Pregnane X Receptor (PXR) Polymorphisms and Cancer
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Comprehensive Study of Nuclear Receptor DNA Binding Provides a Revised Framework for Understanding Receptor Specificity
ARTICLE https://doi.org/10.1038/s41467-019-10264-3 OPEN Comprehensive study of nuclear receptor DNA binding provides a revised framework for understanding receptor specificity Ashley Penvose 1,2,4, Jessica L. Keenan 2,3,4, David Bray2,3, Vijendra Ramlall 1,2 & Trevor Siggers 1,2,3 The type II nuclear receptors (NRs) function as heterodimeric transcription factors with the retinoid X receptor (RXR) to regulate diverse biological processes in response to endogenous 1234567890():,; ligands and therapeutic drugs. DNA-binding specificity has been proposed as a primary mechanism for NR gene regulatory specificity. Here we use protein-binding microarrays (PBMs) to comprehensively analyze the DNA binding of 12 NR:RXRα dimers. We find more promiscuous NR-DNA binding than has been reported, challenging the view that NR binding specificity is defined by half-site spacing. We show that NRs bind DNA using two distinct modes, explaining widespread NR binding to half-sites in vivo. Finally, we show that the current models of NR specificity better reflect binding-site activity rather than binding-site affinity. Our rich dataset and revised NR binding models provide a framework for under- standing NR regulatory specificity and will facilitate more accurate analyses of genomic datasets. 1 Department of Biology, Boston University, Boston, MA 02215, USA. 2 Biological Design Center, Boston University, Boston, MA 02215, USA. 3 Bioinformatics Program, Boston University, Boston, MA 02215, USA. 4These authors contributed equally: Ashley Penvose, Jessica L. Keenan. Correspondence -
Xenobiotic-Sensing Nuclear Receptors Involved in Drug Metabolism: a Structural Perspective
HHS Public Access Author manuscript Author ManuscriptAuthor Manuscript Author Drug Metab Manuscript Author Rev. Author Manuscript Author manuscript; available in PMC 2016 May 24. Published in final edited form as: Drug Metab Rev. 2013 February ; 45(1): 79–100. doi:10.3109/03602532.2012.740049. Xenobiotic-sensing nuclear receptors involved in drug metabolism: a structural perspective Bret D. Wallace and Matthew R. Redinbo Departments of Chemistry, Biochemistry, and Microbiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA Abstract Xenobiotic compounds undergo a critical range of biotransformations performed by the phase I, II, and III drug-metabolizing enzymes. The oxidation, conjugation, and transportation of potentially harmful xenobiotic and endobiotic compounds achieved by these catalytic systems are significantly regulated, at the gene expression level, by members of the nuclear receptor (NR) family of ligand-modulated transcription factors. Activation of NRs by a variety of endo- and exogenous chemicals are elemental to induction and repression of drug-metabolism pathways. The master xenobiotic sensing NRs, the promiscuous pregnane X receptor and less-promiscuous constitutive androstane receptor are crucial to initial ligand recognition, jump-starting the metabolic process. Other receptors, including farnesoid X receptor, vitamin D receptor, hepatocyte nuclear factor 4 alpha, peroxisome proliferator activated receptor, glucocorticoid receptor, liver X receptor, and RAR-related orphan receptor, are not directly linked to promiscuous xenobiotic binding, but clearly play important roles in the modulation of metabolic gene expression. Crystallographic studies of the ligand-binding domains of nine NRs involved in drug metabolism provide key insights into ligand-based and constitutive activity, coregulator recruitment, and gene regulation. -
Pharmacogenomics to Predict Tumor Therapy Response: a Focus on ATP-Binding Cassette Transporters and Cytochromes P450
Journal of Personalized Medicine Review Pharmacogenomics to Predict Tumor Therapy Response: A Focus on ATP-Binding Cassette Transporters and Cytochromes P450 Viktor Hlaváˇc 1,2,* , Petr Holý 1,2,3 and Pavel Souˇcek 1,2 1 Toxicogenomics Unit, National Institute of Public Health, 100 00 Prague, Czech Republic; [email protected] (P.H.); [email protected] (P.S.) 2 Laboratory of Pharmacogenomics, Biomedical Center, Faculty of Medicine in Pilsen, Charles University, 306 05 Pilsen, Czech Republic 3 Third Faculty of Medicine, Charles University, 100 00 Prague, Czech Republic * Correspondence: [email protected]; Tel.: +420-267082681; Fax: +420-267311236 Received: 31 July 2020; Accepted: 26 August 2020; Published: 28 August 2020 Abstract: Pharmacogenomics is an evolving tool of precision medicine. Recently,due to the introduction of next-generation sequencing and projects generating “Big Data”, a plethora of new genetic variants in pharmacogenes have been discovered. Cancer resistance is a major complication often preventing successful anticancer treatments. Pharmacogenomics of both somatic mutations in tumor cells and germline variants may help optimize targeted treatments and improve the response to conventional oncological therapy. In addition, integrative approaches combining copy number variations and long noncoding RNA profiling with germline and somatic variations seem to be a promising approach as well. In pharmacology, expression and enzyme activity are traditionally the more studied aspects of ATP-binding cassette transporters and cytochromes P450. In this review, we briefly introduce the field of pharmacogenomics and the advancements driven by next-generation sequencing and outline the possible roles of genetic variation in the two large pharmacogene superfamilies. -
Somatic Pharmacogenomics in Cancer
The Pharmacogenomics Journal (2008) 8, 305–314 & 2008 Nature Publishing Group All rights reserved 1470-269X/08 $30.00 www.nature.com/tpj REVIEW Somatic pharmacogenomics in cancer ON Ikediobi Many of the initial examples of the clinical utility of pharmacogenetics were elucidated in the field of oncology. Those examples were largely based on Department of Clinical Pharmacy, School of the existence of germline genetic variation that influences the metabolism of Pharmacy, University of California, San Francisco, cytotoxic drugs. However, with the development of kinase inhibitors, drugs CA, USA designed to preferentially target altered proteins driving oncogenesis, pharmacogenetics in cancer has shifted to understanding the somatic Correspondence: Dr ON Ikediobi, Department of Clinical differences that determine response to these targeted agents. It is becoming Pharmacy, School of Pharmacy, University of increasingly clear that understanding the molecular genetics of cancer will California, 3333 California Street, Box 0613, lead to the further development of targeted therapeutics. Therefore, it is San Francisco, CA 94118, USA. imperative that pharmacogenomics researchers understand the motivations E-mail: [email protected] and challenges of developing targeted therapies to treat cancer as a paradigm for personalized medicine. However, much of the discussion in the pharmacogenomics community in cancer is still largely focused on the germline variants as predictors of drug toxicity. In light of that fact, this review presents a detailed -
Appendix E Papers That Were Accepted for ECOTOX
Appendix E Papers that Were Accepted for ECOTOX E1. Acceptable for ECOTOX and OPP 1. Aitken, R. J., Ryan, A. L., Baker, M. A., and McLaughlin, E. A. (2004). Redox Activity Associated with the Maturation and Capacitation of Mammalian Spermatozoa. Free Rad.Biol.Med. 36: 994-1010. EcoReference No.: 100193 Chemical of Concern: RTN,CPS; Habitat: T; Effect Codes: BCM,CEL; Rejection Code: LITE EVAL CODED(RTN,CPS). 2. Akpinar, M. B., Erdogan, H., Sahin, S., Ucar, F., and Ilhan, A. (2005). Protective Effects of Caffeic Acid Phenethyl Ester on Rotenone-Induced Myocardial Oxidative Injury. Pestic.Biochem.Physiol. 82: 233- 239. EcoReference No.: 99975 Chemical of Concern: RTN; Habitat: T; Effect Codes: BCM,PHY; Rejection Code: LITE EVAL CODED(RTN). 3. Amer, S. M. and Aboul-Ela, E. I. (1985). Cytogenetic Effects of Pesticides. III. Induction of Micronuclei in Mouse Bone Marrow by the Insecticides Cypermethrin and Rotenone. Mutation Res. 155: 135-142. EcoReference No.: 99593 Chemical of Concern: CYP,RTN; Habitat: T; Effect Codes: CEL,PHY,MOR; Rejection Code: LITE EVAL CODED(RTN),OK(CYP). 4. Bartlett, B. R. (1966). Toxicity and Acceptance of Some Pesticides Fed to Parasitic Hymenoptera and Predatory Coccinellids. J.Econ.Entomol. 59: 1142-1149. EcoReference No.: 98221 Chemical of Concern: AND,ARM,AZ,DCTP,Captan,CBL,CHD,CYT,DDT,DEM,DZ,DCF,DLD,DMT,DINO,ES,EN,ETN,F NTH,FBM,HPT,HCCH,MLN,MXC,MVP,Naled,KER,PRN,RTN,SBDA,SFR,TXP,TCF,Zineb; Habitat: T; Effect Codes: MOR; Rejection Code: LITE EVAL CODED(RTN),OK(ARM,AZ,Captan,CBL,DZ,DCF,DMT,ES,MLN,MXC,MVP,Naled,SFR). -
A Yeast Phenomic Model for the Influence of Warburg Metabolism on Genetic Buffering of Doxorubicin Sean M
Santos and Hartman Cancer & Metabolism (2019) 7:9 https://doi.org/10.1186/s40170-019-0201-3 RESEARCH Open Access A yeast phenomic model for the influence of Warburg metabolism on genetic buffering of doxorubicin Sean M. Santos and John L. Hartman IV* Abstract Background: The influence of the Warburg phenomenon on chemotherapy response is unknown. Saccharomyces cerevisiae mimics the Warburg effect, repressing respiration in the presence of adequate glucose. Yeast phenomic experiments were conducted to assess potential influences of Warburg metabolism on gene-drug interaction underlying the cellular response to doxorubicin. Homologous genes from yeast phenomic and cancer pharmacogenomics data were analyzed to infer evolutionary conservation of gene-drug interaction and predict therapeutic relevance. Methods: Cell proliferation phenotypes (CPPs) of the yeast gene knockout/knockdown library were measured by quantitative high-throughput cell array phenotyping (Q-HTCP), treating with escalating doxorubicin concentrations under conditions of respiratory or glycolytic metabolism. Doxorubicin-gene interaction was quantified by departure of CPPs observed for the doxorubicin-treated mutant strain from that expected based on an interaction model. Recursive expectation-maximization clustering (REMc) and Gene Ontology (GO)-based analyses of interactions identified functional biological modules that differentially buffer or promote doxorubicin cytotoxicity with respect to Warburg metabolism. Yeast phenomic and cancer pharmacogenomics data were integrated to predict differential gene expression causally influencing doxorubicin anti-tumor efficacy. Results: Yeast compromised for genes functioning in chromatin organization, and several other cellular processes are more resistant to doxorubicin under glycolytic conditions. Thus, the Warburg transition appears to alleviate requirements for cellular functions that buffer doxorubicin cytotoxicity in a respiratory context. -
Access to Guideline-Recommended Pharmacogenomic Tests for Cancer Treatments: Experience of Providers and Patients
Access to Guideline-Recommended Pharmacogenomic Tests for Cancer Treatments: Experience of Providers and Patients The Harvard community has made this article openly available. Please share how this access benefits you. Your story matters Citation Wu, Ann Chen, Kathleen M. Mazor, Rachel Ceccarelli, Stephanie Loomer, and Christine Y. Lu. 2017. “Access to Guideline-Recommended Pharmacogenomic Tests for Cancer Treatments: Experience of Providers and Patients.” Journal of Personalized Medicine 7 (4): 17. doi:10.3390/jpm7040017. http:// dx.doi.org/10.3390/jpm7040017. Published Version doi:10.3390/jpm7040017 Citable link http://nrs.harvard.edu/urn-3:HUL.InstRepos:34868910 Terms of Use This article was downloaded from Harvard University’s DASH repository, and is made available under the terms and conditions applicable to Other Posted Material, as set forth at http:// nrs.harvard.edu/urn-3:HUL.InstRepos:dash.current.terms-of- use#LAA Journal of Personalized Medicine Article Access to Guideline-Recommended Pharmacogenomic Tests for Cancer Treatments: Experience of Providers and Patients Ann Chen Wu 1,*, Kathleen M. Mazor 2, Rachel Ceccarelli 1, Stephanie Loomer 1 and Christine Y. Lu 1 1 Precision Medicine Translational Research (PROMoTeR) Center, Department of Population Medicine, Harvard Pilgrim Health Care Institute and Harvard Medical School, 401 Park Drive, Suite 401, Boston, MA 02215, USA; [email protected] (R.C.); [email protected] (S.L.); [email protected] (C.Y.L.) 2 Meyers Primary Care Institute, A Joint Endeavor of the University of Massachusetts Medical School, Reliant Medical Group and Fallon Health; 630 Plantation Street, Worcester, MA 02215, USA; [email protected] * Correspondence: [email protected]; Tel.: +1-617-867-4823; Fax: +1-617-859-8112 Academic Editor: Stephen B. -
BMAL1 and Modulates Tissue-Specific Circadian Networks
Nuclear receptor HNF4A transrepresses CLOCK: BMAL1 and modulates tissue-specific circadian networks Meng Qua, Tomas Duffyb, Tsuyoshi Hirotac, and Steve A. Kaya,1 aKeck School of Medicine, University of Southern California, Los Angeles, CA 90089; bDepartment of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037; and cInstitute of Transformative Bio-Molecules, Nagoya University, 464-8602 Nagoya, Japan Contributed by Steve A. Kay, November 6, 2018 (sent for review September 24, 2018; reviewed by Carla B. Green and John B. Hogenesch) Either expression level or transcriptional activity of various nuclear NRs canonically function as ligand-activated transcription receptors (NRs) have been demonstrated to be under circadian factors that regulate the expression of their target genes to control. With a few exceptions, little is known about the roles of affect physiological pathways (19). The importance of NRs in NRs as direct regulators of the circadian circuitry. Here we show maintaining optimal physiological homeostasis is illustrated in that the nuclear receptor HNF4A strongly transrepresses the their identification as potential targets for therapeutic drug transcriptional activity of the CLOCK:BMAL1 heterodimer. We development to combat a diverse array of diseases, including define a central role for HNF4A in maintaining cell-autonomous reproductive disorders, inflammation, cancer, diabetes, car- circadian oscillations in a tissue-specific manner in liver and colon diovascular disease, and obesity (20). Various NRs have been cells. Not only transcript level but also genome-wide chromosome implicated as targets of the circadian clock, which may con- binding of HNF4A is rhythmically regulated in the mouse liver. tribute to the circadian regulation of nutrient and energy me- ChIP-seq analyses revealed cooccupancy of HNF4A and CLOCK: tabolism. -
Cphi & P-MEC China Exhibition List展商名单version版本20180116
CPhI & P-MEC China Exhibition List展商名单 Version版本 20180116 Booth/ Company Name/公司中英文名 Product/产品 展位号 Carbosynth Ltd E1A01 Toronto Research Chemicals Inc E1A08 SiliCycle Inc. E1A10 SA TOURNAIRE E1A11 Indena SpA E1A17 Trifarma E1A21 LLC Velpharma E1A25 Anuh Pharma E1A31 Chemclone Industries E1A51 Hetero Labs Limited E1B09 Concord Biotech Limited E1B10 ScinoPharm Taiwan Ltd E1B11 Dongkook Pharmaceutical Co., Ltd. E1B19 Shenzhen Salubris Pharmaceuticals Co., Ltd E1B22 GfM mbH E1B25 Leawell International Ltd E1B28 DCS Pharma AG E1B31 Agno Pharma E1B32 Newchem Spa E1B35 APEX HEALTHCARE LIMITED E1B51 AMRI E1C21 Aarti Drugs Limited E1C25 Espee Group Innovators E1C31 Ruland Chemical Co., Ltd. E1C32 Merck Chemicals (Shanghai) Co., Ltd. E1C51 Mediking Pharmaceutical Group Ltd E1C57 珠海联邦制药股份有限公司/The United E1D01 Laboratories International Holdings Ltd. FMC Corporation E1D02 Kingchem (Liaoning) Chemical Co., Ltd E1D10 Doosan Corporation E1D22 Sunasia Co., Ltd. E1D25 Bolon Pharmachem Co., Ltd. E1D26 Savior Lifetec Corporation E1D27 Alchem International Pvt Ltd E1D31 Polish Investment and Trade Agency E1D57 Fischer Chemicals AG E1E01 NGL Fine Chem Limited E1E24 常州艾柯轧辊有限公司/ECCO Roller E1E25 Linnea SA E1E26 Everlight Chemical Industrial Corporation E1E27 HARMAN FINOCHEM E1E28 Zhechem Co Ltd E1F01 Midas Pharma GmbH Shanghai Representativ E1F03 Supriya Lifescience Ltd E1F10 KOA Shoji Co Ltd E1F22 NOF Corporation E1F24 上海贺利氏工业技术材料有限公司/Heraeus E1F26 Materials Technology Shanghai Ltd. Novacyl Asia Pacific Ltd E1F28 PharmSol Europe Limited E1F32 Bachem AG E1F35 Louston International Inc. E1F51 High Science Co Ltd E1F55 Chemsphere Technology Inc. E1F57a PharmaCore Biotech Co., Ltd. E1F57b Rockwood Lithium GmbH E1G51 Sarv Bio Labs Pvt Ltd E1G57 抗病毒类、抗肿瘤类、抗感染类和甾体类中间体、原料药和药物制剂及医药合约研发和加工服务 上海创诺医药集团有限公司/Shanghai Desano APIs and Finished products of ARV, Oncology, Anti-infection and Hormone drugs and E1H01 Pharmaceuticals Co., Ltd. -
Pregnane X Receptor (PXR)-Mediated Gene Repression and Cross-Talk of PXR with Other Nuclear Receptors Via Coactivator Interactions
fphar-07-00456 November 23, 2016 Time: 17:3 # 1 REVIEW published: 25 November 2016 doi: 10.3389/fphar.2016.00456 Pregnane X Receptor (PXR)-Mediated Gene Repression and Cross-Talk of PXR with Other Nuclear Receptors via Coactivator Interactions Petr Pavek* Department of Pharmacology and Toxicology and Centre for Drug Development, Faculty of Pharmacy in Hradec Kralove, Charles University in Prague, Hradec Kralove, Czechia Pregnane X receptor is a ligand-activated nuclear receptor (NR) that mainly controls inducible expression of xenobiotics handling genes including biotransformation enzymes and drug transporters. Nowadays it is clear that PXR is also involved in regulation of intermediate metabolism through trans-activation and trans-repression of genes controlling glucose, lipid, cholesterol, bile acid, and bilirubin homeostasis. In these processes PXR cross-talks with other NRs. Accumulating evidence suggests that the cross-talk is often mediated by competing for common coactivators or by disruption Edited by: of coactivation and activity of other transcription factors by the ligand-activated PXR. Ulrich M. Zanger, In this respect mainly PXR-CAR and PXR-HNF4a interference have been reported Dr. Margarete Fischer-Bosch-Institute and several cytochrome P450 enzymes (such as CYP7A1 and CYP8B1), phase II of Clinical Pharmacology, Germany enzymes (SULT1E1, Gsta2, Ugt1a1), drug and endobiotic transporters (OCT1, Mrp2, Reviewed by: Ramiro Jover, Mrp3, Oatp1a, and Oatp4) as well as intermediate metabolism enzymes (PEPCK1 and University of Valencia, Spain G6Pase) have been shown as down-regulated genes after PXR activation. In this review, Yuji Ishii, Kyushu University, Japan I summarize our current knowledge of PXR-mediated repression and coactivation *Correspondence: interference in PXR-controlled gene expression regulation. -
S41598-020-68561-7.Pdf
www.nature.com/scientificreports OPEN Prolongation of metallothionein induction combats Aß and α‑synuclein toxicity in aged transgenic Caenorhabditis elegans Dagmar Pretsch1*, Judith Maria Rollinger2, Axel Schmid3, Miroslav Genov 1, Teresa Wöhrer1, Liselotte Krenn2, Mark Moloney4, Ameya Kasture3, Thomas Hummel3 & Alexander Pretsch1 Neurodegenerative disorders (ND) like Alzheimer’s (AD), Parkinson’s (PD), Huntington’s or Prion diseases share similar pathological features. They are all age dependent and are often associated with disruptions in analogous metabolic processes such as protein aggregation and oxidative stress, both of which involve metal ions like copper, manganese and iron. Bush and Tanzi proposed 2008 in the ‘metal hypothesis of Alzheimer’s disease’ that a breakdown in metal homeostasis is the main cause of NDs, and drugs restoring metal homeostasis are promising novel therapeutic strategies. We report here that metallothionein (MT), an endogenous metal detoxifying protein, is increased in young amyloid ß (Aß) expressing Caenorhabditis elegans, whereas it is not in wild type strains. Further MT induction collapsed in 8 days old transgenic worms, indicating the age dependency of disease outbreak, and sharing intriguing parallels to diminished MT levels in human brains of AD. A medium throughput screening assay method was established to search for compounds increasing the MT level. Compounds known to induce MT release like progesterone, ZnSO 4, quercetin, dexamethasone and apomorphine were active in models of AD and PD. Thiofavin T, clioquinol and emodin are promising leads in AD and PD research, whose mode of action has not been fully established yet. In this study, we could show that the reduction of Aß and α‑synuclein toxicity in transgenic C. -
Expression of C-Terminal Modified Serine Palmitoyltransferase-1 Alters Chemosensitivity of Inflammation-Associated Human Cancer Cell Lines
Journal of Cancer Therapy, 2014, 5, 902-919 Published Online September 2014 in SciRes. http://www.scirp.org/journal/jct http://dx.doi.org/10.4236/jct.2014.510097 Expression of C-Terminal Modified Serine Palmitoyltransferase-1 Alters Chemosensitivity of Inflammation-Associated Human Cancer Cell Lines Tokunbo Yerokun Department of Biology, Spelman College, Atlanta, Georgia, USA Email: [email protected] Received 21 June 2014; revised 20 July 2014; accepted 15 August 2014 Copyright © 2014 by author and Scientific Research Publishing Inc. This work is licensed under the Creative Commons Attribution International License (CC BY). http://creativecommons.org/licenses/by/4.0/ Abstract Background: The human serine palmitoyltransferase-1, SPTLC1, subunit is emerging as a stress responsive protein with putative role in modulating cellular stress response behavior. When compared to the parental cell line, recombinant Glioma cells expressing C-terminal modified SPTLC1 are found to show resistance to the cytotoxic effect of polycyclic hydrocarbons, PHs, in- cluding the environmental contaminant 3-methylcholanthrene. This novel functional association of SPTLC1 expression with proliferative capacity is thought to be due, in part, to its ability for crosstalk with protein regulators of different biological processes. Whether the effect of SPTLC1 on sensitivity to PHs extends to therapeutic drugs and the progression of the malignant phenotype is of research interest. Methods: In the current study, sub-cellular localization was by immunos- taining for SPTLC1 in untreated and chemical treated cells and detection with confocal microscopy. The effect expressing C-terminal modified SPTLC1, in cancer cell lines of the inflammation-asso- ciated type, has on chemosensitivity and gene expression was also assessed.