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Rizvi AA, Abbas M, Verma S, Verma S, Khan A, Raza ST, Mahdi F. Determinants in Tailoring Antidiabetic Therapies: A Personalized Approach. Glob Med Genet 2022; 9:63-71. [PMID: 35707783 PMCID: PMC9192178 DOI: 10.1055/s-0041-1741109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 11/20/2021] [Indexed: 11/02/2022] Open
Abstract
AbstractDiabetes has become a pandemic as the number of diabetic people continues to rise globally. Being a heterogeneous disease, it has different manifestations and associated complications in different individuals like diabetic nephropathy, neuropathy, retinopathy, and others. With the advent of science and technology, this era desperately requires increasing the pace of embracing precision medicine and tailoring of drug treatment based on the genetic composition of individuals. It has been previously established that response to antidiabetic drugs, like biguanides, sulfonylureas, dipeptidyl peptidase-4 (DPP-4) inhibitors, glucagon-like peptide 1 (GLP-1) agonists, and others, depending on variations in their transporter genes, metabolizing genes, genes involved in their action, etc. Responsiveness of these drugs also relies on epigenetic factors, including histone modifications, miRNAs, and DNA methylation, as well as environmental factors and the lifestyle of an individual. For precision medicine to make its way into clinical procedures and come into execution, all these factors must be reckoned with. This review provides an insight into several factors oscillating around the idea of precision medicine in type-2 diabetes mellitus.
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Affiliation(s)
- Aliya A. Rizvi
- Department of Personalized and Molecular Medicine, Era University, Lucknow, Uttar Pradesh, India
| | - Mohammad Abbas
- Department of Personalized and Molecular Medicine, Era University, Lucknow, Uttar Pradesh, India
| | - Sushma Verma
- Department of Personalized and Molecular Medicine, Era University, Lucknow, Uttar Pradesh, India
| | - Shrikant Verma
- Department of Personalized and Molecular Medicine, Era University, Lucknow, Uttar Pradesh, India
| | - Almas Khan
- Department of Personalized and Molecular Medicine, Era University, Lucknow, Uttar Pradesh, India
| | - Syed T. Raza
- Department of Biochemistry, Era University, Lucknow Medical College and Hospital, Lucknow, Uttar Pradesh, India
| | - Farzana Mahdi
- Department of Personalized and Molecular Medicine, Era University, Lucknow, Uttar Pradesh, India
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2
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Poku VO, Iram SH. A critical review on modulators of Multidrug Resistance Protein 1 in cancer cells. PeerJ 2022; 10:e12594. [PMID: 35036084 PMCID: PMC8742536 DOI: 10.7717/peerj.12594] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 11/14/2021] [Indexed: 01/11/2023] Open
Abstract
Multidrug resistance protein 1 (MRP1/ABCC1) is an ATP-dependent efflux transporter, and responsible for the transport of a broad spectrum of xenobiotics, toxins, and physiological substrates across the plasma membrane. As an efflux pump, it plays a significant role in the absorption and disposition of drugs including anticancer drugs, antivirals, antimalarials, and antibiotics and their metabolites across physiological barriers in cells. MRP1 is also known to aid in the regulation of several physiological processes such as redox homeostasis, steroid metabolism, and tissue defense. However, its overexpression has been reported to be a key clinical marker associated with multidrug resistance (MDR) of several types of cancers including lung cancer, childhood neuroblastoma, breast and prostate carcinomas, often resulting in a higher risk of treatment failure and shortened survival rates in cancer patients. Aside MDR, overexpression of MRP1 is also implicated in the development of neurodegenerative and cardiovascular diseases. Due to the cellular importance of MRP1, the identification and biochemical/molecular characterization of modulators of MRP1 activity and expression levels are of key interest to cancer research and beyond. This review primarily aims at highlighting the physiological and pharmacological importance of MRP1, known MRP1 modulators, current challenges encountered, and the potential benefits of conducting further research on the MRP1 transporter.
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Affiliation(s)
- Vivian Osei Poku
- Department of Chemistry and Biochemistry, South Dakota State University, Brookings, SD, United States of America
| | - Surtaj Hussain Iram
- Department of Chemistry and Biochemistry, South Dakota State University, Brookings, SD, United States of America,American University of Iraq, Sulaimaniya, Sulaimani, KRG, Iraq
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3
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Yee SW, Giacomini KM. Emerging Roles of the Human Solute Carrier 22 Family. Drug Metab Dispos 2021; 50:DMD-MR-2021-000702. [PMID: 34921098 PMCID: PMC9488978 DOI: 10.1124/dmd.121.000702] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 11/22/2021] [Accepted: 12/08/2021] [Indexed: 11/22/2022] Open
Abstract
The human Solute Carrier 22 family (SLC22), also termed the organic ion transporter family, consists of 28 distinct multi-membrane spanning proteins, which phylogenetically cluster together according to their charge specificity for organic cations (OCTs), organic anions (OATs) and organic zwitterion/cations (OCTNs). Some SLC22 family members are well characterized in terms of their substrates, transport mechanisms and expression patterns, as well as their roles in human physiology and pharmacology, whereas others remain orphans with no known ligands. Pharmacologically, SLC22 family members play major roles as determinants of the absorption and disposition of many prescription drugs, and several including the renal transporters, OCT2, OAT1 and OAT3 are targets for many clinically important drug-drug interactions. In addition, mutations in some of these transporters (SLC22A5 (OCTN2) and SLC22A12 (URAT1) lead to rare monogenic disorders. Genetic polymorphisms in SLC22 transporters have been associated with common human disease, drug response and various phenotypic traits. Three members in this family were deorphaned in very recently: SLC22A14, SLC22A15 and SLC22A24, and found to transport specific compounds such as riboflavin (SLC22A14), anti-oxidant zwitterions (SLC22A15) and steroid conjugates (SLC22A24). Their physiologic and pharmacological roles need further investigation. This review aims to summarize the substrates, expression patterns and transporter mechanisms of individual SLC22 family members and their roles in human disease and drug disposition and response. Gaps in our understanding of SLC22 family members are described. Significance Statement In recent years, three members of the SLC22 family of transporters have been deorphaned and found to play important roles in the transport of diverse solutes. New research has furthered our understanding of the mechanisms, pharmacological roles, and clinical impact of SLC22 transporters. This minireview provides overview of SLC22 family members of their physiologic and pharmacologic roles, the impact of genetic variants in the SLC22 family on disease and drug response, and summary of recent studies deorphaning SLC22 family members.
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Affiliation(s)
- Sook Wah Yee
- Bioengineering and Therapeutic Sciences, Univerity of California, San Francisco, United States
| | - Kathleen M Giacomini
- Bioengineering and Therapeutic Sciences, Univerity of California, San Francisco, United States
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Gonzalez-Covarrubias V, Sánchez-Ibarra H, Lozano-Gonzalez K, Villicaña S, Texis T, Rodríguez-Dorantes M, Cortés-Ramírez S, Lavalle-Gonzalez F, Soberón X, Barrera-Saldaña H. Transporters, TBC1D4, and ARID5B Variants to Explain Glycated Hemoglobin Variability in Patients with Type 2 Diabetes. Pharmacology 2021; 106:588-596. [PMID: 34265779 DOI: 10.1159/000517462] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2021] [Accepted: 05/15/2021] [Indexed: 11/19/2022]
Abstract
INTRODUCTION Genetic variants could aid in predicting antidiabetic drug response by associating them with markers of glucose control, such as glycated hemoglobin (HbA1c). However, pharmacogenetic implementation for antidiabetics is still under development, as the list of actionable markers is being populated and validated. This study explores potential associations between genetic variants and plasma levels of HbA1c in 100 patients under treatment with metformin. METHODS HbA1c was measured in a clinical chemistry analyzer (Roche), genotyping was performed in an Illumina-GSA array and data were analyzed using PLINK. Association and prediction models were developed using R and a 10-fold cross-validation approach. RESULTS We identified genetic variants on SLC47A1, SLC28A1, ABCG2, TBC1D4, and ARID5B that can explain up to 55% of the interindividual variability of HbA1c plasma levels in diabetic patients under treatment. Variants on SLC47A1, SLC28A1, and ABCG2 likely impact the pharmacokinetics (PK) of metformin, while the role of the two latter can be related to insulin resistance and regulation of adipogenesis. CONCLUSIONS Our results confirm previous genetic associations and point to previously unassociated gene variants for metformin PK and glucose control.
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Affiliation(s)
| | | | | | - Sergio Villicaña
- Pharmacogenomics Laboratory, Instituto Nacional de Medicina Genómica, CDMX, Mexico
| | - Tomas Texis
- Pharmacogenomics Laboratory, Instituto Nacional de Medicina Genómica, CDMX, Mexico
| | | | | | - Fernando Lavalle-Gonzalez
- University Hospital Dr. José E. González, Endocrinology, Universidad Autónoma de Nuevo León, San Nicolás de los Garza, Mexico
| | - Xavier Soberón
- Instituto de Biotecnología, Universidad Autónoma de México, UNAM, Cuernavaca, Mexico
| | - Hugo Barrera-Saldaña
- Genetics Laboratory, Vitagénesis, Monterrey, Mexico.,Medicine and Health Sciences Department, Tecnológico de Monterrey, Monterrey, Mexico
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Cano L, Soto-Ospina A, Araque P, Caro-Gomez MA, Parra-Marin MV, Bedoya G, Duque C. Diffusion Mechanism Modeling of Metformin in Human Organic Cationic Amino Acid Transporter one and Functional Impact of S189L, R206C, and G401S Mutation. Front Pharmacol 2021; 11:587590. [PMID: 33658930 PMCID: PMC7917475 DOI: 10.3389/fphar.2020.587590] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2020] [Accepted: 12/23/2020] [Indexed: 12/25/2022] Open
Abstract
Metformin used as a first-line drug to treat Type 2 Diabetes Mellitus is transported via organic cation channels to soft tissues. Mutations in the SLC22A1 gene, such as Gly401Ser, Ser189Leu, and Arg206Cys, may affect the drug’s therapeutic effect on these patients. This study aims at proposing a potential structural model for drug interactions with the hOCT1 transporter, as well as the impact of these mutations at both topological and electronic structure levels on the channel’s surface, from a chemical point of view with, in addition to exploring the frequency distribution. To chemically understand metformin diffusion, we used an open model from the protein model database, with ID PM0080367, viewed through UCSF Chimera. The effect of the mutations was assessed using computational hybrid Quantum Mechanics/Molecular Mechanics, based on the Austin Model 1 semi-empirical method using Spartan 18’ software. The results demonstrate coupling energy for metformin with amino acids F, W, H and Y, because of the interaction between the metformin dication and the electron cloud of π orbitals. The mutations analyzed showed changes in the chemical polarity and topology of the structure. The proposed diffusion model is a possible approach to the interaction mechanism between metformin and its transporter, as well as the impacts of variants, suggesting structural changes in the action of the drug. Metformin efficacy considerably varies from one patient to another; this may be largely attributed to the presence of mutations on the SLC22A1 gene. This study aims at proposing a potential structural model for metformin-hOCT1 (SLC22A1) transporter interaction, as well as the identification of the effect of mutations G401S (rs34130495), S189L (rs34104736), and R206C (616C > T) of the SLC22A1 gene at the topological and electronic structure levels on the channel surfaces, from a chemical viewpoint. Our results demonstrated that the coupling energies for metformin with aromatic amino acids F, W, H and Y, because of the interaction between the metformin dication and the electron cloud of π orbitals. Changes in the chemical environment’s polarity and the structure’s topology were reported in the mutations assessed. The diffusion model proposed is a potential approach for the mechanism of interaction of metformin with its transporter and the effects of variants on the efficacy of the drug in the treatment of type 2 diabetes. The assessment of the frequency of these mutations in a sample of Colombian type 2 diabetes patients suggests that different SLC22A1 gene variants might be involved in reduced OCT1 activity in the Colombian population since none of these mutations were detected.
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Affiliation(s)
- Leydy Cano
- Universidad de Antioquia, Medellín, Colombia
| | | | - Pedronel Araque
- Universidad EIA, Envigado, Colombia.,Cecoltec, Medellin, Colombia
| | | | | | | | - Constanza Duque
- Universidad de Antioquia, Medellín, Colombia.,Universidad Cooperativa de Colombia, Medellín, Colombia
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Zazuli Z, Duin NJCB, Jansen K, Vijverberg SJH, Maitland-van der Zee AH, Masereeuw R. The Impact of Genetic Polymorphisms in Organic Cation Transporters on Renal Drug Disposition. Int J Mol Sci 2020; 21:ijms21186627. [PMID: 32927790 PMCID: PMC7554776 DOI: 10.3390/ijms21186627] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 09/05/2020] [Accepted: 09/07/2020] [Indexed: 12/18/2022] Open
Abstract
A considerable number of drugs and/or their metabolites are excreted by the kidneys through glomerular filtration and active renal tubule secretion via transporter proteins. Uptake transporters in the proximal tubule are part of the solute carrier (SLC) superfamily, and include the organic cation transporters (OCTs). Several studies have shown that specific genetic polymorphisms in OCTs alter drug disposition and may lead to nephrotoxicity. Multiple single nucleotide polymorphisms (SNPs) have been reported for the OCT genes (SLC22A1, SLC22A2 and SLC22A3), which can influence the proteins’ structure and expression levels and affect their transport function. A gain-in-function mutation may lead to accumulation of drugs in renal proximal tubule cells, eventually leading to nephrotoxicity. This review illustrates the impact of genetic polymorphisms in OCTs on renal drug disposition and kidney injury, the clinical significances and how to personalize therapies to minimize the risk of drug toxicity.
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Affiliation(s)
- Zulfan Zazuli
- Department of Respiratory Medicine, Amsterdam UMC, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands; (S.J.H.V.); (A.H.M.-v.d.Z.)
- Department of Pharmacology-Clinical Pharmacy, School of Pharmacy, Bandung Institute of Technology, Jawa Barat 40132, Indonesia
- Correspondence: (Z.Z.); (R.M.)
| | - Naut J. C. B. Duin
- Division of Pharmacology, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, 3584 CG Utrecht, The Netherlands; (N.J.C.B.D.); (K.J.)
| | - Katja Jansen
- Division of Pharmacology, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, 3584 CG Utrecht, The Netherlands; (N.J.C.B.D.); (K.J.)
| | - Susanne J. H. Vijverberg
- Department of Respiratory Medicine, Amsterdam UMC, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands; (S.J.H.V.); (A.H.M.-v.d.Z.)
| | - Anke H. Maitland-van der Zee
- Department of Respiratory Medicine, Amsterdam UMC, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands; (S.J.H.V.); (A.H.M.-v.d.Z.)
| | - Rosalinde Masereeuw
- Division of Pharmacology, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, 3584 CG Utrecht, The Netherlands; (N.J.C.B.D.); (K.J.)
- Correspondence: (Z.Z.); (R.M.)
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7
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Pawar G, Madden JC, Ebbrell D, Firman JW, Cronin MTD. In Silico Toxicology Data Resources to Support Read-Across and (Q)SAR. Front Pharmacol 2019; 10:561. [PMID: 31244651 PMCID: PMC6580867 DOI: 10.3389/fphar.2019.00561] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Accepted: 05/03/2019] [Indexed: 12/14/2022] Open
Abstract
A plethora of databases exist online that can assist in in silico chemical or drug safety assessment. However, a systematic review and grouping of databases, based on purpose and information content, consolidated in a single source, has been lacking. To resolve this issue, this review provides a comprehensive listing of the key in silico data resources relevant to: chemical identity and properties, drug action, toxicology (including nano-material toxicity), exposure, omics, pathways, Absorption, Distribution, Metabolism and Elimination (ADME) properties, clinical trials, pharmacovigilance, patents-related databases, biological (genes, enzymes, proteins, other macromolecules etc.) databases, protein-protein interactions (PPIs), environmental exposure related, and finally databases relating to animal alternatives in support of 3Rs policies. More than nine hundred databases were identified and reviewed against criteria relating to accessibility, data coverage, interoperability or application programming interface (API), appropriate identifiers, types of in vitro, in vivo,-clinical or other data recorded and suitability for modelling, read-across, or similarity searching. This review also specifically addresses the need for solutions for mapping and integration of databases into a common platform for better translatability of preclinical data to clinical data.
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Affiliation(s)
| | | | | | | | - Mark T. D. Cronin
- School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, Liverpool, United Kingdom
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8
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Modeling Gadoxetate Liver Uptake and Efflux Using Dynamic Contrast-Enhanced Magnetic Resonance Imaging Enables Preclinical Quantification of Transporter Drug-Drug Interactions. Invest Radiol 2019; 53:563-570. [PMID: 29771727 DOI: 10.1097/rli.0000000000000480] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
OBJECTIVES The aim of this study was to model the in vivo transporter-mediated uptake and efflux of the hepatobiliary contrast agent gadoxetate in the liver. The efficacy of the proposed technique was assessed for its ability to provide quantitative insights into drug-drug interactions (DDIs), using rifampicin as inhibitor. MATERIALS AND METHODS Three groups of C57 mice were scanned twice with a dynamic gadoxetate-enhanced magnetic resonance imaging protocol, using a 3-dimensional spoiled gradient-echo sequence for approximately 72 minutes. Before the second magnetic resonance imaging session, 2 of the groups received a rifampicin dose of 20 (n = 7) or 40 (n = 7) mg/kg, respectively. Data from regions of interest in the liver were analyzed using 2 simplifications of a 2-compartment uptake and efflux model to provide estimates for the gadoxetate uptake rate (ki) into the hepatocytes and its efflux rate (kef) into the bile. Both models were assessed for goodness-of-fit in the group without rifampicin (n = 9), and the appropriate model was selected for assessing the ability to monitor DDIs in vivo. RESULTS Seven of 9 mice from the group without rifampicin were assessed for model implementation and reproducibility. A simple 3 parameter model (ki, kef, and extracellular space, vecs) adequately described the observed liver concentration time series with mean ki = 0.47 ± 0.11 min and mean kef = 0.039 ± 0.016 min. Visually, the area under the liver concentration time profile was reduced for the groups receiving rifampicin. Furthermore, tracer kinetic modeling demonstrated a significant dose-dependent decrease in the uptake (5.9- and 17.3-fold decrease for 20 mg/kg and 40 mg/kg, respectively) and efflux rates (2.2- and 7.9-fold decrease) compared with the first scan for each group. CONCLUSIONS This study presents the first in vivo implementation of a 2-compartment uptake and efflux model to monitor DDIs at the transporter-protein level, using the clinically relevant organic anion transporting polypeptide inhibitor rifampicin. The technique has the potential to be a novel alternative to other methods, allowing real-time changes in transporter DDIs to be measured directly in vivo.
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9
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Wevers RA, Christensen M, Engelke UFH, Geuer S, Coene KLM, Kwast JT, Lund AM, Vissers LELM. Functional disruption of pyrimidine nucleoside transporter CNT1 results in a novel inborn error of metabolism with high excretion of uridine and cytidine. J Inherit Metab Dis 2019; 42:494-500. [PMID: 30847922 DOI: 10.1002/jimd.12081] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Accepted: 03/05/2019] [Indexed: 12/31/2022]
Abstract
Genetic defects in the pyrimidine nucleoside transporters of the CNT transporter family have not yet been reported. Metabolic investigations in a patient with infantile afebrile tonic-clonic seizures revealed increased urinary uridine and cytidine excretion. Segregation of this metabolic trait in the family showed the same biochemical phenotype in a healthy older brother of the index. Whole exome sequencing revealed biallelic mutations in SLC28A1 encoding the pyrimidine nucleoside transporter CNT1 in the index and his brother. Both parents and unaffected sibs showed the variant in heterozygous state. The transporter is expressed in the kidneys. Compelling evidence is available for the disrupting effect of the mutation on the transport function thus explaining the increased excretion of the pyrimidine nucleosides. The exome analysis also revealed a pathogenic mutation in PRRT2 in the index, explaining the epilepsy phenotype in infancy. At present, both the index (10 years) and his older brother are asymptomatic. Mutations in SLC28A1 cause a novel inborn error of metabolism that can be explained by the disrupted activity of the pyrimidine nucleoside transporter CNT1. This is the first report describing a defect in the family of CNT concentrative pyrimidine nucleoside transporter proteins encoded by the SLC28 gene family. In all likelihood, the epilepsy phenotype in the index is unrelated to the SLC28A1 defect, as this can be fully explained by the pathogenic PRRT2 variant. Clinical data on more patients are required to prove whether pathogenic mutations in SLC28A1 have any clinical consequences or are to be considered a benign metabolic phenotype.
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Affiliation(s)
- R A Wevers
- Department Laboratory Medicine, Translational Metabolic Laboratory, Radboudumc, Nijmegen, The Netherlands
| | - M Christensen
- Department of Clinical Genetics, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - U F H Engelke
- Department Laboratory Medicine, Translational Metabolic Laboratory, Radboudumc, Nijmegen, The Netherlands
| | - S Geuer
- Department Human Genetics, Donders Institute for Brain, Cognition, and Behaviour, Radboudumc, Nijmegen, The Netherlands
- Institut für Medizinische Diagnostik GmbH, Ingelheim, Germany
| | - K L M Coene
- Department Laboratory Medicine, Translational Metabolic Laboratory, Radboudumc, Nijmegen, The Netherlands
| | - J T Kwast
- Department Laboratory Medicine, Translational Metabolic Laboratory, Radboudumc, Nijmegen, The Netherlands
| | - A M Lund
- Department of Paediatrics and Clinical Genetics, Centre for Inherited Metabolic Diseases, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - L E L M Vissers
- Department Human Genetics, Donders Institute for Brain, Cognition, and Behaviour, Radboudumc, Nijmegen, The Netherlands
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10
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Moketla MB, Wadley AL, Kamerman P, de Assis Rosa D. Pharmacogenetic variation influences sensory neuropathy occurrence in Southern Africans treated with stavudine-containing antiretroviral therapy. PLoS One 2018; 13:e0204111. [PMID: 30273369 PMCID: PMC6166924 DOI: 10.1371/journal.pone.0204111] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Accepted: 09/03/2018] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND The use of the HIV antiretroviral drug stavudine (d4T), a thymidine analogue, is associated with the development of mitochondrial toxicities such as sensory neuropathy (SN). Genetic variation in genes relating to d4T transport and metabolism, as well as genetic variation in the thymidine synthesis pathway, could influence occurrence of d4T-related toxicity. METHODS We examined this hypothesis in a cohort of HIV-positive South African adults exposed to d4T, including 143 cases with SN and 120 controls without SN. Ten SNPs in four genes associated with stavudine transport, and 16 SNPs in seven genes of the thymidine synthesis / phosphorylation pathway were genotyped using Agena mass spectrometry methods. Associations between sensory neuropathy and genetic variants were evaluated using PLINK by univariate and multivariable analyses. RESULTS Age and height were significantly associated with SN occurrence. Using logistic regression with age and height as covariates, and uncorrected empirical p-values, genetic variation in SLC28A1, SAMHD1, MTHFR and RRM2B was associated with SN in South Africans using d4T. CONCLUSION Variation in genes relating to d4T transport and metabolism, as well as genetic variation in the thymidine synthesis pathway may influence occurrence of d4T-related SN. These data contribute to the characterisation of African pharmacogenetic variation and its role in adverse response to antiretroviral therapy.
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Affiliation(s)
- Marvin Blessings Moketla
- School of Molecular and Cell Biology, Faculty of Science, University of the Witwatersrand, Johannesburg, South Africa
| | - Antonia L. Wadley
- Brain Function Research Group, School of Physiology, Faculty of Health Science, University of the Witwatersrand, Johannesburg, South Africa
| | - Peter Kamerman
- Brain Function Research Group, School of Physiology, Faculty of Health Science, University of the Witwatersrand, Johannesburg, South Africa
- School of Pharmacy and Biomedical Sciences, Faculty of Health Sciences, Curtin University, Perth, Australia
| | - Debra de Assis Rosa
- School of Molecular and Cell Biology, Faculty of Science, University of the Witwatersrand, Johannesburg, South Africa
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11
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Yee SW, Brackman DJ, Ennis EA, Sugiyama Y, Kamdem LK, Blanchard R, Galetin A, Zhang L, Giacomini KM. Influence of Transporter Polymorphisms on Drug Disposition and Response: A Perspective From the International Transporter Consortium. Clin Pharmacol Ther 2018; 104:803-817. [PMID: 29679469 DOI: 10.1002/cpt.1098] [Citation(s) in RCA: 82] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Revised: 04/10/2018] [Accepted: 04/11/2018] [Indexed: 12/21/2022]
Abstract
Advances in genomic technologies have led to a wealth of information identifying genetic polymorphisms in membrane transporters, specifically how these polymorphisms affect drug disposition and response. This review describes the current perspective of the International Transporter Consortium (ITC) on clinically important polymorphisms in membrane transporters. ITC suggests that, in addition to previously recommended polymorphisms in ABCG2 (BCRP) and SLCO1B1 (OATP1B1), polymorphisms in the emerging transporter, SLC22A1 (OCT1), be considered during drug development. Collectively, polymorphisms in these transporters are important determinants of interindividual differences in the levels, toxicities, and response to many drugs.
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Affiliation(s)
- Sook Wah Yee
- Department of Bioengineering and Therapeutic Sciences, Schools of Pharmacy and Medicine, University of California, San Francisco, San Francisco, California, USA
| | - Deanna J Brackman
- Department of Bioengineering and Therapeutic Sciences, Schools of Pharmacy and Medicine, University of California, San Francisco, San Francisco, California, USA
| | - Elizabeth A Ennis
- Department of Bioengineering and Therapeutic Sciences, Schools of Pharmacy and Medicine, University of California, San Francisco, San Francisco, California, USA
| | - Yuichi Sugiyama
- Sugiyama Laboratory, RIKEN Innovation Center, Research Cluster for Innovation, RIKEN, Yokohama, Japan
| | - Landry K Kamdem
- Department of Pharmaceutical Sciences, Harding University College of Pharmacy, Searcy, Arkansas, USA
| | | | - Aleksandra Galetin
- Centre for Applied Pharmacokinetic Research, School of Health Sciences, University of Manchester, UK
| | - Lei Zhang
- Office of Research and Standards, Office of Generic Drugs, Center for Drug Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland, USA
| | - Kathleen M Giacomini
- Department of Bioengineering and Therapeutic Sciences, Schools of Pharmacy and Medicine, University of California, San Francisco, San Francisco, California, USA.,Institute of Human Genetics, University of California, San Francisco, San Francisco, California, USA
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12
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Eclov RJ, Kim MJ, Smith R, Ahituv N, Kroetz DL. Rare Variants in the ABCG2 Promoter Modulate In Vivo Activity. Drug Metab Dispos 2018; 46:636-642. [PMID: 29467213 PMCID: PMC5896364 DOI: 10.1124/dmd.117.079541] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Accepted: 02/15/2018] [Indexed: 11/22/2022] Open
Abstract
ABCG2 encodes the breast cancer resistance protein (BCRP), an efflux membrane transporter important in the detoxification of xenobiotics. In the present study, the basal activity of the ABCG2 promoter in liver, kidney, intestine, and breast cell lines was examined using luciferase reporter assays. The promoter activities of reference and variant ABCG2 sequences were compared in human hepatocellular carcinoma cell (HepG2), human embryonic kidney cell (HEK293T), human colorectal carcinoma cell (HCT116), and human breast adenocarcinoma cell (MCF-7) lines. The ABCG2 promoter activity was strongest in the kidney and intestine cell lines. Four variants in the basal ABCG2 promoter (rs76656413, rs66664036, rs139256004, and rs59370292) decreased the promoter activity by 25%-50% in at least three of the four cell lines. The activity of these four variants was also examined in vivo using the hydrodynamic tail vein assay, and two single nucleotide polymorphisms (rs76656413 and rs59370292) significantly decreased in vivo liver promoter activity by 50%-80%. Electrophoretic mobility shift assays confirmed a reduction in nuclear protein binding to the rs59370292 variant probe, whereas the rs76656413 probe had a shift in transcription factor binding specificity. Although both rs59370292 and rs76656413 are rare variants in all populations, they could contribute to patient-level variation in ABCG2 expression in the kidney, liver, and intestine.
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Affiliation(s)
- Rachel J Eclov
- Department of Bioengineering and Therapeutic Sciences (R.J.E., M.J.K., R.S., N.A., D.L.K.) and Institute for Human Genetics (N.A., M.J.K., R.S., D.L.K.), University of California San Francisco, San Francisco, California
| | - Mee J Kim
- Department of Bioengineering and Therapeutic Sciences (R.J.E., M.J.K., R.S., N.A., D.L.K.) and Institute for Human Genetics (N.A., M.J.K., R.S., D.L.K.), University of California San Francisco, San Francisco, California
| | - Robin Smith
- Department of Bioengineering and Therapeutic Sciences (R.J.E., M.J.K., R.S., N.A., D.L.K.) and Institute for Human Genetics (N.A., M.J.K., R.S., D.L.K.), University of California San Francisco, San Francisco, California
| | - Nadav Ahituv
- Department of Bioengineering and Therapeutic Sciences (R.J.E., M.J.K., R.S., N.A., D.L.K.) and Institute for Human Genetics (N.A., M.J.K., R.S., D.L.K.), University of California San Francisco, San Francisco, California
| | - Deanna L Kroetz
- Department of Bioengineering and Therapeutic Sciences (R.J.E., M.J.K., R.S., N.A., D.L.K.) and Institute for Human Genetics (N.A., M.J.K., R.S., D.L.K.), University of California San Francisco, San Francisco, California
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13
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Eclov RJ, Kim MJ, Chhibber A, Smith RP, Ahituv N, Kroetz DL. ABCG2 regulatory single-nucleotide polymorphisms alter in vivo enhancer activity and expression. Pharmacogenet Genomics 2018; 27:454-463. [PMID: 28930109 DOI: 10.1097/fpc.0000000000000312] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
OBJECTIVES The expression and activity of the breast cancer resistance protein (ABCG2) contributes toward the pharmacokinetics of endogenous and xenobiotic substrates. The effect of genetic variation on the activity of cis-regulatory elements and nuclear response elements in the ABCG2 locus and their contribution toward ABCG2 expression have not been investigated systematically. In this study, the effect of genetic variation on the in vitro and in vivo enhancer activity of six previously identified liver enhancers in the ABCG2 locus was examined. METHODS Reference and variant liver enhancers were tested for their ability to alter luciferase activity in vitro in HepG2 and HEK293T cell lines and in vivo using a hydrodynamic tail vein assay. Positive in vivo single-nucleotide polymorphisms (SNPs) were tested for association with gene expression and for altered protein binding in electrophoretic mobility shift assays. RESULTS Multiple SNPs were found to alter enhancer activity in vitro. Four of these variants (rs9999111, rs12508471, ABCG2RE1*2, and rs149713212) decreased and one (rs2725263) increased enhancer activity in vivo. In addition, rs9999111 and rs12508471 were associated with ABCG2 expression in lymphoblastoid cell lines, lymphocytes, and T cells, and showed increased HepG2 nuclear protein binding. CONCLUSION This study identifies SNPs within regulatory regions of the ABCG2 locus that alter enhancer activity in vitro and in vivo. Several of these SNPs correlate with tissue-specific ABCG2 expression and alter DNA/protein binding. These SNPs could contribute toward reported tissue-specific variability in ABCG2 expression and may influence the correlation between ABCG2 expression and disease risk or the pharmacokinetics and pharmacodynamics of breast cancer resistance protein substrates.
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Affiliation(s)
- Rachel J Eclov
- aDepartment of Bioengineering and Therapeutic Sciences bInstitute for Human Genetics, University of California San Francisco, San Francisco, California, USA
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Pearce B, Jacobs C, Hoosain N, Benjeddou M. SLC22A2 - mapping genomic variations within South African indigenous and admixed populations. Drug Metab Pers Ther 2017; 31:213-220. [PMID: 27828777 DOI: 10.1515/dmpt-2016-0022] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Accepted: 09/26/2016] [Indexed: 11/15/2022]
Abstract
BACKGROUND The SLC22A2 gene is a polyspecific transporter that mediates the electrogenic transport of small organic cations with different molecular structures. Furthermore, single-nucleotide polymorphisms (SNPs) of SLC22A2 are clinically significant because they can alter the transport of substrate drugs and may, thus, influence the efficacy and toxicity thereof. Additionally, further studies have reported that SLC22A2 is responsible for 80% of the total metformin clearance. Therefore, loss-of-function variants of SLC22A2 could affect the pharmacokinetic and pharmacodynamic characteristics of metformin. Although it is widely accepted that African populations harbor a greater amount of genomic diversity compared to other populations, limited information is available regarding genetic polymorphisms in SLC genes among African populations, specifically those related to impaired functional activity of hOCT2. Therefore, the aim of this study was to map known impaired function variants in the SLC22A2 gene. METHODS Development of multiplex SNaPshot™ genotyping assay for 20 previously reported SLC22A2 nonsynonymous SNPs and the assessment of baseline allele frequencies of these variants in 140 Cape Admixed, 148 Xhosa and 152 Zulu individuals residing in Cape Town, South Africa. RESULTS We identified three nonsynonymous SNPs, namely, A270S, R400C and K432Q in the population studied at minor allele frequencies of 6.1%, 3.4% and 0.7%, respectively. The most frequently observed haplotypes across all three populations were CATAATGCGTACGCGCGACG (~85%), CATAATGATTACGCGCGACG (~7%) and CATAATGAGTACGCGCGACG (~4.5%). CONCLUSIONS In addition to SNPs, the haplotypes identified in this study can in future also aid in identifying associations between causative genetic variants and drug response. This study contributes in filling the gap that exists with regards to genetic information about important variations in organic cation transporter genes for the indigenous populations of South Africa.
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Brian W, Tremaine LM, Arefayene M, de Kanter R, Evers R, Guo Y, Kalabus J, Lin W, Loi CM, Xiao G. Assessment of drug metabolism enzyme and transporter pharmacogenetics in drug discovery and early development: perspectives of the I-PWG. Pharmacogenomics 2016; 17:615-31. [PMID: 27045656 DOI: 10.2217/pgs.16.9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Genetic variants of drug metabolism enzymes and transporters can result in high pharmacokinetic and pharmacodynamic variability, unwanted characteristics of efficacious and safe drugs. Ideally, the contributions of these enzymes and transporters to drug disposition can be predicted from in vitro experiments and in silico modeling in discovery or early development, and then be utilized during clinical development. Recently, regulatory agencies have provided guidance on the preclinical investigation of pharmacogenetics, for application to clinical drug development. This white paper summarizes the results of an industry survey conducted by the Industry Pharmacogenomics Working Group on current practice and challenges with using in vitro systems and in silico models to understand pharmacogenetic causes of variability in drug disposition.
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Affiliation(s)
- William Brian
- Sanofi, Translational Medicine and Early Development, 55 Corporate Drive, Bridgewater, NJ 08807, USA
| | - Larry M Tremaine
- Pfizer Inc., Worldwide Research and Development, Department of Pharmacokinetics, Dynamics and Metabolism, Eastern Point Road, Groton, CT 06340, USA
| | - Million Arefayene
- Biogen, Early Development Sciences, 14 Cambridge Center, Cambridge, MA 02142, USA
| | - Ruben de Kanter
- Preclinical Pharmacokinetics and Metabolism, Actelion Pharmaceuticals Ltd., Gewerbestrasse 16, CH-4123 Allschwil, Switzerland
| | - Raymond Evers
- Merck & Co, Pharmacodynamics, Pharmacokinetics and Drug Metabolism, 2000 Galloping Hill Road, Kenilworth, NJ07033, USA
| | - Yingying Guo
- Eli Lilly and Company, Drug Disposition, LillyCorporate Center, Indianapolis, IN 46285, USA
| | - James Kalabus
- Novartis Pharmaceuticals, 1 Health Plaza, EastHanover, NJ 07936, USA
| | - Wen Lin
- Novartis Institutes for Biomedical Research, Drug Metabolism and Pharmacokinetics, One Health Plaza, East Hanover, NJ07936-1080, USA
| | - Cho-Ming Loi
- Pfizer Inc., Worldwide Research and Development, Department of Pharmacokinetics, Dynamics and Metabolism,10646 Science Center Drive, San Diego, CA 92121, USA
| | - Guangqing Xiao
- Biogen, Preclinical PK and In vitro ADME, 14 Cambridge Center, Cambridge, MA 02142, USA
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16
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Kim DS, Sung JH, Lee JM. Robust parameter estimation for physiologically based pharmacokinetic model of Tegafur with dissolution dynamics. Chem Eng Res Des 2015. [DOI: 10.1016/j.cherd.2015.10.029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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17
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Atomic-level characterization of transport cycle thermodynamics in the glycerol-3-phosphate:phosphate antiporter. Nat Commun 2015; 6:8393. [PMID: 26417850 PMCID: PMC4598623 DOI: 10.1038/ncomms9393] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2015] [Accepted: 08/18/2015] [Indexed: 01/09/2023] Open
Abstract
Membrane transporters actively translocate their substrate by undergoing large-scale structural transitions between inward- (IF) and outward-facing (OF) states ('alternating-access' mechanism). Despite extensive structural studies, atomic-level mechanistic details of such structural transitions, and as importantly, their coupling to chemical events supplying the energy, remain amongst the most elusive aspects of the function of these proteins. Here we present a quantitative, atomic-level description of the functional thermodynamic cycle for the glycerol-3-phosphate:phosphate antiporter GlpT by using a novel approach in reconstructing the free energy landscape governing the IF↔OF transition along a cyclic transition pathway involving both apo and substrate-bound states. Our results provide a fully atomic description of the complete transport process, offering a structural model for the alternating-access mechanism and substantiating the close coupling between global structural transitions and local chemical events.
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18
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Gonzalez FJ, Fang ZZ, Ma X. Transgenic mice and metabolomics for study of hepatic xenobiotic metabolism and toxicity. Expert Opin Drug Metab Toxicol 2015; 11:869-81. [PMID: 25836352 DOI: 10.1517/17425255.2015.1032245] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
INTRODUCTION The study of xenobiotic metabolism and toxicity has been greatly aided by the use of genetically modified mouse models and metabolomics. AREAS COVERED Gene knockout mice can be used to determine the enzymes responsible for the metabolism of xenobiotics in vivo and to examine the mechanisms of xenobiotic-induced toxicity. Humanized mouse models are especially important because there exist marked species differences in the xenobiotic-metabolizing enzymes and the nuclear receptors that regulate these enzymes. Humanized mice expressing CYPs and nuclear receptors including the pregnane X receptor, the major regulator of xenobiotic metabolism and transport were produced. With genetically modified mouse models, metabolomics can determine the metabolic map of many xenobiotics with a level of sensitivity that allows the discovery of even minor metabolites. This technology can be used for determining the mechanism of xenobiotic toxicity and to find early biomarkers for toxicity. EXPERT OPINION Metabolomics and genetically modified mouse models can be used for the study of xenobiotic metabolism and toxicity by: i) comparison of the metabolomics profiles between wild-type and genetically modified mice, and searching for genotype-dependent endogenous metabolites; ii) searching for and elucidating metabolites derived from xenobiotics; and iii) discovery of specific alterations of endogenous compounds induced by xenobiotics-induced toxicity.
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Affiliation(s)
- Frank J Gonzalez
- National Institutes of Health, National Cancer Institute, Center for Cancer Research, Laboratory of Metabolism , Bethesda, MD 20892 , USA +1 301 496 9067 ; +1 301 496 8419 ;
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19
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Clinical Relevance of Multidrug-Resistance-Proteins (MRPs) for Anticancer Drug Resistance and Prognosis. ACTA ACUST UNITED AC 2014. [DOI: 10.1007/978-3-319-09801-2_2] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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20
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Klamerus KJ, Alvey C, Li L, Feng B, Wang R, Kaplan I, Shi H, Dowty ME, Krishnaswami S. Evaluation of the potential interaction between tofacitinib and drugs that undergo renal tubular secretion using metformin, an in vivo marker of renal organic cation transporter 2. Clin Pharmacol Drug Dev 2014; 3:499-507. [PMID: 27129125 DOI: 10.1002/cpdd.120] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2013] [Accepted: 03/20/2014] [Indexed: 12/23/2022]
Abstract
Tofacitinib is a novel, oral Janus kinase inhibitor. The potential for drug-drug interactions (DDIs) between tofacitinib and drugs that undergo renal tubular secretion was evaluated using metformin as a probe transporter substrate, and genotyping for organic cation transporter (OCT) 1, OCT2 and multidrug and toxin extrusion 1 polymorphisms. Twenty-four healthy male subjects completed this open-label, fixed-sequence study. Subjects were administered a single oral metformin 500 mg dose on Days 1 and 4, and multiple oral tofacitinib 30 mg twice daily doses on Days 2, 3, and 4. Subjects underwent serial blood and urine samplings (Days 1 and 4) to estimate metformin pharmacokinetics. A single blood sample for tofacitinib was collected 2 hours after the morning dose (Day 4). The 90% confidence intervals for the ratios of maximum plasma concentration, area under the curve and renal clearance of metformin, with and without tofacitinib, were contained within the 80-125% acceptance range commonly used to establish a lack of DDI. No deaths, serious adverse events (AEs), severe AEs or discontinuations due to AEs were reported. The study confirms tofacitinib is unlikely to impact the pharmacokinetics of drugs that undergo renal tubular secretion, and concurs with its weak in vitro OCT2 inhibitory profile.
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Affiliation(s)
| | | | - Lei Li
- Pfizer Inc, San Diego, CA, USA
| | - Bo Feng
- Pfizer Inc, San Diego, CA, USA
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21
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Nicol MR, Fedoriw Y, Mathews M, Prince HMA, Patterson KB, Geller E, Mollan K, Mathews S, Kroetz DL, Kashuba ADM. Expression of six drug transporters in vaginal, cervical, and colorectal tissues: Implications for drug disposition in HIV prevention. J Clin Pharmacol 2014; 54:574-83. [PMID: 24343710 PMCID: PMC4061289 DOI: 10.1002/jcph.248] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2013] [Accepted: 12/09/2013] [Indexed: 11/11/2022]
Abstract
Effective antiretroviral (ARV)-based HIV prevention strategies require optimizing drug exposure in mucosal tissues; yet factors influencing mucosal tissue disposition remain unknown. We hypothesized drug transporter expression in vaginal, cervical, and colorectal tissues is a contributing factor and selected 3 efflux (ABCB1/MDR1, ABCC2/MRP2, ABCC4/MRP4) and 3 uptake (SLC22A6/OAT1, SLC22A8/OAT3, SLCO1B1/OATP1B1) transporters to further investigate based on their affinity for 2 ARVs central to prevention (tenofovir, maraviroc). Tissue was collected from 98 donors. mRNA and protein expression were quantified using qPCR and immunohistochemistry (IHC). Hundred percent of tissues expressed efflux transporter mRNA. IHC localized them to the epithelium and/or submucosa. Multivariable analysis adjusted for age, smoking, and co-medications revealed significant (P < 0.05) differences in efflux transporter mRNA between tissue types (vaginal ABCB1 3.9-fold > colorectal; vaginal ABCC2 2.9-fold > colorectal; colorectal ABCC4 2.0-fold > cervical). In contrast, uptake transporter mRNA was expressed in <25% of tissues. OAT1 protein was detected in 0% of female genital tissues and in 100% of colorectal tissues, but only in rare epithelial cells. These data support clinical findings of higher maraviroc and tenofovir concentrations in rectal tissue compared to vaginal or cervical tissue after oral dosing. Quantifying mucosal transporter expression and localization can facilitate ARV selection to target these tissues.
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Affiliation(s)
- Melanie R Nicol
- Eshelman School of Pharmacy, University of North Carolina at Chapel Hill
| | - Yuri Fedoriw
- UNC School of Medicine, University of North Carolina at Chapel Hill
| | - Michelle Mathews
- UNC School of Medicine, University of North Carolina at Chapel Hill
| | - Heather MA Prince
- UNC School of Medicine, University of North Carolina at Chapel Hill
- Center for AIDS Research, University of North Carolina at Chapel Hill
| | | | - Elizabeth Geller
- UNC School of Medicine, University of North Carolina at Chapel Hill
| | - Katie Mollan
- Center for AIDS Research, University of North Carolina at Chapel Hill
| | | | - Deanna L Kroetz
- UCSF School of Pharmacy, University of California, San Francisco
| | - Angela DM Kashuba
- Eshelman School of Pharmacy, University of North Carolina at Chapel Hill
- UNC School of Medicine, University of North Carolina at Chapel Hill
- Center for AIDS Research, University of North Carolina at Chapel Hill
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Ishikawa T, Wakabayashi-Nakao K, Nakagawa H. Methods to examine the impact of nonsynonymous SNPs on protein degradation and function of human ABC transporter. Methods Mol Biol 2014; 1015:225-50. [PMID: 23824860 DOI: 10.1007/978-1-62703-435-7_15] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Abstract
Clinical studies have strongly suggested that genetic polymorphisms and/or mutations of certain ATP-binding cassette (ABC) transporter genes might be regarded as significant factors affecting patients' responses to medication and/or the risk of diseases. In the case of ABCG2, certain single nucleotide polymorphisms (SNPs) in the encoding gene alter the substrate specificity and/or enhance endoplasmic reticulum-associated degradation (ERAD) of the de novo synthesized ABCG2 protein via the ubiquitin-mediated proteasomal proteolysis pathway. Hitherto accumulated clinical data imply that several nonsynonymous SNPs affect the ABCG2-mediated clearance of drugs or cellular metabolites, although some controversies still exist. Therefore, we recently developed high-speed functional screening and ERAD of ABC transporters so as to evaluate the effect of genetic polymorphisms on their function and protein expression levels in vitro. In this chapter we present in vitro experimental methods to elucidate the impact of nonsynonymous SNPs on protein degradation of ABCG2 as well as on its transport function.
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A Microscopic View of the Mechanisms of Active Transport Across the Cellular Membrane. ANNUAL REPORTS IN COMPUTATIONAL CHEMISTRY 2014. [DOI: 10.1016/b978-0-444-63378-1.00004-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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Conseil G, Cole SP. Two Polymorphic Variants of ABCC1 Selectively Alter Drug Resistance and Inhibitor Sensitivity of the Multidrug and Organic Anion Transporter Multidrug Resistance Protein 1. Drug Metab Dispos 2013; 41:2187-96. [DOI: 10.1124/dmd.113.054213] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
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25
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Cole SPC. Targeting multidrug resistance protein 1 (MRP1, ABCC1): past, present, and future. Annu Rev Pharmacol Toxicol 2013; 54:95-117. [PMID: 24050699 DOI: 10.1146/annurev-pharmtox-011613-135959] [Citation(s) in RCA: 228] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The human ATP-binding cassette transporter multidrug resistance protein 1 (MRP1), encoded by ABCC1, was initially identified because of its ability to confer multidrug resistance in lung cancer cells. It is now established that MRP1 plays a role in protecting certain tissues from xenobiotic insults and that it mediates the cellular efflux of the proinflammatory cysteinyl leukotriene C4 as well as a vast array of other endo- and xenobiotic organic anions. Many of these are glutathione (GSH) or glucuronide conjugates, the products of Phase II drug metabolism. MRP1 also plays a role in the cellular efflux of the reduced and oxidized forms of GSH and thus contributes to the many physiological and pathophysiological processes influenced by these small peptides, including oxidative stress. In this review, the pharmacological and physiological aspects of MRP1 are considered in the context of the current status and future prospects of pharmacological and genetic modulation of MRP1 activity.
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Affiliation(s)
- Susan P C Cole
- Department of Pathology and Molecular Medicine, and Division of Cancer Biology and Genetics, Queen's University Cancer Research Institute, Kingston, Ontario K7L 3N6, Canada;
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26
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Yang L, Price ET, Chang CW, Li Y, Huang Y, Guo LW, Guo Y, Kaput J, Shi L, Ning B. Gene expression variability in human hepatic drug metabolizing enzymes and transporters. PLoS One 2013; 8:e60368. [PMID: 23637747 PMCID: PMC3634068 DOI: 10.1371/journal.pone.0060368] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2012] [Accepted: 02/26/2013] [Indexed: 12/17/2022] Open
Abstract
Interindividual variability in the expression of drug-metabolizing enzymes and transporters (DMETs) in human liver may contribute to interindividual differences in drug efficacy and adverse reactions. Published studies that analyzed variability in the expression of DMET genes were limited by sample sizes and the number of genes profiled. We systematically analyzed the expression of 374 DMETs from a microarray data set consisting of gene expression profiles derived from 427 human liver samples. The standard deviation of interindividual expression for DMET genes was much higher than that for non-DMET genes. The 20 DMET genes with the largest variability in the expression provided examples of the interindividual variation. Gene expression data were also analyzed using network analysis methods, which delineates the similarities of biological functionalities and regulation mechanisms for these highly variable DMET genes. Expression variability of human hepatic DMET genes may affect drug-gene interactions and disease susceptibility, with concomitant clinical implications.
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Affiliation(s)
- Lun Yang
- Division of Systems Biology, National Center for Toxicological Research, Food and Drug Administration, Jefferson, Arkansas, United States of America
| | - Elvin T. Price
- Department of Pharmaceutical Sciences, University of Arkansas for Medical Sciences, Little Rock, Arkansas, United States of America
| | - Ching-Wei Chang
- Division of Systems Biology, National Center for Toxicological Research, Food and Drug Administration, Jefferson, Arkansas, United States of America
| | - Yan Li
- Division of Systems Biology, National Center for Toxicological Research, Food and Drug Administration, Jefferson, Arkansas, United States of America
| | - Ying Huang
- Department of Pharmaceutical Sciences, College of Pharmacy, Western University of Health Sciences, Pomona, California, United States of America
| | - Li-Wu Guo
- Division of Systems Biology, National Center for Toxicological Research, Food and Drug Administration, Jefferson, Arkansas, United States of America
| | - Yongli Guo
- Division of Systems Biology, National Center for Toxicological Research, Food and Drug Administration, Jefferson, Arkansas, United States of America
| | - Jim Kaput
- Division of Systems Biology, National Center for Toxicological Research, Food and Drug Administration, Jefferson, Arkansas, United States of America
| | - Leming Shi
- Division of Systems Biology, National Center for Toxicological Research, Food and Drug Administration, Jefferson, Arkansas, United States of America
- * E-mail: (BN); (LS)
| | - Baitang Ning
- Division of Systems Biology, National Center for Toxicological Research, Food and Drug Administration, Jefferson, Arkansas, United States of America
- * E-mail: (BN); (LS)
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Shaikh S, Li J, Enkavi G, Wen PC, Huang Z, Tajkhorshid E. Visualizing functional motions of membrane transporters with molecular dynamics simulations. Biochemistry 2013; 52:569-87. [PMID: 23298176 PMCID: PMC3560430 DOI: 10.1021/bi301086x] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2012] [Revised: 12/21/2012] [Indexed: 01/08/2023]
Abstract
Computational modeling and molecular simulation techniques have become an integral part of modern molecular research. Various areas of molecular sciences continue to benefit from, indeed rely on, the unparalleled spatial and temporal resolutions offered by these technologies, to provide a more complete picture of the molecular problems at hand. Because of the continuous development of more efficient algorithms harvesting ever-expanding computational resources, and the emergence of more advanced and novel theories and methodologies, the scope of computational studies has expanded significantly over the past decade, now including much larger molecular systems and far more complex molecular phenomena. Among the various computer modeling techniques, the application of molecular dynamics (MD) simulation and related techniques has particularly drawn attention in biomolecular research, because of the ability of the method to describe the dynamical nature of the molecular systems and thereby to provide a more realistic representation, which is often needed for understanding fundamental molecular properties. The method has proven to be remarkably successful in capturing molecular events and structural transitions highly relevant to the function and/or physicochemical properties of biomolecular systems. Herein, after a brief introduction to the method of MD, we use a number of membrane transport proteins studied in our laboratory as examples to showcase the scope and applicability of the method and its power in characterizing molecular motions of various magnitudes and time scales that are involved in the function of this important class of membrane proteins.
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Affiliation(s)
- Saher
A. Shaikh
- Department of Biochemistry, Beckman Institute for Advanced
Science and Technology, and Center for Biophysics and Computational
Biology, University of Illinois at Urbana-Champaign, 405 North Mathews Avenue, Urbana, Illinois 61801, United States
| | - Jing Li
- Department of Biochemistry, Beckman Institute for Advanced
Science and Technology, and Center for Biophysics and Computational
Biology, University of Illinois at Urbana-Champaign, 405 North Mathews Avenue, Urbana, Illinois 61801, United States
| | - Giray Enkavi
- Department of Biochemistry, Beckman Institute for Advanced
Science and Technology, and Center for Biophysics and Computational
Biology, University of Illinois at Urbana-Champaign, 405 North Mathews Avenue, Urbana, Illinois 61801, United States
| | - Po-Chao Wen
- Department of Biochemistry, Beckman Institute for Advanced
Science and Technology, and Center for Biophysics and Computational
Biology, University of Illinois at Urbana-Champaign, 405 North Mathews Avenue, Urbana, Illinois 61801, United States
| | - Zhijian Huang
- Department of Biochemistry, Beckman Institute for Advanced
Science and Technology, and Center for Biophysics and Computational
Biology, University of Illinois at Urbana-Champaign, 405 North Mathews Avenue, Urbana, Illinois 61801, United States
| | - Emad Tajkhorshid
- Department of Biochemistry, Beckman Institute for Advanced
Science and Technology, and Center for Biophysics and Computational
Biology, University of Illinois at Urbana-Champaign, 405 North Mathews Avenue, Urbana, Illinois 61801, United States
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Rowland M, Noe CR, Smith DA, Tucker GT, Crommelin DJA, Peck CC, Rocci ML, Besançon L, Shah VP. Impact of the pharmaceutical sciences on health care: a reflection over the past 50 years. J Pharm Sci 2012; 101:4075-99. [PMID: 22911654 DOI: 10.1002/jps.23295] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2012] [Revised: 07/10/2012] [Accepted: 07/31/2012] [Indexed: 11/07/2022]
Abstract
During the last century, particularly the latter half, spectacular progress has been made in improving the health and longevity of people. The reasons are many, but the development of medicines has played a critical role. This report documents and reflects on the impressive contribution that those working in the pharmaceutical sciences have made to healthcare over the past 50 years. It is divided into six sections (drug discovery; absorption, distribution, metabolism, and excretion; pharmacokinetics and pharmacodynamics; drug formulation; drug regulation; and drug utilization), each describing key contributions that have been made in the progression of medicines, from conception to use. A common thread throughout is the application of translational science to the improvement of drug discovery, development, and therapeutic application. Each section has been coordinated by a leading scientist who was asked, after consulting widely with many colleagues across the globe, to identify "The five most influential ideas/concepts/developments introduced by 'pharmaceutical scientists' (in their field) over the past 50 years?" Although one cannot predict where the important breakthroughs will come in the future to meet the unmet medical needs, the evidence presented in this report should leave no doubt that those engaged in the pharmaceutical sciences will continue to make their contributions heavily felt.
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Affiliation(s)
- Malcolm Rowland
- School of Pharmacy and Pharmaceutical Sciences, University of Manchester, Manchester, UK.
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Stieger B, Meier PJ. Pharmacogenetics of drug transporters in the enterohepatic circulation. Pharmacogenomics 2012; 12:611-31. [PMID: 21619426 DOI: 10.2217/pgs.11.53] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
This article summarizes the impact of the pharmacogenetics of drug transporters expressed in the enterohepatic circulation on the pharmacokinetics and pharmacodynamics of drugs. The role of pharmacogenetics in the function of drug transporter proteins in vitro is now well established and evidence is rapidly accumulating from in vivo pharmacokinetic studies, which suggests that genetic variants of drug transporter proteins can translate into clinically relevant phenotypes. However, a large amount of conflicting information on the clinical relevance of drug transporter proteins has so far precluded the emergence of a clear picture regarding the role of drug transporter pharmacogenetics in medical practice. This is very well exemplified by the case of P-glycoprotein (MDR1, ABCB1). The challenge is now to develop pharmacogenetic models with sufficient predictive power to allow for translation into drug therapy. This will require a combination of pharmacogenetics of drug transporters, drug metabolism and pharmacodynamics of the respective drugs.
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Affiliation(s)
- Bruno Stieger
- Division of Clinical Pharmacology & Toxicology, University Hospital, 8091 Zurich, Switzerland
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Abstract
Clinical genetic testing has grown substantially over the past 30 years as the causative mutations for Mendelian diseases have been identified, particularly aided in part by the recent advances in molecular-based technologies. Importantly, the adoption of new tests and testing strategies (e.g., diagnostic confirmation, prenatal testing, and population-based carrier screening) has often been met with caution and careful consideration before clinical implementation, which facilitates the appropriate use of new genetic tests. Although the field of pharmacogenetics was established in the 1950s, clinical testing for constitutional pharmacogenetic variants implicated in interindividual drug response variability has only recently become available to help clinicians guide pharmacotherapy, in part due to US Food and Drug Administration-mediated product insert revisions that include pharmacogenetic information for selected drugs. However, despite pharmacogenetic associations with adverse outcomes, physician uptake of clinical pharmacogenetic testing has been slow. Compared with testing for Mendelian diseases, pharmacogenetic testing for certain indications can have a lower positive predictive value, which is one reason for underutilization. A number of other barriers remain with implementing clinical pharmacogenetics, including clinical utility, professional education, and regulatory and reimbursement issues, among others. This review presents some of the current opportunities and challenges with implementing clinical pharmacogenetic testing.
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Waldman SA, Terzic A. Patient-centric clinical pharmacology advances the path to personalized medicine. Biomark Med 2012; 5:697-700. [PMID: 22103605 DOI: 10.2217/bmm.11.78] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Affiliation(s)
- Scott A Waldman
- Department of Pharmacology and Experimental Therapeutics, Division of Clinical Pharmacology, Department of Medicine, 132 South 10th Street, 1170 Main Philadelphia, PA 19107, USA
| | - Andre Terzic
- Division of Cardiovascular Diseases, Departments of Medicine, Molecular Pharmacology and Experimental Therapeutics and Medical Genetics, Mayo Clinic, 200, First Street SW, Rochester, MN 55905, USA
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Cano-Soldado P, Gorraitz E, Errasti-Murugarren E, Casado FJ, Lostao MP, Pastor-Anglada M. Functional analysis of the human concentrative nucleoside transporter-1 variant hCNT1S546P provides insight into the sodium-binding pocket. Am J Physiol Cell Physiol 2012; 302:C257-66. [DOI: 10.1152/ajpcell.00198.2011] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
SLC28 genes, encoding concentrative nucleoside transporter proteins (CNT), show little genetic variability, although a few single nucleotide polymorphisms (SNPs) have been associated with marked functional disturbances. In particular, human CNT1S546P had been reported to result in negligible thymidine uptake. In this study we have characterized the molecular mechanisms responsible for this apparent loss of function. The hCNT1S546P variant showed an appropriate endoplasmic reticulum export and insertion into the plasma membrane, whereas loss of nucleoside translocation ability affected all tested nucleoside and nucleoside-derived drugs. Site-directed mutagenesis analysis revealed that it is the lack of the serine residue itself responsible for the loss of hCNT1 function. This serine residue is highly conserved, and mutation of the analogous serine in hCNT2 (Ser541) and hCNT3 (Ser568) resulted in total and partial loss of function, respectively. Moreover, hCNT3, the only member that shows a 2Na+/1 nucleoside stoichiometry, showed altered Na+ binding properties associated with a shift in the Hill coefficient, consistent with one Na+ binding site being affected by the mutation. Two-electrode voltage-clamp studies using the hCNT1S546P mutant revealed the occurrence of Na+ leak, which was dependent on the concentration of extracellular Na+ indicating that, although the variant is unable to transport nucleosides, there is an uncoupled sodium transport.
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Affiliation(s)
- Pedro Cano-Soldado
- Departament de Bioquímica i Biologia Molecular, Institut de Biomedicina (IBUB), Universitat de Barcelona and CIBER EHD, Barcelona
| | - Edurne Gorraitz
- Department of Food Science, Physiology and Toxicology, University of Navarra, Pamplona, Spain
| | - Ekaitz Errasti-Murugarren
- Departament de Bioquímica i Biologia Molecular, Institut de Biomedicina (IBUB), Universitat de Barcelona and CIBER EHD, Barcelona
| | - F. Javier Casado
- Departament de Bioquímica i Biologia Molecular, Institut de Biomedicina (IBUB), Universitat de Barcelona and CIBER EHD, Barcelona
| | - M. Pilar Lostao
- Department of Food Science, Physiology and Toxicology, University of Navarra, Pamplona, Spain
| | - Marçal Pastor-Anglada
- Departament de Bioquímica i Biologia Molecular, Institut de Biomedicina (IBUB), Universitat de Barcelona and CIBER EHD, Barcelona
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Fardel O, Kolasa E, Le Vee M. Environmental chemicals as substrates, inhibitors or inducers of drug transporters: implication for toxicokinetics, toxicity and pharmacokinetics. Expert Opin Drug Metab Toxicol 2011; 8:29-46. [DOI: 10.1517/17425255.2012.637918] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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Silverton L, Dean M, Moitra K. Variation and evolution of the ABC transporter genes ABCB1, ABCC1, ABCG2, ABCG5 and ABCG8: implication for pharmacogenetics and disease. ACTA ACUST UNITED AC 2011; 26:169-79. [PMID: 22098604 DOI: 10.1515/dmdi.2011.027] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
The ATP-binding cassette (ABC) transporter genes are ubiquitous in the genomes of all vertebrates. Some of these transporters play a key role in xenobiotic defense and are endowed with the capacity to efflux harmful toxic substances. A major role in the evolution of the vertebrate ABC genes is played by gene duplication. Multiple gene duplication and deletion events have been identified in ABC genes, resulting in either gene birth or gene death indicating that the process of gene evolution is still ongoing in this group of transporters. Additionally, polymorphisms in these genes are linked to variations in expression, function, drug disposition and drug response. Single nucleotide polymorphisms in the ABC genes may be considered as markers of individual risk for adverse drug reactions or susceptibility to complex diseases as they can uniquely influence the quality and quantity of gene product. As the ABC genes continue to evolve, globalization will yield additional migration and racial admixtures that will have far reaching implications for the pharmacogenetics of this unique family of transporters in the context of human health.
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MESH Headings
- ATP Binding Cassette Transporter, Subfamily B
- ATP Binding Cassette Transporter, Subfamily B, Member 1/genetics
- ATP Binding Cassette Transporter, Subfamily G, Member 2
- ATP Binding Cassette Transporter, Subfamily G, Member 5
- ATP Binding Cassette Transporter, Subfamily G, Member 8
- ATP-Binding Cassette Transporters/genetics
- Animals
- Evolution, Molecular
- Genetic Variation
- Humans
- Lipoproteins/genetics
- Multidrug Resistance-Associated Proteins/genetics
- Neoplasm Proteins/genetics
- Pharmacogenetics
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Affiliation(s)
- Latoya Silverton
- Laboratory of Experimental Immunology, Cancer and Inflammation Program, National Cancer Institute at Frederick, Frederick, MD 21702, USA
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Design and coverage of high throughput genotyping arrays optimized for individuals of East Asian, African American, and Latino race/ethnicity using imputation and a novel hybrid SNP selection algorithm. Genomics 2011; 98:422-30. [PMID: 21903159 DOI: 10.1016/j.ygeno.2011.08.007] [Citation(s) in RCA: 120] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2011] [Accepted: 08/22/2011] [Indexed: 12/24/2022]
Abstract
Four custom Axiom genotyping arrays were designed for a genome-wide association (GWA) study of 100,000 participants from the Kaiser Permanente Research Program on Genes, Environment and Health. The array optimized for individuals of European race/ethnicity was previously described. Here we detail the development of three additional microarrays optimized for individuals of East Asian, African American, and Latino race/ethnicity. For these arrays, we decreased redundancy of high-performing SNPs to increase SNP capacity. The East Asian array was designed using greedy pairwise SNP selection. However, removing SNPs from the target set based on imputation coverage is more efficient than pairwise tagging. Therefore, we developed a novel hybrid SNP selection method for the African American and Latino arrays utilizing rounds of greedy pairwise SNP selection, followed by removal from the target set of SNPs covered by imputation. The arrays provide excellent genome-wide coverage and are valuable additions for large-scale GWA studies.
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Kell DB, Dobson PD, Oliver SG. Pharmaceutical drug transport: the issues and the implications that it is essentially carrier-mediated only. Drug Discov Today 2011; 16:704-14. [PMID: 21624498 DOI: 10.1016/j.drudis.2011.05.010] [Citation(s) in RCA: 148] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2010] [Revised: 04/04/2011] [Accepted: 05/11/2011] [Indexed: 01/04/2023]
Abstract
All cells necessarily contain tens, if not hundreds, of carriers for nutrients and intermediary metabolites, and the human genome codes for more than 1000 carriers of various kinds. Here, we illustrate using a typical literature example the widespread but erroneous nature of the assumption that the 'background' or 'passive' permeability to drugs occurs in the absence of carriers. Comparison of the rate of drug transport in natural versus artificial membranes shows discrepancies in absolute magnitudes of 100-fold or more, with the carrier-containing cells showing the greater permeability. Expression profiling data show exactly which carriers are expressed in which tissues. The recognition that drugs necessarily require carriers for uptake into cells provides many opportunities for improving the effectiveness of the drug discovery process.
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Affiliation(s)
- Douglas B Kell
- School of Chemistry, The University of Manchester, 131 Princess St, Manchester, M1 7DN, UK.
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Hoffmann TJ, Kvale MN, Hesselson SE, Zhan Y, Aquino C, Cao Y, Cawley S, Chung E, Connell S, Eshragh J, Ewing M, Gollub J, Henderson M, Hubbell E, Iribarren C, Kaufman J, Lao RZ, Lu Y, Ludwig D, Mathauda GK, McGuire W, Mei G, Miles S, Purdy MM, Quesenberry C, Ranatunga D, Rowell S, Sadler M, Shapero MH, Shen L, Shenoy TR, Smethurst D, Van den Eeden SK, Walter L, Wan E, Wearley R, Webster T, Wen CC, Weng L, Whitmer RA, Williams A, Wong SC, Zau C, Finn A, Schaefer C, Kwok PY, Risch N. Next generation genome-wide association tool: design and coverage of a high-throughput European-optimized SNP array. Genomics 2011; 98:79-89. [PMID: 21565264 DOI: 10.1016/j.ygeno.2011.04.005] [Citation(s) in RCA: 145] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2011] [Accepted: 04/15/2011] [Indexed: 10/18/2022]
Abstract
The success of genome-wide association studies has paralleled the development of efficient genotyping technologies. We describe the development of a next-generation microarray based on the new highly-efficient Affymetrix Axiom genotyping technology that we are using to genotype individuals of European ancestry from the Kaiser Permanente Research Program on Genes, Environment and Health (RPGEH). The array contains 674,517 SNPs, and provides excellent genome-wide as well as gene-based and candidate-SNP coverage. Coverage was calculated using an approach based on imputation and cross validation. Preliminary results for the first 80,301 saliva-derived DNA samples from the RPGEH demonstrate very high quality genotypes, with sample success rates above 94% and over 98% of successful samples having SNP call rates exceeding 98%. At steady state, we have produced 462 million genotypes per week for each Axiom system. The new array provides a valuable addition to the repertoire of tools for large scale genome-wide association studies.
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Affiliation(s)
- Thomas J Hoffmann
- Institute for Human Genetics, University of California, San Francisco 94143-0794, CA, USA.
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Sim SC, Altman RB, Ingelman-Sundberg M. Databases in the area of pharmacogenetics. Hum Mutat 2011; 32:526-31. [PMID: 21309040 DOI: 10.1002/humu.21454] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2010] [Accepted: 01/13/2011] [Indexed: 11/10/2022]
Abstract
In the area of pharmacogenetics and personalized health care it is obvious that databases, providing important information of the occurrence and consequences of variant genes encoding drug metabolizing enzymes, drug transporters, drug targets, and other proteins of importance for drug response or toxicity, are of critical value for scientists, physicians, and industry. The primary outcome of the pharmacogenomic field is the identification of biomarkers that can predict drug toxicity and drug response, thereby individualizing and improving drug treatment of patients. The drug in question and the polymorphic gene exerting the impact are the main issues to be searched for in the databases. Here, we review the databases that provide useful information in this respect, of benefit for the development of the pharmacogenomic field.
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Affiliation(s)
- Sarah C Sim
- Section of Pharmacogenetics, Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden.
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40
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Smith DE, Hu Y, Shen H, Nagaraja TN, Fenstermacher JD, Keep RF. Distribution of glycylsarcosine and cefadroxil among cerebrospinal fluid, choroid plexus, and brain parenchyma after intracerebroventricular injection is markedly different between wild-type and Pept2 null mice. J Cereb Blood Flow Metab 2011; 31:250-61. [PMID: 20571525 PMCID: PMC2965812 DOI: 10.1038/jcbfm.2010.84] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The purpose of this study was to define the cerebrospinal fluid (CSF) clearance kinetics, choroid plexus uptake, and parenchymal penetration of PEPT2 substrates in different regions of the brain after intracerebroventricular administration. To accomplish these objectives, we performed biodistribution studies using [(14)C]glycylsarcosine (GlySar) and [(3)H]cefadroxil, along with quantitative autoradiography of [(14)C]GlySar, in wild-type and Pept2 null mice. We found that PEPT2 deletion markedly reduced the uptake of GlySar and cefadroxil in choroid plexuses at 60 mins by 94% and 82% (P<0.001), respectively, and lowered their CSF clearances by about fourfold. Autoradiography showed that GlySar concentrations in the lateral, third, and fourth ventricle choroid plexuses were higher in wild-type as compared with Pept2 null mice (P<0.01). Uptake of GlySar by the ependymal-subependymal layer and septal region was higher in wild-type than in null mice, but the half-distance of penetration into parenchyma was significantly less in wild-type mice. The latter is probably because of the clearance of GlySar from interstitial fluid by brain cells expressing PEPT2, which stops further penetration. These studies show that PEPT2 knockout can significantly modify the spatial distribution of GlySar and cefadroxil (and presumably other peptides/mimetics and peptide-like drugs) in brain.
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Affiliation(s)
- David E Smith
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Michigan, Ann Arbor, Michigan 48109-5633, USA.
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Abstract
Large inter-individual variability in drug response and toxicity, as well as in drug concentrations after application of the same dosage, can be of genetic, physiological, pathophysiological, or environmental origin. Absorption, distribution and metabolism of a drug and interactions with its target often are determined by genetic differences. Pharmacokinetic and pharmacodynamic variations can appear at the level of drug metabolizing enzymes (e.g., the cytochrome P450 system), drug transporters, drug targets or other biomarker genes. Pharmacogenetics or toxicogenetics can therefore be relevant in forensic toxicology. This review presents relevant aspects together with some examples from daily routines.
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[Recent developments of pharmacogenomics in the treatment of colorectal cancers]. ANNALES PHARMACEUTIQUES FRANÇAISES 2010; 68:233-53. [PMID: 20637356 DOI: 10.1016/j.pharma.2010.04.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2010] [Revised: 04/16/2010] [Accepted: 04/16/2010] [Indexed: 12/27/2022]
Abstract
Colorectal cancer (CCR), which is one of the most common causes of cancer, has benefited from the major advances in the understanding of the intracellular signaling pathways implicated in the initiation, growing and local and metastasis dissemination of tumor, which have occurred during the 20 past years. The pharmacogenomics approach, especially the determination of the genetic polymorphisms, tries to find prognosis and predictive biomarkers permitting to identify patients who could benefit from a particular treatment or those exhibiting higher risks of toxicity. Among the numerous biomarkers, which have been studied, few are currently in use in clinical practice. The phenotyping of DPD and UGT1A1 activities, and to a lesser extent, its genotyping, appears as the most useful tool in terms of prediction of toxicities induced by two major drugs: 5-FU and irinotecan. For oxaliplatin, the determination of the polymorphisms of reparases and detoxification systems such as GSTpi seems interesting, but its exact place should be more defined. It is in the field of targeted therapies that the pharmacogenomics approach seems to be the more relevant. KRAS mutation is a dramatic example of single nucleotide polymorphism, which is able to identify a priori patients that could receive or not an anti-EGFR monoclonal antibody such as cetuximab or panitumumab. It is obvious that pre-clinical identification of molecular biomarkers predictive of the sensitivity of the drug targets, which subsequently implicate the selection of patients and the rational evaluation of responses, will be the cornerstone of any clinical trials concerning targeted therapies. Besides the determination of drug target polymorphisms, it is also important to consider those related to the distribution and metabolism. In this area, the determination of enzymatic activities should recover its place besides the genomic profiling.
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Yee SW, Chen L, Giacomini KM. Pharmacogenomics of membrane transporters: past, present and future. Pharmacogenomics 2010; 11:475-9. [PMID: 20350125 DOI: 10.2217/pgs.10.22] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Membrane transporters are major determinants of the absorption, distribution and elimination of many of the most commonly used drugs. In the past decade, the field of membrane transporter pharmacogenomics has undergone enormous growth. In particular, functional genomic and clinical studies have provided new information regarding the contribution of coding variants in transporters to drug disposition and response. With continuing advances in sequencing technologies and large-scale human variation studies, over the next decade, knowledge in the field will be transformed. In particular, functional variants in noncoding regions of transporters will be discovered, and large clinical studies will result in the identification of variants in multiple genes, including transporter genes, which contribute to variation in clinical drug response.
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Affiliation(s)
- Sook Wah Yee
- School of Pharmacy, University of California San Francisco, CA 94143-2911, USA
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44
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Errasti-Murugarren E, Molina-Arcas M, Casado FJ, Pastor-Anglada M. The human concentrative nucleoside transporter-3 C602R variant shows impaired sorting to lipid rafts and altered specificity for nucleoside-derived drugs. Mol Pharmacol 2010; 78:157-65. [PMID: 20421346 DOI: 10.1124/mol.110.063552] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
The human concentrative nucleoside transporter-3 C602R (hCNT3C602R), a recently identified human concentrative nucleoside transporter-3 (hCNT3) variant, has been shown to interact with natural nucleosides with apparent K(m) values similar to those of the wild-type transporter, although binding of one of the two sodium ions required for nucleoside translocation is impaired, resulting in decreased V(max) values (Mol Pharmacol 73:379-386, 2008). We have further analyzed the properties of this hCNT3 variant by determining its localization in plasma membrane lipid domains and its interaction with nucleoside-derived drugs used in anticancer and antiviral therapies. When expressed heterologously in HeLa cells, wild-type hCNT3 localized to both lipid raft and nonlipid raft domains. Treatment of cells with the cholesterol-depleting agent methyl-beta-cyclodextrin resulted in a marked decrease in hCNT3-related transport activity that was associated with the loss of wild-type hCNT3 from lipid rafts. It is noteworthy that although exogenously expressed hCNT3C602R was present in nonlipid raft domains at a level similar to that of the wild-type transporter, the mutant transporter was present at much lower amounts in lipid rafts. A substrate profile analysis showed that interactions with a variety of nucleoside-derived drugs were altered in the hCNT3C602R variant and revealed that sugar hydroxyl residues are key structural determinants for substrate recognition by the hCNT3C602R variant.
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Affiliation(s)
- Ekaitz Errasti-Murugarren
- Departament de Bioquímica i Biologia Molecular, Facultat de Biologia, Universitat de Barcelona and CIBER EHD, Avda Diagonal 645, Edifici annex, Planta-1, 08028 Barcelona, Spain
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