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Ball AL, Bloch KM, Rainbow L, Liu X, Kenny J, Lyon JJ, Gregory R, Alfirevic A, Chadwick AE. Assessment of the impact of mitochondrial genotype upon drug-induced mitochondrial dysfunction in platelets derived from healthy volunteers. Arch Toxicol 2021; 95:1335-1347. [PMID: 33585966 PMCID: PMC8032628 DOI: 10.1007/s00204-021-02988-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 01/21/2021] [Indexed: 12/02/2022]
Abstract
Mitochondrial DNA (mtDNA) is highly polymorphic and encodes 13 proteins which are critical to the production of ATP via oxidative phosphorylation. As mtDNA is maternally inherited and undergoes negligible recombination, acquired mutations have subdivided the human population into several discrete haplogroups. Mitochondrial haplogroup has been found to significantly alter mitochondrial function and impact susceptibility to adverse drug reactions. Despite these findings, there are currently limited models to assess the effect of mtDNA variation upon susceptibility to adverse drug reactions. Platelets offer a potential personalised model of this variation, as their anucleate nature offers a source of mtDNA without interference from the nuclear genome. This study, therefore, aimed to determine the effect of mtDNA variation upon mitochondrial function and drug-induced mitochondrial dysfunction in a platelet model. The mtDNA haplogroup of 383 healthy volunteers was determined using next-generation mtDNA sequencing (Illumina MiSeq). Subsequently, 30 of these volunteers from mitochondrial haplogroups H, J, T and U were recalled to donate fresh, whole blood from which platelets were isolated. Platelet mitochondrial function was tested at basal state and upon treatment with compounds associated with both mitochondrial dysfunction and adverse drug reactions, flutamide, 2-hydroxyflutamide and tolcapone (10–250 μM) using extracellular flux analysis. This study has demonstrated that freshly-isolated platelets are a practical, primary cell model, which is amenable to the study of drug-induced mitochondrial dysfunction. Specifically, platelets from donors of haplogroup J have been found to have increased susceptibility to the inhibition of complex I-driven respiration by 2-hydroxyflutamide. At a time when individual susceptibility to adverse drug reactions is not fully understood, this study provides evidence that inter-individual variation in mitochondrial genotype could be a factor in determining sensitivity to mitochondrial toxicants associated with costly adverse drug reactions.
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Affiliation(s)
- Amy L Ball
- Department of Pharmacology and Therapeutics, MRC Centre for Drug Safety Science, University of Liverpool, Liverpool, UK
| | - Katarzyna M Bloch
- The Wolfson Centre for Personalised Medicine, Department of Pharmacology and Therapeutics, University of Liverpool, Liverpool, UK
| | - Lucille Rainbow
- Centre for Genomic Research, Institute of Integrative Biology, University of Liverpool, Liverpool, UK
| | - Xuan Liu
- Centre for Genomic Research, Institute of Integrative Biology, University of Liverpool, Liverpool, UK
| | - John Kenny
- Centre for Genomic Research, Institute of Integrative Biology, University of Liverpool, Liverpool, UK
| | | | - Richard Gregory
- Centre for Genomic Research, Institute of Integrative Biology, University of Liverpool, Liverpool, UK
| | - Ana Alfirevic
- The Wolfson Centre for Personalised Medicine, Department of Pharmacology and Therapeutics, University of Liverpool, Liverpool, UK
| | - Amy E Chadwick
- Department of Pharmacology and Therapeutics, MRC Centre for Drug Safety Science, University of Liverpool, Liverpool, UK.
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2
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Maroteau C, Siddiqui MK, Veluchamy A, Carr F, White M, Cassidy AJ, Baranova EV, Rasmussen ER, Eriksson N, Bloch KM, Brown NJ, Bygum A, Hallberg P, Karawajczyk M, Magnusson PKE, Yue QY, Syvänen AC, von Buchwald C, Alfirevic A, Maitland-van der Zee AH, Wadelius M, Palmer CNA. Exome Sequencing Reveals Common and Rare Variants in F5 Associated With ACE Inhibitor and Angiotensin Receptor Blocker-Induced Angioedema. Clin Pharmacol Ther 2020; 108:1195-1202. [PMID: 32496628 PMCID: PMC10306231 DOI: 10.1002/cpt.1927] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Accepted: 05/08/2020] [Indexed: 12/14/2022]
Abstract
Angioedema occurring in the head and neck region is a rare and sometimes life-threatening adverse reaction to angiotensin-converting enzyme inhibitors (ACEIs) and angiotensin receptor blockers (ARBs). Few studies have investigated the association of common variants with this extreme reaction, but none have explored the combined influence of rare variants yet. Adjudicated cases of ACEI-induced angioedema (ACEI-AE) or ARB-induced angioedema (ARB-AE) and controls were recruited at five different centers. Sequencing of 1,066 samples (408 ACEI-AE, ARB-AE, and 658 controls) was performed using exome-enriched sequence data. A common variant of the F5 gene that causes an increase in blood clotting (rs6025, p.Arg506Gln, also called factor V Leiden), was significantly associated with both ACEI-AE and ARB-AE (odds ratio: 2.85, 95% confidence interval (CI), 1.89-4.25). A burden test analysis of five rare missense variants in F5 was also found to be associated with ACEI-AE or ARB-AE, P = 2.09 × 10-3 . A combined gene risk score of these variants, and the common variants rs6025 and rs6020, showed that individuals carrying at least one variant had 2.21 (95% CI, 1.49-3.27, P = 6.30 × 10-9 ) times the odds of having ACEI-AE or ARB-AE. The increased risk due to the common Leiden allele was confirmed in a genome-wide association study from the United States. A high risk of angioedema was also observed for the rs6020 variant that is the main coagulation defect-causing variant in black African and Asian populations. We found that deleterious missense variants in F5 are associated with an increased risk of ACEI-AE or ARB-AE.
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Affiliation(s)
- Cyrielle Maroteau
- Division of Population Health and Genomics, Ninewells Hospital and Medical School, University of Dundee, Dundee, UK
| | - Moneeza Kalhan Siddiqui
- Division of Population Health and Genomics, Ninewells Hospital and Medical School, University of Dundee, Dundee, UK
| | - Abirami Veluchamy
- Division of Population Health and Genomics, Ninewells Hospital and Medical School, University of Dundee, Dundee, UK
| | - Fiona Carr
- Division of Population Health and Genomics, Ninewells Hospital and Medical School, University of Dundee, Dundee, UK
| | - Myra White
- Division of Population Health and Genomics, Ninewells Hospital and Medical School, University of Dundee, Dundee, UK
| | - Andrew J. Cassidy
- Tayside Centre for Genomic Analysis, School of Medicine, University of Dundee, Dundee, UK
| | - Ekaterina V. Baranova
- Division of Pharmacoepidemiology and Clinical Pharmacology, Utrecht University, Utrecht, The Netherlands
| | - Eva R. Rasmussen
- Department of Otorhinolaryngology, Head & Neck Surgery and Audiology, Rigshospitalet, University of Copenhagen, Denmark
- OPEN Patient data Explorative Network, Odense University Hospital, Odense, Denmark
| | - Niclas Eriksson
- Department of Medical Sciences, Clinical Pharmacology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
- Uppsala Clinical Research Centre, Uppsala, Sweden
| | - Katarzyna M. Bloch
- Department of Molecular and Clinical Pharmacology, University of Liverpool, Liverpool, UK
| | - Nancy J. Brown
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Anette Bygum
- OPEN Patient data Explorative Network, Odense University Hospital, Odense, Denmark
| | - Par Hallberg
- Department of Medical Sciences, Clinical Pharmacology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | | | - Patrik K. E. Magnusson
- Swedish Twin Registry, Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Qun-Ying Yue
- Uppsala Monitoring Centre, WHO Collaborating Centre, Uppsala, Sweden
| | - Ann-Christine Syvänen
- Department of Medical Sciences, Molecular Medicine and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Christian von Buchwald
- Department of Otorhinolaryngology, Head & Neck Surgery and Audiology, Rigshospitalet, University of Copenhagen, Denmark
| | - Ana Alfirevic
- Department of Molecular and Clinical Pharmacology, University of Liverpool, Liverpool, UK
| | - Anke H. Maitland-van der Zee
- Division of Pharmacoepidemiology and Clinical Pharmacology, Utrecht University, Utrecht, The Netherlands
- Department of Respiratory Medicine, Amsterdam University Medical Centre, location AMC, University of Amsterdam, The Netherlands
| | - Mia Wadelius
- Department of Medical Sciences, Clinical Pharmacology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Colin N. A. Palmer
- Division of Population Health and Genomics, Ninewells Hospital and Medical School, University of Dundee, Dundee, UK
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3
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Yaqoob N, Bloch KM, Evans AR, Lock EA. The effect of trichloroethylene metabolites on the hepatic vitamin B12-dependent methionine salvage pathway and its relevance to increased excretion of formic acid in the rat. Toxicol Res (Camb) 2020; 9:117-126. [DOI: 10.1093/toxres/tfaa006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Revised: 12/31/2019] [Accepted: 02/25/2020] [Indexed: 11/13/2022] Open
Abstract
Abstract
The industrial solvent trichloroethylene (TCE) and its two major metabolites trichloroethanol (TCE-OH) and trichloroacetic acid (TCA) cause formic aciduria in male F344 rats. Prior treatment of male F344 rats with 1-aminobenzotriazole a cytochrome P450 inhibitor, followed by TCE (16mk/kg, po), completely prevented formic aciduria, but had no effect on formic acid excretion produced by TCA (8 or 16 mg/kg, po), suggesting TCA may be the proximate metabolite producing this response. Dow and Green reported an increase in the concentration of 5-methyltetrahydrofolate (5-MTHF) in the plasma of rats treated with TCE-OH, suggesting a block in the cycling of 5-MTHF to tetrahydrofolate (THF). This pathway is under the control of the vitamin B12-dependent methionine salvage pathway. We therefore treated rats with three daily doses of methylcobalamin (CH3Cbl) or hydroxocobalamin (OHCbl), a cofactor for methionine synthase, or L-methionine, followed by TCE (16 mg/kg) to determine if they could alleviate the formic aciduria. These pretreatments only partially reduced the excretion of formic acid in the urine. Although prior treatment with S-adenosyl-L-methionine had no effect on formic acid excretion. Consistent with these findings, the activity of methionine synthase in the liver of TCE-treated rats was not inhibited. Transcriptomic analysis of the liver-identified nine differential expressed genes, of note, was downregulation of Lmbrd1 involved in the conversion of vitamin B12 into CH3Cbl, a cofactor for methionine synthase. Our findings indicate that the formic aciduria produced by TCE-OH and TCA may be the result of a block in the recycling of 5-MTHF to THF, the effect on the methionine salvage pathway being a secondary response following acute exposure.
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Affiliation(s)
- Noreen Yaqoob
- School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, Byrom Street, Liverpool, L3 3AF, UK
| | - Katarzyna M Bloch
- School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, Byrom Street, Liverpool, L3 3AF, UK
| | - Andrew R Evans
- School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, Byrom Street, Liverpool, L3 3AF, UK
| | - Edward A Lock
- School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, Byrom Street, Liverpool, L3 3AF, UK
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4
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Floyd JS, Bloch KM, Brody JA, Maroteau C, Siddiqui MK, Gregory R, Carr DF, Molokhia M, Liu X, Bis JC, Ahmed A, Liu X, Hallberg P, Yue QY, Magnusson PKE, Brisson D, Wiggins KL, Morrison AC, Khoury E, McKeigue P, Stricker BH, Lapeyre-Mestre M, Heckbert SR, Gallagher AM, Chinoy H, Gibbs RA, Bondon-Guitton E, Tracy R, Boerwinkle E, Gaudet D, Conforti A, van Staa T, Sitlani CM, Rice KM, Maitland-van der Zee AH, Wadelius M, Morris AP, Pirmohamed M, Palmer CAN, Psaty BM, Alfirevic A. Pharmacogenomics of statin-related myopathy: Meta-analysis of rare variants from whole-exome sequencing. PLoS One 2019; 14:e0218115. [PMID: 31242253 PMCID: PMC6594672 DOI: 10.1371/journal.pone.0218115] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Accepted: 05/25/2019] [Indexed: 11/25/2022] Open
Abstract
AIMS Statin-related myopathy (SRM), which includes rhabdomyolysis, is an uncommon but important adverse drug reaction because the number of people prescribed statins world-wide is large. Previous association studies of common genetic variants have had limited success in identifying a genetic basis for this adverse drug reaction. We conducted a multi-site whole-exome sequencing study to investigate whether rare coding variants confer an increased risk of SRM. METHODS AND RESULTS SRM 3-5 cases (N = 505) and statin treatment-tolerant controls (N = 2047) were recruited from multiple sites in North America and Europe. SRM 3-5 was defined as symptoms consistent with muscle injury and an elevated creatine phosphokinase level >4 times upper limit of normal without another likely cause of muscle injury. Whole-exome sequencing and variant calling was coordinated from two analysis centres, and results of single-variant and gene-based burden tests were meta-analysed. No genome-wide significant associations were identified. Given the large number of cases, we had 80% power to identify a variant with minor allele frequency of 0.01 that increases the risk of SRM 6-fold at genome-wide significance. CONCLUSIONS In this large whole-exome sequencing study of severe statin-related muscle injury conducted to date, we did not find evidence that rare coding variants are responsible for this adverse drug reaction. Larger sample sizes would be required to identify rare variants with small effects, but it is unclear whether such findings would be clinically actionable.
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Affiliation(s)
- James S. Floyd
- Department of Medicine, University of Washington, Seattle, Washington, United States of America
| | - Katarzyna M. Bloch
- MRC Centre for Drug Safety Science, Department of Molecular and Clinical Pharmacology, University of Liverpool, Liverpool, United Kingdom
| | - Jennifer A. Brody
- Department of Medicine, University of Washington, Seattle, Washington, United States of America
| | - Cyrielle Maroteau
- Division of Molecular and Clinical Medicine, University of Dundee, Dundee, United Kingdom
| | - Moneeza K. Siddiqui
- Division of Molecular and Clinical Medicine, University of Dundee, Dundee, United Kingdom
| | - Richard Gregory
- Functional and Comparative Genomics, Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Daniel F. Carr
- Department of Medicine, University of Washington, Seattle, Washington, United States of America
| | - Mariam Molokhia
- School of Population Health and Environmental Sciences, London, United Kingdom
| | - Xiaoming Liu
- Human Genetics Center, University of Texas Health Science Center, Houston, United States of America
| | - Joshua C. Bis
- Department of Medicine, University of Washington, Seattle, Washington, United States of America
| | - Ammar Ahmed
- Medical School, University of Liverpool, Liverpool, United Kingdom
| | - Xuan Liu
- Functional and Comparative Genomics, Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Pär Hallberg
- Department of Medical Sciences, Clinical Pharmacology and Science for Life Laboratory, Uppsala University, Uppsala University Hospital, Uppsala, Sweden
| | | | - Patrik K. E. Magnusson
- Swedish Twin Registry, Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Diane Brisson
- Clinical Lipidology and Rare Lipid Disorders Unit, Department of Medicine, Université de Montréal Community Gene Medicine Center, Lipid Clinic Chicoutimi Hospital and ECOGENE-21 Clinical and Translational Research Center, Chicoutimi, Quebec, Canada
| | - Kerri L. Wiggins
- Department of Medicine, University of Washington, Seattle, Washington, United States of America
| | - Alanna C. Morrison
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, Texas, United States of America
| | - Etienne Khoury
- Clinical Lipidology and Rare Lipid Disorders Unit, Department of Medicine, Université de Montréal Community Gene Medicine Center, Lipid Clinic Chicoutimi Hospital and ECOGENE-21 Clinical and Translational Research Center, Chicoutimi, Quebec, Canada
| | - Paul McKeigue
- Usher Institute of Population Health Sciences and Informatics, University of Edinburgh Medical School, Edinburgh, Scotland, United Kingdom
| | - Bruno H. Stricker
- Department of Epidemiology, Erasmus Medical Centre, Rotterdam, the Netherlands
| | - Maryse Lapeyre-Mestre
- Paul Sabatier University - Toulouse III, UPS Toulouse, Laboratoire de Pharmacologie Medicale et Clinique, Toulouse, France
| | - Susan R. Heckbert
- Department of Epidemiology, University of Washington, Seattle, Washington, United States of America
| | - Arlene M. Gallagher
- Clinical Practice Research Datalink (CPRD) Medicines and Healthcare Products Regulatory Agency, London, United Kingdom
| | - Hector Chinoy
- Rheumatology Department, Salford Royal NHS Foundation Trust, Manchester Academic Health Science Centre, Salford, United Kingdom
| | - Richard A. Gibbs
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, United States of America
| | - Emmanuelle Bondon-Guitton
- Centre Hospitalier Universitaire de Toulouse, CHU Toulouse, Centre de Pharmacovigilance, Toulouse, France
| | - Russell Tracy
- Departments of Pathology & Laboratory Medicine and Biochemistry, Larner College of Medicine, University of Vermont, Burlington, Vermont, United States of America
| | - Eric Boerwinkle
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, Texas, United States of America
| | - Daniel Gaudet
- Clinical Lipidology and Rare Lipid Disorders Unit, Department of Medicine, Université de Montréal Community Gene Medicine Center, Lipid Clinic Chicoutimi Hospital and ECOGENE-21 Clinical and Translational Research Center, Chicoutimi, Quebec, Canada
| | - Anita Conforti
- U.O. Farmacologia, Policlinico "Gb Rossi", Verona, Italy
| | - Tjeerd van Staa
- Division of Informatics, Imaging & Data Sciences, University of Manchester, Manchester, United Kingdom
| | - Colleen M. Sitlani
- Department of Medicine, University of Washington, Seattle, Washington, United States of America
| | - Kenneth M. Rice
- Department of Biostatistics, University of Washington, Seattle, Washington, United States of America
| | | | - Mia Wadelius
- Medical School, University of Liverpool, Liverpool, United Kingdom
| | - Andrew P. Morris
- Department of Biostatistics, University of Liverpool, Liverpool, United Kingdom
| | - Munir Pirmohamed
- MRC Centre for Drug Safety Science, Department of Molecular and Clinical Pharmacology, University of Liverpool, Liverpool, United Kingdom
| | - Colin A. N. Palmer
- Division of Molecular and Clinical Medicine, University of Dundee, Dundee, United Kingdom
| | - Bruce M. Psaty
- Department of Medicine, University of Washington, Seattle, Washington, United States of America
| | - Ana Alfirevic
- MRC Centre for Drug Safety Science, Department of Molecular and Clinical Pharmacology, University of Liverpool, Liverpool, United Kingdom
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5
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Hawcutt DB, Francis B, Carr DF, Jorgensen AL, Yin P, Wallin N, O'Hara N, Zhang EJ, Bloch KM, Ganguli A, Thompson B, McEvoy L, Peak M, Crawford AA, Walker BR, Blair JC, Couriel J, Smyth RL, Pirmohamed M. Susceptibility to corticosteroid-induced adrenal suppression: a genome-wide association study. Lancet Respir Med 2018; 6:442-450. [PMID: 29551627 PMCID: PMC5971210 DOI: 10.1016/s2213-2600(18)30058-4] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Revised: 01/24/2018] [Accepted: 01/25/2018] [Indexed: 12/21/2022]
Abstract
BACKGROUND A serious adverse effect of corticosteroid therapy is adrenal suppression. Our aim was to identify genetic variants affecting susceptibility to corticosteroid-induced adrenal suppression. METHODS We enrolled children with asthma who used inhaled corticosteroids as part of their treatment from 25 sites across the UK (discovery cohort), as part of the Pharmacogenetics of Adrenal Suppression with Inhaled Steroids (PASS) study. We included two validation cohorts, one comprising children with asthma (PASS study) and the other consisting of adults with chronic obstructive pulmonary disorder (COPD) who were recruited from two UK centres for the Pharmacogenomics of Adrenal Suppression in COPD (PASIC) study. Participants underwent a low-dose short synacthen test. Adrenal suppression was defined as peak cortisol less than 350 nmol/L (in children) and less than 500 nmol/L (in adults). A case-control genome-wide association study was done with the control subset augmented by Wellcome Trust Case Control Consortium 2 (WTCCC2) participants. Single nucleotide polymorphisms (SNPs) that fulfilled criteria to be advanced to replication were tested by a random-effects inverse variance meta-analysis. This report presents the primary analysis. The PASS study is registered in the European Genome-phenome Archive (EGA). The PASS study is complete whereas the PASIC study is ongoing. FINDINGS Between November, 2008, and September, 2011, 499 children were enrolled to the discovery cohort. Between October, 2011, and December, 2012, 81 children were enrolled to the paediatric validation cohort, and from February, 2010, to June, 2015, 78 adults were enrolled to the adult validation cohort. Adrenal suppression was present in 35 (7%) children in the discovery cohort and six (7%) children and 17 (22%) adults in the validation cohorts. In the discovery cohort, 40 SNPs were found to be associated with adrenal suppression (genome-wide significance p<1 × 10-6), including an intronic SNP within the PDGFD gene locus (rs591118; odds ratio [OR] 7·32, 95% CI 3·15-16·99; p=5·8 × 10-8). This finding for rs591118 was validated successfully in both the paediatric asthma (OR 3·86, 95% CI 1·19-12·50; p=0·02) and adult COPD (2·41, 1·10-5·28; p=0·03) cohorts. The proportions of patients with adrenal suppression by rs591118 genotype were six (3%) of 214 patients with the GG genotype, 15 (6%) of 244 with the AG genotype, and 22 (25%) of 87 with the AA genotype. Meta-analysis of the paediatric cohorts (discovery and validation) and all three cohorts showed genome-wide significance of rs591118 (respectively, OR 5·89, 95% CI 2·97-11·68; p=4·3 × 10-9; and 4·05, 2·00-8·21; p=3·5 × 10-10). INTERPRETATION Our findings suggest that genetic variation in the PDGFD gene locus increases the risk of adrenal suppression in children and adults who use corticosteroids to treat asthma and COPD, respectively. FUNDING Department of Health Chair in Pharmacogenetics.
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Affiliation(s)
- Daniel B Hawcutt
- Department of Women's and Children's Health, University of Liverpool, Liverpool, UK; Wolfson Centre for Personalised Medicine, Medical Research Council (MRC) Centre for Drug Safety Science, Department of Molecular and Clinical Pharmacology, University of Liverpool, Liverpool, UK
| | - Ben Francis
- Department of Biostatistics, University of Liverpool, Liverpool, UK
| | - Daniel F Carr
- Wolfson Centre for Personalised Medicine, Medical Research Council (MRC) Centre for Drug Safety Science, Department of Molecular and Clinical Pharmacology, University of Liverpool, Liverpool, UK
| | | | - Peng Yin
- Department of Biostatistics, University of Liverpool, Liverpool, UK
| | - Naomi Wallin
- Department of Women's and Children's Health, University of Liverpool, Liverpool, UK
| | - Natalie O'Hara
- Wolfson Centre for Personalised Medicine, Medical Research Council (MRC) Centre for Drug Safety Science, Department of Molecular and Clinical Pharmacology, University of Liverpool, Liverpool, UK
| | - Eunice J Zhang
- Wolfson Centre for Personalised Medicine, Medical Research Council (MRC) Centre for Drug Safety Science, Department of Molecular and Clinical Pharmacology, University of Liverpool, Liverpool, UK
| | - Katarzyna M Bloch
- Wolfson Centre for Personalised Medicine, Medical Research Council (MRC) Centre for Drug Safety Science, Department of Molecular and Clinical Pharmacology, University of Liverpool, Liverpool, UK
| | - Amitava Ganguli
- Wolfson Centre for Personalised Medicine, Medical Research Council (MRC) Centre for Drug Safety Science, Department of Molecular and Clinical Pharmacology, University of Liverpool, Liverpool, UK
| | - Ben Thompson
- Wolfson Centre for Personalised Medicine, Medical Research Council (MRC) Centre for Drug Safety Science, Department of Molecular and Clinical Pharmacology, University of Liverpool, Liverpool, UK
| | - Laurence McEvoy
- Wolfson Centre for Personalised Medicine, Medical Research Council (MRC) Centre for Drug Safety Science, Department of Molecular and Clinical Pharmacology, University of Liverpool, Liverpool, UK
| | - Matthew Peak
- National Institute for Health Research (NIHR) Alder Hey Clinical Research Facility, Alder Hey Children's Hospital, Liverpool, UK
| | - Andrew A Crawford
- British Heart Foundation (BHF) Centre for Cardiovascular Science, University of Edinburgh, Edinburgh, UK; MRC Integrated Epidemiology Unit at the University of Bristol, Bristol, UK
| | - Brian R Walker
- British Heart Foundation (BHF) Centre for Cardiovascular Science, University of Edinburgh, Edinburgh, UK; Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, UK
| | - Joanne C Blair
- Department of Endocrinology, Alder Hey Children's Hospital, Liverpool, UK
| | - Jonathan Couriel
- Department of Respiratory Medicine, Alder Hey Children's Hospital, Liverpool, UK
| | - Rosalind L Smyth
- Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Munir Pirmohamed
- Wolfson Centre for Personalised Medicine, Medical Research Council (MRC) Centre for Drug Safety Science, Department of Molecular and Clinical Pharmacology, University of Liverpool, Liverpool, UK.
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6
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Herwig R, Gmuender H, Corvi R, Bloch KM, Brandenburg A, Castell J, Ceelen L, Chesne C, Doktorova TY, Jennen D, Jennings P, Limonciel A, Lock EA, McMorrow T, Phrakonkham P, Radford R, Slattery C, Stierum R, Vilardell M, Wittenberger T, Yildirimman R, Ryan M, Rogiers V, Kleinjans J. Inter-laboratory study of human in vitro toxicogenomics-based tests as alternative methods for evaluating chemical carcinogenicity: a bioinformatics perspective. Arch Toxicol 2015; 90:2215-2229. [PMID: 26525393 DOI: 10.1007/s00204-015-1617-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Accepted: 10/19/2015] [Indexed: 01/29/2023]
Abstract
The assessment of the carcinogenic potential of chemicals with alternative, human-based in vitro systems has become a major goal of toxicogenomics. The central read-out of these assays is the transcriptome, and while many studies exist that explored the gene expression responses of such systems, reports on robustness and reproducibility, when testing them independently in different laboratories, are still uncommon. Furthermore, there is limited knowledge about variability induced by the data analysis protocols. We have conducted an inter-laboratory study for testing chemical carcinogenicity evaluating two human in vitro assays: hepatoma-derived cells and hTERT-immortalized renal proximal tubule epithelial cells, representing liver and kidney as major target organs. Cellular systems were initially challenged with thirty compounds, genome-wide gene expression was measured with microarrays, and hazard classifiers were built from this training set. Subsequently, each system was independently established in three different laboratories, and gene expression measurements were conducted using anonymized compounds. Data analysis was performed independently by two separate groups applying different protocols for the assessment of inter-laboratory reproducibility and for the prediction of carcinogenic hazard. As a result, both workflows came to very similar conclusions with respect to (1) identification of experimental outliers, (2) overall assessment of robustness and inter-laboratory reproducibility and (3) re-classification of the unknown compounds to the respective toxicity classes. In summary, the developed bioinformatics workflows deliver accurate measures for inter-laboratory comparison studies, and the study can be used as guidance for validation of future carcinogenicity assays in order to implement testing of human in vitro alternatives to animal testing.
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Affiliation(s)
- R Herwig
- Department Computational Molecular Biology, Max-Planck-Institute for Molecular Genetics, Ihnestr. 73, 14195, Berlin, Germany.
| | - H Gmuender
- Genedata AG, Margarethenstrasse 38, 4053, Basel, Switzerland
| | - R Corvi
- European Union Reference Laboratory for Alternatives to Animal Testing (EURL ECVAM), Institute for Health and Consumer Protection (IHCP), European Commission Joint Research Centre, TP 126, Via E. Fermi 2749, 21027, Ispra, Italy
| | - K M Bloch
- School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, Byrom Street, Liverpool, L3 3AF, UK
| | - A Brandenburg
- Genedata AG, Margarethenstrasse 38, 4053, Basel, Switzerland
| | - J Castell
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Valencia, Av. Blasco Ibanez 15, 46010, Valencia, Spain
| | - L Ceelen
- Department of In Vitro Toxicology and Dermato-Cosmetology, Vrije Universiteit Brussel, Laarbeeklaan 103, 1090, Brussels, Belgium
| | - C Chesne
- Biopredic International, Parc d'affaires de la Bretèche, Bldg. A4, 35760, St Gregoire, France
| | - T Y Doktorova
- Department of In Vitro Toxicology and Dermato-Cosmetology, Vrije Universiteit Brussel, Laarbeeklaan 103, 1090, Brussels, Belgium
| | - D Jennen
- Department of Toxicogenomics, Maastricht University, Maastricht, The Netherlands
| | - P Jennings
- Division of Physiology, Department of Physiology and Medical Physics, Medical University of Innsbruck, Innsbruck, Austria
| | - A Limonciel
- Division of Physiology, Department of Physiology and Medical Physics, Medical University of Innsbruck, Innsbruck, Austria
| | - E A Lock
- School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, Byrom Street, Liverpool, L3 3AF, UK
| | - T McMorrow
- Conway Institute, School of Biomolecular and Biomedical Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - P Phrakonkham
- European Union Reference Laboratory for Alternatives to Animal Testing (EURL ECVAM), Institute for Health and Consumer Protection (IHCP), European Commission Joint Research Centre, TP 126, Via E. Fermi 2749, 21027, Ispra, Italy
| | - R Radford
- Conway Institute, School of Biomolecular and Biomedical Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - C Slattery
- Conway Institute, School of Biomolecular and Biomedical Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - R Stierum
- Department of Risk Analysis for Products in Development, Netherlands Organisation for Applied Scientific Research (TNO), Utrechtseweg 48, 3704 HE, Zeist, The Netherlands
| | - M Vilardell
- Department Computational Molecular Biology, Max-Planck-Institute for Molecular Genetics, Ihnestr. 73, 14195, Berlin, Germany
| | - T Wittenberger
- Genedata AG, Margarethenstrasse 38, 4053, Basel, Switzerland
| | - R Yildirimman
- Department Computational Molecular Biology, Max-Planck-Institute for Molecular Genetics, Ihnestr. 73, 14195, Berlin, Germany
| | - M Ryan
- Conway Institute, School of Biomolecular and Biomedical Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - V Rogiers
- Department of In Vitro Toxicology and Dermato-Cosmetology, Vrije Universiteit Brussel, Laarbeeklaan 103, 1090, Brussels, Belgium
| | - J Kleinjans
- Department of Toxicogenomics, Maastricht University, Maastricht, The Netherlands
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7
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Bloch KM, Evans A, Lock EA. Aristolochic acids - Induced transcriptomic responses in rat renal proximal tubule cells in vitro. Genom Data 2015; 5:254-6. [PMID: 26484264 PMCID: PMC4584013 DOI: 10.1016/j.gdata.2015.05.028] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/13/2015] [Accepted: 05/23/2015] [Indexed: 12/04/2022]
Abstract
Aristolochic acids (AAs) are the active components of herbal drugs derived from Aristolochia species that have been used for medicinal purposes since antiquity. However, AAs have recently been discovered to be highly nephrotoxic and induced urothelial cancer in humans and malignant tumors in the kidney and urinary tract of rodents. In this study, we exposed rat renal proximal tubule cells in vitro to a sub-cytotoxic level of AAs at three different time points (6 h, 24 h and 72 h). We then analyzed the gene expression profile after the compound exposure. Functional analysis with Ingenuity Pathways Analysis and DAVID tools revealed that at the late time point (72 h) there are many significantly altered genes involved in cancer-related pathways such as p53 signaling. MIAMI-compliant microarray data are deposited in the NCBI GEO database under accession number GSE68687 and can be found at: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE68687.
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8
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Bloch KM, Yaqoob N, Sharma S, Evans A, Aschauer L, Radford R, Jennings P, Ryan MP, van Delft JHM, Lock EA. Transcriptomic alterations induced by Monuron in rat and human renal proximal tubule cells in vitro and comparison to rat renal-cortex in vivo. Toxicol Res (Camb) 2015. [DOI: 10.1039/c4tx00113c] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Monuron (1,1-dimethyl-3-(4-chlorophenyl)urea) is a widely used herbicide in developing countries although concerns have been raised about its toxicity and carcinogenicity.
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Affiliation(s)
- Katarzyna M. Bloch
- School of Pharmacy and Biomolecular Sciences
- Liverpool John Moores University
- Liverpool
- UK
| | - Noreen Yaqoob
- School of Pharmacy and Biomolecular Sciences
- Liverpool John Moores University
- Liverpool
- UK
| | - Sikander Sharma
- School of Pharmacy and Biomolecular Sciences
- Liverpool John Moores University
- Liverpool
- UK
| | - Andrew Evans
- School of Pharmacy and Biomolecular Sciences
- Liverpool John Moores University
- Liverpool
- UK
| | - Lydia Aschauer
- Division of Physiology
- Department of Physiology and Medical Physics
- Innsbruck Medical University
- Innsbruck
- Austria
| | - Robert Radford
- Renal Disease Research Group
- School of Biomolecular and Biomedical Science
- UCD Conway Institute
- University College Dublin
- Ireland
| | - Paul Jennings
- Division of Physiology
- Department of Physiology and Medical Physics
- Innsbruck Medical University
- Innsbruck
- Austria
| | - Michael P. Ryan
- Renal Disease Research Group
- School of Biomolecular and Biomedical Science
- UCD Conway Institute
- University College Dublin
- Ireland
| | - Joost H. M. van Delft
- Department of Health Risk Analyses and Toxicology
- Faculty of Health
- Medicine and Life Sciences
- Maastricht University
- Maastricht
| | - Edward A. Lock
- School of Pharmacy and Biomolecular Sciences
- Liverpool John Moores University
- Liverpool
- UK
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9
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Alfirevic A, Neely D, Armitage J, Chinoy H, Cooper RG, Laaksonen R, Carr DF, Bloch KM, Fahy J, Hanson A, Yue QY, Wadelius M, Maitland-van Der Zee AH, Voora D, Psaty BM, Palmer CNA, Pirmohamed M. Phenotype standardization for statin-induced myotoxicity. Clin Pharmacol Ther 2014; 96:470-6. [PMID: 24897241 PMCID: PMC4172546 DOI: 10.1038/clpt.2014.121] [Citation(s) in RCA: 137] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2014] [Accepted: 05/27/2014] [Indexed: 11/12/2022]
Abstract
Statins are widely used lipid-lowering drugs that are effective in reducing cardiovascular disease risk. Although they are generally well tolerated, they can cause muscle toxicity, which can lead to severe rhabdomyolysis. Research in this area has been hampered to some extent by the lack of standardized nomenclature and phenotypic definitions. We have used numerical and descriptive classifications and developed an algorithm to define statin-related myotoxicity phenotypes, including myalgia, myopathy, rhabdomyolysis, and necrotizing autoimmune myopathy.
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Affiliation(s)
- A Alfirevic
- Department of Molecular and Clinical Pharmacology, TheWolfson Centre for Personalised Medicine, Institute of Translational Medicine, University of Liverpool, Liverpool, UK
| | - D Neely
- Department of Clinical Biochemistry, Newcastle upon Tyne Hospitals NHS Foundation Trust, Royal Victoria Infirmary, Newcastle upon Tyne, UK
| | | | - H Chinoy
- Centre for Musculoskeletal Research/NIHR Manchester Musculoskeletal Biomedical Research Unit, University of Manchester, Manchester, UK
| | - R G Cooper
- MRC/ARUK Institute of Ageing and Chronic Disease, Faculty of Health & Life Sciences, University of Liverpool, Liverpool, UK
| | - R Laaksonen
- Zora Biosciences Ltd, Tieotie 2, Espoo, Finland
| | - D F Carr
- Department of Molecular and Clinical Pharmacology, TheWolfson Centre for Personalised Medicine, Institute of Translational Medicine, University of Liverpool, Liverpool, UK
| | - K M Bloch
- Department of Molecular and Clinical Pharmacology, TheWolfson Centre for Personalised Medicine, Institute of Translational Medicine, University of Liverpool, Liverpool, UK
| | - J Fahy
- Department of Molecular and Clinical Pharmacology, TheWolfson Centre for Personalised Medicine, Institute of Translational Medicine, University of Liverpool, Liverpool, UK
| | - A Hanson
- Department of Molecular and Clinical Pharmacology, TheWolfson Centre for Personalised Medicine, Institute of Translational Medicine, University of Liverpool, Liverpool, UK
| | - Q-Y Yue
- The Medical Products Agency, Uppsala, Sweden
| | - M Wadelius
- Department of Medical Sciences, Clinical Pharmacology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - A H Maitland-van Der Zee
- Division of Pharmacoepidemiology and Clinical Pharmacology, Utrecht University, Faculty of Science, Utrecht Institute for Pharmaceutical Sciences, Utrecht, The Netherlands
| | - D Voora
- Duke Institute for Genome Sciences and Policy, Durham, North Carolina, USA
| | - B M Psaty
- Cardiovascular Health Research Unit, Departments of Medicine, Epidemiology and Health Services, University of Washington, Seattle, Washington, USA
- Group Health Research Institute, Group Health Cooperative, Seattle, Washington, USA
| | - C N A Palmer
- Medical Research Institute, Ninewells Hospital and Medical School, Dundee, UK
| | - M Pirmohamed
- Department of Molecular and Clinical Pharmacology, TheWolfson Centre for Personalised Medicine, Institute of Translational Medicine, University of Liverpool, Liverpool, UK
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10
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Abstract
Antiepileptic drugs can induce potentially life-threatening hypersensitivity reactions such as Stevens–Johnson syndrome at a frequency of one in 10,000 to one in 1000 treated patients. There is a considerable cross-reactivity among different antiepileptic drugs but the mechanisms are not known. In this review we have summarized current evidence on antiepileptic drug-induced hypersensitivity reactions and performed meta-analyses of published case–control studies that investigated associations between HLA alleles and several antiepileptic drugs in diverse populations. As the heterogeneity between studies was high, we conducted subsequent subgroup analyses and showed that HLA-B*15:02 was associated with carbamazepine, lamotrigine and phenytoin-induced Stevens–Johnson syndrome in Asian populations indicating that pretreatment testing may prevent cross-reactivity. Additionally, we explored the potential of new, high-throughput technologies that may help to understand the mechanisms and predict the risk of adverse drug reactions in the future.
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Affiliation(s)
- Katarzyna M Bloch
- The Wolfson Centre for Personalised Medicine, Department of Molecular & Clinical Pharmacology, University of Liverpool, Block A: Waterhouse Buildings, 1–5 Brownlow Street, Liverpool, L69 3GL, UK
| | - Graeme J Sills
- The Wolfson Centre for Personalised Medicine, Department of Molecular & Clinical Pharmacology, University of Liverpool, Block A: Waterhouse Buildings, 1–5 Brownlow Street, Liverpool, L69 3GL, UK
| | - Munir Pirmohamed
- The Wolfson Centre for Personalised Medicine, Department of Molecular & Clinical Pharmacology, University of Liverpool, Block A: Waterhouse Buildings, 1–5 Brownlow Street, Liverpool, L69 3GL, UK
| | - Ana Alfirevic
- The Wolfson Centre for Personalised Medicine, Department of Molecular & Clinical Pharmacology, University of Liverpool, Block A: Waterhouse Buildings, 1–5 Brownlow Street, Liverpool, L69 3GL, UK
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11
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Limonciel A, Wilmes A, Aschauer L, Radford R, Bloch KM, McMorrow T, Pfaller W, van Delft JH, Slattery C, Ryan MP, Lock EA, Jennings P. Oxidative stress induced by potassium bromate exposure results in altered tight junction protein expression in renal proximal tubule cells. Arch Toxicol 2012; 86:1741-51. [DOI: 10.1007/s00204-012-0897-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2012] [Accepted: 06/18/2012] [Indexed: 12/11/2022]
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12
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Bloch KM, Yaqoob N, Evans A, Radford R, Jennings P, Boei JJWA, McMorrow T, Slattery C, Ryan MP, Gmuender H, van Delft JHM, Lock EA. Detection of genotoxic and non-genotoxic renal carcinogens in vitro in NRK-52E cells using a transcriptomics approach. Toxicol Res (Camb) 2012. [DOI: 10.1039/c2tx20023f] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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13
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Jennings P, Weiland C, Limonciel A, Bloch KM, Radford R, Aschauer L, McMorrow T, Wilmes A, Pfaller W, Ahr HJ, Slattery C, Lock EA, Ryan MP, Ellinger-Ziegelbauer H. Transcriptomic alterations induced by Ochratoxin A in rat and human renal proximal tubular in vitro models and comparison to a rat in vivo model. Arch Toxicol 2011; 86:571-89. [DOI: 10.1007/s00204-011-0780-4] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2011] [Accepted: 11/07/2011] [Indexed: 12/15/2022]
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