Human Cytochrome P450 CYP2A13
Total Page:16
File Type:pdf, Size:1020Kb
Load more
Recommended publications
-
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. -
Cytochrome P450 Enzymes in Oxygenation of Prostaglandin Endoperoxides and Arachidonic Acid
Comprehensive Summaries of Uppsala Dissertations from the Faculty of Pharmacy 231 _____________________________ _____________________________ Cytochrome P450 Enzymes in Oxygenation of Prostaglandin Endoperoxides and Arachidonic Acid Cloning, Expression and Catalytic Properties of CYP4F8 and CYP4F21 BY JOHAN BYLUND ACTA UNIVERSITATIS UPSALIENSIS UPPSALA 2000 Dissertation for the Degree of Doctor of Philosophy (Faculty of Pharmacy) in Pharmaceutical Pharmacology presented at Uppsala University in 2000 ABSTRACT Bylund, J. 2000. Cytochrome P450 Enzymes in Oxygenation of Prostaglandin Endoperoxides and Arachidonic Acid: Cloning, Expression and Catalytic Properties of CYP4F8 and CYP4F21. Acta Universitatis Upsaliensis. Comprehensive Summaries of Uppsala Dissertations from Faculty of Pharmacy 231 50 pp. Uppsala. ISBN 91-554-4784-8. Cytochrome P450 (P450 or CYP) is an enzyme system involved in the oxygenation of a wide range of endogenous compounds as well as foreign chemicals and drugs. This thesis describes investigations of P450-catalyzed oxygenation of prostaglandins, linoleic and arachidonic acids. The formation of bisallylic hydroxy metabolites of linoleic and arachidonic acids was studied with human recombinant P450s and with human liver microsomes. Several P450 enzymes catalyzed the formation of bisallylic hydroxy metabolites. Inhibition studies and stereochemical analysis of metabolites suggest that the enzyme CYP1A2 may contribute to the biosynthesis of bisallylic hydroxy fatty acid metabolites in adult human liver microsomes. 19R-Hydroxy-PGE and 20-hydroxy-PGE are major components of human and ovine semen, respectively. They are formed in the seminal vesicles, but the mechanism of their biosynthesis is unknown. Reverse transcription-polymerase chain reaction using degenerate primers for mammalian CYP4 family genes, revealed expression of two novel P450 genes in human and ovine seminal vesicles. -
Transcriptomic Characterization of Fibrolamellar Hepatocellular
Transcriptomic characterization of fibrolamellar PNAS PLUS hepatocellular carcinoma Elana P. Simona, Catherine A. Freijeb, Benjamin A. Farbera,c, Gadi Lalazara, David G. Darcya,c, Joshua N. Honeymana,c, Rachel Chiaroni-Clarkea, Brian D. Dilld, Henrik Molinad, Umesh K. Bhanote, Michael P. La Quagliac, Brad R. Rosenbergb,f, and Sanford M. Simona,1 aLaboratory of Cellular Biophysics, The Rockefeller University, New York, NY 10065; bPresidential Fellows Laboratory, The Rockefeller University, New York, NY 10065; cDivision of Pediatric Surgery, Department of Surgery, Memorial Sloan-Kettering Cancer Center, New York, NY 10065; dProteomics Resource Center, The Rockefeller University, New York, NY 10065; ePathology Core Facility, Memorial Sloan-Kettering Cancer Center, New York, NY 10065; and fJohn C. Whitehead Presidential Fellows Program, The Rockefeller University, New York, NY 10065 Edited by Susan S. Taylor, University of California, San Diego, La Jolla, CA, and approved September 22, 2015 (received for review December 29, 2014) Fibrolamellar hepatocellular carcinoma (FLHCC) tumors all carry a exon of DNAJB1 and all but the first exon of PRKACA. This deletion of ∼400 kb in chromosome 19, resulting in a fusion of the produced a chimeric RNA transcript and a translated chimeric genes for the heat shock protein, DNAJ (Hsp40) homolog, subfam- protein that retains the full catalytic activity of wild-type PKA. ily B, member 1, DNAJB1, and the catalytic subunit of protein ki- This chimeric protein was found in 15 of 15 FLHCC patients nase A, PRKACA. The resulting chimeric transcript produces a (21) in the absence of any other recurrent mutations in the DNA fusion protein that retains kinase activity. -
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. -
© Copyright 2017 Yichen
© Copyright 2017 Yichen Jia Prediction of CYP3A4 metabolic activity from whole genome RNA-seq data with feature selection machine learning methods Yichen Jia A thesis submitted in partial fulfillment of the requirements for the degree of Master of Science University of Washington 2017 Reading Committee: Timothy A. Thornton, PhD; Chair Michael C. Wu, PhD Program Authorized to Offer Degree: Biostatistics University of Washington Abstract Prediction of CYP3A4 metabolic activity from whole genome RNA-seq data with feature selection machine learning methods Yichen Jia Chair of the Supervisory Committee: Timothy A. Thornton, Robert W. Day Endowed Professor of Public Health, Associate Professor Department of Biostatistics CYP3A4, one of the isozyme of the cytochromes P450 (CYPs), contributes significantly to drug clearance and drug-drug interactions. The goals of this project are to identify hepatically- expressed genes that are associated with CYP3A4 metabolic activity in human liver tissue and to predict CYP3A4 activity using gene expression data from whole genome RNA sequences. Due to the high-dimensionality of the dataset, we applied lasso and elastic net, two feature selection machine learning methods, for prediction and graphical lasso was used for constructing gene network graphs. A simulation study was performed to assess the performance of the prediction algorithms and to evaluate the efficiency of gene selection using the machine learning methods. We assessed prediction performance based on correlations, and the correlation between measured CYP3A4 activity and predicted activity was approximately 0.4 and 0.5 when reductase was excluded and included, respectively, for both lasso and elastic net. In addition to the CYP3A4 gene, we also identified the GZMA gene as a strong candidate for prediction of CYP3A4 activity that should be investigated in future studies. -
Altered Levels of Cytochrome P450 Genes in Hepatitis B Or C Virus-Infected Liver Identified by Oligonucleotide Microarray
CANCER GENOMICS & PROTEOMICS 1: 53-58 (2004) Altered Levels of Cytochrome P450 Genes in Hepatitis B or C Virus-infected Liver Identified by Oligonucleotide Microarray NORIO IIZUKA1,2, MASAAKI OKA1, YOSHIHIKO HAMAMOTO3, NAOHIDE MORI1, TAKAO TAMESA1, AKIRA TANGOKU1, TAKANOBU MIYAMOTO3, SHUNJI UCHIMURA3, HIRONOBU NAKAYAMA4, KENJI HAMADA4 and HISAFUMI YAMADA-OKABE4 1Department of Surgery II and 2Department of Bioregulatory Function, Yamaguchi University School of Medicine, 1-1-1 Minami-kogushi, Ube, Yamaguchi 755-8505; 3Department of Computer Science and Systems Engineering, Faculty of Engineering, Yamaguchi University, 2-16-1 Tokiwadai, Ube, Yamaguchi 755-8611; 4Pharmaceutical Research Department 4, Kamakaura Research Laboratories, Chugai Pharmaceutical Co. Ltd., 200 Kajiwara, Kamakura, Kanagawa 247-8530, Japan Abstract. Background: Molecular pathogenesis of hepatocellular (1,2). However, the genetic basis underlying these diseases carcinoma (HCC) remains to be clarified. Many studies with DNA remains unclear. To overcome this dilemma, many chip technology have revealed altered levels of several cytochrome researchers have applied DNA chip technology to elucidate P450 (CYP) family genes in human HCC. However, little is known genome-wide changes in these diseases (3-13). Interestingly, about their alterations in hepatitis B virus (HBV)- and hepatitis C as summarized in Table I, commonly found in those studies virus (HCV)-infected livers. Materials and Methods: We here used are altered levels of several cytochrome P450 family genes high-density oligonucleotide arrays to evaluate alterations of CYP (CYPs), such as CYP2E, CYP2A6 and CYP2A7, in HCC genes in five of each HBV- or HCV-infected livers in comparison versus non-cancerous liver. with six normal livers. We extracted the data of 32 CYP genes from The cytochrome P450 system is a group of enzymes that are those of 12600 genes. -
CYP2A7 (NM 000764) Human Recombinant Protein Product Data
OriGene Technologies, Inc. 9620 Medical Center Drive, Ste 200 Rockville, MD 20850, US Phone: +1-888-267-4436 [email protected] EU: [email protected] CN: [email protected] Product datasheet for TP313527 CYP2A7 (NM_000764) Human Recombinant Protein Product data: Product Type: Recombinant Proteins Description: Recombinant protein of human cytochrome P450, family 2, subfamily A, polypeptide 7 (CYP2A7), transcript variant 1 Species: Human Expression Host: HEK293T Tag: C-Myc/DDK Predicted MW: 56.2 kDa Concentration: >50 ug/mL as determined by microplate BCA method Purity: > 80% as determined by SDS-PAGE and Coomassie blue staining Buffer: 25 mM Tris.HCl, pH 7.3, 100 mM glycine, 10% glycerol Preparation: Recombinant protein was captured through anti-DDK affinity column followed by conventional chromatography steps. Storage: Store at -80°C. Stability: Stable for 12 months from the date of receipt of the product under proper storage and handling conditions. Avoid repeated freeze-thaw cycles. RefSeq: NP_000755 Locus ID: 1549 UniProt ID: P20853 RefSeq Size: 2281 Cytogenetics: 19q13.2 RefSeq ORF: 1482 Synonyms: CPA7; CPAD; CYP2A; CYPIIA7; P450-IIA4 This product is to be used for laboratory only. Not for diagnostic or therapeutic use. View online » ©2021 OriGene Technologies, Inc., 9620 Medical Center Drive, Ste 200, Rockville, MD 20850, US 1 / 2 CYP2A7 (NM_000764) Human Recombinant Protein – TP313527 Summary: This gene encodes a member of the cytochrome P450 superfamily of enzymes. The cytochrome P450 proteins are monooxygenases which catalyze many reactions involved in drug metabolism and synthesis of cholesterol, steroids and other lipids. This protein localizes to the endoplasmic reticulum; its substrate has not yet been determined. -
Simulation of Physicochemical and Pharmacokinetic Properties of Vitamin D3 and Its Natural Derivatives
pharmaceuticals Article Simulation of Physicochemical and Pharmacokinetic Properties of Vitamin D3 and Its Natural Derivatives Subrata Deb * , Anthony Allen Reeves and Suki Lafortune Department of Pharmaceutical Sciences, College of Pharmacy, Larkin University, Miami, FL 33169, USA; [email protected] (A.A.R.); [email protected] (S.L.) * Correspondence: [email protected] or [email protected]; Tel.: +1-224-310-7870 or +1-305-760-7479 Received: 9 June 2020; Accepted: 20 July 2020; Published: 23 July 2020 Abstract: Vitamin D3 is an endogenous fat-soluble secosteroid, either biosynthesized in human skin or absorbed from diet and health supplements. Multiple hydroxylation reactions in several tissues including liver and small intestine produce different forms of vitamin D3. Low serum vitamin D levels is a global problem which may origin from differential absorption following supplementation. The objective of the present study was to estimate the physicochemical properties, metabolism, transport and pharmacokinetic behavior of vitamin D3 derivatives following oral ingestion. GastroPlus software, which is an in silico mechanistically-constructed simulation tool, was used to simulate the physicochemical and pharmacokinetic behavior for twelve vitamin D3 derivatives. The Absorption, Distribution, Metabolism, Excretion and Toxicity (ADMET) Predictor and PKPlus modules were employed to derive the relevant parameters from the structural features of the compounds. The majority of the vitamin D3 derivatives are lipophilic (log P values > 5) with poor water solubility which are reflected in the poor predicted bioavailability. The fraction absorbed values for the vitamin D3 derivatives were low except for calcitroic acid, 1,23S,25-trihydroxy-24-oxo-vitamin D3, and (23S,25R)-1,25-dihydroxyvitamin D3-26,23-lactone each being greater than 90% fraction absorbed. -
Diazepam Therapy and CYP2C19 Genotype
NLM Citation: Dean L. Diazepam Therapy and CYP2C19 Genotype. 2016 Aug 25. In: Pratt VM, McLeod HL, Rubinstein WS, et al., editors. Medical Genetics Summaries [Internet]. Bethesda (MD): National Center for Biotechnology Information (US); 2012-. Bookshelf URL: https://www.ncbi.nlm.nih.gov/books/ Diazepam Therapy and CYP2C19 Genotype Laura Dean, MD1 Created: August 25, 2016. Introduction Diazepam is a benzodiazepine with several clinical uses, including the management of anxiety, insomnia, muscle spasms, seizures, and alcohol withdrawal. The clinical response to benzodiazepines, such as diazepam, varies widely between individuals (1, 2). Diazepam is primarily metabolized by CY2C19 and CYP3A4 to the major active metabolite, desmethyldiazepam. Approximately 3% of Caucasians and 15 to 20% of Asians have reduced or absent CYP2C19 enzyme activity (“poor metabolizers”). In these individuals, standard doses of diazepam may lead to a higher exposure to diazepam. The FDA-approved drug label for diazepam states that “The marked inter-individual variability in the clearance of diazepam reported in the literature is probably attributable to variability of CYP2C19 (which is known to exhibit genetic polymorphism; about 3-5% of Caucasians have little or no activity and are “poor metabolizers”) and CYP3A4” (1). Drug: Diazepam Diazepam is used in the management of anxiety disorders or for the short-term relief of the symptoms of anxiety. In acute alcohol withdrawal, diazepam may provide symptomatic relief from agitation, tremor, delirium tremens, and hallucinations. Diazepam is also useful as an adjunct treatment for the relief of acute skeletal muscle spasms, as well as spasticity caused by upper motor neuron disorders (3). There are currently 16 benzodiazepines licensed by the FDA. -
Variation in CYP2A6 Activity and Personalized Medicine
Journal of Personalized Medicine Review Variation in CYP2A6 Activity and Personalized Medicine Julie-Anne Tanner 1,2 and Rachel F. Tyndale 1,2,3,* 1 Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health (CAMH), Toronto, ON M5T 1R8, Canada; [email protected] 2 Department of Pharmacology and Toxicology, University of Toronto, Toronto, ON M5S 1A8, Canada 3 Department of Psychiatry, University of Toronto, Toronto, ON M5T 1R8, Canada * Correspondence: [email protected]; Tel.: +1-416-978-6374; Fax: +1-416-978-6395 Academic Editor: Stephen B. Liggett Received: 7 October 2017; Accepted: 27 November 2017; Published: 1 December 2017 Abstract: The cytochrome P450 2A6 (CYP2A6) enzyme metabolizes several clinically relevant substrates, including nicotine—the primary psychoactive component in cigarette smoke. The gene that encodes the CYP2A6 enzyme is highly polymorphic, resulting in extensive interindividual variation in CYP2A6 enzyme activity and the rate of metabolism of nicotine and other CYP2A6 substrates including cotinine, tegafur, letrozole, efavirenz, valproic acid, pilocarpine, artemisinin, artesunate, SM-12502, caffeine, and tyrosol. CYP2A6 expression and activity are also impacted by non-genetic factors, including induction or inhibition by pharmacological, endogenous, and dietary substances, as well as age-related changes, or interactions with other hepatic enzymes, co-enzymes, and co-factors. As variation in CYP2A6 activity is associated with smoking behavior, smoking cessation, tobacco-related lung cancer risk, and with altered metabolism and resulting clinical responses for several therapeutics, CYP2A6 expression and enzyme activity is an important clinical consideration. This review will discuss sources of variation in CYP2A6 enzyme activity, with a focus on the impact of CYP2A6 genetic variation on metabolism of the CYP2A6 substrates. -
Metabolic Activation and Toxicological Evaluation of Polychlorinated Biphenyls in Drosophila Melanogaster T
www.nature.com/scientificreports OPEN Metabolic activation and toxicological evaluation of polychlorinated biphenyls in Drosophila melanogaster T. Idda1,7, C. Bonas1,7, J. Hofmann1, J. Bertram1, N. Quinete1,2, T. Schettgen1, K. Fietkau3, A. Esser1, M. B. Stope4, M. M. Leijs3, J. M. Baron3, T. Kraus1, A. Voigt5,6 & P. Ziegler1* Degradation of polychlorinated biphenyls (PCBs) is initiated by cytochrome P450 (CYP) enzymes and includes PCB oxidation to OH-metabolites, which often display a higher toxicity than their parental compounds. In search of an animal model refecting PCB metabolism and toxicity, we tested Drosophila melanogaster, a well-known model system for genetics and human disease. Feeding Drosophila with lower chlorinated (LC) PCB congeners 28, 52 or 101 resulted in the detection of a human-like pattern of respective OH-metabolites in fy lysates. Feeding fies high PCB 28 concentrations caused lethality. Thus we silenced selected CYPs via RNA interference and analyzed the efect on PCB 28-derived metabolite formation by assaying 3-OH-2′,4,4′-trichlorobiphenyl (3-OHCB 28) and 3′-OH-4′,4,6′-trichlorobiphenyl (3′-OHCB 28) in fy lysates. We identifed several drosophila CYPs (dCYPs) whose knockdown reduced PCB 28-derived OH-metabolites and suppressed PCB 28 induced lethality including dCYP1A2. Following in vitro analysis using a liver-like CYP-cocktail, containing human orthologues of dCYP1A2, we confrm human CYP1A2 as a PCB 28 metabolizing enzyme. PCB 28-induced mortality in fies was accompanied by locomotor impairment, a common phenotype of neurodegenerative disorders. Along this line, we show PCB 28-initiated caspase activation in diferentiated fy neurons. -
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