151
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Kato H. Computational prediction of cytochrome P450 inhibition and induction. Drug Metab Pharmacokinet 2019; 35:30-44. [PMID: 31902468 DOI: 10.1016/j.dmpk.2019.11.006] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Revised: 10/27/2019] [Accepted: 11/17/2019] [Indexed: 12/14/2022]
Abstract
Cytochrome P450 (CYP) enzymes play an important role in the phase I metabolism of many xenobiotics. Most drug-drug interactions (DDIs) associated with CYP are caused by either CYP inhibition or induction. The early detection of potential DDIs is highly desirable in the pharmaceutical industry because DDIs can cause serious adverse events, which can lead to poor patient health and drug development failures. Recently, many computational studies predicting CYP inhibition and induction have been reported. The current computational modeling approaches for CYP metabolism are classified as ligand- and structure-based; various techniques, such as quantitative structure-activity relationships, machine learning, docking, and molecular dynamic simulation, are involved in both the approaches. Recently, combining these two approaches have resulted in improvements in the prediction accuracy of DDIs. In this review, we present important, recent developments in the computational prediction of the inhibition of four clinically crucial CYP isoforms (CYP1A2, 2C9, 2D6, and 3A4) and three nuclear receptors (aryl hydrocarbon receptor, constitutive androstane receptor, and pregnane X receptor) involved in the induction of CYP1A2, 2B6, and 3A4, respectively.
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Affiliation(s)
- Harutoshi Kato
- DMPK Research Laboratories, Mitsubishi Tanabe Pharma Corporation, Aoba-ku, Yokohama-shi, 227-0033, Japan.
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152
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Omics in schizophrenia: current progress and future directions of antipsychotic treatments. JOURNAL OF BIO-X RESEARCH 2019. [DOI: 10.1097/jbr.0000000000000049] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
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153
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Chen G, Chen J, Liu H, Chen S, Zhang Y, Li P, Thierry-Mieg D, Thierry-Mieg J, Mattes W, Ning B, Shi T. Comprehensive Identification and Characterization of Human Secretome Based on Integrative Proteomic and Transcriptomic Data. Front Cell Dev Biol 2019; 7:299. [PMID: 31824949 PMCID: PMC6881247 DOI: 10.3389/fcell.2019.00299] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Accepted: 11/07/2019] [Indexed: 12/25/2022] Open
Abstract
Secreted proteins (SPs) play important roles in diverse important biological processes; however, a comprehensive and high-quality list of human SPs is still lacking. Here we identified 6,943 high-confidence human SPs (3,522 of them are novel) based on 330,427 human proteins derived from databases of UniProt, Ensembl, AceView, and RefSeq. Notably, 6,267 of 6,943 (90.3%) SPs have the supporting evidences from a large amount of mass spectrometry (MS) and RNA-seq data. We found that the SPs were broadly expressed in diverse tissues as well as human body fluid, and a significant portion of them exhibited tissue-specific expression. Moreover, 14 cancer-specific SPs that their expression levels were significantly associated with the patients’ survival of eight different tumors were identified, which could be potential prognostic biomarkers. Strikingly, 89.21% of 6,943 SPs (2,927 novel SPs) contain known protein domains. Those novel SPs we mainly enriched with the known domains regarding immunity, such as Immunoglobulin V-set and C1-set domain. Specifically, we constructed a user-friendly and freely accessible database, SPRomeDB (www.unimd.org/SPRomeDB), to catalog those SPs. Our comprehensive SP identification and characterization gain insights into human secretome and provide valuable resource for future researches.
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Affiliation(s)
- Geng Chen
- The Center for Bioinformatics and Computational Biology, Shanghai Key Laboratory of Regulatory Biology, The Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China
| | - Jiwei Chen
- The Center for Bioinformatics and Computational Biology, Shanghai Key Laboratory of Regulatory Biology, The Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China
| | - Huanlong Liu
- The Center for Bioinformatics and Computational Biology, Shanghai Key Laboratory of Regulatory Biology, The Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China
| | - Shuangguan Chen
- The Center for Bioinformatics and Computational Biology, Shanghai Key Laboratory of Regulatory Biology, The Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China
| | - Yang Zhang
- The Center for Bioinformatics and Computational Biology, Shanghai Key Laboratory of Regulatory Biology, The Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China
| | - Peng Li
- The Center for Bioinformatics and Computational Biology, Shanghai Key Laboratory of Regulatory Biology, The Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China
| | - Danielle Thierry-Mieg
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, United States
| | - Jean Thierry-Mieg
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, United States
| | - William Mattes
- National Center for Toxicological Research, Food and Drug Administration, Jefferson City, AR, United States
| | - Baitang Ning
- National Center for Toxicological Research, Food and Drug Administration, Jefferson City, AR, United States
| | - Tieliu Shi
- The Center for Bioinformatics and Computational Biology, Shanghai Key Laboratory of Regulatory Biology, The Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China
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154
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Axelrad DA, Setzer RW, Bateson TF, DeVito M, Dzubow RC, Fitzpatrick JW, Frame AM, Hogan KA, Houck K, Stewart M. Methods for evaluating variability in human health dose-response characterization. HUMAN AND ECOLOGICAL RISK ASSESSMENT : HERA 2019; 25:1-24. [PMID: 31404325 PMCID: PMC6688638 DOI: 10.1080/10807039.2019.1615828] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Accepted: 05/03/2019] [Indexed: 05/21/2023]
Abstract
The Reference Dose (RfD) and Reference Concentration (RfC) are human health reference values (RfVs) representing exposure concentrations at or below which there is presumed to be little risk of adverse effects in the general human population. The 2009 National Research Council report Science and Decisions recommended redefining RfVs as "a risk-specific dose (for example, the dose associated with a 1 in 100,000 risk of a particular end point)." Distributions representing variability in human response to environmental contaminant exposures are critical for deriving risk-specific doses. Existing distributions estimating the extent of human toxicokinetic and toxicodynamic variability are based largely on controlled human exposure studies of pharmaceuticals. New data and methods have been developed that are designed to improve estimation of the quantitative variability in human response to environmental chemical exposures. Categories of research with potential to provide new database useful for developing updated human variability distributions include controlled human experiments, human epidemiology, animal models of genetic variability, in vitro estimates of toxicodynamic variability, and in vitro-based models of toxicokinetic variability. In vitro approaches, with further development including studies of different cell types and endpoints, and approaches to incorporate non-genetic sources of variability, appear to provide the greatest opportunity for substantial near-term advances.
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Affiliation(s)
- Daniel A. Axelrad
- Office of Policy, U.S. Environmental Protection Agency, Washington, DC, USA
| | - R. Woodrow Setzer
- Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, NC, USA
| | - Thomas F. Bateson
- Office of Research and Development, U.S. Environmental Protection Agency, Washington, DC, USA
| | - Michael DeVito
- National Institute of Environmental Health Sciences, National Toxicology Program, Research Triangle Park, NC, USA
| | - Rebecca C. Dzubow
- Office of Children’s Health Protection, U.S. Environmental Protection Agency, Washington, DC, USA
| | - Julie W. Fitzpatrick
- Office of the Science Advisor, U.S. Environmental Protection Agency, Washington, DC, USA
| | - Alicia M. Frame
- Office of Land and Emergency Management, U.S. Environmental Protection Agency, Washington, DC, USA
| | - Karen A. Hogan
- Office of Research and Development, U.S. Environmental Protection Agency, Washington, DC, USA
| | - Keith Houck
- Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, NC, USA
| | - Michael Stewart
- Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, NC, USA
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155
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156
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Feng L, Ning J, Tian X, Wang C, Zhang L, Ma X, James TD. Fluorescent probes for bioactive detection and imaging of phase II metabolic enzymes. Coord Chem Rev 2019. [DOI: 10.1016/j.ccr.2019.213026] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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157
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Chen G, Fan M, Liu Y, Sun B, Liu M, Wu J, Li N, Guo M. Advances in MS Based Strategies for Probing Ligand-Target Interactions: Focus on Soft Ionization Mass Spectrometric Techniques. Front Chem 2019; 7:703. [PMID: 31709232 PMCID: PMC6819514 DOI: 10.3389/fchem.2019.00703] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Accepted: 10/08/2019] [Indexed: 12/12/2022] Open
Abstract
The non-covalent interactions between small drug molecules and disease-related proteins (ligand-target interactions) mediate various pharmacological processes in the treatment of different diseases. The development of the analytical methods to assess those interactions, including binding sites, binding energies, stoichiometry and association-dissociation constants, could assist in clarifying the mechanisms of action, precise treatment of targeted diseases as well as the targeted drug discovery. For the last decades, mass spectrometry (MS) has been recognized as a powerful tool to study the non-covalent interactions of the ligand-target complexes with the characteristics of high sensitivity, high-resolution, and high-throughput. Soft ionization mass spectrometry, especially the electrospray mass spectrometry (ESI-MS) and matrix assisted laser desorption ionization mass spectrometry (MALDI-MS), could achieve the complete transformation of the target analytes into the gas phase, and subsequent detection of the small drug molecules and disease-related protein complexes, and has exerted great advantages for studying the drug ligands-protein targets interactions, even in case of identifying active components as drug ligands from crude extracts of medicinal plants. Despite of other analytical techniques for this purpose, such as the NMR and X-ray crystallography, this review highlights the principles, research hotspots and recent applications of the soft ionization mass spectrometry and its hyphenated techniques, including hydrogen-deuterium exchange mass spectrometry (HDX-MS), chemical cross-linking mass spectrometry (CX-MS), and ion mobility spectrometry mass spectrometry (IMS-MS), in the study of the non-covalent interactions between small drug molecules and disease-related proteins.
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Affiliation(s)
- Guilin Chen
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, China
| | - Minxia Fan
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, China
- Graduate University of Chinese Academy of Sciences, Beijing, China
| | - Ye Liu
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, China
| | - Baoqing Sun
- State Key Laboratory of Respiratory Disease, National Clinical Center for Respiratory Diseases, Guangzhou Institute of Respiratory Diseases, First Affiliated Hospital, Guangzhou Medical University, Guangzhou, China
| | - Meixian Liu
- State Key Laboratory for Quality Research of Chinese Medicines, Macau University of Science and Technology, Taipa, Macau
| | - Jianlin Wu
- State Key Laboratory for Quality Research of Chinese Medicines, Macau University of Science and Technology, Taipa, Macau
| | - Na Li
- State Key Laboratory for Quality Research of Chinese Medicines, Macau University of Science and Technology, Taipa, Macau
| | - Mingquan Guo
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, China
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158
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Fuselli S. Beyond drugs: the evolution of genes involved in human response to medications. Proc Biol Sci 2019; 286:20191716. [PMID: 31640517 DOI: 10.1098/rspb.2019.1716] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
The genetic variation of our species reflects human demographic history and adaptation to diverse local environments. Part of this genetic variation affects individual responses to exogenous substances, such as food, pollutants and drugs, and plays an important role in drug efficacy and safety. This review provides a synthesis of the evolution of loci implicated in human pharmacological response and metabolism, interpreted within the theoretical framework of population genetics and molecular evolution. In particular, I review and discuss key evolutionary aspects of different pharmacogenes in humans and other species, such as the relationship between the type of substrates and rate of evolution; the selective pressure exerted by landscape variables or dietary habits; expected and observed patterns of rare genetic variation. Finally, I discuss how this knowledge can be translated directly or after the implementation of specific studies, into practical guidelines.
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Affiliation(s)
- Silvia Fuselli
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
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159
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Lin Y, Wang S, Zhou Z, Guo L, Yu F, Wu B. Bmal1 regulates circadian expression of cytochrome P450 3a11 and drug metabolism in mice. Commun Biol 2019; 2:378. [PMID: 31633069 PMCID: PMC6795895 DOI: 10.1038/s42003-019-0607-z] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2019] [Accepted: 09/10/2019] [Indexed: 12/17/2022] Open
Abstract
Metabolism is a major defense mechanism of the body against xenobiotic threats. Here we unravel a critical role of Bmal1 for circadian clock-controlled Cyp3a11 expression and xenobiotic metabolism. Bmal1 deficiency decreases the mRNA, protein and microsomal activity of Cyp3a11, and blunts their circadian rhythms in mice. A screen for Cyp3a11 regulators identifies two circadian genes Dbp and Hnf4α as potential regulatory mediators. Cell-based experiments confirm that Dbp and Hnf4α activate Cyp3a11 transcription by their binding to a D-box and a DR1 element in the Cyp3a11 promoter, respectively. Bmal1 binds to the P1 distal promoter to regulate Hnf4α transcriptionally. Cellular regulation of Cyp3a11 by Bmal1 is Dbp- and Hnf4α-dependent. Bmal1 deficiency sensitizes mice to toxicities of drugs such as aconitine and triptolide (and blunts circadian toxicity rhythmicities) due to elevated drug exposure. In summary, Bmal1 connects circadian clock and Cyp3a11 metabolism, thereby impacting drug detoxification as a function of daily time.
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Affiliation(s)
- Yanke Lin
- Research Center for Biopharmaceutics and Pharmacokinetics, College of Pharmacy, Jinan University, 601 Huangpu Avenue West, 510632 Guangzhou, China
| | - Shuai Wang
- Research Center for Biopharmaceutics and Pharmacokinetics, College of Pharmacy, Jinan University, 601 Huangpu Avenue West, 510632 Guangzhou, China
- Integrated Chinese and Western Medicine Postdoctoral research station, Jinan University, 601 Huangpu Avenue West, Guangzhou, China
| | - Ziyue Zhou
- Research Center for Biopharmaceutics and Pharmacokinetics, College of Pharmacy, Jinan University, 601 Huangpu Avenue West, 510632 Guangzhou, China
| | - Lianxia Guo
- Research Center for Biopharmaceutics and Pharmacokinetics, College of Pharmacy, Jinan University, 601 Huangpu Avenue West, 510632 Guangzhou, China
| | - Fangjun Yu
- Research Center for Biopharmaceutics and Pharmacokinetics, College of Pharmacy, Jinan University, 601 Huangpu Avenue West, 510632 Guangzhou, China
| | - Baojian Wu
- Research Center for Biopharmaceutics and Pharmacokinetics, College of Pharmacy, Jinan University, 601 Huangpu Avenue West, 510632 Guangzhou, China
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160
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Metabolism of carcinogenic alpha-asarone by human cytochrome P450 enzymes. Naunyn Schmiedebergs Arch Pharmacol 2019; 393:213-223. [DOI: 10.1007/s00210-019-01724-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Accepted: 08/28/2019] [Indexed: 01/23/2023]
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161
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Jessurun NT, Drent M, van Puijenbroek EP, Bekers O, Wijnen PA, Bast A. Drug-induced interstitial lung disease: role of pharmacogenetics in predicting cytotoxic mechanisms and risks of side effects. Curr Opin Pulm Med 2019; 25:468-477. [PMID: 31365381 DOI: 10.1097/mcp.0000000000000590] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
PURPOSE OF REVIEW The diagnosis of drug-induced interstitial lung disease (DI-ILD) is challenging and mainly made by exclusion of other possible causes. Toxicity can occur as a cause of drug(s) or drug-drug interactions. In this review, we summarize the possible role of pharmacogenetics of metabolizing enzymes in DI-ILD. RECENT FINDINGS Knowledge of the genetic predispositions of enzymes involved in drug metabolization and their relation with proposed cytotoxic mechanisms of DI-ILD, in particular direct cell toxicity and free oxygen radical production is increasing. The cytochrome P450 enzyme family and other enzymes play an important role in the metabolism of all sorts of ingested, injected, or inhaled xenobiotic substances. The liver is the major site for metabolism. Metabolic cytotoxic mechanisms have however also been detected in lung tissue. Polymorphisms in genes coding for enzymes that influence metabolic activity may lead to localized (toxic) reactions and tissue damage. This knowledge may be helpful in preventing the risk of DI-ILD. SUMMARY Drug toxicity can be the consequence of absence or very poor enzyme activity, especially if no other metabolic route is available. In the case of reduced enzyme activity, it is recommended to reduce the dose or to prescribe an alternative drug, which is metabolized by a different, unaffected enzyme system to prevent toxic side effects. However, enhanced enzyme activity may lead to excessive formation of toxic and sometimes reactive metabolites. Therefore, knowing a patient's drug-metabolizing profile before drug prescription is a promising way to prevent or explain DI-ILD.
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Affiliation(s)
- Naomi T Jessurun
- Netherlands Pharmacovigilance Centre Lareb, 's-Hertogenbosch, The Netherlands
- ILD Care Foundation Research Team, Ede, The Netherlands
| | - Marjolein Drent
- ILD Care Foundation Research Team, Ede, The Netherlands
- Department of Pharmacology and Toxicology, Faculty of Health, Medicine and Life Science, Maastricht University, Maastricht, The Netherlands
- ILD Center of Excellence, St. Antonius Hospital, Nieuwegein, The Netherlands
| | - Eugène P van Puijenbroek
- Netherlands Pharmacovigilance Centre Lareb, 's-Hertogenbosch, The Netherlands
- Groningen Research Institute of Pharmacy, University of Groningen, Groningen, The Netherlands
| | - Otto Bekers
- ILD Care Foundation Research Team, Ede, The Netherlands
- Department of Clinical Chemistry, Central Diagnostic Laboratory, Maastricht University Medical Centre, Maastricht, The Netherlands
| | - Petal A Wijnen
- ILD Care Foundation Research Team, Ede, The Netherlands
- Department of Clinical Chemistry, Central Diagnostic Laboratory, Maastricht University Medical Centre, Maastricht, The Netherlands
| | - Aalt Bast
- ILD Care Foundation Research Team, Ede, The Netherlands
- Department of Pharmacology and Toxicology, Faculty of Health, Medicine and Life Science, Maastricht University, Maastricht, The Netherlands
- Venlo Campus, Maastricht University, Venlo, The Netherlands
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162
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Lorenzo-Pouso AI, Pérez-Sayáns M, Rodríguez-Zorrilla S, Chamorro-Petronacci C, García-García A. Dissecting the Proton Transport Pathway in Oral Squamous Cell Carcinoma: State of the Art and Theranostics Implications. Int J Mol Sci 2019; 20:ijms20174222. [PMID: 31470498 PMCID: PMC6747091 DOI: 10.3390/ijms20174222] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Revised: 08/27/2019] [Accepted: 08/28/2019] [Indexed: 12/12/2022] Open
Abstract
Cancer cells overexpress proton exchangers at the plasma membrane in order acidify the extracellular matrix and maintain the optimal pH for sustaining cancer growth. Among the families of proton exchangers implicated in carcinogenesis, carbonic anhydrases (CAs), monocarboxylate transporters (MCTs), Na+/H+ exchangers (NHEs), sodium bicarbonate cotransporters (NBCs), and vacuolar ATPases (V-ATPases) are highlighted. Considerable research has been carried out into the utility of the understanding of these machineries in the diagnosis and prognosis of several solid tumors. In addition, as therapeutic targets, the interference of their functions has contributed to the discovery or optimization of cancer therapies. According to recent reports, the study of these mechanisms seems promising in the particular case of oral squamous cell carcinoma (OSCC). In the present review, the latest advances in these fields are summarized, in particular, the usefulness of proton exchangers as potential prognostic biomarkers and therapeutic targets in OSCC.
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Affiliation(s)
- Alejandro I Lorenzo-Pouso
- Oral Medicine, Oral Surgery and Implantology Unit, Faculty of Medicine and Odontology, University of Santiago de Compostela, GI-1319 Research Group, Health Research Institute of Santiago de Compostela (IDIS), Santiago de Compostela, 15782, Spain.
| | - Mario Pérez-Sayáns
- Oral Medicine, Oral Surgery and Implantology Unit, Faculty of Medicine and Odontology, University of Santiago de Compostela, GI-1319 Research Group, Health Research Institute of Santiago de Compostela (IDIS), Santiago de Compostela, 15782, Spain.
| | - Samuel Rodríguez-Zorrilla
- Oral Medicine, Oral Surgery and Implantology Unit, Faculty of Medicine and Odontology, University of Santiago de Compostela, GI-1319 Research Group, Health Research Institute of Santiago de Compostela (IDIS), Santiago de Compostela, 15782, Spain
| | - Cintia Chamorro-Petronacci
- Oral Medicine, Oral Surgery and Implantology Unit, Faculty of Medicine and Odontology, University of Santiago de Compostela, GI-1319 Research Group, Health Research Institute of Santiago de Compostela (IDIS), Santiago de Compostela, 15782, Spain
| | - Abel García-García
- Oral Medicine, Oral Surgery and Implantology Unit, Faculty of Medicine and Odontology, University of Santiago de Compostela, GI-1319 Research Group, Health Research Institute of Santiago de Compostela (IDIS), Santiago de Compostela, 15782, Spain
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163
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Petrović J, Pešić V, Lauschke VM. Frequencies of clinically important CYP2C19 and CYP2D6 alleles are graded across Europe. Eur J Hum Genet 2019; 28:88-94. [PMID: 31358955 PMCID: PMC6906321 DOI: 10.1038/s41431-019-0480-8] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Revised: 07/03/2019] [Accepted: 07/17/2019] [Indexed: 11/23/2022] Open
Abstract
CYP2C19 and CYP2D6 are important drug-metabolizing enzymes that are involved in the metabolism of around 30% of all medications. Importantly, the corresponding genes are highly polymorphic and these genetic differences contribute to interindividual and interethnic differences in drug pharmacokinetics, response, and toxicity. In this study we systematically analyzed the frequency distribution of clinically relevant CYP2C19 and CYP2D6 alleles across Europe based on data from 82,791 healthy individuals extracted from 79 original publications and, for the first time, provide allele confidence intervals for the general population. We found that frequencies of CYP2D6 gene duplications showed a clear South-East to North-West gradient ranging from <1% in Sweden and Denmark to 6% in Greece and Turkey. In contrast, an inverse distribution was observed for the loss-of-function alleles CYP2D6*4 and CYP2D6*5. Similarly, frequencies of the inactive CYP2C19*2 allele were graded from North-West to South-East Europe. In important contrast to previous work we found that the increased activity allele CYP2C19*17 was most prevalent in Central Europe (25–33%) with lower prevalence in Mediterranean-South Europeans (11–24%). In summary, we provide a detailed European map of common CYP2C19 and CYP2D6 variants and find that frequencies of the most clinically relevant alleles are geographically graded reflective of Europe’s migratory history. These findings emphasize the importance of generating pharmacogenomic data sets with high spatial resolution to improve precision public health across Europe.
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Affiliation(s)
- Jelena Petrović
- Department of Physiology and Pharmacology, Section of Pharmacogenetics, Karolinska Institutet, Stockholm, Sweden.,Faculty of Pharmacy, Department of Physiology, University of Belgrade, Belgrade, Serbia
| | - Vesna Pešić
- Faculty of Pharmacy, Department of Physiology, University of Belgrade, Belgrade, Serbia
| | - Volker M Lauschke
- Department of Physiology and Pharmacology, Section of Pharmacogenetics, Karolinska Institutet, Stockholm, Sweden.
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164
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Li H, Toth E, Cherrington NJ. Alcohol Metabolism in the Progression of Human Nonalcoholic Steatohepatitis. Toxicol Sci 2019; 164:428-438. [PMID: 29718361 DOI: 10.1093/toxsci/kfy106] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Alcohol metabolism is a well-characterized biological process that is dominated by the alcohol dehydrogenase (ADH) and aldehyde dehydrogenase (ALDH) families. Nonalcoholic steatohepatitis (NASH) is the advanced inflammatory stage of nonalcoholic fatty liver disease (NAFLD) and is known to alter the metabolism and disposition of numerous drugs. The purpose of this study was to investigate the alterations in alcohol metabolism processes in response to human NASH progression. Expression and function of ADHs, ALDHs, and catalase were examined in normal, steatosis, NASH (fatty) and NASH (not fatty) human liver samples. ALDH4A1 mRNA was significantly decreased in both NASH groups, while no significant changes were observed in the mRNA levels of other alcohol-related enzymes. The protein levels of ADH1A, ADH1B, and ADH4 were each decreased in the NASH groups, which was consistent with a decreased overall ADH activity. The protein level of ALDH2 was significantly increased in both NASH groups, while ALDH1A1 and ALDH1B1 were only decreased in NASH (fatty) samples. ALDH activity represented by oxidation of acetaldehyde was decreased in the NASH (fatty) group. The protein level of catalase was decreased in both NASH groups, though activity was unchanged. Furthermore, the significant accumulation of 4-hydroxynonenal protein adduct in NASH indicated significant oxidative stress and a potential reduction in ALDH activity. Collectively, ADH and ALDH expression and function are profoundly altered in the progression of NASH, which may have a notable impact on ADH- and ALDH-associated cellular metabolism processes and lead to significant alterations in drug metabolism mediated by these enzymes.
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Affiliation(s)
- Hui Li
- Pharmacology and Toxicology, University of Arizona, Tucson, Arizona 85721
| | - Erica Toth
- Pharmacology and Toxicology, University of Arizona, Tucson, Arizona 85721
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165
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Xu ZY, Li JL. Comparative review of drug-drug interactions with epidermal growth factor receptor tyrosine kinase inhibitors for the treatment of non-small-cell lung cancer. Onco Targets Ther 2019; 12:5467-5484. [PMID: 31371986 PMCID: PMC6636179 DOI: 10.2147/ott.s194870] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Accepted: 03/12/2019] [Indexed: 12/13/2022] Open
Abstract
The development of small-molecule tyrosine kinase inhibitors (TKIs) that target the epidermal growth factor receptor (EGFR) has revolutionized the management of non-small-cell lung cancer (NSCLC). Because these drugs are commonly used in combination with other types of medication, the risk of clinically significant drug–drug interactions (DDIs) is an important consideration, especially for patients using multiple drugs for coexisting medical conditions. Clinicians need to be aware of the potential for clinically important DDIs when considering therapeutic options for individual patients. In this article, we describe the main mechanisms underlying DDIs with the EGFR-TKIs that are currently approved for the treatment of NSCLC, and, specifically, the potential for interactions mediated via effects on gastrointestinal pH, cytochrome P450-dependent metabolism, uridine diphosphate-glucuronosyltransferase, and transporter proteins. We review evidence of such DDIs with the currently approved EGFR-TKIs (gefitinib, erlotinib, afatinib, osimertinib, and icotinib) and discuss several information sources that are available online to aid clinical decision-making. We conclude by summarizing the most clinically relevant DDIs with these EFGR-TKIs and provide recommendations for managing, minimizing, or avoiding DDIs with the different agents.
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Affiliation(s)
- Zi-Yi Xu
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, People's Republic of China
| | - Jun-Ling Li
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, People's Republic of China
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166
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Kwapiszewska G, Johansen AKZ, Gomez-Arroyo J, Voelkel NF. Role of the Aryl Hydrocarbon Receptor/ARNT/Cytochrome P450 System in Pulmonary Vascular Diseases. Circ Res 2019; 125:356-366. [PMID: 31242807 DOI: 10.1161/circresaha.119.315054] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
RATIONALE CYPs (cytochrome p450) are critically involved in the metabolism of xenobiotics and toxins. Given that pulmonary hypertension is strongly associated with environmental exposure, we hypothesize that CYPs play a role in the development and maintenance of pathological vascular remodeling. OBJECTIVE We sought to identify key CYPs that could link drug or hormone metabolism to the development of pulmonary hypertension. METHODS AND RESULTS We searched in Medline (PubMed) database, as well as http://www.clinicaltrials.gov, for CYPs associated with many key aspects of pulmonary arterial hypertension including, but not limited to, severe pulmonary hypertension, estrogen metabolism, inflammation mechanisms, quasi-malignant cell growth, drug susceptibility, and metabolism of the pulmonary arterial hypertension-specific drugs. CONCLUSIONS We postulate a hypothesis where the AhR (aryl hydrocarbon receptor) mediates aberrant cell growth via expression of different CYPs associated with estrogen metabolism and inflammation.
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Affiliation(s)
- Grazyna Kwapiszewska
- From the Ludwig Boltzmann Institute for Lung Vascular Research, Medical University of Graz, Austria (G.K.)
| | - Anne Katrine Z Johansen
- Department of Pediatrics, Cincinnati Children's Hospital Medical Center, University of Cincinnati, OH (A.K.Z.J.)
| | - Jose Gomez-Arroyo
- Division of Pulmonary and Critical Care Medicine, University of Cincinnati College of Medicine, OH (J.G.-A.)
- Division of Pulmonary Biology, Perinatal Institute of Cincinnati Children's Hospital Research Foundation, OH (J.G.-A.)
| | - Norbert F Voelkel
- Department of Pulmonary Medicine, Amsterdam University Medical Centers, the Netherlands (N.F.V.)
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167
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Crisafulli C, Romeo PD, Calabrò M, Epasto LM, Alberti S. Pharmacogenetic and pharmacogenomic discovery strategies. CANCER DRUG RESISTANCE (ALHAMBRA, CALIF.) 2019; 2:225-241. [PMID: 35582724 PMCID: PMC8992635 DOI: 10.20517/cdr.2018.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Revised: 03/22/2019] [Accepted: 03/26/2019] [Indexed: 11/12/2022]
Abstract
Genetic/genomic profiling at a single-patient level is expected to provide critical information for determining inter-individual drug toxicity and potential efficacy in cancer therapy. A better definition of cancer subtypes at a molecular level, may correspondingly complement such pharmacogenetic and pharmacogenomic approaches, for more effective personalized treatments. Current pharmacogenetic/pharmacogenomic strategies are largely based on the identification of known polymorphisms, thus limiting the discovery of novel or rarer genetic variants. Recent improvements in cost and throughput of next generation sequencing (NGS) are now making whole-genome profiling a plausible alternative for clinical procedures. Beyond classical pharmacogenetic/pharmacogenomic traits for drug metabolism, NGS screening programs of cancer genomes may lead to the identification of novel cancer-driving mutations. These may not only constitute novel therapeutic targets, but also effector determinants for metabolic pathways linked to drug metabolism. An additional advantage is that cancer NGS profiling is now leading to discovering targetable mutations, e.g., in glioblastomas and pancreatic cancers, which were originally discovered in other tumor types, thus allowing for effective repurposing of active drugs already on the market.
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Affiliation(s)
- Concetta Crisafulli
- Department of Biomedical Sciences - BIOMORF, University of Messina, via Consolare Valeria, 98125 Messina, Italy
| | | | - Marco Calabrò
- Department of Biomedical Sciences - BIOMORF, University of Messina, via Consolare Valeria, 98125 Messina, Italy
| | - Ludovica Martina Epasto
- Unit of Medical Genetics, University of Messina, via Consolare Valeria, 98125 Messina, Italy
| | - Saverio Alberti
- Department of Biomedical Sciences - BIOMORF, University of Messina, via Consolare Valeria, 98125 Messina, Italy.,Unit of Medical Genetics, University of Messina, via Consolare Valeria, 98125 Messina, Italy.,Correspondence Address: Prof. Saverio Alberti, Unit of Medical Genetics, BIOMORF Department of Biomedical Sciences, University of Messina, via Consolare Valeria, 98125 Messina, Italy. E-mail:
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168
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Abstract
![]()
A correct estimate
of ligand binding modes and a ratio of their
occupancies is crucial for calculations of binding free energies.
The newly developed method BLUES combines molecular dynamics with
nonequilibrium candidate Monte Carlo. Nonequilibrium candidate Monte
Carlo generates a plethora of possible binding modes and molecular
dynamics enables the system to relax. We used BLUES to investigate
binding modes of caffeine in the active site of its metabolizing enzyme
Cytochrome P450 1A2 with the aim of elucidating metabolite-formation
profiles at different concentrations. Because the activation energies
of all sites of metabolism do not show a clear preference for one
metabolite over the others, the orientations in the active site must
play a key role. In simulations with caffeine located in a spacious
pocket above the I-helix, it points N3 and N1 to the heme iron, whereas
in simulations where caffeine is in close proximity to the heme N7
and C8 are preferably oriented toward the heme iron. We propose a
mechanism where at low caffeine concentrations caffeine binds to the
upper part of the active site, leading to formation of the main metabolite
paraxanthine. On the other hand, at high concentrations two molecules
are located in the active site, forcing one molecule into close proximity
to the heme and yielding metabolites theophylline and trimethyluretic
acid. Our results offer an explanation of previously published experimental
results.
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Affiliation(s)
- Zuzana Jandova
- Institute of Molecular Modeling and Simulation , University of Natural Resources and Life Sciences, Vienna , 1180 Vienna , Austria
| | | | | | | | - Chris Oostenbrink
- Institute of Molecular Modeling and Simulation , University of Natural Resources and Life Sciences, Vienna , 1180 Vienna , Austria
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169
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Gulilat M, Lamb T, Teft WA, Wang J, Dron JS, Robinson JF, Tirona RG, Hegele RA, Kim RB, Schwarz UI. Targeted next generation sequencing as a tool for precision medicine. BMC Med Genomics 2019; 12:81. [PMID: 31159795 PMCID: PMC6547602 DOI: 10.1186/s12920-019-0527-2] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Accepted: 05/13/2019] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND Targeted next-generation sequencing (NGS) enables rapid identification of common and rare genetic variation. The detection of variants contributing to therapeutic drug response or adverse effects is essential for implementation of individualized pharmacotherapy. Successful application of short-read based NGS to pharmacogenes with high sequence homology, nearby pseudogenes and complex structure has been previously shown despite anticipated technical challenges. However, little is known regarding the utility of such panels to detect copy number variation (CNV) in the highly polymorphic cytochrome P450 (CYP) 2D6 gene, or to identify the promoter (TA)7 TAA repeat polymorphism UDP glucuronosyltransferase (UGT) 1A1*28. Here we developed and validated PGxSeq, a targeted exome panel for pharmacogenes pertinent to drug disposition and/or response. METHODS A panel of capture probes was generated to assess 422 kb of total coding region in 100 pharmacogenes. NGS was carried out in 235 subjects, and sequencing performance and accuracy of variant discovery validated in clinically relevant pharmacogenes. CYP2D6 CNV was determined using the bioinformatics tool CNV caller (VarSeq). Identified SNVs were assessed in terms of population allele frequency and predicted functional effects through in silico algorithms. RESULTS Adequate performance of the PGxSeq panel was demonstrated with a depth-of-coverage (DOC) ≥ 20× for at least 94% of the target sequence. We showed accurate detection of 39 clinically relevant gene variants compared to standard genotyping techniques (99.9% concordance), including CYP2D6 CNV and UGT1A1*28. Allele frequency of rare or novel variants and predicted function in 235 subjects mirrored findings from large genomic datasets. A large proportion of patients (78%, 183 out of 235) were identified as homozygous carriers of at least one variant necessitating altered pharmacotherapy. CONCLUSIONS PGxSeq can serve as a comprehensive, rapid, and reliable approach for the detection of common and novel SNVs in pharmacogenes benefiting the emerging field of precision medicine.
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Affiliation(s)
- Markus Gulilat
- Division of Clinical Pharmacology, Department of Medicine, Western University, London Health Sciences Centre - University Hospital, 339 Windermere Road, London, ON, N6A 5A5, Canada.,Department of Physiology and Pharmacology, Western University, Medical Sciences Building, Room 216, London, ON, N6A 5C1, Canada
| | - Tyler Lamb
- Department of Physiology and Pharmacology, Western University, Medical Sciences Building, Room 216, London, ON, N6A 5C1, Canada
| | - Wendy A Teft
- Division of Clinical Pharmacology, Department of Medicine, Western University, London Health Sciences Centre - University Hospital, 339 Windermere Road, London, ON, N6A 5A5, Canada
| | - Jian Wang
- Robarts Research Institute, Western University, 1151 Richmond St. N, London, ON, N6A 5B7, Canada
| | - Jacqueline S Dron
- Robarts Research Institute, Western University, 1151 Richmond St. N, London, ON, N6A 5B7, Canada
| | - John F Robinson
- Robarts Research Institute, Western University, 1151 Richmond St. N, London, ON, N6A 5B7, Canada
| | - Rommel G Tirona
- Division of Clinical Pharmacology, Department of Medicine, Western University, London Health Sciences Centre - University Hospital, 339 Windermere Road, London, ON, N6A 5A5, Canada.,Department of Physiology and Pharmacology, Western University, Medical Sciences Building, Room 216, London, ON, N6A 5C1, Canada
| | - Robert A Hegele
- Robarts Research Institute, Western University, 1151 Richmond St. N, London, ON, N6A 5B7, Canada
| | - Richard B Kim
- Division of Clinical Pharmacology, Department of Medicine, Western University, London Health Sciences Centre - University Hospital, 339 Windermere Road, London, ON, N6A 5A5, Canada.,Department of Physiology and Pharmacology, Western University, Medical Sciences Building, Room 216, London, ON, N6A 5C1, Canada
| | - Ute I Schwarz
- Division of Clinical Pharmacology, Department of Medicine, Western University, London Health Sciences Centre - University Hospital, 339 Windermere Road, London, ON, N6A 5A5, Canada.
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170
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Hebenstreit D, Pichler R, Heidegger I. Drug-Drug Interactions in Prostate Cancer Treatment. Clin Genitourin Cancer 2019; 18:e71-e82. [PMID: 31677899 DOI: 10.1016/j.clgc.2019.05.016] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Revised: 05/16/2019] [Accepted: 05/20/2019] [Indexed: 12/24/2022]
Abstract
Polypharmacy is associated with an increased risk of drug-drug interactions (DDIs), which can cause serious and debilitating drug-induced adverse events. With a steadily aging population and associated increasing multimorbidity and polypharmacy, the potential for DDIs becomes considerably important. Prostate cancer (PCa) is the most common cancer in men and occurs mostly in elderly men in the Western world. Therefore, the aim of this review is to give an overview of DDIs in PCa therapy to better understand pharmacodynamic and pharm kinetic side effects as well as their interactions with other medications. Last, we explore potential future strategies, which might help to optimize treatment and reduce adverse events patients with polypharmacy and PCa.
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Affiliation(s)
- Doris Hebenstreit
- Department of Urology, Medical University Innsbruck, Innsbruck, Austria
| | - Renate Pichler
- Department of Urology, Medical University Innsbruck, Innsbruck, Austria
| | - Isabel Heidegger
- Department of Urology, Medical University Innsbruck, Innsbruck, Austria.
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171
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Expression of drug metabolizing enzymes and transporters in the cochlea: Implications for drug delivery and ototoxicity. Hear Res 2019; 379:98-102. [PMID: 31121337 DOI: 10.1016/j.heares.2019.05.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Revised: 04/24/2019] [Accepted: 05/13/2019] [Indexed: 11/22/2022]
Abstract
Inner ear drug delivery is a major area of research and development, but relatively little is known about basic drug metabolism in the cochlea. Additionally, the use of potentially ototoxic drugs such as NSAIDs, chemotherapeutics and aminoglycosides is common, but little is known about the role of metabolism in ototoxicity of those drugs. To address those issues, we compared expression of major Cytochromes P450 (Cyps), UDP-glucuronosyl-transferases (Ugts), sulfotransferases (Sults), and drug transporters between cochleae and liver, an organ with high expression, in mice using qPCR and enzyme kinetics. Together, the tested drug-metabolizing enzymes (DMEs) and transporters account for metabolism of approximately 70-80% of all medically important drugs in the body. Expression of most Cyps was low in the cochlea compared to liver, but three displayed similar expression levels to the liver, and one (Cyp2c65) had significantly higher levels of expression in the cochlea (1.9 ± 0.06 fold vs. liver). Enzyme kinetics revealed undetectable levels of p450 activity in the cochlea, especially as compared to the liver. Similar results were obtained for expression of Ugts and Sults. Interestingly, expression of most transporters was also low, with one major exception: Mdr1/P-glycoprotein (P-gp), which is generally thought to be highly expressed in liver and poorly expressed in most of the nervous system, was 3-fold greater in cochlea. Importantly, P-gp is known to protect other tissues from toxicity of cancer drugs by acting as an efflux pump. Our data demonstrate overall low levels of expression of DMEs and transporters in the cochlea, and identify a few that may be important to consider when designing and testing drugs for local delivery to the inner ear.
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172
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Scheffler L, Sharapa C, Buettner A. Quantification of Volatile Metabolites Derived From Garlic ( Allium sativum) in Human Urine. Front Nutr 2019; 6:43. [PMID: 31111029 PMCID: PMC6499206 DOI: 10.3389/fnut.2019.00043] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Accepted: 03/26/2019] [Indexed: 01/08/2023] Open
Abstract
The consumption of garlic (Allium sativum) is widely known to (negatively) impact body odor, in particular breath and sweat, but also urine. Despite this common phenomenon, the underlying processes in the body that lead to the malodor are not yet fully understood. In previous studies we identified three volatile garlic-derived metabolites in human milk and urine, namely allyl methyl sulfide (AMS), allyl methyl sulfoxide (AMSO), and allyl methyl sulfone (AMSO2). In the present study, we monitored the excretion processes of these metabolites via human urine after consumption of garlic over time, whereby 19 sets of eight urine samples (one sample pre-ingestion and seven samples post-ingestion) were analyzed using two-dimensional high resolution gas chromatography-mass spectrometry/olfactometry (HRGC-GC-MS/O). The highest concentrations of these metabolites were detected in urine ~1–2 h after garlic ingestion, with a second increase observed after 6–8 h in the urine of some participants. Moreover, the highest observed concentrations differed between the individual participants or test series by up to one order of magnitude.
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Affiliation(s)
- Laura Scheffler
- Chair of Aroma and Smell Research, Department of Chemistry and Pharmacy, Emil Fischer Center, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Constanze Sharapa
- Chair of Aroma and Smell Research, Department of Chemistry and Pharmacy, Emil Fischer Center, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Andrea Buettner
- Chair of Aroma and Smell Research, Department of Chemistry and Pharmacy, Emil Fischer Center, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany.,Department Sensorical Analytics, Fraunhofer Institute for Process Engineering and Packaging (IVV), Freising, Germany
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173
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Jin Y, Chen G, Xiao W, Hong H, Xu J, Guo Y, Xiao W, Shi T, Shi L, Tong W, Ning B. Sequencing XMET genes to promote genotype-guided risk assessment and precision medicine. SCIENCE CHINA-LIFE SCIENCES 2019; 62:895-904. [PMID: 31114935 DOI: 10.1007/s11427-018-9479-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Accepted: 12/06/2018] [Indexed: 12/26/2022]
Abstract
High-throughput next generation sequencing (NGS) is a shotgun approach applied in a parallel fashion by which the genome is fragmented and sequenced through small pieces and then analyzed either by aligning to a known reference genome or by de novo assembly without reference genome. This technology has led researchers to conduct an explosion of sequencing related projects in multidisciplinary fields of science. However, due to the limitations of sequencing-based chemistry, length of sequencing reads and the complexity of genes, it is difficult to determine the sequences of some portions of the human genome, leaving gaps in genomic data that frustrate further analysis. Particularly, some complex genes are difficult to be accurately sequenced or mapped because they contain high GC-content and/or low complexity regions, and complicated pseudogenes, such as the genes encoding xenobiotic metabolizing enzymes and transporters (XMETs). The genetic variants in XMET genes are critical to predicate inter-individual variability in drug efficacy, drug safety and susceptibility to environmental toxicity. We summarized and discussed challenges, wet-lab methods, and bioinformatics algorithms in sequencing "complex" XMET genes, which may provide insightful information in the application of NGS technology for implementation in toxicogenomics and pharmacogenomics.
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Affiliation(s)
- Yaqiong Jin
- Beijing Key Laboratory for Pediatric Diseases of Otolaryngology, Head and Neck Surgery, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, 100045, China
| | - Geng Chen
- Center for Bioinformatics and Computational Biology, and the Institute of Biomedical Sciences, Shanghai Key Laboratory of Regulatory Biology, the Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - Wenming Xiao
- National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR, 72079, USA
| | - Huixiao Hong
- National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR, 72079, USA
| | - Joshua Xu
- National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR, 72079, USA
| | - Yongli Guo
- Beijing Key Laboratory for Pediatric Diseases of Otolaryngology, Head and Neck Surgery, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, 100045, China
| | - Wenzhong Xiao
- Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, 02114, USA
| | - Tieliu Shi
- Center for Bioinformatics and Computational Biology, and the Institute of Biomedical Sciences, Shanghai Key Laboratory of Regulatory Biology, the Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - Leming Shi
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Cancer Center; Collaborative Innovation Center for Genetics and Development, Fudan University, Shanghai, 200433, China
| | - Weida Tong
- National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR, 72079, USA
| | - Baitang Ning
- National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR, 72079, USA.
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174
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Influence of ABCB1 polymorphisms on the pharmacokinetics and toxicity of lenalidomide in patients with multiple myeloma. Med Oncol 2019; 36:55. [PMID: 31089832 DOI: 10.1007/s12032-019-1280-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Accepted: 05/05/2019] [Indexed: 10/26/2022]
Abstract
Individual diversity in plasma concentrations of lenalidomide occurs despite dosage modifications based on creatinine clearance (CCr), which can lead to unexpected toxicity. We have previously identified a cutoff value of area under the concentration-time curve (AUC0-24) for lenalidomide to avoid severe toxicity. Here, we investigated the association between ABCB1 polymorphisms and pharmacokinetics of lenalidomide in patients with multiple myeloma (MM) treated with lenalidomide and dexamethasone. Plasma concentrations of lenalidomide were analyzed using liquid chromatography-tandem mass spectrometry. Genotyping for ABCB1 1236C>T, 2677G>A/T, and 3435C>T polymorphisms was performed, and the effects of ABCB1 polymorphisms on AUC0-24 for lenalidomide were compared in 36 patients with MM who were administered lenalidomide according to the drug label based on CCr. Genotyping analysis showed that although there were no differences in AUC0-24 in 1236C>T and 2677G>A/T polymorphisms. AUC0-24 was significantly higher in patients with the T allele of 3435C>T (n = 15) than in those without (n = 21) (median 6324.6 ng h/mL vs. 2857.4 ng h/mL, p = 0.028). The AUC0-24 value exceeded the aforementioned cutoff value in 95% of the patients with the T allele of 3435C>T but in 60% with C/C genotype (p = 0.013). Multivariate logistic analysis confirmed the significance of T allele of ABCB1 3435C>T as a factor due to which the AUC0-24 cutoff value was exceeded (hazard ratio of 15.0, p = 0.019). We show that lenalidomide pharmacokinetics is influenced by the ABCB1 3435C>T polymorphism, which could be useful to individualize dosage design and reduce unexpected toxicity.
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175
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Sharma A, Buschmann MM, Gilbert JA. Pharmacomicrobiomics: The Holy Grail to Variability in Drug Response? Clin Pharmacol Ther 2019; 106:317-328. [PMID: 30937887 DOI: 10.1002/cpt.1437] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Accepted: 03/11/2019] [Indexed: 12/23/2022]
Abstract
The human body, with 3.0 × 1013 cells and more than 3.8 × 1013 microorganisms, has nearly a one-to-one ratio of resident microbes to human cells. Initiatives like the Human Microbiome Project, American Gut, and Flemish Gut have identified associations between microbial taxa and human health. The study of interactions between microbiome and pharmaceutical agents, i.e., pharmacomicrobiomics, has revealed an instrumental role of the microbiome in modulating drug response that alters the therapeutic outcomes. In this review, we present our current comprehension of the relationship of the microbiome, host biology, and pharmaceutical agents such as cardiovascular drugs, analgesics, and chemotherapeutic agents to human disease and treatment outcomes. We also discuss the significance of studying diet-gene-drug interactions and further address the key challenges associated with pharmacomicrobiomics. Finally, we examine proposed models employing systems biology for the application of pharmacomicrobiomics and other -omics data, and provide approaches to elucidate microbiome-drug interactions to improve future translation to personalized medicine.
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Affiliation(s)
- Anukriti Sharma
- Department of Pediatrics, University of California San Diego School of Medicine, La Jolla, California, USA
| | | | - Jack A Gilbert
- Department of Pediatrics, University of California San Diego School of Medicine, La Jolla, California, USA.,Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, USA
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176
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Zhang L, Xu P, Cheng Y, Wang P, Ma X, Liu M, Wang X, Xu F. Diet-induced obese alters the expression and function of hepatic drug-metabolizing enzymes and transporters in rats. Biochem Pharmacol 2019; 164:368-376. [PMID: 31063713 DOI: 10.1016/j.bcp.2019.05.002] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Accepted: 05/02/2019] [Indexed: 01/16/2023]
Abstract
Obesity increases the incidences of metabolic syndrome, including type 2 diabete, fatty liver, dyslipidemia, hyperglycemia, heart disease, hypertension and cancer. In particular, pharmacokinetics and pharmacodynamics of many drugs have changed in obese patients. However, little is known about the hepatic drug-metabolizing enzymes and transporters that are influenced by diet-induced obese. In this report, we established obesity and fatty liver models in male rats by high-fat diet. The expression profiles of drug-metabolizing enzymes and transporters were studied by quantitative real-timePCR and Western blotting analysis. The function of these enzymes and transporters were assessed by their substrates and cocktail methods. The expression and activity of phase I enzymes (CYP1A2, CYP2B1, CYP2C11, CYP3A1, CYP4A1 and FMO1) and phase II enzymes (UGT1A1, UGT1A3, UGT1A6, UGT1A9, UGT2B7, NAT1 and GSTT1) were decreased in the liver of obese rats. In addition, the mRNA levels of hepatic transporter Slco1a2, Slco1b2, Slc22a5, Abcc2, Abcc3, Abcb1a and Abcg2 decreased significantly in obese animals, while Abcb1b increased significantly. Furthermore, the decreased expression of hepatic phase I and II enzymes and transporter may be due to changes of Hnf4α, LXRα and FXR. In conclusion, the diet-induced obese altered the expression and function of hepatic drug-metabolizing enzymes and transporters in male rats, thereby impacting drug metabolism and pharmacokinetics.
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Affiliation(s)
- Lei Zhang
- Fengxian Hospital and East China Normal University Joint Research Centre for Translational Medicine, Department of Pharmacy, Fengxian Hospital, Shanghai, China; Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China
| | - Peipei Xu
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China
| | - Yi Cheng
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China
| | - Peili Wang
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China
| | - Xinrun Ma
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China
| | - Mingyao Liu
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China; Department of Molecular and Cellular Medicine, Institute of Biosciences and Technology, Texas A&M University Health Science Centre, Houston, TX, USA
| | - Xin Wang
- Fengxian Hospital and East China Normal University Joint Research Centre for Translational Medicine, Department of Pharmacy, Fengxian Hospital, Shanghai, China; Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China.
| | - Feng Xu
- Fengxian Hospital and East China Normal University Joint Research Centre for Translational Medicine, Department of Pharmacy, Fengxian Hospital, Shanghai, China.
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177
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López-Valverde N, López-Valverde A, Gómez de Diego R, Cieza-Borrella C, Ramírez JM, González-Sarmiento R. Genetic study in patients operated dentally and anesthetized with articaine-epinephrine. J Pain Res 2019; 12:1371-1384. [PMID: 31118755 PMCID: PMC6499144 DOI: 10.2147/jpr.s193745] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Accepted: 03/26/2019] [Indexed: 12/01/2022] Open
Abstract
Aims: In this study we wanted to figure out if there was a correlation between OPRM1 N40D, TRPV1 I316M, TRPV1 I585V, NOS3 −786T>C and IL6 −174C>G polymorphisms and the response to locally applied articaine-epinephrine anesthetic. Methods: In this observational study, 114 oral cell samples of patients anesthetized with articaine-epinephrine (54 from men 60 from women), were collected from dental centers in Madrid (Spain). High molecular weight DNA was obtained from oral mucosa cells. The analysis of OPRM1 N40D (rs1799971), TRPV1 I316M (rs222747), TRPV1 I585V (rs8065080) and IL6 −174C>G polymorphism was performed through real-time PCR allelic discrimination using TaqMan probes. Polymorphism NOS3 −786T> C (rs2070744) was analyzed using RFLP-PCR. Results: The studied polymorphisms are involved neither in the response to the anesthetic, nor in the intensity of perceived dental pain. However, in a subset of female patients we found that TRPV1 I316M was associated with a delayed onset of anesthesia. Conclusions: There is no association among these polymorphisms and the time elapsed between the application of the anesthetic and the onset of its effect.
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Affiliation(s)
- Nansi López-Valverde
- Dental Clinic, Department of Surgery, Biomedical Research Institute of Salamanca (IBSAL), Salamanca, Spain
| | - Antonio López-Valverde
- Dental Clinic, Department of Surgery, Biomedical Research Institute of Salamanca (IBSAL), Salamanca, Spain
| | | | - Clara Cieza-Borrella
- Molecular Medicine Unit, Department of Medicine, Biomedical Research Institute of Salamanca (IBSAL), Salamanca, Spain
| | - Juan M Ramírez
- Department of Morphological Sciences, School of Medicine, University of Córdoba, Córdoba, Spain
| | - Rogelio González-Sarmiento
- Molecular Medicine Unit, Department of Medicine, Biomedical Research Institute of Salamanca (IBSAL), Salamanca, Spain
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178
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179
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Changing paradigm of antibiotic resistance amongst Escherichia coli isolates in Indian pediatric population. PLoS One 2019; 14:e0213850. [PMID: 30995225 PMCID: PMC6469777 DOI: 10.1371/journal.pone.0213850] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Accepted: 03/02/2019] [Indexed: 12/14/2022] Open
Abstract
Antimicrobial resistance happens when microorganisms mutates in manners that render the drugs like antibacterial, antiviral, antiparasitic and antifungal, ineffective. The normal mutation process is encouraged by the improper use of antibiotics. Mutations leading to quinolone resistance occur in a highly conserved region of the quinolone resistance-determining region (QRDR) of DNA gyrAse and topoisomerase IV gene. We analyzed antibiotic resistant genes and single nucleotide polymorphism (SNP) in gyrA and parC genes in QRDR in 120 E. coli isolates (both diarrheagenic and non-pathogenic) recovered from fresh stool samples collected from children aged less than 5 years from Delhi, India. Antibiotic susceptibility testing was performed according to standard clinical and laboratory standards institute (CLSI) guidelines. Phylogenetic analysis showed the clonal diversity and phylogenetic relationships among the E. coli isolates. The SNP analysis depicted mutations in gyrA and parC genes in QRDR. The sul1 gene, responsible for sulfonamide resistance, was present in almost half (47.5%) of the isolates across the diseased and healthy samples. The presence of antibiotic resistance genes in E. coli isolates from healthy children indicate the development, dissemination and carriage of antibiotic resistance in their gut. Our observations suggest the implementation of active surveillance and stewardship programs to promote appropriate antibiotic use and minimizing further danger.
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180
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Coecke S, Ahr H, Blaauboer BJ, Bremer S, Casati S, Castell J, Combes R, Corvi R, Crespi CL, Cunningham ML, Elaut G, Eletti B, Freidig A, Gennari A, Ghersi-Egea JF, Guillouzo A, Hartung T, Hoet P, Ingelman-Sundberg M, Munn S, Janssens W, Ladstetter B, Leahy D, Long A, Meneguz A, Monshouwer M, Morath S, Nagelkerke F, Pelkonen O, Ponti J, Prieto P, Richert L, Sabbioni E, Schaack B, Steiling W, Testai E, Vericat JA, Worth A. Metabolism: A Bottleneck in In Vitro Toxicological Test Development. Altern Lab Anim 2019; 34:49-84. [PMID: 16522150 DOI: 10.1177/026119290603400113] [Citation(s) in RCA: 106] [Impact Index Per Article: 21.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Sandra Coecke
- ECVAM, Institute for Health and Consumer Protection, European Commission Joint Research Centre, Ispra, Italy
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181
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Giannopoulou E, Katsila T, Mitropoulou C, Tsermpini EE, Patrinos GP. Integrating Next-Generation Sequencing in the Clinical Pharmacogenomics Workflow. Front Pharmacol 2019; 10:384. [PMID: 31024324 PMCID: PMC6460422 DOI: 10.3389/fphar.2019.00384] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Accepted: 03/27/2019] [Indexed: 12/12/2022] Open
Abstract
Pharmacogenomics has been recognized as a fundamental tool in the era of personalized medicine with up to 266 drug labels, approved by major regulatory bodies, currently containing pharmacogenomics information. Next-generation sequencing analysis assumes a critical role in personalized medicine, providing a comprehensive profile of an individual's variome, particularly that of clinical relevance, comprising of pathogenic variants and pharmacogenomic biomarkers. Here, we propose a strategy to integrate next-generation sequencing into the current clinical pharmacogenomics workflow from deep resequencing to pharmacogenomics consultation, according to the existing guidelines and recommendations.
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Affiliation(s)
| | - Theodora Katsila
- Department of Pharmacy, School of Health Sciences, University of Patras, Patras, Greece
| | | | | | - George P Patrinos
- Department of Pharmacy, School of Health Sciences, University of Patras, Patras, Greece.,Department of Pathology, College of Medicine and Health Sciences, United Arab Emirates University, Al-Ain, United Arab Emirates.,Zayed Center of Health Sciences, United Arab Emirates University, Al-Ain, United Arab Emirates
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182
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Miyauchi Y, Kimura S, Kimura A, Kurohara K, Hirota Y, Fujimoto K, Mackenzie PI, Tanaka Y, Ishii Y. Investigation of the Endoplasmic Reticulum Localization of UDP-Glucuronosyltransferase 2B7 with Systematic Deletion Mutants. Mol Pharmacol 2019; 95:551-562. [PMID: 30944207 DOI: 10.1124/mol.118.113902] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Accepted: 03/05/2019] [Indexed: 11/22/2022] Open
Abstract
UDP-Glucuronosyltransferase (UGT) plays an important role in the metabolism of endogenous and exogenous compounds. UGT is a type I membrane protein, and has a dilysine motif (KKXX/KXKXX) in its C-terminal cytoplasmic domain. Although a dilysine motif is defined as an endoplasmic reticulum (ER) retrieval signal, it remains a matter of debate whether this motif functions in the ER localization of UGT. To address this issue, we generated systematic deletion mutants of UGT2B7, a major human isoform, and compared their subcellular localizations with that of an ER marker protein calnexin (CNX), using subcellular fractionation and immunofluorescent microscopy. We found that although the dilysine motif functioned as the ER retention signal in a chimera that replaced the cytoplasmic domain of CD4 with that of UGT2B7, UGT2B7 truncated mutants lacking this motif extensively colocalized with CNX, indicating dilysine motif-independent ER retention of UGT2B7. Moreover, deletion of the C-terminal transmembrane and cytoplasmic domains did not affect ER localization of UGT2B7, suggesting that the signal necessary for ER retention of UGT2B7 is present in its luminal domain. Serial deletions of the luminal domain, however, did not affect the ER retention of the mutants. Further, a cytoplasmic and transmembrane domain-deleted mutant of UGT2B7 was localized to the ER without being secreted. These results suggest that UGT2B7 could localize to the ER without any retention signal, and lead to the conclusion that the static localization of UGT results from lack of a signal for export from the ER.
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Affiliation(s)
- Yuu Miyauchi
- Division of Pharmaceutical Cell Biology, Graduate School of Pharmaceutical Sciences (Y.M., A.K., K.K., Y.H., K.F., Y.T.) and Laboratory of Molecular Life Sciences, Graduate School of Pharmaceutical Sciences (Y.M., S.K., Y.I.), Kyushu University, Fukuoka, Japan; and Department of Clinical Pharmacology, Flinders Medical Centre and Flinders University, Adelaide, South Australia, Australia (P.I.M.)
| | - Sora Kimura
- Division of Pharmaceutical Cell Biology, Graduate School of Pharmaceutical Sciences (Y.M., A.K., K.K., Y.H., K.F., Y.T.) and Laboratory of Molecular Life Sciences, Graduate School of Pharmaceutical Sciences (Y.M., S.K., Y.I.), Kyushu University, Fukuoka, Japan; and Department of Clinical Pharmacology, Flinders Medical Centre and Flinders University, Adelaide, South Australia, Australia (P.I.M.)
| | - Akane Kimura
- Division of Pharmaceutical Cell Biology, Graduate School of Pharmaceutical Sciences (Y.M., A.K., K.K., Y.H., K.F., Y.T.) and Laboratory of Molecular Life Sciences, Graduate School of Pharmaceutical Sciences (Y.M., S.K., Y.I.), Kyushu University, Fukuoka, Japan; and Department of Clinical Pharmacology, Flinders Medical Centre and Flinders University, Adelaide, South Australia, Australia (P.I.M.)
| | - Ken Kurohara
- Division of Pharmaceutical Cell Biology, Graduate School of Pharmaceutical Sciences (Y.M., A.K., K.K., Y.H., K.F., Y.T.) and Laboratory of Molecular Life Sciences, Graduate School of Pharmaceutical Sciences (Y.M., S.K., Y.I.), Kyushu University, Fukuoka, Japan; and Department of Clinical Pharmacology, Flinders Medical Centre and Flinders University, Adelaide, South Australia, Australia (P.I.M.)
| | - Yuko Hirota
- Division of Pharmaceutical Cell Biology, Graduate School of Pharmaceutical Sciences (Y.M., A.K., K.K., Y.H., K.F., Y.T.) and Laboratory of Molecular Life Sciences, Graduate School of Pharmaceutical Sciences (Y.M., S.K., Y.I.), Kyushu University, Fukuoka, Japan; and Department of Clinical Pharmacology, Flinders Medical Centre and Flinders University, Adelaide, South Australia, Australia (P.I.M.)
| | - Keiko Fujimoto
- Division of Pharmaceutical Cell Biology, Graduate School of Pharmaceutical Sciences (Y.M., A.K., K.K., Y.H., K.F., Y.T.) and Laboratory of Molecular Life Sciences, Graduate School of Pharmaceutical Sciences (Y.M., S.K., Y.I.), Kyushu University, Fukuoka, Japan; and Department of Clinical Pharmacology, Flinders Medical Centre and Flinders University, Adelaide, South Australia, Australia (P.I.M.)
| | - Peter I Mackenzie
- Division of Pharmaceutical Cell Biology, Graduate School of Pharmaceutical Sciences (Y.M., A.K., K.K., Y.H., K.F., Y.T.) and Laboratory of Molecular Life Sciences, Graduate School of Pharmaceutical Sciences (Y.M., S.K., Y.I.), Kyushu University, Fukuoka, Japan; and Department of Clinical Pharmacology, Flinders Medical Centre and Flinders University, Adelaide, South Australia, Australia (P.I.M.)
| | - Yoshitaka Tanaka
- Division of Pharmaceutical Cell Biology, Graduate School of Pharmaceutical Sciences (Y.M., A.K., K.K., Y.H., K.F., Y.T.) and Laboratory of Molecular Life Sciences, Graduate School of Pharmaceutical Sciences (Y.M., S.K., Y.I.), Kyushu University, Fukuoka, Japan; and Department of Clinical Pharmacology, Flinders Medical Centre and Flinders University, Adelaide, South Australia, Australia (P.I.M.)
| | - Yuji Ishii
- Division of Pharmaceutical Cell Biology, Graduate School of Pharmaceutical Sciences (Y.M., A.K., K.K., Y.H., K.F., Y.T.) and Laboratory of Molecular Life Sciences, Graduate School of Pharmaceutical Sciences (Y.M., S.K., Y.I.), Kyushu University, Fukuoka, Japan; and Department of Clinical Pharmacology, Flinders Medical Centre and Flinders University, Adelaide, South Australia, Australia (P.I.M.)
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183
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Choi J, Tantisira KG, Duan QL. Whole genome sequencing identifies high-impact variants in well-known pharmacogenomic genes. THE PHARMACOGENOMICS JOURNAL 2019; 19:127-135. [PMID: 30214008 PMCID: PMC6417988 DOI: 10.1038/s41397-018-0048-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Revised: 07/10/2018] [Accepted: 08/10/2018] [Indexed: 01/21/2023]
Abstract
More than 1100 genetic loci have been correlated with drug response outcomes but disproportionately few have been translated into clinical practice. One explanation for the low rate of clinical implementation is that the majority of associated variants may be in linkage disequilibrium (LD) with the causal variants, which are often elusive. This study aims to identify and characterize likely causal variants within well-established pharmacogenomic genes using next-generation sequencing data from the 1000 Genomes Project. We identified 69,319 genetic variations within 160 pharmacogenomic genes, of which 8207 variants are in strong LD (r2>0.8) with known pharmacogenomic variants. Of the latter, eight are coding or structural variants predicted to have high impact, with 19 additional missense variants that are predicted to have moderate impact. In conclusion, we identified putatively functional variants within known pharmacogenomics loci that could account for the association signals and represent the missing causative variants underlying drug response phenotypes.
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Affiliation(s)
- Jihoon Choi
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, ON, Canada
- School of Computing, Queen's University, Kingston, ON, Canada
| | - Kelan G Tantisira
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Qing Ling Duan
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, ON, Canada.
- School of Computing, Queen's University, Kingston, ON, Canada.
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184
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Abstract
The emergence of new biotechnologies provides great promise for biodefense, especially for key objectives of biosurveillance and early warning, microbial forensics, risk and threat assessment, horizon scanning in biotechnology, and medical countermeasure (MCM) development, scale-up, and delivery. Understanding and leveraging the newly developed capabilities afforded by emerging biotechnologies require knowledge about cutting-edge research and its real or proposed application(s), the process through which biotechnologies advance, and the educational and research infrastructure that promotes multi-disciplinary science. Innovation in research and technology development are driven by sector-specific needs and the convergence of the physical, chemical, material, computer, engineering, and/or life sciences. Biotechnologies developed for other sectors could be applied to biodefense, especially if the individuals involved are able to innovate in concept design and development. Of all biodefense objectives, biosurveillance seems to have reaped the most benefit from emerging biotechnologies, specifically the integration and analysis of diverse clinical, biological, demographic, and other relevant data. More recently, scientists have begun applying synthetic biology, genomics, and microfluidics to the development of new products and platforms for MCMs. Unlike these objectives, investments in microbial forensics have been few, limiting its ability to harness biotechnology advances for collecting and analyzing data. Looking to the future, emerging biotechnologies can provide new opportunities for enhancing biodefense by addressing capability gaps.
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Affiliation(s)
- Sunit K. Singh
- Molecular Biology Unit, Institute of Medical Sciences, Banaras Hindu University, Varanasi, India
| | - Jens H. Kuhn
- NIH/NIAID, Division of Clinical Research, Integrated Research Facility at Fort Detrick, Frederick, MD USA
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185
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Nelson G, Bakkum-Gamez J, Kalogera E, Glaser G, Altman A, Meyer LA, Taylor JS, Iniesta M, Lasala J, Mena G, Scott M, Gillis C, Elias K, Wijk L, Huang J, Nygren J, Ljungqvist O, Ramirez PT, Dowdy SC. Guidelines for perioperative care in gynecologic/oncology: Enhanced Recovery After Surgery (ERAS) Society recommendations-2019 update. Int J Gynecol Cancer 2019; 29:651-668. [PMID: 30877144 DOI: 10.1136/ijgc-2019-000356] [Citation(s) in RCA: 385] [Impact Index Per Article: 77.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Accepted: 02/18/2019] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND This is the first updated Enhanced Recovery After Surgery (ERAS) Society guideline presenting a consensus for optimal perioperative care in gynecologic/oncology surgery. METHODS A database search of publications using Embase and PubMed was performed. Studies on each item within the ERAS gynecologic/oncology protocol were selected with emphasis on meta-analyses, randomized controlled trials, and large prospective cohort studies. These studies were then reviewed and graded according to the Grading of Recommendations, Assessment, Development and Evaluation (GRADE) system. RESULTS All recommendations on ERAS protocol items are based on best available evidence. The level of evidence for each item is presented accordingly. CONCLUSIONS The updated evidence base and recommendation for items within the ERAS gynecologic/oncology perioperative care pathway are presented by the ERAS® Society in this consensus review.
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Affiliation(s)
- Gregg Nelson
- Division of Gynecologic Oncology, Tom Baker Cancer Centre, Calgary, Alberta, Canada
| | - Jamie Bakkum-Gamez
- Division of Gynecologic Oncology, Mayo Clinic College of Medicine, Rochester, Minnesota, USA
| | - Eleftheria Kalogera
- Division of Gynecologic Oncology, Mayo Clinic College of Medicine, Rochester, Minnesota, USA
| | - Gretchen Glaser
- Division of Gynecologic Oncology, Mayo Clinic College of Medicine, Rochester, Minnesota, USA
| | - Alon Altman
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Larissa A Meyer
- Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Jolyn S Taylor
- Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Maria Iniesta
- Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Javier Lasala
- Department of Anesthesiology and Perioperative Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Gabriel Mena
- Department of Anesthesiology and Perioperative Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Michael Scott
- Department of Anesthesia, Virginia Commonwealth University Hospital, Richmond, Virginia, USA
| | - Chelsia Gillis
- Department of Community Health Sciences, University of Calgary, Calgary, Alberta, Canada
| | - Kevin Elias
- Division of Gynecologic Oncology, Brigham and Women's Hospital, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
| | - Lena Wijk
- Department of Obstetrics and Gynecology, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| | - Jeffrey Huang
- Department of Anesthesiology, Oak Hill Hospital, Brooksville, Florida, USA
| | - Jonas Nygren
- Departments of Surgery and Clinical Sciences, Ersta Hospital and Danderyd Hospital, Karolinska Institutet, Stockholm, Sweden
| | - Olle Ljungqvist
- Department of Surgery, Faculty of Medicine and Health, School of Health and Medical Sciences, Örebro University, Örebro, Sweden
| | - Pedro T Ramirez
- Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Sean C Dowdy
- Division of Gynecologic Oncology, Mayo Clinic College of Medicine, Rochester, Minnesota, USA
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186
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Camilleri M. Implications of Pharmacogenomics to the Management of IBS. Clin Gastroenterol Hepatol 2019; 17:584-594. [PMID: 29709540 DOI: 10.1016/j.cgh.2018.04.052] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Revised: 04/11/2018] [Accepted: 04/21/2018] [Indexed: 02/07/2023]
Abstract
The objectives are to review the role of pharmacogenomics in drug metabolism of medications typically used in patients with irritable bowel syndrome (IBS) focusing predominantly on cytochrome P450 metabolism. Other aims are to provide examples of genetic variation of receptors or intermediary pathways that are targets for IBS drugs and to critically appraise the situations where precision medicine is impacting health in IBS. Pharmacogenomics impacts both pharmacokinetics and pharmacodynamics. Although large clinical trials have not incorporated testing for genetic variations that could impact the efficacy of medications in IBS, there are therapeutic advantages to inclusion of pharmacogenomics testing for individual patients, as has been demonstrated particularly in the treatment with central neuromodulators in psychiatry practice. Clinical practice in IBS is moving in the same direction with the aid of commercially available tests focused on drug metabolism. Specific mechanisms leading to pathophysiology of IBS are still poorly characterized, relative to diseases such as cancer and inflammatory bowel disease, and, therefore, pharmacogenomics related to drug pharmacodynamics is still in its infancy and requires extensive future research. With increased attention to pharmacogenomics affecting drug metabolism, it is anticipated that pharmacogenomics will impact care of IBS.
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Affiliation(s)
- Michael Camilleri
- Clinical Enteric Neuroscience Translational and Epidemiological Research, Mayo Clinic, Rochester, Minnesota.
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187
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S S, Fuke S, Nagasawa H, Tsukahara T. Single nucleotide recognition using a probes-on-carrier DNA chip. Biotechniques 2019; 66:73-78. [PMID: 30744407 DOI: 10.2144/btn-2018-0088] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Following the sequencing of the human genome, SNP analysis of individual patients has become essential for achieving the best drug response and ensuring optimal care. In this study, we developed a cost-effective probes-on-carrier DNA chip for the detection of SNPs. Our chips harbored three different probes against the TP53 gene, and were capable of detecting wild-type TP53 and SNPs such as rs121912651 and rs11540652. Four cell lines were used to validate the specificity of probe hybridization. Strong fluorescence intensity was observed in hybridized spots based on hybridization for perfect base pairing between complementary strands, whereas significantly lower fluorescence (p < 0.05) was observed in nonhybridized spots. These hybridization results indicated that the probes-on-carrier chip is suitable for SNP genotyping.
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Affiliation(s)
- Saifullah S
- Area of Bioscience & Biotechnology, School of Materials Science, Japan Advanced Institute of Science & Technology (JAIST), 1-1 Asahidai, Nomi, Ishikawa 923-1292, Japan
| | - Satoshi Fuke
- Area of Bioscience & Biotechnology, School of Materials Science, Japan Advanced Institute of Science & Technology (JAIST), 1-1 Asahidai, Nomi, Ishikawa 923-1292, Japan
| | - Hiroshi Nagasawa
- Kankyou Resilience, 79-7 Tokiwadai, Hodogaya, Yokohama, 240-0067, Japan
| | - Toshifumi Tsukahara
- Area of Bioscience & Biotechnology, School of Materials Science, Japan Advanced Institute of Science & Technology (JAIST), 1-1 Asahidai, Nomi, Ishikawa 923-1292, Japan.,Division of Transdisciplinary Science, Japan Advanced Institute of Science & Technology, 1-1 Asahidai, Nomi city, Ishikawa 923-1292, Japan
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188
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Ngo LP, Chan TK, Ge J, Samson LD, Engelward BP. Microcolony Size Distribution Assay Enables High-Throughput Cell Survival Quantitation. Cell Rep 2019; 26:1668-1678.e4. [PMID: 30726746 PMCID: PMC6431241 DOI: 10.1016/j.celrep.2019.01.053] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Revised: 11/02/2018] [Accepted: 01/14/2019] [Indexed: 01/14/2023] Open
Abstract
Cell survival is a critical and ubiquitous endpoint in biology. The broadly accepted colony formation assay (CFA) directly measures a cell's ability to divide; however, it takes weeks to perform and is incompatible with high-throughput screening (HTS) technologies. Here, we describe the MicroColonyChip, which exploits microwell array technology to create an array of colonies. Unlike the CFA, where visible colonies are counted by eye, using fluorescence microscopy, microcolonies can be analyzed in days rather than weeks. Using automated analysis of microcolony size distributions, the MicroColonyChip achieves comparable sensitivity to the CFA (and greater sensitivity than the 2,3-bis-(2-methoxy-4-nitro-5-sulfophenyl)-2H-tetrazolium-5-carboxanilide [XTT] assay). Compared to CellTiter-Glo, the MicroColonyChip is as sensitive and also robust to artifacts caused by differences in initial cell seeding density. We demonstrate efficacy via studies of radiosensitivity and chemosensitivity and show that the approach is amenable to multiplexing. We conclude that the MicroColonyChip is a rapid and automated alternative for cell survival quantitation.
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Affiliation(s)
- Le P Ngo
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Tze Khee Chan
- Singapore-MIT Alliance for Research and Technology, Infectious Diseases IRG, Singapore 117600, Singapore
| | - Jing Ge
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Leona D Samson
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Bevin P Engelward
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
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189
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Landolt HP, Holst SC, Valomon A. Clinical and Experimental Human Sleep-Wake Pharmacogenetics. Handb Exp Pharmacol 2019; 253:207-241. [PMID: 30443785 DOI: 10.1007/164_2018_175] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Sleep and wakefulness are highly complex processes that are elegantly orchestrated by fine-tuned neurochemical changes among neuronal and non-neuronal ensembles, nuclei, and networks of the brain. Important neurotransmitters and neuromodulators regulating the circadian and homeostatic facets of sleep-wake physiology include melatonin, γ-aminobutyric acid, hypocretin, histamine, norepinephrine, serotonin, dopamine, and adenosine. Dysregulation of these neurochemical systems may cause sleep-wake disorders, which are commonly classified into insomnia disorder, parasomnias, circadian rhythm sleep-wake disorders, central disorders of hypersomnolence, sleep-related movement disorders, and sleep-related breathing disorders. Sleep-wake disorders can have far-reaching consequences on physical, mental, and social well-being and health and, thus, need be treated with effective and rational therapies. Apart from behavioral (e.g., cognitive behavioral therapy for insomnia), physiological (e.g., chronotherapy with bright light), and mechanical (e.g., continuous positive airway pressure treatment of obstructive sleep apnea) interventions, pharmacological treatments often are the first-line clinical option to improve disturbed sleep and wake states. Nevertheless, not all patients respond to pharmacotherapy in uniform and beneficial fashion, partly due to genetic differences. The improved understanding of the neurochemical mechanisms regulating sleep and wakefulness and the mode of action of sleep-wake therapeutics has provided a conceptual framework, to search for functional genetic variants modifying individual drug response phenotypes. This article will summarize the currently known genetic polymorphisms that modulate drug sensitivity and exposure, to partly determine individual responses to sleep-wake pharmacotherapy. In addition, a pharmacogenetic strategy will be outlined how based upon classical and opto-/chemogenetic strategies in animals, as well as human genetic associations, circuit mechanisms regulating sleep-wake functions in humans can be identified. As such, experimental human sleep-wake pharmacogenetics forms a bridge spanning basic research and clinical medicine and constitutes an essential step for the search and development of novel sleep-wake targets and therapeutics.
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Affiliation(s)
- Hans-Peter Landolt
- Institute of Pharmacology and Toxicology, University of Zürich, Zürich, Switzerland.
- Zürich Center for Interdisciplinary Sleep Research (ZiS), University of Zürich, Zürich, Switzerland.
| | - Sebastian C Holst
- Neurobiology Research Unit and Neuropharm, Department of Neurology, Rigshospitalet, Copenhagen, Denmark
| | - Amandine Valomon
- Wisconsin Institute for Sleep and Consciousness, University of Wisconsin Madison, Madison, WI, USA
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190
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Zhang S, Bamakan SMH, Qu Q, Li S. Learning for Personalized Medicine: A Comprehensive Review From a Deep Learning Perspective. IEEE Rev Biomed Eng 2019; 12:194-208. [DOI: 10.1109/rbme.2018.2864254] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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191
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Next Generation Sequencing (NGS): A Revolutionary Technology in Pharmacogenomics and Personalized Medicine in Cancer. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1168:9-30. [DOI: 10.1007/978-3-030-24100-1_2] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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192
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A single inhalation of vapor from dried toad secretion containing 5-methoxy-N,N-dimethyltryptamine (5-MeO-DMT) in a naturalistic setting is related to sustained enhancement of satisfaction with life, mindfulness-related capacities, and a decrement of psychopathological symptoms. Psychopharmacology (Berl) 2019; 236:2653-2666. [PMID: 30982127 PMCID: PMC6695371 DOI: 10.1007/s00213-019-05236-w] [Citation(s) in RCA: 81] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Accepted: 03/19/2019] [Indexed: 12/22/2022]
Abstract
BACKGROUND 5-methoxy-N,N-dimethyltryptamine (hereinafter referred to as 5-MeO-DMT) is a psychedelic substance found in the secretion from the parotoid glands of the Bufo alvarius toad. Inhalation of vapor from toad secretion containing 5-MeO-DMT has become popular in naturalistic settings as a treatment of mental health problems or as a means for spiritual exploration. However, knowledge of the effects of 5-MeO-DMT in humans is limited. AIMS The first objective of this study was to assess sub-acute and long-term effects of inhaling vapor from dried toad secretion containing 5-MeO-DMT on affect and cognition. The second objective was to assess whether any changes were associated with the psychedelic experience. METHODS Assessments at baseline, within 24 h and 4 weeks following intake, were made in 42 individuals who inhaled vapor from dried toad secretion at several European locations. RESULTS Relative to baseline, ratings of satisfaction with life and convergent thinking significantly increased right after intake and were maintained at follow-up 4 weeks later. Ratings of mindfulness also increased over time and reached statistical significance at 4 weeks. Ratings of depression, anxiety, and stress decreased after the session, and reached significance at 4 weeks. Participants that experienced high levels of ego dissolution or oceanic boundlessness during the session displayed higher ratings of satisfaction with life and lower ratings of depression and stress. CONCLUSION A single inhalation of vapor from dried toad secretion containing 5-MeO-DMT produces sub-acute and long-term changes in affect and cognition in volunteers. These results warrant exploratory research into therapeutic applications of 5-MeO-DMT.
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193
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Susanto AH, Widodo, Rohman MS, Utomo DH, Lukitasari M. Analysis in silico of the single nucleotide polymorphism G–152A in the promoter of the angiotensinogen gene of Indonesian patients with essential hypertension. ASIAN BIOMED 2018. [DOI: 10.1515/abm-2018-0027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Abstract
Background
Single nucleotide polymorphism (SNP) G–152A (rs11568020) in the promoter of the angiotensinogen gene (AGT) may modulate its transcription. Translation of mRNA to angiotensinogen induces hypertension during hypoxia. The G allele at position –152 is located within the hypoxia-response element (HRE) transcription factor-binding site for the hypoxia-inducible factor 1 (HIF-1) heterodimer. However, the function of the –152 site in HIF-1 binding is not fully elucidated.
Objectives
To determine the frequency of SNP G–152A in Indonesian patients with hypertension and the function of this SNP.
Methods
We determined the frequency of the SNP in 100 patients by direct sequencing, and the influence of SNP G–152A on predicted binding of HIF-1 to the HRE using a docking approach in silico.
Results
The AGT promoter in our patients had genetic variants –152G and –152A (19:1). Predicted binding indicated that HIF-1 directly contacts the major groove of the G allele, but not the A allele. Scoring according to weighted sum High Ambiguity Driven biomolecular DOCKing showed that the score for the A allele–HIF-1 complex (–47.1 ± 6.9 kcal/mol) was higher than that for the G allele–HIF-1 complex (–94.6 ± 14.1 kcal/mol), indicating more favorable binding of HIF-1 to the G allele.
Conclusions
SNP G–152A reduces the favorability of binding of HIF-1 to the HRE. The occurrence of this SNP in the AGT promoter of Indonesian patients with essential hypertension suggests that the G allele is a genetic susceptibility factor in hypertension regulated by HIF-1.
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Affiliation(s)
- Akhiyan Hadi Susanto
- Basic Nursing Department , School of Nursing, Faculty of Medicine , Universitas Brawijaya , Malang 65145 , Indonesia
| | - Widodo
- Biology Department , Faculty of Mathematics and Natural Sciences , Universitas Brawijaya , Malang 65145 , Indonesia
| | - Mohammad Saifur Rohman
- Department of Cardiology and Vascular Medicine , Faculty of Medicine , Universitas Brawijaya – Saiful Anwar General Hospital , Malang 65145 , Indonesia
| | - Didik Huswo Utomo
- Biology Department , Faculty of Mathematics and Natural Sciences , Universitas Brawijaya , Malang 65145 , Indonesia
| | - Mifetika Lukitasari
- Medical Surgical Nursing Department , School of Nursing, Faculty of Medicine , Universitas Brawijaya , Malang 65145 , Indonesia
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194
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Peters FT, Steuer AE. Antemortem and postmortem influences on drug concentrations and metabolite patterns in postmortem specimens. ACTA ACUST UNITED AC 2018. [DOI: 10.1002/wfs2.1297] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Frank T. Peters
- Institute of Forensic Medicine Jena University Hospital Jena Germany
| | - Andrea E. Steuer
- Department of Forensic Pharmacology and Toxicology, Zurich Institute of Forensic Medicine University of Zurich Zurich Switzerland
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195
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Jensen KP, DeVito EE, Yip S, Carroll KM, Sofuoglu M. The Cholinergic System as a Treatment Target for Opioid Use Disorder. CNS Drugs 2018; 32:981-996. [PMID: 30259415 PMCID: PMC6314885 DOI: 10.1007/s40263-018-0572-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Opioid overdoses recently became the leading cause of accidental death in the US, marking an increase in the severity of the opioid use disorder (OUD) epidemic that is impacting global health. Current treatment protocols for OUD are limited to opioid medications, including methadone, buprenorphine, and naltrexone. While these medications are effective in many cases, new treatments are required to more effectively address the rising societal and interpersonal costs associated with OUD. In this article, we review the opioid and cholinergic systems, and examine the potential of acetylcholine (ACh) as a treatment target for OUD. The cholinergic system includes enzymes that synthesize and degrade ACh and receptors that mediate the effects of ACh. ACh is involved in many central nervous system functions that are critical to the development and maintenance of OUD, such as reward and cognition. Medications that target the cholinergic system have been approved for the treatment of Alzheimer's disease, tobacco use disorder, and nausea. Clinical and preclinical studies suggest that medications such as cholinesterase inhibitors and scopolamine, which target components of the cholinergic system, show promise for the treatment of OUD and further investigations are warranted.
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Affiliation(s)
- Kevin P Jensen
- Department of Psychiatry and VA Connecticut Healthcare System, Yale University, School of Medicine, 950 Campbell Ave, Bldg 36/116A4, West Haven, CT, 06516, USA
| | - Elise E DeVito
- Department of Psychiatry and VA Connecticut Healthcare System, Yale University, School of Medicine, 950 Campbell Ave, Bldg 36/116A4, West Haven, CT, 06516, USA
| | - Sarah Yip
- Department of Psychiatry and VA Connecticut Healthcare System, Yale University, School of Medicine, 950 Campbell Ave, Bldg 36/116A4, West Haven, CT, 06516, USA
| | - Kathleen M Carroll
- Department of Psychiatry and VA Connecticut Healthcare System, Yale University, School of Medicine, 950 Campbell Ave, Bldg 36/116A4, West Haven, CT, 06516, USA
| | - Mehmet Sofuoglu
- Department of Psychiatry and VA Connecticut Healthcare System, Yale University, School of Medicine, 950 Campbell Ave, Bldg 36/116A4, West Haven, CT, 06516, USA.
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196
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Fritz A, Busch D, Lapczuk J, Ostrowski M, Drozdzik M, Oswald S. Expression of clinically relevant drug-metabolizing enzymes along the human intestine and their correlation to drug transporters and nuclear receptors: An intra-subject analysis. Basic Clin Pharmacol Toxicol 2018; 124:245-255. [PMID: 30253071 DOI: 10.1111/bcpt.13137] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Accepted: 09/18/2018] [Indexed: 12/23/2022]
Abstract
The oral bioavailability of many drugs is highly influenced not only by hepatic but also by intestinal biotransformation. To estimate the impact of intestinal phase I and II metabolism on oral drug absorption, knowledge on the expression levels of the respective enzymes is an essential prerequisite. In addition, the potential interplay of metabolism and transport contributes to drug disposition. Both mechanisms may be subjected to coordinative regulation by nuclear receptors, leading to unwanted drug-drug interactions due to induction of intestinal metabolism and transport. Thus, it was the aim of this study to comprehensively analyse the regional expression of clinically relevant phase I and II enzymes along the entire human intestine and to correlate these data to expression data of drug transporters and nuclear receptors of pharmacokinetic relevance. Gene expression of 11 drug-metabolizing enzymes (CYP2B6, 2C8, 2C9, 2C19, 2D6, 3A4, 3A5, SULT1A, UGT1A, UGT2B7, UGT2B15) was studied in duodenum, jejunum, ileum and colon from six organ donors by real-time RT-PCR. Enzyme expression was correlated with expression data of the nuclear receptors PXR, CAR and FXR as well as drug transporters observed in the same cohort. Intestinal expression of all studied metabolizing enzymes was significantly higher in the small intestine compared to colonic tissue. CYP2B6, CYP2C9, CYP2C19, CYP2D6, CYP3A4/5, SULT1A, UGT1A and UGT2B7 expression increased from the duodenum to jejunum but was markedly lower in the ileum. In the small intestine, that is, the predominant site of drug absorption, the highest expression has been observed for CYP3A4, CYP2C9, SULT1A and UGT1A. In addition, significant correlations were found between several enzymes and PXR as well as ABC transporters in the small intestine. In conclusion, the observed substantial site-dependent intestinal expression of several enzymes may explain regional differences in intestinal drug absorption. The detected correlations between intestinal enzymes, transporters and nuclear receptors provide indirect evidence for their coordinative expression, regulation and function in the human small intestine.
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Affiliation(s)
- Anja Fritz
- Department of Clinical Pharmacology, Center of Drug Absorption and Transport, University Medicine Greifswald, Greifswald, Germany
| | - Diana Busch
- Department of Clinical Pharmacology, Center of Drug Absorption and Transport, University Medicine Greifswald, Greifswald, Germany
| | - Joanna Lapczuk
- Department of Experimental and Clinical Pharmacology, Pomeranian Medical University, Szczecin, Poland
| | - Marek Ostrowski
- Department of General and Transplantation Surgery, Pomeranian Medical University, Szczecin, Poland
| | - Marek Drozdzik
- Department of Experimental and Clinical Pharmacology, Pomeranian Medical University, Szczecin, Poland
| | - Stefan Oswald
- Department of Clinical Pharmacology, Center of Drug Absorption and Transport, University Medicine Greifswald, Greifswald, Germany
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197
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Zhang T, Yu F, Guo L, Chen M, Yuan X, Wu B. Small Heterodimer Partner Regulates Circadian Cytochromes p450 and Drug-Induced Hepatotoxicity. Theranostics 2018; 8:5246-5258. [PMID: 30555544 PMCID: PMC6276094 DOI: 10.7150/thno.28676] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2018] [Accepted: 09/24/2018] [Indexed: 01/01/2023] Open
Abstract
The role of small heterodimer partner (SHP) in regulation of xenobiotic detoxification remains elusive. Here, we uncover a critical role for SHP in circadian regulation of cytochromes P450 (CYPs) and drug-induced hepatotoxicity. Methods: The mRNA and protein levels of CYPs in the livers of wild-type and SHP-/- mice were measured by quantitative real-time polymerase chain reaction and Western blotting, respectively. Regulation of CYP by SHP was investigated using luciferase reporter, mobility shift, chromatin immunoprecipitation, and/or co-immunoprecipitation assays. Results: The circadian rhythmicities of xenobiotic-detoxifying CYP mRNAs and proteins were disrupted in SHP-deficient mice. Of note, SHP ablation up-regulated Cyp2c38 and Cyp2c39, whereas it down-regulated all other CYP genes. Moreover, SHP regulated the expression of CYP genes through different mechanisms. SHP repressed Lrh-1/Hnf4α to down-regulate Cyp2c38, E4bp4 to up-regulate Cyp2a5, Dec2/HNF1α axis to up-regulate Cyp1a2, Cyp2e1 and Cyp3a11, and Rev-erbα to up-regulate Cyp2b10, Cyp4a10 and Cyp4a14. Furthermore, SHP ablation sensitized mice to theophylline (or mitoxantrone)-induced toxicity. Higher level of toxicity was correlated with down-regulated metabolism and clearance of theophylline (or mitoxantrone). In contrast, SHP ablation blunted the circadian rhythmicity of acetaminophen-induced hepatotoxicity and alleviated the toxicity by down-regulating Cyp2e1-mediated metabolism and reducing formation of the toxic metabolite. Toxicity alleviation by SHP ablation was also observed for aflatoxin B1 due to reduced formation of the toxic epoxide metabolite. Conclusion: SHP participates in circadian regulation of CYP enzymes, thereby impacting xenobiotic metabolism and drug-induced hepatotoxicity.
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198
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Winkler M, Geier M, Hanlon SP, Nidetzky B, Glieder A. Human Enzymes for Organic Synthesis. Angew Chem Int Ed Engl 2018; 57:13406-13423. [PMID: 29600541 PMCID: PMC6334177 DOI: 10.1002/anie.201800678] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Indexed: 02/06/2023]
Abstract
Human enzymes have been widely studied in various disciplines. The number of reactions taking place in the human body is vast, and so is the number of potential catalysts for synthesis. Herein, we focus on the application of human enzymes that catalyze chemical reactions in course of the metabolism of drugs and xenobiotics. Some of these reactions have been explored on the preparative scale. The major field of application of human enzymes is currently drug development, where they are applied for the synthesis of drug metabolites.
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Affiliation(s)
- Margit Winkler
- Institute for Molecular BiotechnologyGraz University of TechnologyPetersgasse 148010GrazAustria
- acib GmbHPetersgasse 148010GrazAustria
| | | | | | - Bernd Nidetzky
- acib GmbHPetersgasse 148010GrazAustria
- Institute of Biotechnology and Biochemical EngineeringGraz University of TechnologyPetersgasse 128010GrazAustria
| | - Anton Glieder
- Institute for Molecular BiotechnologyGraz University of TechnologyPetersgasse 148010GrazAustria
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199
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Spooner W, McLaren W, Slidel T, Finch DK, Butler R, Campbell J, Eghobamien L, Rider D, Kiefer CM, Robinson MJ, Hardman C, Cunningham F, Vaughan T, Flicek P, Huntington CC. Haplosaurus computes protein haplotypes for use in precision drug design. Nat Commun 2018; 9:4128. [PMID: 30297836 PMCID: PMC6175845 DOI: 10.1038/s41467-018-06542-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Accepted: 09/07/2018] [Indexed: 01/08/2023] Open
Abstract
Selecting the most appropriate protein sequences is critical for precision drug design. Here we describe Haplosaurus, a bioinformatic tool for computation of protein haplotypes. Haplosaurus computes protein haplotypes from pre-existing chromosomally-phased genomic variation data. Integration into the Ensembl resource provides rapid and detailed protein haplotypes retrieval. Using Haplosaurus, we build a database of unique protein haplotypes from the 1000 Genomes dataset reflecting real-world protein sequence variability and their prevalence. For one in seven genes, their most common protein haplotype differs from the reference sequence and a similar number differs on their most common haplotype between human populations. Three case studies show how knowledge of the range of commonly encountered protein forms predicted in populations leads to insights into therapeutic efficacy. Haplosaurus and its associated database is expected to find broad applications in many disciplines using protein sequences and particularly impactful for therapeutics design.
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Affiliation(s)
- William Spooner
- Eagle Genomics Ltd., Biodata Innovation Centre, Wellcome Genome Campus, Hinxton, Cambridge, CB10 3DR UK
- Genomics England, QMUL Dawson Hall, London, EC1M 6BQ UK
| | - William McLaren
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD UK
| | | | | | - Robin Butler
- MedImmune Ltd., Granta Park, Cambridge, CB21 4QR UK
| | | | | | - David Rider
- MedImmune Ltd., Granta Park, Cambridge, CB21 4QR UK
| | | | | | | | - Fiona Cunningham
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD UK
| | | | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD UK
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200
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Abstract
As a result of an increasing aging population, the number of individuals taking multiple medications simultaneously has grown considerably. For these individuals, taking multiple medications has increased the risk of undesirable drug–drug interactions (DDIs), which can cause serious and debilitating adverse drug reactions (ADRs). A comprehensive understanding of DDIs is needed to combat these deleterious outcomes. This review provides a synopsis of the pharmacokinetic (PK) and pharmacodynamic (PD) mechanisms that underlie DDIs. PK-mediated DDIs affect all aspects of drug disposition: absorption, distribution, metabolism and excretion (ADME). In this review, the cells that play a major role in ADME and have been investigated for DDIs are discussed. Key examples of drug metabolizing enzymes and drug transporters that are involved in DDIs and found in these cells are described. The effect of inhibiting or inducing these proteins through DDIs on the PK parameters is also reviewed. Despite most DDI studies being focused on the PK effects, DDIs through PD can also lead to significant and harmful effects. Therefore, this review outlines specific examples and describes the additive, synergistic and antagonistic mechanisms of PD-mediated DDIs. The effects DDIs on the maximum PD response (Emax) and the drug dose or concentration (EDEC50) that lead to 50% of Emax are also examined. Significant gaps in our understanding of DDIs remain, so innovative and emerging approaches are critical for overcoming them.
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Affiliation(s)
- Arthur G Roberts
- Pharmaceutical and Biomedical Sciences, University of Georgia, Athens, GA, USA,
| | - Morgan E Gibbs
- Pharmaceutical and Biomedical Sciences, University of Georgia, Athens, GA, USA,
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