367 tumor vs. normal surrounding tissue comparisons from 6 human organs, (ii) MCF-7 cells after activation of ER, (iii) after partial hepatectomy in mice and rats, and (iv) the livers of mice and rats after exposure to nongenotoxic hepatocarcinogens. The biomarker identified suppression of CP (i) under conditions of p53 activation by DNA damaging agents in human cells, (ii) in human A549 lung cells exposed to therapeutic anticancer kinase inhibitors (dasatinib, nilotnib), and (iii) in the mouse liver when comparing high levels of CP at birth to the low background levels in the adult. The responses using the biomarker were similar to those observed using conventional markers of CP including PCNA, Ki67, and BrdU labeling. The CP biomarker will be a useful tool for interpretation of HTTr data streams to identify CP status after exposure to chemicals in human cells or in rodent tissues.
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Affiliation(s)
- J Christopher Corton
- Center for Computational Toxicology and Exposure, US Environmental Protection Agency, Research Triangle Park, NC 27711, United States
| | - Victoria Ledbetter
- Center for Computational Toxicology and Exposure, US Environmental Protection Agency, Research Triangle Park, NC 27711, United States
| | - Samuel M Cohen
- Department of Pathology and Microbiology and Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 69198-3135, United States
| | - Ella Atlas
- Environmental Health Science and Research Bureau, Healthy Environments and Consumer Safety Branch (HECSB) Health Canada, Ottawa, ON K2K 0K9, Canada
| | - Carole L Yauk
- Department of Biology, University of Ottawa, Ottawa, ON, Canada
| | - Jie Liu
- Center for Computational Toxicology and Exposure, US Environmental Protection Agency, Research Triangle Park, NC 27711, United States
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Alvergnas M, Richert L, Blanchard N, Abadie C, Heyd B, Mantion G, Gallemann D, Martin H. Regulation of CYP4A expression by bezafibrate in primary culture of rat and human hepatocytes: interspecies difference and influence of N-acetylcysteine. Toxicol In Vitro 2009; 23:1259-67. [PMID: 19647067 DOI: 10.1016/j.tiv.2009.07.027] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2008] [Revised: 07/23/2009] [Accepted: 07/24/2009] [Indexed: 10/20/2022]
Abstract
The effects of fibrates on cytochrome P450 4A (CYP4A) expression have not been clearly evaluated in human hepatocytes, human being reported as a non-responsive species. We have evaluated the effects of clofibrate, bezafibrate (BEZA), WY-14643, nafenopin and ciprofibrate at the concentration of 250 microM on CYP4A expression in primary cultures of rat and human hepatocytes. BEZA greatly induced mRNA expression in both species. Eight out of 10 human cultures responded to BEZA 250 microM. CYP4A-dependent activity was increased in rat, but not in human hepatocytes. The antioxidant N-acetylcysteine (Nac) enhanced the inducing effect of BEZA on mRNA expression, this potentialization being higher in human compared to rat hepatocytes. By contrast, Nac decreased the inducing effect of BEZA on CYP4A-dependent activity in rat and had either no effect or decreased the activity in BEZA-treated human hepatocytes. In conclusion, the cellular environment appears as an important parameter to take into account when studying CYP4A induction and could partly explain interspecies differences in the complex regulation of CYP4A expression.
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Affiliation(s)
- M Alvergnas
- Laboratoire de Toxicologie Cellulaire, EA 4267, UFR des Sciences Médicales et Pharmaceutiques, 25030 Besançon cedex, France
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Trapp C, Schwarz M, Epe B. The Peroxisome Proliferator WY-14,643 Promotes Hepatocarcinogenesis Caused by Endogenously Generated Oxidative DNA Base Modifications in Repair-Deficient Csbm/m/Ogg1−/− Mice. Cancer Res 2007; 67:5156-61. [PMID: 17545594 DOI: 10.1158/0008-5472.can-07-0335] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Basal levels of endogenously generated oxidative DNA modifications such as 7,8-dihydro-8-oxoguanine (8-oxoG) are present in apparently all mammalian cells, but their relevance for the generation of spontaneous cancers remains to be established. Both the 8-oxoG levels and the resulting spontaneous mutations are increased in the livers of Csb(m/m)/Ogg1(-/-) mice, which are deficient in the repair of 8-oxoG. In order to determine the consequences of these additional oxidative DNA modifications and mutations and thus assess the tumor initiating potency of this type of endogenous DNA damage, we treated Csb(m/m)/Ogg1(-/-) mice and repair-proficient controls with the peroxisome proliferator WY-14,643 (0.025% ad libitum), a potent inducer of liver cell proliferation. The treatment did not generate any additional oxidative DNA damage; the elevated levels of 8-oxoG in the Csb(m/m)/Ogg1(-/-) mice even decreased. Also, the spontaneous mutation frequencies observed in the lacI gene of BigBlue Csb(m/m)/Ogg1(-/-) mice, which were approximately 3-fold higher than in the repair-proficient mice, declined by 39% under the treatment, whereas the frequencies in the livers of the repair-proficient animals remained unchanged. Preneoplastic lesions (staining positive or negative for glucose-6-phoshatase) developed in the livers of both wild-type and Csb(m/m)/Ogg1(-/-) mice after 30 weeks. Both the numbers and the total volumes of the lesions were approximately 6-fold higher in the repair-deficient mice than in the wild-type mice. The results indicate that spontaneous mutations generated from endogenous oxidative DNA base damage efficiently translate into increased tumorigenesis when cell proliferation is stimulated.
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Rajaraman G, Wang GQ, Yan J, Jiang P, Gong Y, Burczynski FJ. Role of cytosolic liver fatty acid binding protein in hepatocellular oxidative stress: effect of dexamethasone and clofibrate treatment. Mol Cell Biochem 2006; 295:27-34. [PMID: 16924418 DOI: 10.1007/s11010-006-9268-6] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2006] [Accepted: 06/26/2006] [Indexed: 12/13/2022]
Abstract
The presence of cysteine and methionine groups together with an ability to bind long-chain fatty acid (LCFA) oxidation products makes liver fatty acid binding protein (L-FABP) an attractive candidate against hepatocellular oxidative stress. In this report, we show that pharmacological treatment directed at modulating L-FABP level affected hepatocellular oxidant status. L-FABP expressing 1548-hepatoma cells, treated with dexamethasone or clofibrate, decreased and increased intracellular L-FABP levels, respectively. Oxidative stress was induced by H2O2 incubation or hypoxia-reoxygenation. The fluorescent marker, dichlorofluorescein (DCF), was employed to measure intracellular reactive oxygen species (ROS). Hepatocellular damage was assessed by lactate dehydrogenase (LDH) level. Dexamethasone treatment resulted in a significant increase in DCF fluorescence with higher LDH release compared to control cells. Clofibrate treatment, however, resulted in a significant decrease in both parameters (p<0.05). Drug treatments did not affect cytosolic activities of glutathione peroxidase (GPx), superoxide dismutase (SOD), or catalase suggesting that the differences between treated and control cells may likely be associated with varying L-FABP levels. We conclude that L-FABP may act as an effective endogenous cytoprotectant against hepatocellular oxidative stress.
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Affiliation(s)
- G Rajaraman
- Faculty of Pharmacy, University of Manitoba, 50 Sifton Road, R3T 2N2, Winnipeg, Manitoba, Canada
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Khor TO, Ibrahim S, Kong ANT. Toxicogenomics in Drug Discovery and Drug Development: Potential Applications and Future Challenges. Pharm Res 2006; 23:1659-64. [PMID: 16858654 DOI: 10.1007/s11095-006-9003-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2005] [Accepted: 03/07/2006] [Indexed: 10/24/2022]
Abstract
Despite the massive investments made by pharmaceutical companies on drug research and development, the number of new drug approvals has remained stagnant in the past decades. It is well known that developing safe and effective new drugs is a long, difficult, and expensive process. While the cost of developing new drugs is increasing rapidly, withdrawals of drugs from the marketplace due to adverse drug reactions (ADR) and/or toxicity is increasing concurrently. The recent advent of high-throughput in silico (computer softwares) and in vitro (cell cultures) screenings have somewhat alleviated some, but not all, of these challenges by providing an efficient and effective way for developing safer and better drugs. This emerging technology, known as toxicogenomics, has great potential to facilitate the development of methodologies that could predict the long-term toxic effects of compounds using relatively short-term bioassays. This review is aimed at discussing the potential applications and future challenges of toxicogenomics in drug discovery and drug development.
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Affiliation(s)
- Tin Oo Khor
- Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers University, 160 Frelinghuysen Road, Piscataway, New Jersey 08854, USA
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Rajaraman G, Burczynski FJ. Effect of dexamethasone, 2-bromopalmitate and clofibrate on L-FABP mediated hepatoma proliferation. J Pharm Pharmacol 2004; 56:1155-61. [PMID: 15324484 DOI: 10.1211/0022357044111] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
Abstract
Cytosolic liver fatty acid binding protein (L-FABP) is involved in many intracellular functions including cellular mitogenesis. We investigated the role of L-FABP and the plasma membrane liver fatty acid binding proteins (L-FABP(pm)) in the modulation of hepatoma growth and proliferation, hypothesizing that agents that affect either the content of, or ligand binding to, L-FABP would affect hepatocellular mitogenesis. L-FABP expressing 1548-rat hepatoma cells were treated with 0.5 microM dexamethasone or 500 microM clofibrate for 4 days to downregulate and upregulate L-FABP expression, respectively. The competitive inhibitor 2-bromopalmitate (BrPA, 600 microM) was used to inhibit ligand binding to L-FABP. The peripherally present plasma membrane fatty acid transporter was inactivated by treating cells with 1:50 rabbit antisera (FABP-Ab) raised against L-FABP. Western blot analysis was used to monitor L-FABP levels while [(3)H]-thymidine incorporation and growth curves were used to monitor hepatocellular proliferation. [(3)H]-Palmitate clearance studies were performed using monolayer cultures. Palmitate clearance in dexamethasone-, BrPA- and FABP-Ab-treated cells was significantly reduced when compared with control (P < 0.05), while clofibrate treatment moderately increased the rate. [(3)H]-Thymidine incorporation by dexamethasone- and BrPA-treated cells was significantly lower than control (P < 0.05), suggesting that hepatocellular proliferation was inhibited. Clofibrate treatment did not statistically affect growth rate. Lowering L-FABP using dexamethasone or interfering with its activity using BrPA significantly affected hepatocellular proliferation. This may be due to the non-availability of long-chain fatty acids or other intracellular mediators that are transported by L-FABP to the nucleus.
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Affiliation(s)
- G Rajaraman
- Faculty of Pharmacy, University of Manitoba, 50 Sifton Road, Winnipeg, Manitoba R3T 2N2, Canada
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Kramer JA, Blomme EAG, Bunch RT, Davila JC, Jackson CJ, Jones PF, Kolaja KL, Curtiss SW. Transcription profiling distinguishes dose-dependent effects in the livers of rats treated with clofibrate. Toxicol Pathol 2003; 31:417-31. [PMID: 12851107 DOI: 10.1080/01926230390202353] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Peroxisome proliferators such as the fibrates act via the peroxisome proliferator activated receptor (PPAR)-alpha as hypolipidemic agents. Many peroxisome proliferators are also nongenotoxic hepatic carcinogens and hepatotoxicants in rodents. We performed transcription profiling using cDNA microarrays on livers of rats treated for 5 days with 3 doses of the peroxisome proliferator clofibrate. All 3 doses had hepatic effects as assessed by liver to body weight ratio, alanine aminotransferase (ALT) increases and histopathology examination. Analysis of the transcription profiling data identified changes in the expression of many genes within several mechanistic pathways that support existing hypotheses regarding peroxisome proliferator mediated carcinogenicity. Additionally, the transcription profiling, histopathology, and clinical chemistry results suggested a biphasic response to clofibrate. These findings provide insight into the pathogenesis of toxic and carcinogenic effects of clofibrate in rodents and demonstrate the ability of cDNA microarrays to provide information regarding mechanisms of toxicity identified during the drug development process.
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Affiliation(s)
- Jeffrey A Kramer
- Pharmacia Corporation, Global Toxicology, 800 N. Lindbergh Blvd., St Louis, Missouri 63167, USA.
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Ziouzenkova O, Perrey S, Asatryan L, Hwang J, MacNaul KL, Moller DE, Rader DJ, Sevanian A, Zechner R, Hoefler G, Plutzky J. Lipolysis of triglyceride-rich lipoproteins generates PPAR ligands: evidence for an antiinflammatory role for lipoprotein lipase. Proc Natl Acad Sci U S A 2003; 100:2730-5. [PMID: 12606719 PMCID: PMC151409 DOI: 10.1073/pnas.0538015100] [Citation(s) in RCA: 174] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Increased levels of triglyceride-rich lipoproteins provoke lipid accumulation in the artery wall, triggering early inflammatory responses central to atherosclerosis like endothelial adhesion molecule expression. The endogenous mechanisms limiting such reactions remain poorly defined. Lipoprotein lipase (LPL) plays a central role in lipid metabolism by hydrolyzing triglyceride rich lipoproteins and releasing fatty acids. We found that LPL treatment reversed tumor necrosis factor alpha and very low-density lipoprotein (VLDL)-stimulated endothelial vascular cell adhesion molecule 1 (VCAM1) induction and VCAM1 promoter responses, thus recapitulating effects reported with synthetic peroxisome proliferator-activated receptor (PPAR) agonists. In fact, these LPL effects on VCAM1 were absent in endothelial cells isolated from PPAR alpha-deficient mice. This finding suggests a novel antiinflammatory role for LPL. Further studies reveal specificity for PPAR activation through lipolysis in regards to lipoprotein substrate (VLDL >> LDL > HDL), PPAR isoform (PPAR alpha >> PPAR delta > PPAR gamma), and among fatty acid-releasing lipases. These PPAR responses required intact LPL catalytic activity. In vivo, transgenic mice overexpressing LPL had increased peroxisome proliferation, but not in the genetic absence of PPAR alpha. Although human plasma possesses minimal PPAR alpha activation despite containing abundant free fatty acids, marked PPAR alpha activation is seen with human plasma after LPL is added in vitro or systemically released in vivo. These data suggest a previously uncharacterized pathway in which the key lipolytic enzyme LPL can act on circulating lipoproteins to generate PPAR alpha ligands, providing a potentially important link between lipoprotein metabolism and distal PPAR alpha transcriptional effects.
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MESH Headings
- Animals
- Anti-Inflammatory Agents/pharmacology
- Blotting, Northern
- Cells, Cultured
- Dose-Response Relationship, Drug
- Fatty Acids/metabolism
- Humans
- Immunohistochemistry
- Ligands
- Lipid Metabolism
- Lipolysis
- Lipoprotein Lipase/physiology
- Lipoproteins/metabolism
- Lipoproteins, VLDL/metabolism
- Mice
- Mice, Transgenic
- Microscopy, Fluorescence
- Models, Biological
- Protein Isoforms
- Receptors, Cytoplasmic and Nuclear/genetics
- Receptors, Cytoplasmic and Nuclear/metabolism
- Transcription Factors/genetics
- Transcription Factors/metabolism
- Transcription, Genetic
- Transfection
- Triglycerides/metabolism
- Vascular Cell Adhesion Molecule-1/metabolism
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Affiliation(s)
- Ouliana Ziouzenkova
- Cardiovascular Division, Brigham and Women's Hospital, Harvard University, Boston, MA 02115, USA
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Anderson SP, Yoon L, Richard EB, Dunn CS, Cattley RC, Corton JC. Delayed liver regeneration in peroxisome proliferator-activated receptor-alpha-null mice. Hepatology 2002; 36:544-54. [PMID: 12198646 DOI: 10.1053/jhep.2002.35276] [Citation(s) in RCA: 116] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Peroxisome proliferator chemicals, acting via the peroxisome proliferator-activated receptor-alpha (Pparalpha), are potent hepatic mitogens and carcinogens in mice and rats. To test whether Pparalpha is required for hepatic growth in response to other stimuli, we studied liver regeneration and hepatic gene expression following partial hepatectomy (PH) of wild-type and Pparalpha-null mice. Pparalpha-null mice had a 12- to 24-hour delay in liver regeneration associated with a delayed onset and lower peak magnitude of hepatocellular DNA synthesis. Furthermore, these mice had a 24-hour lag in the hepatic expression of the G(1)/S checkpoint regulator genes Ccnd1 and cMyc and increased expression of the IL-1beta cytokine gene. Hepatic expression of Ccnd1, cMyc, IL-1r1, and IL-6r was induced in wild-type mice, but not Pparalpha-null mice, after acute exposure to the potent Pparalpha agonist Wy-14,643, indicating a role for Pparalpha in regulating the expression of these genes. Expression of the fatty acid omega-hydroxylase gene Cyp4a14, a commonly used indicator gene for Pparalpha activation, was strongly induced in wild-type mice after hepatectomy, suggesting that altered hepatocyte lipid processing may also contribute to the impaired regeneration in mice lacking the Pparalpha gene. In conclusion, liver regeneration in Pparalpha-null mice is transiently impaired and is associated with altered expression of genes involved in cell cycle control, cytokine signaling, and fat metabolism.
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Affiliation(s)
- Steven P Anderson
- Toxicogenomics Group, GlaxoSmithKline Research and Development, Research Triangle Park, NC 27709, USA.
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Coste H, Rodríguez JC. Orphan nuclear hormone receptor Rev-erbalpha regulates the human apolipoprotein CIII promoter. J Biol Chem 2002; 277:27120-9. [PMID: 12021280 DOI: 10.1074/jbc.m203421200] [Citation(s) in RCA: 63] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Apolipoprotein CIII (apoCIII) plays an important role in plasma triglyceride and remnant lipoprotein metabolism. Because hypertriglyceridemia is an independent risk factor in coronary artery disease and the presence in plasma of triglyceride-rich remnant lipoproteins is correlated with atherosclerosis, considerable research efforts have been focused on the identification of factors regulating apoCIII gene expression to decrease its production. Here we report that the orphan nuclear hormone receptor Rev-erbalpha regulates the human apoCIII gene promoter. In apoCIII expressing human hepatic HepG2 cells, transfection of Rev-erbalpha specifically repressed apoCIII gene promoter activity. We determined by deletion and site-directed mutagenesis experiments that Rev-erbalpha dependent repression is mainly due to an element present in the proximal promoter of the apoCIII gene. In contrast, we found no functional Rev-erbalpha response elements in the convergently transcribed human apoAI gene or the common regulatory enhancer. The identified Rev-erbalpha response element coincides with a RORalpha1 element, and in the present study we provide evidence that functional cross-talk between these orphan receptors modulates the apoCIII promoter. In vitro binding analysis showed that monomers of Rev-erbalpha bound this element but not another upstream RORalpha1 response element. In addition, we showed that the closely related nuclear orphan receptor RVR also specifically repressed the human apoCIII gene. These studies underscore a novel physiological role for members of the Rev-erb family of nuclear receptors in the regulation of genes involved in triglyceride metabolism and the pathogenesis of atherosclerosis.
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Affiliation(s)
- Hervé Coste
- GlaxoSmithKline, 25 avenue du Québec, 91951 Les Ulis cedex, France.
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