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Identification and Developmental Expression of the Full Complement Of
Goldstone et al. BMC Genomics 2010, 11:643 http://www.biomedcentral.com/1471-2164/11/643 RESEARCH ARTICLE Open Access Identification and developmental expression of the full complement of Cytochrome P450 genes in Zebrafish Jared V Goldstone1, Andrew G McArthur2, Akira Kubota1, Juliano Zanette1,3, Thiago Parente1,4, Maria E Jönsson1,5, David R Nelson6, John J Stegeman1* Abstract Background: Increasing use of zebrafish in drug discovery and mechanistic toxicology demands knowledge of cytochrome P450 (CYP) gene regulation and function. CYP enzymes catalyze oxidative transformation leading to activation or inactivation of many endogenous and exogenous chemicals, with consequences for normal physiology and disease processes. Many CYPs potentially have roles in developmental specification, and many chemicals that cause developmental abnormalities are substrates for CYPs. Here we identify and annotate the full suite of CYP genes in zebrafish, compare these to the human CYP gene complement, and determine the expression of CYP genes during normal development. Results: Zebrafish have a total of 94 CYP genes, distributed among 18 gene families found also in mammals. There are 32 genes in CYP families 5 to 51, most of which are direct orthologs of human CYPs that are involved in endogenous functions including synthesis or inactivation of regulatory molecules. The high degree of sequence similarity suggests conservation of enzyme activities for these CYPs, confirmed in reports for some steroidogenic enzymes (e.g. CYP19, aromatase; CYP11A, P450scc; CYP17, steroid 17a-hydroxylase), and the CYP26 retinoic acid hydroxylases. Complexity is much greater in gene families 1, 2, and 3, which include CYPs prominent in metabolism of drugs and pollutants, as well as of endogenous substrates. -
Synonymous Single Nucleotide Polymorphisms in Human Cytochrome
DMD Fast Forward. Published on February 9, 2009 as doi:10.1124/dmd.108.026047 DMD #26047 TITLE PAGE: A BIOINFORMATICS APPROACH FOR THE PHENOTYPE PREDICTION OF NON- SYNONYMOUS SINGLE NUCLEOTIDE POLYMORPHISMS IN HUMAN CYTOCHROME P450S LIN-LIN WANG, YONG LI, SHU-FENG ZHOU Department of Nutrition and Food Hygiene, School of Public Health, Peking University, Beijing 100191, P. R. China (LL Wang & Y Li) Discipline of Chinese Medicine, School of Health Sciences, RMIT University, Bundoora, Victoria 3083, Australia (LL Wang & SF Zhou). 1 Copyright 2009 by the American Society for Pharmacology and Experimental Therapeutics. DMD #26047 RUNNING TITLE PAGE: a) Running title: Prediction of phenotype of human CYPs. b) Author for correspondence: A/Prof. Shu-Feng Zhou, MD, PhD Discipline of Chinese Medicine, School of Health Sciences, RMIT University, WHO Collaborating Center for Traditional Medicine, Bundoora, Victoria 3083, Australia. Tel: + 61 3 9925 7794; fax: +61 3 9925 7178. Email: [email protected] c) Number of text pages: 21 Number of tables: 10 Number of figures: 2 Number of references: 40 Number of words in Abstract: 249 Number of words in Introduction: 749 Number of words in Discussion: 1459 d) Non-standard abbreviations: CYP, cytochrome P450; nsSNP, non-synonymous single nucleotide polymorphism. 2 DMD #26047 ABSTRACT Non-synonymous single nucleotide polymorphisms (nsSNPs) in coding regions that can lead to amino acid changes may cause alteration of protein function and account for susceptivity to disease. Identification of deleterious nsSNPs from tolerant nsSNPs is important for characterizing the genetic basis of human disease, assessing individual susceptibility to disease, understanding the pathogenesis of disease, identifying molecular targets for drug treatment and conducting individualized pharmacotherapy. -
Novel Copy-Number Variations in Pharmacogenes Contribute to Interindividual Differences in Drug Pharmacokinetics
ORIGINAL RESEARCH ARTICLE © American College of Medical Genetics and Genomics Novel copy-number variations in pharmacogenes contribute to interindividual differences in drug pharmacokinetics María Santos, MSc1, Mikko Niemi, PhD2, Masahiro Hiratsuka, PhD3, Masaki Kumondai, BSc3, Magnus Ingelman-Sundberg, PhD4, Volker M. Lauschke, PhD4 and Cristina Rodríguez-Antona, PhD1,5 Purpose: Variability in pharmacokinetics and drug response is of the genes studied. We experimentally confirmed novel deletions shaped by single-nucleotide variants (SNVs) as well as copy- in CYP2C19, CYP4F2, and SLCO1B3 by Sanger sequencing and number variants (CNVs) in genes with importance for drug validated their allelic frequencies in selected populations. absorption, distribution, metabolism, and excretion (ADME). Conclusion: CNVs are an additional source of pharmacogenetic While SNVs have been extensively studied, a systematic assessment variability with important implications for drug response and of the CNV landscape in ADME genes is lacking. personalized therapy. This, together with the important contribu- Methods: We integrated data from 2,504 whole genomes from the tion of rare alleles to the variability of pharmacogenes, emphasizes 1000 Genomes Project and 59,898 exomes from the Exome the necessity of comprehensive next-generation sequencing–based Aggregation Consortium to identify CNVs in 208 relevant genotype identification for an accurate prediction of the genetic pharmacogenes. variability of drug pharmacokinetics. Results: We describe novel exonic deletions -
Rapid Birth–Death Evolution Specific to Xenobiotic Cytochrome P450 Genes in Vertebrates
Rapid Birth–Death Evolution Specific to Xenobiotic Cytochrome P450 Genes in Vertebrates James H. Thomas* Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America Genes vary greatly in their long-term phylogenetic stability and there exists no general explanation for these differences. The cytochrome P450 (CYP450) gene superfamily is well suited to investigating this problem because it is large and well studied, and it includes both stable and unstable genes. CYP450 genes encode oxidase enzymes that function in metabolism of endogenous small molecules and in detoxification of xenobiotic compounds. Both types of enzymes have been intensively studied. My analysis of ten nearly complete vertebrate genomes indicates that each genome contains 50–80 CYP450 genes, which are about evenly divided between phylogenetically stable and unstable genes. The stable genes are characterized by few or no gene duplications or losses in species ranging from bony fish to mammals, whereas unstable genes are characterized by frequent gene duplications and losses (birth–death evolution) even among closely related species. All of the CYP450 genes that encode enzymes with known endogenous substrates are phylogenetically stable. In contrast, most of the unstable genes encode enzymes that function as xenobiotic detoxifiers. Nearly all unstable CYP450 genes in the mouse and human genomes reside in a few dense gene clusters, forming unstable gene islands that arose by recurrent local gene duplication. Evidence for positive selection in amino acid sequence is restricted to these unstable CYP450 genes, and sites of selection are associated with substrate-binding regions in the protein structure. These results can be explained by a general model in which phylogenetically stable genes have core functions in development and physiology, whereas unstable genes have accessory functions associated with unstable environmental interactions such as toxin and pathogen exposure. -
Conformational Changes in Binding of Substrates with Human Cytochrome P450 Enzymes
Book of oral abstracts 100 Conformational changes in binding of substrates with human cytochrome P450 enzymes F. Peter Guengerich, Clayton J. Wilkey, Michael J. Reddish, Sarah M. Glass, and Thanh T. N. Phan Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN, USA Introduction. Extensive evidence now exists that P450 enzymes can exist in multiple conformations, at least in the substrate-bound forms (e.g., crystallography). This multiplicity can be the result of either an induced fit mechanism or conformational selection (selective substrate binding to one of two or more equilibrating P450 conformations). Aims. Kinetic approaches can be used to distinguish between induced fit and conformational selection models. The same energy is involved in reaching the final state, regardless of the kinetic path. Methods. Stopped-flow absorbance and fluorescence measurements were made with recombinant human P450 enzymes. Analysis utilized kinetic modeling software (KinTek Explorer®). Results. P450 17A1 binding to its steroid ligands (pregnenolone and progesterone and the 17-hydroxy derivatives) is dominated by a conformational selection process, as judged by (a) decreasing rates of substrate binding as a function of substrate concentration, (b) opposite patterns of the dependence of binding rates as a function of varying concentrations of (i) substrate and (ii) enzyme, and (c) modeling of the data in KinTek Explorer. The inhibitory drugs orteronel and abiraterone bind P450 17A1 in multi-step processes, apparently in different ways. The dye Nile Red is also a substrate for P450 17A1 and its sequential binding to the enzyme can be resolved in fluorescence and absorbance changes. P450s 2C8, 2D6, 2E1, and 4A11 have also been analyzed with regard to substrate binding and utilize primarily conformational selection models, as revealed by analysis of binding rates vs. -
Expression of CYP2S1 in Human Hepatic Stellate Cells
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Elsevier - Publisher Connector FEBS Letters 581 (2007) 781–786 Expression of CYP2S1 in human hepatic stellate cells Carylyn J. Mareka, Steven J. Tuckera, Matthew Korutha, Karen Wallacea,b, Matthew C. Wrighta,b,* a School of Medical Sciences, Institute of Medical Science, University of Aberdeen, Aberdeen, UK b Liver Faculty Research Group, School of Clinical and Laboratory Sciences, University of Newcastle, Newcastle, UK Received 22 November 2006; revised 16 January 2007; accepted 23 January 2007 Available online 2 February 2007 Edited by Laszlo Nagy the expression and accumulation of scarring extracellular Abstract Activated stellate cells are myofibroblast-like cells associated with the generation of fibrotic scaring in chronically fibrotic matrix protein [2]. It is currently thought an inhibition damaged liver. Gene chip analysis was performed on cultured fi- of fibrosis in liver diseases may be an effective approach to brotic stellate cells. Of the 51 human CYP genes known, 13 treating patients for which the cause is refractive to current CYP and 5 CYP reduction-related genes were detected with 4 treatments (e.g. in approx. 30% of hepatitis C infected CYPs (CYP1A1, CYP2E1, CY2S1 and CYP4F3) consistently patients) [2,3]. At present, there is no approved treatment for present in stellate cells isolated from three individuals. Quantita- fibrosis. tive RT-PCR indicated that CYP2S1 was a major expressed Inadvertent toxicity of drugs is often associated with a ‘‘met- CYP mRNA transcript. The presence of a CYP2A-related pro- abolic activation’’ by CYPs [1]. -
Rapid Birth–Death Evolution Specific to Xenobiotic Cytochrome P450 Genes in Vertebrates
Rapid Birth–Death Evolution Specific to Xenobiotic Cytochrome P450 Genes in Vertebrates James H. Thomas* Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America Genes vary greatly in their long-term phylogenetic stability and there exists no general explanation for these differences. The cytochrome P450 (CYP450) gene superfamily is well suited to investigating this problem because it is large and well studied, and it includes both stable and unstable genes. CYP450 genes encode oxidase enzymes that function in metabolism of endogenous small molecules and in detoxification of xenobiotic compounds. Both types of enzymes have been intensively studied. My analysis of ten nearly complete vertebrate genomes indicates that each genome contains 50–80 CYP450 genes, which are about evenly divided between phylogenetically stable and unstable genes. The stable genes are characterized by few or no gene duplications or losses in species ranging from bony fish to mammals, whereas unstable genes are characterized by frequent gene duplications and losses (birth–death evolution) even among closely related species. All of the CYP450 genes that encode enzymes with known endogenous substrates are phylogenetically stable. In contrast, most of the unstable genes encode enzymes that function as xenobiotic detoxifiers. Nearly all unstable CYP450 genes in the mouse and human genomes reside in a few dense gene clusters, forming unstable gene islands that arose by recurrent local gene duplication. Evidence for positive selection in amino acid sequence is restricted to these unstable CYP450 genes, and sites of selection are associated with substrate-binding regions in the protein structure. These results can be explained by a general model in which phylogenetically stable genes have core functions in development and physiology, whereas unstable genes have accessory functions associated with unstable environmental interactions such as toxin and pathogen exposure. -
Biodiversity of P-450 Monooxygenase: Cross-Talk
Cytochrome P450: Oxygen activation and biodiversty 1 Biodiversity of P-450 monooxygenase: Cross-talk between chemistry and biology Heme Fe(II)-CO complex 450 nm, different from those of hemoglobin and other heme proteins 410-420 nm. Cytochrome Pigment of 450 nm Cytochrome P450 CYP3A4…. 2 High Energy: Ultraviolet (UV) Low Energy: Infrared (IR) Soret band 420 nm or g-band Mb Fe(II) ---------- Mb Fe(II) + CO - - - - - - - Visible region Visible bands Q bands a-band, b-band b a 3 H2O/OH- O2 CO Fe(III) Fe(II) Fe(II) Fe(II) Soret band at 420 nm His His His His metHb deoxy Hb Oxy Hb Carbon monoxy Hb metMb deoxy Mb Oxy Mb Carbon monoxy Mb H2O/Substrate O2-Substrate CO Substrate Soret band at 450 nm Fe(III) Fe(II) Fe(II) Fe(II) Cytochrome P450 Cys Cys Cys Cys Active form 4 Monooxygenase Reactions by Cytochromes P450 (CYP) + + RH + O2 + NADPH + H → ROH + H2O + NADP RH: Hydrophobic (lipophilic) compounds, organic compounds, insoluble in water ROH: Less hydrophobic and slightly soluble in water. Drug metabolism in liver ROH + GST → R-GS GST: glutathione S-transferase ROH + UGT → R-UG UGT: glucuronosyltransferaseGlucuronic acid Insoluble compounds are converted into highly hydrophilic (water soluble) compounds. 5 Drug metabolism at liver: Sleeping pill, pain killer (Narcotic), carcinogen etc. Synthesis of steroid hormones (steroidgenesis) at adrenal cortex, brain, kidney, intestine, lung, Animal (Mammalian, Fish, Bird, Insect), Plants, Fungi, Bacteria 6 NSAID: non-steroid anti-inflammatory drug 7 8 9 10 11 Cytochrome P450: Cysteine-S binding to Fe(II) heme is important for activation of O2. -
Differential Expression of Prostaglandin I2 Synthase Associated with Arachidonic Acid Pathway in the Oral Squamous Cell Carcinoma
Hindawi Journal of Oncology Volume 2018, Article ID 6301980, 13 pages https://doi.org/10.1155/2018/6301980 Research Article Differential Expression of Prostaglandin I2 Synthase Associated with Arachidonic Acid Pathway in the Oral Squamous Cell Carcinoma Anelise Russo ,1 Patr-cia M. Biselli-Chicote ,1 Rosa S. Kawasaki-Oyama,1 Márcia M. U. Castanhole-Nunes,1 José V. Maniglia,2 Dal-sio de Santi Neto,3 Érika C. Pavarino ,1 and Eny M. Goloni-Bertollo 1 1 Department of Molecular Biology: Biological and Genetics and Molecular Biology Research Unit – UPGEM, Sao˜ Jose´ do Rio Preto Medical School – FAMERP, Sao˜ Jose´ do Rio Preto, SP 15090-000, Brazil 2Department of Otorhinolaryngology and Head and Neck Surgery, FAMERP, Sao˜ Jose´ do Rio Preto, SP 15090-000, Brazil 3Department of Pathology, FAMERP, Sao˜ Jose´ do Rio Preto, SP 15090-000, Brazil Correspondence should be addressed to Anelise Russo; [email protected] and Eny M. Goloni-Bertollo; [email protected] Received 17 July 2018; Accepted 16 October 2018; Published 8 November 2018 Academic Editor: Tomas R. Chauncey Copyright © 2018 Anelise Russo et al. Tis is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Introduction. Diferential expression of genes encoding cytochrome P450 (CYP) and other oxygenases enzymes involved in biotransformation mechanisms of endogenous and exogenous compounds can lead to oral tumor development. Objective.We aimed to identify the expression profle of these genes, searching for susceptibility biomarkers in oral squamous cell carcinoma. -
The Common Analgesic Paracetamol Enhances the Anti-Tumour Activity of Decitabine Through Exacerbation of Oxidative Stress
Supplementary information for: The common analgesic paracetamol enhances the anti-tumour activity of decitabine through exacerbation of oxidative stress Hannah J. Gleneadie, Amy Baker, Nikolaos Batis, Jennifer Bryant, Yao Jiang, Samuel J.H. Clokie, Hisham Mehanna, Paloma Garcia, Deena M.A. Gendoo, Sally Roberts, Alfredo A. Molinolo, J. Silvio Gutkind, Ben A. Scheven, Paul R. Cooper, Farhat L. Khanim, Malgorzata Wiench. The Appendix contains the following supplementary information: SI Tables S1 to S7 (Tables S3 and S4 as separate .xlsx files) SI Figures S1 to S7 1 SI Supplementary Tables Table S1. DRI (Dose Reduction Index) for VU40T, combined treatment. VU40T Fa Dose DRI (%) DAC Para DAC Para 10 0.01 105 0.30 10.18 25 0.16 251 1.22 7.11 50 2.26 595 4.99 4.97 75 31 1414 20.35 3.47 97 9300 9200 426 1.59 Table S2. DRI for HN12, combined treatment. HN12 Fa Dose DRI (%) DAC Para DAC Para 10 0.004 186 0.49 80 25 0.06 1962 1.19 147 50 0.85 20653 2.92 269 75 11.92 217412 7.15 493 97 3630 3.55E+07 49.5 1827 2 Table S3. Differentially expressed (increased and decreased) genes in VU40T cells following DAC, paracetamol and DAC+paracetamol treatments. See the Table_S3.xlsx file. Table S4. Full list of GO terms from REVIGO for differentially expressed groups (DAC, paracetamol and DAC+paracetamol treatments). See the Table_S4.xlsx file. 3 Table S5. cBioPortal RNA-seq data (for cancers with provisional TCGA data): frequency of expression alterations (%) in genes from COX-2-PGE2 pathway and correlation to survival (Logrank test p-value). -
The Cytochrome P450 (CYP) Superfamily in Cnidarians Kirill V
www.nature.com/scientificreports OPEN The cytochrome P450 (CYP) superfamily in cnidarians Kirill V. Pankov1,2, Andrew G. McArthur1, David A. Gold3, David R. Nelson4, Jared V. Goldstone5 & Joanna Y. Wilson2* The cytochrome P450 (CYP) superfamily is a diverse and important enzyme family, playing a central role in chemical defense and in synthesis and metabolism of major biological signaling molecules. The CYPomes of four cnidarian genomes (Hydra vulgaris, Acropora digitifera, Aurelia aurita, Nematostella vectensis) were annotated; phylogenetic analyses determined the evolutionary relationships amongst the sequences and with existing metazoan CYPs. 155 functional CYPs were identifed and 90 fragments. Genes were from 24 new CYP families and several new subfamilies; genes were in 9 of the 12 established metazoan CYP clans. All species had large expansions of clan 2 diversity, with H. vulgaris having reduced diversity for both clan 3 and mitochondrial clan. We identifed potential candidates for xenobiotic metabolism and steroidogenesis. That each genome contained multiple, novel CYP families may refect the large evolutionary distance within the cnidarians, unique physiology in the cnidarian classes, and/or diferent ecology of the individual species. The cytochrome P450 superfamily. Te cytochrome P450 (CYP) superfamily consists of a large group of hemeproteins that catalyze a wide range of reactions, playing important roles in several fundamental bio- logical processes (e.g. steroid synthesis, fatty acid metabolism, chemical defense)1. CYPs primarily perform a monooxygenase function, adding polar hydroxyl groups to a substrate, making it more reactive and hydrophilic2. Each individual CYP has a specifc suite of compounds that ft into its active site, ofen with a structure–activ- ity relationship. -
Genome-Based Analysis of the Nonhuman Primate Macaca Fascicularis As a Model for Drug Safety Assessment
Downloaded from genome.cshlp.org on October 8, 2021 - Published by Cold Spring Harbor Laboratory Press Resource Genome-based analysis of the nonhuman primate Macaca fascicularis as a model for drug safety assessment Martin Ebeling,1 Erich Ku¨ng,2 Angela See,3 Clemens Broger,4 Guido Steiner,1 Marco Berrera,1 Tobias Heckel,2 Leonardo Iniguez,3 Thomas Albert,3 Roland Schmucki,1 Hermann Biller,4 Thomas Singer,2 and Ulrich Certa2,5 1Translational Research Sciences, F. Hoffmann-La Roche AG, Pharmaceutical Research and Early Development (pRED), 4070 Basel, Switzerland; 2Global Non-clinical Safety, F. Hoffmann-La Roche AG, Pharmaceutical Research and Early Development (pRED), 4070 Basel, Switzerland; 3Roche NimbleGen, Inc., Madison, Wisconsin 53719, USA; 4Research Informatics, F. Hoffmann-La Roche AG, Pharmaceutical Research and Early Development (pRED), 4070 Basel, Switzerland The long-tailed macaque, also referred to as cynomolgus monkey (Macaca fascicularis), is one of the most important nonhuman primate animal models in basic and applied biomedical research. To improve the predictive power of primate experiments for humans, we determined the genome sequence of a Macaca fascicularis female of Mauritian origin using a whole-genome shotgun sequencing approach. We applied a template switch strategy that uses either the rhesus or the human genome to assemble sequence reads. The sixfold sequence coverage of the draft genome sequence enabled dis- covery of about 2.1 million potential single-nucleotide polymorphisms based on occurrence of a dimorphic nucleotide at a given position in the genome sequence. Homology-based annotation allowed us to identify 17,387 orthologs of human protein-coding genes in the M.