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Abrahams-October Z, Lloyd S, Pearce B, Johnson R, Benjeddou M. Promoter haplotype structure of solute carrier 22 member 2 (SLC22A2) in the Xhosa population of South Africa and their differential effect on gene expression. Gene X 2022; 820:146292. [PMID: 35143948 DOI: 10.1016/j.gene.2022.146292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 01/06/2022] [Accepted: 02/03/2022] [Indexed: 11/20/2022] Open
Abstract
SLC22A2 is abundantly expressed in the kidney and facilitates the transport of endogenous and exogenous cationic compounds. It plays a pivotal role in the transport of pharmacologically important compounds such as metformin, cisplatin, lamivudine and cimetidine. Polymorphisms within SLC22A2 could potentially contribute to the inter-individual variable response to drugs. The SLC22A2 gene is known to show polymorphism variability amongst populations of different ethnicities. The present study was undertaken to characterize the promoter haplotype structure of the SLC22A2 gene in the Xhosa population of South Africa. In addition to this, we also investigate the effects of the observed promoter haplotypes on gene expression levels in vitro. We identified six known single nucleotide polymorphisms in the promoter region, namely rs60249401 (G424A), rs113150889 (G289A), rs55920607 (C246T), rs59695691 (A195G), rs572296424 (G156A), rs150063153 (A95C/G) and one novel SNP at location 6:160258967 (A209T). While these polymorphisms appeared in other African and non-African populations, their minor allele frequencies differed considerably from the non-African populations and could be considered to be African specific. A total of nine promoter haplotypes were characterized and the functional significance of each haplotype on promoter activity was determined using a luciferase reporter assay system. Amongst the nine observed haplotypes, three haplotypes (i.e. haplotypes 7, 8 and 9) displayed a significant decrease in expression level when compared to the wild-type with p -values of: 0.0317, <0.0001 and 0.0013 respectively. The data presented here shows African specific promoter haplotypes to cause a decrease in SLC22A2 gene expression levels, which in turn may have an impact on the pharmacokinetic profiles of cationic drugs.
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Affiliation(s)
- Zainonesa Abrahams-October
- Precision Medicine Unit, Department of Biotechnology, Faculty of Natural Sciences, University of the Western Cape, Robert Sobukwe Road, Bellville 7535, South Africa.
| | - Sheridon Lloyd
- Precision Medicine Unit, Department of Biotechnology, Faculty of Natural Sciences, University of the Western Cape, Robert Sobukwe Road, Bellville 7535, South Africa
| | - Brendon Pearce
- Precision Medicine Unit, Department of Biotechnology, Faculty of Natural Sciences, University of the Western Cape, Robert Sobukwe Road, Bellville 7535, South Africa
| | - Rabia Johnson
- Biomedical Research and Innovation Platform, South African Medical Research Council, Tygerberg, 7505 Cape Town, South Africa; Division of Medical Physiology, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg 7505, South Africa
| | - Mongi Benjeddou
- Precision Medicine Unit, Department of Biotechnology, Faculty of Natural Sciences, University of the Western Cape, Robert Sobukwe Road, Bellville 7535, South Africa
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Kumar A, Jaitak V. Natural products as multidrug resistance modulators in cancer. Eur J Med Chem 2019; 176:268-291. [PMID: 31103904 DOI: 10.1016/j.ejmech.2019.05.027] [Citation(s) in RCA: 186] [Impact Index Per Article: 37.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Revised: 05/07/2019] [Accepted: 05/07/2019] [Indexed: 01/21/2023]
Abstract
Cancer is a prominent cause of death globally. Currently, many drugs that are in clinical practice are having a high prevalence of side effect and multidrug resistance. Risk of tumors acquiring resistance to chemotherapy (multidrug resistance) remains a significant hurdle to the successful treatment of various types of cancer. Membrane-embedded drug transporters, generally overexpressed in cancer, are the leading cause among multiple mechanisms of multidrug resistance (MDR). P-glycoprotein (P-gp) also MDR1/ABCB1, multidrug resistance associated protein 1 (MRP1/ABCC1), MRP2 and breast cancer resistance protein (BCRP/ABCG2) are considered to be a prime factor for induction of MDR. To date, several chemical substances have been tested in a number of clinical trials for their MDR modulatory activity which are not having devoid of any side effects that necessitates to find newer and safer way to tackle the current problem of multidrug resistance in cancer. The present study systematically discusses the various classes of natural products i.e flavonoids, alkaloids, terpenoids, coumarins (from plants, marine, and microorganisms) as potential MDR modulators and/or as a source of promising lead compounds. Recently a bisbenzyl isoquinoline alkaloid namely tetrandrine, isolated from Chinese herb Stephania tetrandra (Han-Fang-Chi) is in clinical trials for its MDR reversal activity.
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Affiliation(s)
- Amit Kumar
- Laboratory of Natural Products, Department of Pharmaceutical Sciences and Natural Products, Central University of Punjab, Mansa Road, Bathinda, 151001, India
| | - Vikas Jaitak
- Laboratory of Natural Products, Department of Pharmaceutical Sciences and Natural Products, Central University of Punjab, Mansa Road, Bathinda, 151001, India.
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3
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Bokelmann K, Brockmöller J, Tzvetkov MV. Impact of Promoter Polymorphisms on the Transcriptional Regulation of the Organic Cation Transporter OCT1 (SLC22A1). J Pers Med 2018; 8:jpm8040042. [PMID: 30544975 PMCID: PMC6313513 DOI: 10.3390/jpm8040042] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Revised: 11/20/2018] [Accepted: 12/05/2018] [Indexed: 01/12/2023] Open
Abstract
The organic cation transporter 1 (OCT1, SLC22A1) is strongly expressed in the human liver and facilitates the hepatic uptake of drugs such as morphine, metformin, tropisetron, sumatriptan and fenoterol and of endogenous substances such as thiamine. OCT1 expression is inter-individually highly variable. Here, we analyzed SNPs in the OCT1 promoter concerning their potential contribution to the variability in OCT1 expression. Using electrophoretic mobility shift and luciferase reporter gene assays in HepG2, Hep3B, and Huh7 cell lines, we identified the SNPs −1795G>A (rs6935207) and −201C>G (rs58812592) as having effects on transcription factor binding and/or promoter activity. The A-allele of the −1795G>A SNP showed allele-specific binding of the transcription factor NF-Y leading to 2.5-fold increased enhancer activity of the artificial SV40 promoter. However, the −1795G>A SNP showed no significant effects on the native OCT1 promoter activity. Furthermore, the −1795G>A SNP was not associated with the pharmacokinetics of metformin, fenoterol, sumatriptan and proguanil in healthy individuals or tropisetron efficacy in patients undergoing chemotherapy. Allele-dependent differences in USF1/2 binding and nearly total loss in OCT1 promoter activity were detected for the G-allele of −201C>G, but the SNP is apparently very rare. In conclusion, common OCT1 promoter SNPs have only minor effects on OCT1 expression.
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Affiliation(s)
- Kristin Bokelmann
- Institute of Clinical Pharmacology, University Medical Center, Georg-August-University, 37075 Göttingen, Germany.
| | - Jürgen Brockmöller
- Institute of Clinical Pharmacology, University Medical Center, Georg-August-University, 37075 Göttingen, Germany.
| | - Mladen V Tzvetkov
- Institute of Pharmacology, Center of Drug Absorption and Transport (C_DAT), University Medicine Greifswald, 17487 Greifswald, Germany.
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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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Jaruskova M, Curik N, Hercog R, Polivkova V, Motlova E, Benes V, Klamova H, Pecherkova P, Belohlavkova P, Vrbacky F, Machova Polakova K. Genotypes of SLC22A4 and SLC22A5 regulatory loci are predictive of the response of chronic myeloid leukemia patients to imatinib treatment. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2017; 36:55. [PMID: 28420426 PMCID: PMC5395939 DOI: 10.1186/s13046-017-0523-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Accepted: 03/31/2017] [Indexed: 01/06/2023]
Abstract
Background Through high-throughput next-generation sequencing of promoters of solute carrier and ATP-binding cassette genes, which encode drug transporters, we aimed to identify SNPs associated with the response to imatinib administered for first-line treatment of patients with chronic myeloid leukemia. Methods In silico analysis using publicly available databases was done to select the SLC and ABC genes and their promoters for the next-generation sequencing. SNPs associated with the imatinib response were identified using Fisher’s exact probability tests and subjected to the linkage disequilibrium analyses with regulatory loci of concerned genes. We analyzed cumulative achievement of major molecular response and probability of event free survival in relation to identified SNP genotypes in 129 CML patients and performed multivariate analysis for determination of genotypes as independent predictors of outcome. Gene expression analysis of eight cell lines naturally carrying different genotypes was performed to outline an impact of genotypes on the gene expression. Results We observed significant differences in the frequencies of the rs460089-GC and rs460089-GG (SLC22A4) genotypes among rs2631365-TC (SLC22A5) genotype carriers that were associated with optimal and non-optimal responses, respectively. Loci rs460089 and rs2631365 were in highly significant linkage disequilibrium with 12 regulatory loci in introns of SLC22A4 and SLC22A5 encoding imatinib transporters. Genotype association analysis with the response to imatinib indicated that rs460089-GC carriers had a significantly higher probability of achieving a stable major molecular response (BCR-ABL1 transcript level below or equal to 0.1% in the international scale). In contrast, the rs460089-GG represented a risk factor for imatinib failure, which was significantly higher in rs460089-GG_rs2631365-TC carriers. Conclusions This exploratory study depicted potentially important genetic markers predicting outcome of imatinib treatment, which may be helpful for tailoring therapy in clinical practice. Electronic supplementary material The online version of this article (doi:10.1186/s13046-017-0523-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Monika Jaruskova
- Institute of Hematology and Blood Transfusion, U Nemocnice 1, 12820, Prague, Czech Republic.,Institute of Clinical and Experimental Hematology, 1st Medicine Faculty, Charles University, Prague, Czech Republic
| | - Nikola Curik
- Institute of Hematology and Blood Transfusion, U Nemocnice 1, 12820, Prague, Czech Republic.,Institute of Pathophysiology, 1st Medicine Faculty, Charles University, Prague, Czech Republic
| | - Rajna Hercog
- European Molecular Biology Laboratory, Genomics Core Facility, Heidelberg, Germany
| | - Vaclava Polivkova
- Institute of Hematology and Blood Transfusion, U Nemocnice 1, 12820, Prague, Czech Republic.,Faculty of Science, Charles University, Prague, Czech Republic
| | - Eliska Motlova
- Institute of Hematology and Blood Transfusion, U Nemocnice 1, 12820, Prague, Czech Republic
| | - Vladimir Benes
- European Molecular Biology Laboratory, Genomics Core Facility, Heidelberg, Germany
| | - Hana Klamova
- Institute of Hematology and Blood Transfusion, U Nemocnice 1, 12820, Prague, Czech Republic.,Institute of Clinical and Experimental Hematology, 1st Medicine Faculty, Charles University, Prague, Czech Republic.,CELL, the Czech Leukemia Study Group for Life, Brno, Czech Republic
| | - Pavla Pecherkova
- Institute of Hematology and Blood Transfusion, U Nemocnice 1, 12820, Prague, Czech Republic
| | - Petra Belohlavkova
- CELL, the Czech Leukemia Study Group for Life, Brno, Czech Republic.,4th Department of Internal Medicine Hematology, Charles University Faculty Hospital and Faculty of Medicine, Hradec Kralove, Czech Republic
| | - Filip Vrbacky
- 4th Department of Internal Medicine Hematology, Charles University Faculty Hospital and Faculty of Medicine, Hradec Kralove, Czech Republic
| | - Katerina Machova Polakova
- Institute of Hematology and Blood Transfusion, U Nemocnice 1, 12820, Prague, Czech Republic. .,Institute of Clinical and Experimental Hematology, 1st Medicine Faculty, Charles University, Prague, Czech Republic. .,CELL, the Czech Leukemia Study Group for Life, Brno, Czech Republic.
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Cellular Models and In Vitro Assays for the Screening of modulators of P-gp, MRP1 and BCRP. Molecules 2017; 22:molecules22040600. [PMID: 28397762 PMCID: PMC6153761 DOI: 10.3390/molecules22040600] [Citation(s) in RCA: 72] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Revised: 03/24/2017] [Accepted: 03/28/2017] [Indexed: 12/12/2022] Open
Abstract
Adenosine triphosphate (ATP)-binding cassette (ABC) transporters are highly expressed in tumor cells, as well as in organs involved in absorption and secretion processes, mediating the ATP-dependent efflux of compounds, both endogenous substances and xenobiotics, including drugs. Their expression and activity levels are modulated by the presence of inhibitors, inducers and/or activators. In vitro, ex vivo and in vivo studies with both known and newly synthesized P-glycoprotein (P-gp) inducers and/or activators have shown the usefulness of these transport mechanisms in reducing the systemic exposure and specific tissue access of potentially harmful compounds. This article focuses on the main ABC transporters involved in multidrug resistance [P-gp, multidrug resistance-associated protein 1 (MRP1) and breast cancer resistance protein (BCRP)] expressed in tissues of toxicological relevance, such as the blood-brain barrier, cardiovascular system, liver, kidney and intestine. Moreover, it provides a review of the available cellular models, in vitro and ex vivo assays for the screening and selection of safe and specific inducers and activators of these membrane transporters. The available cellular models and in vitro assays have been proposed as high throughput and low-cost alternatives to excessive animal testing, allowing the evaluation of a large number of compounds.
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ABC transporter polymorphisms are associated with irinotecan pharmacokinetics and neutropenia. THE PHARMACOGENOMICS JOURNAL 2016; 18:35-42. [PMID: 27845419 DOI: 10.1038/tpj.2016.75] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2015] [Revised: 05/09/2016] [Accepted: 08/25/2016] [Indexed: 12/22/2022]
Abstract
Neutropenia is a common dose-limiting toxicity associated with irinotecan treatment. Although UGT1A1 variants have been associated with neutropenia, a fraction of neutropenia risk remains unaccounted for. To identify additional genetic markers contributing to variability in irinotecan pharmacokinetics and neutropenia, a regression analysis was performed in 78 irinotecan-treated patients to analyze comprehensively three hepatic efflux transporter genes (ABCB1, ABCC1 and ABCG2). rs6498588 (ABCC1) and rs12720066 (ABCB1) were associated with increased SN-38 exposure, and rs17501331 (ABCC1) and rs12720066 were associated with lower absolute neutrophil count nadir. rs6498588 and a variant in high linkage disequilibrium are located in transcriptionally active regions or are predicted to alter transcription factor binding sites. While enhancer activity was not evident in vitro for genomic regions containing these single-nucleotide polymorphisms, rs6498588 was significantly associated with ABCC1 expression in human liver. These results suggest that genetic variation in ABCC1 and ABCB1 may contribute to irinotecan-induced neutropenia by altering expression of transporters involved in irinotecan metabolite disposition.
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Vatsiou AI, Bazin E, Gaggiotti OE. Changes in selective pressures associated with human population expansion may explain metabolic and immune related pathways enriched for signatures of positive selection. BMC Genomics 2016; 17:504. [PMID: 27444955 PMCID: PMC4955149 DOI: 10.1186/s12864-016-2783-2] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Accepted: 05/26/2016] [Indexed: 12/14/2022] Open
Abstract
Background The study of local adaptation processes is a very important research topic in the field of population genomics. There is a particular interest in the study of human populations because they underwent a process of rapid spatial expansion and faced important environmental changes that translated into changes in selective pressures. New mutations may have been selected for in the new environment and previously existing genetic variants may have become detrimental. Immune related genes may have been released from the selective pressure exerted by pathogens in the ancestral environment and new variants may have been positively selected due to pathogens present in the newly colonized habitat. Also, variants that had a selective advantage in past environments may have become deleterious in the modern world due to external stimuli including climatic, dietary and behavioral changes, which could explain the high prevalence of some polygenic diseases such as diabetes and obesity. Results We performed an enrichment analysis to identify gene sets enriched for signals of positive selection in humans. We used two genome scan methods, XPCLR and iHS to detect selection using a dense coverage of SNP markers combined with two gene set enrichment approaches. We identified immune related gene sets that could be involved in the protection against pathogens especially in the African population. We also identified the glycolysis & gluconeogenesis gene set, related to metabolism, which supports the thrifty genotype hypothesis invoked to explain the current high prevalence of diseases such as diabetes and obesity. Extending our analysis to the gene level, we found signals for 23 candidate genes linked to metabolic syndrome, 13 of which are new candidates for positive selection. Conclusions Our study provides a list of genes and gene sets associated with immunity and metabolic syndrome that are enriched for signals of positive selection in three human populations (Europeans, Africans and Asians). Our results highlight differences in the relative importance of pathogens as drivers of local adaptation in different continents and provide new insights into the evolution and high incidence of metabolic syndrome in modern human populations. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2783-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Alexandra I Vatsiou
- Laboratoire d'Écologie Alpine (LECA), Univesrity Joseph Fourier, 2233 Rue de la Piscine, 38041, Grenoble, Cedex 9, France. .,Scottish Oceans Institute, East Sands, University of St Andrews, St Andrews, KY16 8LB, Scotland, UK. .,Oh no sequences! Research group, Era7Bioinformatics, Plaza de Campo Verde, 3, 18001, Granada, Spain.
| | - Eric Bazin
- Laboratoire d'Écologie Alpine (LECA), Univesrity Joseph Fourier, 2233 Rue de la Piscine, 38041, Grenoble, Cedex 9, France
| | - Oscar E Gaggiotti
- Laboratoire d'Écologie Alpine (LECA), Univesrity Joseph Fourier, 2233 Rue de la Piscine, 38041, Grenoble, Cedex 9, France.,Scottish Oceans Institute, East Sands, University of St Andrews, St Andrews, KY16 8LB, Scotland, UK
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Nigam SK, Wu W, Bush KT, Hoenig MP, Blantz RC, Bhatnagar V. Handling of Drugs, Metabolites, and Uremic Toxins by Kidney Proximal Tubule Drug Transporters. Clin J Am Soc Nephrol 2015; 10:2039-49. [PMID: 26490509 DOI: 10.2215/cjn.02440314] [Citation(s) in RCA: 176] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2014] [Accepted: 09/28/2014] [Indexed: 01/22/2023]
Abstract
The proximal tubule of the kidney plays a crucial role in the renal handling of drugs (e.g., diuretics), uremic toxins (e.g., indoxyl sulfate), environmental toxins (e.g., mercury, aristolochic acid), metabolites (e.g., uric acid), dietary compounds, and signaling molecules. This process is dependent on many multispecific transporters of the solute carrier (SLC) superfamily, including organic anion transporter (OAT) and organic cation transporter (OCT) subfamilies, and the ATP-binding cassette (ABC) superfamily. We review the basic physiology of these SLC and ABC transporters, many of which are often called drug transporters. With an emphasis on OAT1 (SLC22A6), the closely related OAT3 (SLC22A8), and OCT2 (SLC22A2), we explore the implications of recent in vitro, in vivo, and clinical data pertinent to the kidney. The analysis of murine knockouts has revealed a key role for these transporters in the renal handling not only of drugs and toxins but also of gut microbiome products, as well as liver-derived phase 1 and phase 2 metabolites, including putative uremic toxins (among other molecules of metabolic and clinical importance). Functional activity of these transporters (and polymorphisms affecting it) plays a key role in drug handling and nephrotoxicity. These transporters may also play a role in remote sensing and signaling, as part of a versatile small molecule communication network operative throughout the body in normal and diseased states, such as AKI and CKD.
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Affiliation(s)
- Sanjay K Nigam
- Department of Medicine, Department of Pediatrics, Department of Cell & Molecular Medicine,
| | | | | | - Melanie P Hoenig
- Division of Nephrology, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, Massachusetts
| | - Roland C Blantz
- Division of Nephrology-Hypertension, and Veterans Affairs San Diego Healthcare System, San Diego, California; and
| | - Vibha Bhatnagar
- Division of Family & Preventative Medicine, University of California-San Diego, La Jolla, California
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Variability in hepatic expression of organic anion transporter 7/SLC22A9, a novel pravastatin uptake transporter: impact of genetic and regulatory factors. THE PHARMACOGENOMICS JOURNAL 2015; 16:341-51. [PMID: 26239079 DOI: 10.1038/tpj.2015.55] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2015] [Revised: 05/26/2015] [Accepted: 06/23/2015] [Indexed: 02/07/2023]
Abstract
Human organic anion transporter 7 (OAT7, SLC22A9) is a hepatic transport protein poorly characterized so far. We therefore sought to identify novel OAT7 substrates and factors contributing to variable hepatic OAT7 expression. Using OAT7-expressing cells, pravastatin was identified as a substrate. Hepatic SLC22A9/OAT7 mRNA and protein expression varied 28-fold and 15-fold, respectively, in 126 Caucasian liver samples. Twenty-four variants in SLC22A9 were genotyped, including three rare missense variants (rs377211288, rs61742518, rs146027075), which occurred only heterozygously. No variant significantly affected hepatic SLC22A9/OAT7 expression. The three missense variants, however, showed functional consequences when expressed in vitro. Hepatic nuclear factor 4-alpha (HNF4α) emerged as a major transcriptional regulator of SLC22A9 by a series of in silico and in vitro analyses. In conclusion, pravastatin is the first identified OAT7 drug substrate. Substantial inter-individual variability in hepatic OAT7 expression, majorly driven by HNF4α, may contribute to pravastatin drug disposition and might affect response.The Pharmacogenomics Journal advance online publication, 4 August 2015; doi:10.1038/tpj.2015.55.
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Nies AT, Damme K, Schaeffeler E, Schwab M. Multidrug and toxin extrusion proteins as transporters of antimicrobial drugs. Expert Opin Drug Metab Toxicol 2012; 8:1565-77. [PMID: 22970772 DOI: 10.1517/17425255.2012.722996] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
INTRODUCTION Antimicrobial drugs are essential in the treatment of infectious diseases. A better understanding of transport processes involved in drug disposition will improve the predictability of drug-drug interactions with consequences for drug response. Multidrug And Toxin Extrusion (MATE; SLC47A) proteins are efflux transporters mediating the excretion of several antimicrobial drugs as well as other organic compounds into bile and urine, thereby contributing to drug disposition. AREAS COVERED This review summarizes current knowledge of the structural and molecular features of human MATE transporters including their functional role in drug transport with a specific focus on antimicrobial drugs. The PubMed database was searched using the terms "MATE1," "MATE-2K," "MATE2," "SLC47A1," "SLC47A2," and "toxin extrusion protein" (up to June 2012). EXPERT OPINION MATE proteins have been recognized as important transporters mediating the final excretion step of cationic drugs into bile and urine. These include the antiviral drugs acyclovir, amprenavir, and ganciclovir, the antibiotics cephalexin, cephradine and levofloxacin, as well as the antimalarial agents chloroquine and quinine. It is therefore important to enhance our understanding of the role of MATEs in drug extrusion with particular emphasis on the functional consequences of genetic variants on disposition of these antimicrobial drugs.
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Affiliation(s)
- Anne T Nies
- Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart and University of Tübingen, Auerbachstrasse 112, 70376 Stuttgart, Germany.
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12
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Smith RP, Lam ET, Markova S, Yee SW, Ahituv N. Pharmacogene regulatory elements: from discovery to applications. Genome Med 2012; 4:45. [PMID: 22630332 PMCID: PMC3506911 DOI: 10.1186/gm344] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Regulatory elements play an important role in the variability of individual responses to drug treatment. This has been established through studies on three classes of elements that regulate RNA and protein abundance: promoters, enhancers and microRNAs. Each of these elements, and genetic variants within them, are being characterized at an exponential pace by next-generation sequencing (NGS) technologies. In this review, we outline examples of how each class of element affects drug response via regulation of drug targets, transporters and enzymes. We also discuss the impact of NGS technologies such as chromatin immunoprecipitation sequencing (ChIP-Seq) and RNA sequencing (RNA-Seq), and the ramifications of new techniques such as high-throughput chromosome capture (Hi-C), chromatin interaction analysis by paired-end tag sequencing (ChIA-PET) and massively parallel reporter assays (MPRA). NGS approaches are generating data faster than they can be analyzed, and new methods will be required to prioritize laboratory results before they are ready for the clinic. However, there is no doubt that these approaches will bring about a systems-level understanding of the interplay between genetic variants and drug response. An understanding of the importance of regulatory variants in pharmacogenomics will facilitate the identification of responders versus non-responders, the prevention of adverse effects and the optimization of therapies for individual patients.
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Affiliation(s)
- Robin P Smith
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
| | - Ernest T Lam
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
- Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA, USA
| | - Svetlana Markova
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
| | - Sook Wah Yee
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
| | - Nadav Ahituv
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
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13
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Qin S, Chen J, Tanigawa S, Hou DX. Gene expression profiling and pathway network analysis of hepatic metabolic enzymes targeted by baicalein. JOURNAL OF ETHNOPHARMACOLOGY 2012; 140:131-140. [PMID: 22265932 DOI: 10.1016/j.jep.2011.12.046] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2011] [Accepted: 12/21/2011] [Indexed: 05/31/2023]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Baicalein is a flavone originally isolated from the roots of traditional Chinese medicinal herb, Scutellaria baicalensis, which has been proved as a promising chemopreventive compound for many chronic human diseases. AIM OF THE STUDY The present study aimed to clarify the molecular mechanism targeted by baicalein. MATERIALS AND METHODS Gene expression profiling of HepG2 cells treated with baicalein was carried out, using the Affymetrix 42K oligonucleotide microarray in the present study. Microarray data analyzed by Ingenuity Pathway Analysis (IPA), further study performed by real time PCR, reporter gene assay, and Western blot. RESULTS Among total 42K gene probes, baicalein treatment up-regulated the signals of 440 gene probes (1.04% of total gene probes) and down-regulated signals of 254 gene probes (0.6% of total gene probes) by ≥2-fold. These genes were categorized into 35 groups and hit for biological processes, molecular functions, and signaling pathways. The network and pathway analyses of these data further revealed that an Nrf2 (nuclear factor-erythroid 2 p45-related factor 2)-mediated ARE (antioxidant response element) pathway is involved in baicalein-induced gene expression of hepatic metabolic enzymes. The representative enzymes involved in Nrf2/ARE pathway were further confirmed at mRNA level by real time PCR and at protein level by Western blot analysis. Moreover, the ARE-reporter gene assay demonstrated that baicalein stimulated Nrf2-mediated ARE transactivation. CONCLUSIONS Our results provide a comprehensive data for understanding the hepatic metabolism, bioactive role and the molecular mechanisms of baicalein.
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Affiliation(s)
- Si Qin
- Course of Biological Science and Technology, United Graduate School of Agricultural Sciences, Kagoshima University, Korimoto 1-21-24, Kagoshima 890-0065, Japan
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14
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Chen L, Hong C, Chen EC, Yee SW, Xu L, Almof EU, Wen C, Fujii K, Johns SJ, Stryke D, Ferrin TE, Simko J, Chen X, Costello JF, Giacomini KM. Genetic and epigenetic regulation of the organic cation transporter 3, SLC22A3. THE PHARMACOGENOMICS JOURNAL 2012; 13:110-20. [PMID: 22231567 PMCID: PMC3396779 DOI: 10.1038/tpj.2011.60] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Human organic cation transporter 3 (OCT3 and SLC22A3) mediates the uptake of many important endogenous amines and basic drugs in a variety of tissues. OCT3 is identified as one of the important risk loci for prostate cancer, and is markedly underexpressed in aggressive prostate cancers. The goal of this study was to identify genetic and epigenetic factors in the promoter region that influence the expression level of OCT3. Haplotypes that contained the common variants, g.-81G>delGA (rs60515630) (minor allele frequency 11.5% in African American) and g.-2G>A (rs555754) (minor allele frequency>30% in all ethnic groups) showed significant increases in luciferase reporter activities and exhibited stronger transcription factor-binding affinity than the haplotypes that contained the major alleles. Consistent with the reporter assays, OCT3 messenger RNA expression levels were significantly higher in Asian (P<0.001) and Caucasian (P<0.05) liver samples from individuals who were homozygous for g.-2A/A in comparison with those homozygous for the g.-2G/G allele. Studies revealed that the methylation level in the basal promoter region of OCT3 was associated with OCT3 expression level and tumorigenesis capability in various prostate cancer cell lines. The methylation level of the OCT3 promoter was higher in 62% of prostate tumor samples compared with matched normal samples. Our studies demonstrate that genetic polymorphisms in the proximal promoter region of OCT3 alter the transcription rate of the gene and may be associated with altered expression levels of OCT3 in human liver. Aberrant methylation contributes to the reduced expression of OCT3 in prostate cancer.
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Affiliation(s)
- L Chen
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, CA 94158, USA
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15
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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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16
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Interplay of pharmacogenetic variations in ABCB1 transporters and cytochrome P450 enzymes. Arch Pharm Res 2011; 34:1817-28. [DOI: 10.1007/s12272-011-1104-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2011] [Revised: 08/28/2011] [Accepted: 09/05/2011] [Indexed: 01/11/2023]
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17
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Minuesa G, Huber-Ruano I, Pastor-Anglada M, Koepsell H, Clotet B, Martinez-Picado J. Drug uptake transporters in antiretroviral therapy. Pharmacol Ther 2011; 132:268-79. [DOI: 10.1016/j.pharmthera.2011.06.007] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2011] [Accepted: 06/30/2011] [Indexed: 01/11/2023]
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18
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Damme K, Nies AT, Schaeffeler E, Schwab M. Mammalian MATE (SLC47A) transport proteins: impact on efflux of endogenous substrates and xenobiotics. Drug Metab Rev 2011; 43:499-523. [PMID: 21923552 DOI: 10.3109/03602532.2011.602687] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Multidrug and toxin extrusion proteins (MATEs; SLC47A) are mammalian transporters being predominately expressed in the brush-border membrane of proximal tubule epithelial cells in the kidney and the canalicular membrane of hepatocytes. Functionally, MATEs act as efflux transporters for organic compounds, thereby mediating the elimination process. Two isoforms, MATE1 and 2, have been identified, and, so far, only a limited number of substrates, including clinically used drugs such as metformin and cimetidine, are known. A knockout mouse model has been established, as well, and is a valuable tool for further systematic pharmacokinetic analyses. In this review, we summarize the progress in MATE research on structural, molecular, functional, and pathophysiological aspects. Consequences of genetic variants for pharmacokinetic alterations and drug therapy are discussed.
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Affiliation(s)
- Katja Damme
- Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart, Germany
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19
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Saxena M, Stephens MA, Pathak H, Rangarajan A. Transcription factors that mediate epithelial-mesenchymal transition lead to multidrug resistance by upregulating ABC transporters. Cell Death Dis 2011; 2:e179. [PMID: 21734725 PMCID: PMC3199722 DOI: 10.1038/cddis.2011.61] [Citation(s) in RCA: 272] [Impact Index Per Article: 20.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Development of multidrug resistance (MDR) is a major deterrent in the effective treatment of metastatic cancers by chemotherapy. Even though MDR and cancer invasiveness have been correlated, the molecular basis of this link remains obscure. We show here that treatment with chemotherapeutic drugs increases the expression of several ATP binding cassette transporters (ABC transporters) associated with MDR, as well as epithelial–mesenchymal transition (EMT) markers, selectively in invasive breast cancer cells, but not in immortalized or non-invasive cells. Interestingly, the mere induction of an EMT in immortalized and non-invasive cell lines increased their expression of ABC transporters, migration, invasion, and drug resistance. Conversely, reversal of EMT in invasive cells by downregulating EMT-inducing transcription factors reduced their expression of ABC transporters, invasion, and rendered them more chemosensitive. Mechanistically, we demonstrate that the promoters of ABC transporters carry several binding sites for EMT-inducing transcription factors, and overexpression of Twist, Snail, and FOXC2 increases the promoter activity of ABC transporters. Furthermore, chromatin immunoprecipitation studies revealed that Twist binds directly to the E-box elements of ABC transporters. Thus, our study identifies EMT inducers as novel regulators of ABC transporters, thereby providing molecular insights into the long-standing association between invasiveness and MDR. Targeting EMT transcription factors could hence serve as novel strategies to curb both metastasis and the associated drug resistance.
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Affiliation(s)
- M Saxena
- Department of Molecular Reproduction, Development and Genetics, Indian Institute of Science, Bangalore 560012, Karnataka, India
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20
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Functional characterization of liver enhancers that regulate drug-associated transporters. Clin Pharmacol Ther 2011; 89:571-8. [PMID: 21368754 DOI: 10.1038/clpt.2010.353] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Little is known about how genetic variations in enhancers influence drug response. In this study, we investigated whether nucleotide variations in enhancers that regulate drug transporters can alter their expression levels. Using comparative genomics and liver-specific transcription factor binding site (TFBS) analyses, we identified evolutionary conserved regions (ECRs) surrounding nine liver membrane transporters that interact with commonly used pharmaceuticals. The top 50 ECRs were screened for enhancer activity in vivo, of which five--located around ABCB11, SLC10A1, SLCO1B1, SLCO1A2, and SLC47A1--exhibited significant enhancer activity. Common variants identified in a large ethnically diverse cohort (n = 272) were assayed for differential enhancer activity, and three variants were found to have significant effects on reporter activity as compared with the reference allele. In addition, one variant was associated with reduced SLCO1A2 mRNA expression levels in human liver tissues, and another was associated with increased methotrexate (MTX) clearance in patients. This work provides a general model for the rapid characterization of liver enhancers and identifies associations between enhancer variants and drug response.
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21
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Nies AT, Koepsell H, Damme K, Schwab M. Organic cation transporters (OCTs, MATEs), in vitro and in vivo evidence for the importance in drug therapy. Handb Exp Pharmacol 2011:105-67. [PMID: 21103969 DOI: 10.1007/978-3-642-14541-4_3] [Citation(s) in RCA: 267] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Organic cation transporters (OCTs) of the solute carrier family (SLC) 22 and multidrug and toxin extrusion (MATE) transporters of the SLC47 family have been identified as uptake and efflux transporters, respectively, for xenobiotics including several clinically used drugs such as the antidiabetic agent metformin, the antiviral agent lamivudine, and the anticancer drug oxaliplatin. Expression of human OCT1 (SLC22A1) and OCT2 (SLC22A2) is highly restricted to the liver and kidney, respectively. By contrast, OCT3 (SLC22A3) is more widely distributed. MATEs (SLC47A1, SLC47A2) are predominantly expressed in human kidney. Data on in vitro studies reporting a large number of substrates and inhibitors of OCTs and MATEs are systematically summarized. Several genetic variants of human OCTs and in part of MATE1 have been reported, and some of them result in reduced in vitro transport activity corroborating data from studies with knockout mice. A comprehensive overview is given on currently known genotype-phenotype correlations for variants in OCTs and MATE1 related to protein expression, pharmacokinetics/-dynamics of transporter substrates, treatment outcome, and disease susceptibility.
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Affiliation(s)
- Anne T Nies
- Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart, Germany.
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22
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Abstract
Interindividual differences in drug transporter expression can result in variability in drug response. This variation in gene expression is determined, in part, by the actions of nuclear hormone receptors that act as xenobiotic- and endobiotic-sensing transcription factors. Among the ligand-activated nuclear receptors, signaling through the pregnane X receptor (PXR), constitutive androstane receptor (CAR), farnesoid X receptor (FXR), and vitamin D receptor (VDR) constitute major pathways regulating drug transporter expression in tissues. Hence, these endobiotic- and xenobiotic-sensing nuclear receptors are intrinsically involved in environmental influences of drug response. Moreover, because nuclear receptor genes are polymorphic, these transcription factors are also thought to contribute to heritability of variable drug action. In this chapter, the molecular aspects of drug transporter gene regulation by ligand-activated nuclear receptors will be reviewed including their clinical relevance.
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23
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Sequencing of TNFAIP3 and association of variants with multiple autoimmune diseases. Genes Immun 2011; 12:176-82. [PMID: 21326317 DOI: 10.1038/gene.2010.64] [Citation(s) in RCA: 90] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
The TNFAIP3 locus at 6q23, encoding A20, has been associated with multiple autoimmune diseases (AIDs). In this study, we sequence the coding portions of the gene to identify contributing causal polymorphisms that may explain some of the observed associations. A collection of 123 individuals from the Multiple Autoimmune Disease Genetics Consortium (MADGC) collection, each with multiple AIDs (mean=2.2 confirmed diagnoses), and 397 unrelated healthy controls were used for initial sequencing. A total of 32 polymorphisms were identified in the sequencing experiments, including 16 novel and 11 coding variants. Association testing in the entire MADGC collection (1,008 Caucasians with one or more AIDs and 770 unaffected family controls) revealed association of a novel intronic insertion-deletion polymorphism with rheumatoid arthritis (RA) (odds ratio (OR)=2.48, P=0.041). Genotyping of the most common coding polymorphism, rs2230926, in the MADGC collection and additional control individuals revealed a significant association with Sjögren's syndrome (OR=3.38, P=0.038), Crohn's disease (OR=2.25, P=0.041), psoriasis (OR=0.037, P=0.036) and RA (OR=1.9, P=0.025). Finally, haplotype and additional testing of polymorphisms revealed that cases were enriched for 5' and 3' untranslated region variants (one-sided P-value=0.04), but not specifically for common (>2% minor allele frequency), rare, exonic, intronic, non-synonymous or synonymous variants.
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24
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Li J, Zhang L, Zhou H, Stoneking M, Tang K. Global patterns of genetic diversity and signals of natural selection for human ADME genes. Hum Mol Genet 2010; 20:528-40. [DOI: 10.1093/hmg/ddq498] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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25
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Glubb DM, Innocenti F. Mechanisms of genetic regulation in gene expression: examples from drug metabolizing enzymes and transporters. WILEY INTERDISCIPLINARY REVIEWS-SYSTEMS BIOLOGY AND MEDICINE 2010; 3:299-313. [PMID: 20865777 DOI: 10.1002/wsbm.125] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Interindividual variability in the response to drug therapy is due, in part, to genetic mechanisms which influence the expression of genes involved with drug metabolism and transport. Genetic elements and processes such as DNA methylation, histone deacetylation, transcription factors, DNA sequence variants, and microRNAs (miRNAs) can impact at either the transcriptional or translational levels to modulate gene expression. Identification of such genetic regulators has greatly advanced in the last decade. Genome-wide analyses, using different types of approaches and methodologies, have uncovered many potential regulators of the expression of drug metabolizing enzymes and transporters. However, confirming the function of these putative regulators is necessary and requires further work in the laboratory, using techniques which are still evolving. It also still remains to be seen whether these findings have clinical implications for drug therapy but the realization of personalized medicine is a possible consequence of this research.
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Affiliation(s)
- Dylan M Glubb
- Department of Medicine, University of Chicago, Chicago, IL, USA
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26
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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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27
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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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28
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The pharmacogenomics of membrane transporters project: research at the interface of genomics and transporter pharmacology. Clin Pharmacol Ther 2009; 87:109-16. [PMID: 19940846 DOI: 10.1038/clpt.2009.226] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Since the cloning of the first membrane transporter, our understanding of the role of transporters in clinical drug disposition and response has grown enormously. In parallel, large-scale genome-wide variation studies and the emerging field of pharmacogenomics have ushered in a new understanding of variations in drug response. At the crossroads of pharmacogenomics and transporter biology is the National Institutes of Health-funded Pharmacogenomics of Membrane Transporters (PMT) project, centered at the University of California, San Francisco.
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