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Rawls KD, Blais EM, Dougherty BV, Vinnakota KC, Pannala VR, Wallqvist A, Kolling GL, Papin JA. Genome-Scale Characterization of Toxicity-Induced Metabolic Alterations in Primary Hepatocytes. Toxicol Sci 2019; 172:279-291. [PMID: 31501904 PMCID: PMC6876259 DOI: 10.1093/toxsci/kfz197] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Context-specific GEnome-scale metabolic Network REconstructions (GENREs) provide a means to understand cellular metabolism at a deeper level of physiological detail. Here, we use transcriptomics data from chemically-exposed rat hepatocytes to constrain a GENRE of rat hepatocyte metabolism and predict biomarkers of liver toxicity using the Transcriptionally Inferred Metabolic Biomarker Response algorithm. We profiled alterations in cellular hepatocyte metabolism following in vitro exposure to four toxicants (acetaminophen, carbon tetrachloride, 2,3,7,8-tetrachlorodibenzodioxin, and trichloroethylene) for six hour. TIMBR predictions were compared with paired fresh and spent media metabolomics data from the same exposure conditions. Agreement between computational model predictions and experimental data led to the identification of specific metabolites and thus metabolic pathways associated with toxicant exposure. Here, we identified changes in the TCA metabolites citrate and alpha-ketoglutarate along with changes in carbohydrate metabolism and interruptions in ATP production and the TCA Cycle. Where predictions and experimental data disagreed, we identified testable hypotheses to reconcile differences between the model predictions and experimental data. The presented pipeline for using paired transcriptomics and metabolomics data provides a framework for interrogating multiple omics datasets to generate mechanistic insight of metabolic changes associated with toxicological responses.
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Affiliation(s)
- Kristopher D Rawls
- Department of Biomedical Engineering, University of Virginia, Charlottesville, Virginia 22908
| | - Edik M Blais
- Department of Biomedical Engineering, University of Virginia, Charlottesville, Virginia 22908
| | - Bonnie V Dougherty
- Department of Biomedical Engineering, University of Virginia, Charlottesville, Virginia 22908
| | - Kalyan C Vinnakota
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc. (HJF), Bethesda, Maryland 20817
- Department of Defense Biotechnology High Performance Computing Software Applications Institute, Telemedicine and Advanced Technology Research Center, U.S. Army Medical Research and Development Command, Fort Detrick, Maryland 21702
| | - Venkat R Pannala
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc. (HJF), Bethesda, Maryland 20817
- Department of Defense Biotechnology High Performance Computing Software Applications Institute, Telemedicine and Advanced Technology Research Center, U.S. Army Medical Research and Development Command, Fort Detrick, Maryland 21702
| | - Anders Wallqvist
- Department of Defense Biotechnology High Performance Computing Software Applications Institute, Telemedicine and Advanced Technology Research Center, U.S. Army Medical Research and Development Command, Fort Detrick, Maryland 21702
| | - Glynis L Kolling
- Department of Biomedical Engineering, University of Virginia, Charlottesville, Virginia 22908
- Department of Medicine, Division of Infectious Diseases and International Health
| | - Jason A Papin
- Department of Biomedical Engineering, University of Virginia, Charlottesville, Virginia 22908
- Department of Medicine, Division of Infectious Diseases and International Health
- Department of Biochemistry & Molecular Genetics, University of Virginia, Charlottesville, Virginia 22908
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Asai Y, Tanaka H, Nadai M, Katoh M. Status Epilepticus Decreases Brain Cytochrome P450 2D4 Expression in Rats. J Pharm Sci 2017; 107:975-978. [PMID: 29175413 DOI: 10.1016/j.xphs.2017.11.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Revised: 11/09/2017] [Accepted: 11/16/2017] [Indexed: 01/09/2023]
Abstract
Status epilepticus (SE) is a life-threatening neurological emergency characterized by frequent seizures. The present study aims at elucidating the effect of SE on CYP2D4 expression in the rat brain. To create a rat model of SE, Sprague-Dawley rats were intraperitoneally administered 10 mg/kg kainic acid. The CYP2D4 mRNA levels in the cortex and hippocampus of the SE rats were decreased by 0.38- and 0.39-fold, respectively. The protein level of octamer transcription factor 1 (Oct-1), which is involved in the transcriptional activation of CYP2D4 by binding to the CYP2D4 regulatory element, was also attenuated by 0.64- and 0.51-fold in these regions of the SE rat, suggesting that a reduction in Oct-1 may be involved in the CYP2D4 suppression. Yin yang 1 can function as a cofactor of histone deacetylase 1 and inhibit the binding of Oct-1 to the CYP2D4 regulatory element. The coimmunoprecipitation assay revealed that the interaction between yin yang 1 and histone deacetylase 1 in the cortex and hippocampus was enhanced during SE, indicating that this interaction is also responsible for the CYP2D4 suppression. This study clarified that SE led to a decrease in the expression of CYP2D4, thus altering the pharmacokinetics and efficacy of the drugs in the brain.
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Affiliation(s)
- Yuki Asai
- Pharmaceutics, Faculty of Pharmacy, Meijo University, 150 Yagotoyama, Tempaku-ku, Nagoya 468-8503, Japan
| | - Hatsuna Tanaka
- Pharmaceutics, Faculty of Pharmacy, Meijo University, 150 Yagotoyama, Tempaku-ku, Nagoya 468-8503, Japan
| | - Masayuki Nadai
- Pharmaceutics, Faculty of Pharmacy, Meijo University, 150 Yagotoyama, Tempaku-ku, Nagoya 468-8503, Japan
| | - Miki Katoh
- Pharmaceutics, Faculty of Pharmacy, Meijo University, 150 Yagotoyama, Tempaku-ku, Nagoya 468-8503, Japan.
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He ZX, Chen XW, Zhou ZW, Zhou SF. Impact of physiological, pathological and environmental factors on the expression and activity of human cytochrome P450 2D6 and implications in precision medicine. Drug Metab Rev 2015; 47:470-519. [PMID: 26574146 DOI: 10.3109/03602532.2015.1101131] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
With only 1.3-4.3% in total hepatic CYP content, human CYP2D6 can metabolize more than 160 drugs. It is a highly polymorphic enzyme and subject to marked inhibition by a number of drugs, causing a large interindividual variability in drug clearance and drug response and drug-drug interactions. The expression and activity of CYP2D6 are regulated by a number of physiological, pathological and environmental factors at transcriptional, post-transcriptional, translational and epigenetic levels. DNA hypermethylation and histone modifications can repress the expression of CYP2D6. Hepatocyte nuclear factor-4α binds to a directly repeated element in the promoter of CYP2D6 and thus regulates the expression of CYP2D6. Small heterodimer partner represses hepatocyte nuclear factor-4α-mediated transactivation of CYP2D6. GW4064, a farnesoid X receptor agonist, decreases hepatic CYP2D6 expression and activity while increasing small heterodimer partner expression and its recruitment to the CYP2D6 promoter. The genotypes are key determinants of interindividual variability in CYP2D6 expression and activity. Recent genome-wide association studies have identified a large number of genes that can regulate CYP2D6. Pregnancy induces CYP2D6 via unknown mechanisms. Renal or liver diseases, smoking and alcohol use have minor to moderate effects only on CYP2D6 activity. Unlike CYP1 and 3 and other CYP2 members, CYP2D6 is resistant to typical inducers such as rifampin, phenobarbital and dexamethasone. Post-translational modifications such as phosphorylation of CYP2D6 Ser135 have been observed, but the functional impact is unknown. Further functional and validation studies are needed to clarify the role of nuclear receptors, epigenetic factors and other factors in the regulation of CYP2D6.
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Affiliation(s)
- Zhi-Xu He
- a Guizhou Provincial Key Laboratory for Regenerative Medicine, Stem Cell and Tissue Engineering Research Center & Sino-US Joint Laboratory for Medical Sciences, Guizhou Medical University , Guiyang , Guizhou , China
| | - Xiao-Wu Chen
- b Department of General Surgery , The First People's Hospital of Shunde, Southern Medical University , Shunde , Foshan , Guangdong , China , and
| | - Zhi-Wei Zhou
- c Department of Pharmaceutical Science , College of Pharmacy, University of South Florida , Tampa , FL , USA
| | - Shu-Feng Zhou
- a Guizhou Provincial Key Laboratory for Regenerative Medicine, Stem Cell and Tissue Engineering Research Center & Sino-US Joint Laboratory for Medical Sciences, Guizhou Medical University , Guiyang , Guizhou , China .,c Department of Pharmaceutical Science , College of Pharmacy, University of South Florida , Tampa , FL , USA
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New aQTL SNPs for the CYP2D6 identified by a novel mediation analysis of genome-wide SNP arrays, gene expression arrays, and CYP2D6 activity. BIOMED RESEARCH INTERNATIONAL 2013; 2013:493019. [PMID: 24232670 PMCID: PMC3819829 DOI: 10.1155/2013/493019] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/30/2013] [Accepted: 09/16/2013] [Indexed: 12/01/2022]
Abstract
Background. The genome-wide association studies (GWAS) have been successful during the last few years. A key challenge is that the interpretation of the results is not straightforward, especially for transacting SNPs. Integration of transcriptome data into GWAS may provide clues elucidating the mechanisms by which a genetic variant leads to a disease. Methods. Here, we developed a novel mediation analysis approach to identify new expression quantitative trait loci (eQTL) driving CYP2D6 activity by combining genotype, gene expression, and enzyme activity data. Results. 389,573 and 1,214,416 SNP-transcript-CYP2D6 activity trios are found strongly associated (P < 10−5, FDR = 16.6% and 11.7%) for two different genotype platforms, namely, Affymetrix and Illumina, respectively. The majority of eQTLs are trans-SNPs. A single polymorphism leads to widespread downstream changes in the expression of distant genes by affecting major regulators or transcription factors (TFs), which would be visible as an eQTL hotspot and can lead to large and consistent biological effects. Overlapped eQTL hotspots with the mediators lead to the discovery of 64 TFs.
Conclusions. Our mediation analysis is a powerful approach in identifying the trans-QTL-phenotype associations. It improves our understanding of the functional genetic variations for the liver metabolism mechanisms.
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Sakai N, Sakamoto KQ, Fujita S, Ishizuka M. The importance of heterogeneous nuclear ribonucleoprotein K on cytochrome P450 2D2 gene regulation: its binding is reduced in Dark Agouti rats. Drug Metab Dispos 2009; 37:1703-10. [PMID: 19420131 DOI: 10.1124/dmd.109.027284] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Cytochrome P450 (P450) 2D2 (CYP2D2) enzyme is known to metabolize the majority of typical substrates of the human CYP2D6 enzyme, which is the most extensively characterized polymorphic drug-metabolizing enzyme. Despite its impact on drug metabolism in rats, the transcriptional regulation of CYP2D2 remains to be elucidated. We clarified the molecular mechanism of CYP2D2 gene expression. The CYP2D2 gene was positively regulated by the poly(C)-binding protein heterogeneous nuclear ribonucleoprotein K (hnRNP K) through a transcriptional regulatory element located in the 5'-flanking region from -94 to -113. To date, nothing is known about the potential role of hnRNP K in P450 gene regulation. Thus, this is the first report that hnRNP K protein is involved in CYP2D2 gene regulation. Furthermore, we elucidated the genetic basis of the extremely low expression of CYP2D2 mRNA in Dark Agouti (DA) rats. Because of its relatively low abundance, DA rats have been frequently used for the study of CYP2D substrate metabolism as the animal model of the poor metabolizer phenotype for CYP2D6 compared with Sprague-Dawley rats as an extensive metabolizer phenotype. We found a single substitution within the transcriptional regulatory element of the CYP2D2 gene in DA rats. The mutation was detected in the polypyrimidine sequence that is the preferred binding site for hnRNP K protein. The mutation within the transcriptional regulatory element attenuated the binding of hnRNP K protein. In conclusion, decreased recruitment of hnRNP K protein to the mutated sequence causes the low expression of CYP2D2 mRNA in DA rats.
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Affiliation(s)
- Noriaki Sakai
- Laboratory of Toxicology, Department of Environmental Veterinary Sciences, Graduate School of Veterinary Medicine, Hokkaido University, Sapporo, Japan
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David JP, Boyer S, Mesneau A, Ball A, Ranson H, Dauphin-Villemant C. Involvement of cytochrome P450 monooxygenases in the response of mosquito larvae to dietary plant xenobiotics. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2006; 36:410-20. [PMID: 16651188 DOI: 10.1016/j.ibmb.2006.02.004] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2005] [Revised: 02/27/2006] [Accepted: 02/28/2006] [Indexed: 05/08/2023]
Abstract
The response of mosquito larvae to plant toxins found in their breeding sites was investigated by using Aedes aegypti larvae and toxic arborescent leaf litter as experimental models. The relation between larval tolerance to toxic leaf litter and cytochrome P450 monooxygenases (P450s) was examined at the toxicological, biochemical and molecular levels. Larvae pre-exposed to toxic leaf litter show a higher tolerance to those xenobiotics together with a strong increase in P450 activity levels. This enzymatic response is both time- and dose-dependent. The use of degenerate primers from various P450 genes (CYPs) allowed us to isolate 16 new CYP genes belonging to CYP4, CYP6 and CYP9 families. Expression studies revealed a 2.3-fold over-expression of 1 CYP gene (CYP6AL1) after larval pre-exposure to toxic leaf litter, this gene being expressed at a high level in late larval and pupal stages and in fat bodies and midgut. The CYP6AL1 protein has a high level of identity with other insect's CYPs involved in xenobiotic detoxification. The role of CYP genes in tolerance to natural xenobiotics and the importance of such adaptive responses in the capacity of mosquitoes to colonize new habitats and to develop insecticide resistance mechanisms are discussed.
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Affiliation(s)
- J P David
- Laboratoire d'Ecologie Alpine (LECA) UMR 5553, Bâtiment D, rue de la piscine, Université Joseph Fourier, BP53, 38041 Grenoble cedex 9, France.
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Cicatiello L, Addeo R, Sasso A, Altucci L, Petrizzi VB, Borgo R, Cancemi M, Caporali S, Caristi S, Scafoglio C, Teti D, Bresciani F, Perillo B, Weisz A. Estrogens and progesterone promote persistent CCND1 gene activation during G1 by inducing transcriptional derepression via c-Jun/c-Fos/estrogen receptor (progesterone receptor) complex assembly to a distal regulatory element and recruitment of cyclin D1 to its own gene promoter. Mol Cell Biol 2004; 24:7260-74. [PMID: 15282324 PMCID: PMC479712 DOI: 10.1128/mcb.24.16.7260-7274.2004] [Citation(s) in RCA: 125] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2004] [Revised: 02/10/2004] [Accepted: 05/20/2004] [Indexed: 12/31/2022] Open
Abstract
Transcriptional activation of the cyclin D1 gene (CCND1) plays a pivotal role in G(1)-phase progression, which is thereby controlled by multiple regulatory factors, including nuclear receptors (NRs). Appropriate CCND1 gene activity is essential for normal development and physiology of the mammary gland, where it is regulated by ovarian steroids through a mechanism(s) that is not fully elucidated. We report here that CCND1 promoter activation by estrogens in human breast cancer cells is mediated by recruitment of a c-Jun/c-Fos/estrogen receptor alpha complex to the tetradecanoyl phorbol acetate-responsive element of the gene, together with Oct-1 to a site immediately adjacent. This process coincides with the release from the same DNA region of a transcriptional repressor complex including Yin-Yang 1 (YY1) and histone deacetylase 1 and is sufficient to induce the assembly of the basal transcription machinery on the promoter and to lead to initial cyclin D1 accumulation in the cell. Later on in estrogen stimulation, the cyclin D1/Cdk4 holoenzyme associates with the CCND1 promoter, where E2F and pRb can also be found, contributing to the long-lasting gene enhancement required to drive G(1)-phase completion. Interestingly, progesterone triggers similar regulatory events through its own NRs, suggesting that the gene regulation cascade described here represents a crossroad for the transcriptional control of G(1)-phase progression by different classes of NRs.
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Affiliation(s)
- Luigi Cicatiello
- Dipartimento di Patologia Generale, Seconda Università degli Studi di Napoli, 80138 Naples, Italy
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Azuara-Liceaga E, Sandoval M, Corona M, Gariglio P, López-Bayghen E. The human involucrin gene is transcriptionally repressed through a tissue-specific silencer element recognized by Oct-2. Biochem Biophys Res Commun 2004; 318:361-71. [PMID: 15120610 DOI: 10.1016/j.bbrc.2004.04.034] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2004] [Indexed: 11/16/2022]
Abstract
Involucrin is an important marker of epithelial differentiation which expression is upregulated just after basal cells are pushed into the suprabasal layer in stratified epithelia. Several transcription factors and regulatory elements had been described as responsible for turning on the gene. However, it is evident that in basal cell layer, additional mechanisms are involved in keeping the gene silent before the differentiation process starts. In this work, we located a potential transcriptional silencer in a 52bp sequence whose integrity is necessary for silencing the proximal enhancer promoter element (PEP) in multiplying keratinocytes. Octamer-binding sites were noticed in this fragment and the specific binding of Oct-2 transcription factor was detected. Oct-2 appears to be implicated in an epithelial-specific repression activity recorded only in keratinocytes and C33-A cell line. Overexpression of Oct-2 repressed the involucrin promoter activity in epithelial cells and in the presence of the silencer element.
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Affiliation(s)
- Elisa Azuara-Liceaga
- Departamento de Genética y Biología Molecular, Centro de Investigación y Estudios Avanzados del I.P.N., Mexico D.F. 07000, Mexico
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