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Takeji S, Okada M, Hayashi S, Kanamaru K, Uno Y, Imaishi H, Uno T. Metabolism of testosterone and progesterone by cytochrome P450 2C19 allelic variants. Biopharm Drug Dispos 2023; 44:420-430. [PMID: 37815926 DOI: 10.1002/bdd.2378] [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: 04/29/2023] [Revised: 08/29/2023] [Accepted: 09/19/2023] [Indexed: 10/12/2023]
Abstract
CYP2C19 is a member of the human microsomal cytochrome P450 (CYP). Significant variation in CYP2C19 levels and activity can be attributed to polymorphisms in this gene. Wildtype CYP2C19 and 13 mutants (CYP2C19.1B, CYP2C19.5A, CYP2C19.5B, CYP2C19.6, CYP2C19.8, CYP2C19.9, CYP2C19.10, CYP2C19.11, CYP2C19.13, CYP2C19.16, CYP2C19.19, CYP2C19.23, CYP2C19.30, and CYP2C19.33) were coexpressed with NADPH-cytochrome P450 reductase in Escherichia coli. Hydroxylase activity toward testosterone and progesterone was also examined. Ten CYP2C19 variants showed Soret peaks (450 nm) typical of P450 in the reduced CO-difference spectra. CYP2C19.11 and CYP2C19.23 showed higher testosterone 11α, 16α-/17- and progesterone 6β-,21-,16α-/17α-hydroxylase activities than CYP2C19.1B. CYP2C19.6, CYP2C19.16, CYP2C19.19, and CYP2C19.30 showed lower activity than CYP2C19.1B. CYP2C19.9, CYP2C19.10. CYP2C19.13, and CYP2C19.33 showed different hydroxylation activities than CYP2C19.1B. These results indicated that CYP2C19 variants have very different substrate specificities for testosterone and progesterone.
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Affiliation(s)
- Shiori Takeji
- Graduate School of Agricultural Science, Kobe University, Kobe, Japan
| | - Mai Okada
- Graduate School of Agricultural Science, Kobe University, Kobe, Japan
| | - Shu Hayashi
- Graduate School of Agricultural Science, Kobe University, Kobe, Japan
| | - Kengo Kanamaru
- Graduate School of Agricultural Science, Kobe University, Kobe, Japan
| | - Yuichi Uno
- Department of Plant Resource Science, Faculty of Agriculture, Kobe University, Kobe, Japan
| | - Hiromasa Imaishi
- Functional Analysis of Environmental Genes, Research Center for Environmental, Genomics, Kobe University, Kobe, Japan
| | - Tomohide Uno
- Graduate School of Agricultural Science, Kobe University, Kobe, Japan
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2
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Booyse RP, Twesigomwe D, Hazelhurst S. Characterization of CYP2C19 pharmacogenetic variation in African populations and comparison with other global populations. Pharmacogenomics 2023; 24:845-857. [PMID: 37929326 PMCID: PMC10694788 DOI: 10.2217/pgs-2023-0166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Accepted: 10/12/2023] [Indexed: 11/07/2023] Open
Abstract
Background: CYP2C19 is important in the metabolism of clopidogrel and several antidepressants. This study aimed to characterize the distribution of CYP2C19 star alleles (haplotypes) across diverse African populations compared with global populations. Methods: CYP2C19 star alleles and diplotypes were called from high coverage genomes using the StellarPGx pipeline. Results: CYP2C19*1 (51%), *2 (17%) and *17 (22%) were the most common star alleles across African populations in this study. It was observed that 3% of African participants had potentially novel CYP2C19 haplotypes. Conclusion: This study supports the necessity for CYP2C19 pharmacogenetic testing in African and global clinical settings, as well as the importance of comprehensive star allele characterization in the African context.
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Affiliation(s)
- Ross P Booyse
- Division of Human Genetics, National Health Laboratory Service, and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - David Twesigomwe
- Division of Human Genetics, National Health Laboratory Service, and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Scott Hazelhurst
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- School of Electrical & Information Engineering, University of the Witwatersrand, Johannesburg, South Africa
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3
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The efficacy of clopidogrel in preventing recurrent cardiovascular events among Arab population carrying different CYP2C19 mutations: systematic review and meta-analysis. EGYPTIAN JOURNAL OF MEDICAL HUMAN GENETICS 2022. [DOI: 10.1186/s43042-022-00313-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
The prevalence and the role of CYP2C19 gene mutations concerning recurrent Cardiovascular Events (CVEs) among patients treated with clopidogrel is still controversial especially among Arab people. Therefore, this review aimed to determine the frequency of CYP2C19 polymorphic alleles among the Arab population and to investigate the efficacy of clopidogrel as an antiplatelet drug among those carrying different variants of this gene.
Methodology
Two authors independently searched in PubMed, Google Scholar, and EMBASE databases at any year for studies related to the role of CYP2C19 gene on the prognosis of patients with CVEs treated with clopidogrel. The review included Arab people who were genotyped to determine the frequency of CYP2C19 genotypes and alleles (the qualitative part). Concerning the quantitative part (meta-analysis), only patients who previously had CVEs and using clopidogrel as secondary prophylaxis had been included. The Newcastle Ottawa Scale for non-randomizes Studies was utilized to consider the risk of bias among included studies. We analyzed the data using odds ratio at 95% confidence interval and the quality of evidence of each outcome measure was judged using GRADE approach.
Results
The current study revealed that 4% of Arabs reported in the included studies are homozygous, and 25% are heterozygous for the CYP2C19*2 allele. While 3% and 18.5% of them are homozygous and heterozygous of CYP2C19*17 alleles, respectively. A significant increased risk of recurrent CVEs by about threefold was associated with CYP2C19*2 or CYP2C19*3 allele carriers (OR = 3.32, CI = 1.94–5.67, and OR = 3.53, CI = 1.17–10.63, respectively). However, no significant increased risk among carriers of CYP2C19*17 mutation (OR = 0.80, (CI = 0.44–1.44) was documented.
Conclusion
The present study revealed that Arabs carrying CYP2C19*2 and CYP2C19*3 alleles could be at increased risk of decreasing the antiplatelet efficacy of clopidogrel and an alternative drug should be prescribed for those patients to avoid recurrent CVEs. However, few available studies were included in the quantitative part of the analysis and further studies with large sample size are recommended to confirm our results.
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Zhou Y, Lauschke VM. Population pharmacogenomics: an update on ethnogeographic differences and opportunities for precision public health. Hum Genet 2022; 141:1113-1136. [PMID: 34652573 PMCID: PMC9177500 DOI: 10.1007/s00439-021-02385-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 10/05/2021] [Indexed: 11/25/2022]
Abstract
Both safety and efficacy of medical treatment can vary depending on the ethnogeographic background of the patient. One of the reasons underlying this variability is differences in pharmacogenetic polymorphisms in genes involved in drug disposition, as well as in drug targets. Knowledge and appreciation of these differences is thus essential to optimize population-stratified care. Here, we provide an extensive updated analysis of population pharmacogenomics in ten pharmacokinetic genes (CYP2D6, CYP2C19, DPYD, TPMT, NUDT15 and SLC22A1), drug targets (CFTR) and genes involved in drug hypersensitivity (HLA-A, HLA-B) or drug-induced acute hemolytic anemia (G6PD). Combined, polymorphisms in the analyzed genes affect the pharmacology, efficacy or safety of 141 different drugs and therapeutic regimens. The data reveal pronounced differences in the genetic landscape, complexity and variant frequencies between ethnogeographic groups. Reduced function alleles of CYP2D6, SLC22A1 and CFTR were most prevalent in individuals of European descent, whereas DPYD and TPMT deficiencies were most common in Sub-Saharan Africa. Oceanian populations showed the highest frequencies of CYP2C19 loss-of-function alleles while their inferred CYP2D6 activity was among the highest worldwide. Frequencies of HLA-B*15:02 and HLA-B*58:01 were highest across Asia, which has important implications for the risk of severe cutaneous adverse reactions upon treatment with carbamazepine and allopurinol. G6PD deficiencies were most frequent in Africa, the Middle East and Southeast Asia with pronounced differences in variant composition. These variability data provide an important resource to inform cost-effectiveness modeling and guide population-specific genotyping strategies with the goal of optimizing the implementation of precision public health.
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Affiliation(s)
- Yitian Zhou
- Department of Physiology and Pharmacology, Karolinska Institutet, 171 77, Stockholm, Sweden
| | - Volker M Lauschke
- Department of Physiology and Pharmacology, Karolinska Institutet, 171 77, Stockholm, Sweden.
- Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart, Germany.
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Ndadza A, Muyambo S, Mntla P, Wonkam A, Chimusa E, Kengne AP, Ntsekhe M, Dandara C. Profiling of warfarin pharmacokinetics-associated genetic variants: Black Africans portray unique genetic markers important for an African specific warfarin pharmacogenetics-dosing algorithm. J Thromb Haemost 2021; 19:2957-2973. [PMID: 34382722 PMCID: PMC9543705 DOI: 10.1111/jth.15494] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 07/28/2021] [Accepted: 08/09/2021] [Indexed: 11/30/2022]
Abstract
BACKGROUND Warfarin dose variability observed in patients is attributed to variation in genes involved in the warfarin metabolic pathway. Genetic variation in CYP2C9 and VKORC1 has been the traditional focus in evaluating warfarin dose variability, with little focus on other genes. OBJECTIVE We set out to evaluate 27 single nucleotide polymorphisms (SNPs) in the CYP2C cluster loci and 8 genes (VKORC1, ABCB1, CYP2C9, CYP2C19, CYP2C8, CYP1A2, CYP3A4, and CYP3A5) involved in pharmacokinetics of warfarin. PATIENTS/METHODS 503 participants were recruited among black Africans and Mixed Ancestry population groups, from South Africa and Zimbabwe, and a blood sample taken for DNA. Clinical parameters were obtained from patient medical records, and these were correlated with genetic variation. RESULTS Among black Africans, the SNPs CYP2C rs12777823G>A, CYP2C9 c.449G>A (*8), CYP2C9 c.1003C>T (*11) and CYP2C8 c.805A>T (*2) were significantly associated with warfarin maintenance dose. Conversely, CYP2C9 c.430C>T (*2), CYP2C8 c.792C>G (*4) and VKORC1 g.-1639G>A were significantly associated with maintenance dose among the Mixed Ancestry. The presence of CYP2C8*2 and CYP3A5*6 alleles was associated with increased mean warfarin maintenance dose, whereas CYP2C9*8 allele was associated with reduced warfarin maintenance dose. CONCLUSION African populations present with a diversity of variants that are important in predicting pharmacogenetics-based warfarin dosing in addition to those reported in CYP2C9 and VKORC1. It is therefore important, to include African populations in pharmacogenomics studies to be able to identify all possible biomarkers that are potential predictors for drug response.
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Affiliation(s)
- Arinao Ndadza
- Pharmacogenomics and Drug Metabolism Research GroupDivision of Human GeneticsDepartment of Pathology & Institute of Infectious Disease and Molecular Medicine (IDM)Faculty of Health SciencesUniversity of Cape TownCape TownSouth Africa
| | - Sarudzai Muyambo
- Department of Clinical PharmacologyCollege of Health ScienceUniversity of ZimbabweHarareZimbabwe
- Department of Biological SciencesFaculty of Science and EngineeringBindura University of Science and EducationBinduraZimbabwe
| | - Pindile Mntla
- Department of CardiologySefako Makgatho Health Sciences University and Dr. George Mukhari HospitalPretoriaSouth Africa
| | - Ambroise Wonkam
- Pharmacogenomics and Drug Metabolism Research GroupDivision of Human GeneticsDepartment of Pathology & Institute of Infectious Disease and Molecular Medicine (IDM)Faculty of Health SciencesUniversity of Cape TownCape TownSouth Africa
| | - Emile Chimusa
- Pharmacogenomics and Drug Metabolism Research GroupDivision of Human GeneticsDepartment of Pathology & Institute of Infectious Disease and Molecular Medicine (IDM)Faculty of Health SciencesUniversity of Cape TownCape TownSouth Africa
| | - Andre P. Kengne
- Non‐Communicable Diseases Research UnitSouth African Medical Research Council and University of Cape TownCape TownSouth Africa
| | - Mpiko Ntsekhe
- Division of CardiologyDepartment of MedicineFaculty of Health SciencesUniversity of Cape TownCape TownSouth Africa
| | - Collet Dandara
- Pharmacogenomics and Drug Metabolism Research GroupDivision of Human GeneticsDepartment of Pathology & Institute of Infectious Disease and Molecular Medicine (IDM)Faculty of Health SciencesUniversity of Cape TownCape TownSouth Africa
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A Pharmacogenetic Study of CYP2C19 in Acute Coronary Syndrome Patients of Colombian Origin Reveals New Polymorphisms Potentially Related to Clopidogrel Therapy. J Pers Med 2021; 11:jpm11050400. [PMID: 34065778 PMCID: PMC8150782 DOI: 10.3390/jpm11050400] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2021] [Revised: 04/20/2021] [Accepted: 04/22/2021] [Indexed: 12/18/2022] Open
Abstract
Clopidogrel, an oral platelet P2Y12 receptor blocker, is used in the treatment of acute coronary syndrome. Interindividual variability in treatment response and the occurrence of adverse effects has been attributed to genetic variants in CYP2C19. The analysis of relevant pharmacogenes in ethnically heterogeneous and poorly studied populations contributes to the implementation of personalized medicine. We analyzed the coding and regulatory regions of CYP2C19 in 166 patients with acute coronary syndrome (ACS) treated with clopidogrel. The allele frequencies of CYP2C19 alleles *1, *2, *4, *17, *27 and *33 alleles were 86.1%, 7.2%, 0.3%, 10.2%, 0.3% and 0.3%, respectively. A new potentially pathogenic mutation (p.L15H) and five intronic variants with potential splicing effects were detected. In 14.4% of the patients, a new haplotype in strong linkage disequilibrium was identified. The clinical outcome indicated that 13.5% of the patients presented adverse drugs reactions with a predominance of bleeding while 25% of these patients were carriers of at least one polymorphic allele. We propose that new regulatory single-nucleotide variants (SNVs) might potentially influence the response to clopidogrel in Colombian individuals.
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Botton MR, Whirl-Carrillo M, Del Tredici AL, Sangkuhl K, Cavallari LH, Agúndez JAG, Duconge J, Lee MTM, Woodahl EL, Claudio-Campos K, Daly AK, Klein TE, Pratt VM, Scott SA, Gaedigk A. PharmVar GeneFocus: CYP2C19. Clin Pharmacol Ther 2021; 109:352-366. [PMID: 32602114 PMCID: PMC7769975 DOI: 10.1002/cpt.1973] [Citation(s) in RCA: 63] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Accepted: 06/15/2020] [Indexed: 12/17/2022]
Abstract
The Pharmacogene Variation Consortium (PharmVar) catalogues star (*) allele nomenclature for the polymorphic human CYP2C19 gene. CYP2C19 genetic variation impacts the metabolism of many drugs and has been associated with both efficacy and safety issues for several commonly prescribed medications. This GeneFocus provides a comprehensive overview and summary of CYP2C19 and describes how haplotype information catalogued by PharmVar is utilized by the Pharmacogenomics Knowledgebase and the Clinical Pharmacogenetics Implementation Consortium (CPIC).
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Affiliation(s)
| | | | | | - Katrin Sangkuhl
- Department of Biomedical Data Science, Stanford University, Stanford, California, USA
| | | | - José A G Agúndez
- UNEx, ARADyAL, Instituto de Salud Carlos III, University Institute of Molecular Pathology Biomarkers, Cáceres, Spain
| | - Jorge Duconge
- School of Pharmacy, University of Puerto Rico, San Juan, Puerto Rico
| | | | - Erica L Woodahl
- Department of Biomedical and Pharmaceutical Sciences, University of Montana, Missoula, Montana, USA
| | | | - Ann K Daly
- Newcastle University, Newcastle upon Tyne, UK
| | - Teri E Klein
- Department of Biomedical Data Science, Stanford University, Stanford, California, USA
| | - Victoria M Pratt
- Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Stuart A Scott
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Sema4, Stamford, Connecticut, USA
| | - Andrea Gaedigk
- Division of Clinical Pharmacology, Toxicology & Therapeutic Innovation, Children's Mercy, Kansas City, Missouri, USA
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8
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Effects of genetic polymorphisms on the pharmacokinetics and pharmacodynamics of proton pump inhibitors. Pharmacol Res 2020; 152:104606. [DOI: 10.1016/j.phrs.2019.104606] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Revised: 12/13/2019] [Accepted: 12/13/2019] [Indexed: 02/06/2023]
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Martin AR, Teferra S, Möller M, Hoal EG, Daly MJ. The critical needs and challenges for genetic architecture studies in Africa. Curr Opin Genet Dev 2018; 53:113-120. [PMID: 30240950 PMCID: PMC6494470 DOI: 10.1016/j.gde.2018.08.005] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Revised: 08/17/2018] [Accepted: 08/31/2018] [Indexed: 12/11/2022]
Abstract
Human genetic studies have long been vastly Eurocentric, raising a key question about the generalizability of these study findings to other populations. Because humans originated in Africa, these populations retain more genetic diversity, and yet individuals of African descent have been tremendously underrepresented in genetic studies. The diversity in Africa affords ample opportunities to improve fine-mapping resolution for associated loci, discover novel genetic associations with phenotypes, build more generalizable genetic risk prediction models, and better understand the genetic architecture of complex traits and diseases subject to varying environmental pressures. Thus, it is both ethically and scientifically imperative that geneticists globally surmount challenges that have limited progress in African genetic studies to date. Additionally, African investigators need to be meaningfully included, as greater inclusivity and enhanced research capacity afford enormous opportunities to accelerate genomic discoveries that translate more effectively to all populations. We review the advantages, challenges, and examples of genetic architecture studies of complex traits and diseases in Africa. For example, with greater genetic diversity comes greater ancestral heterogeneity; this higher level of understudied diversity can yield novel genetic findings, but some methods that assume homogeneous population structure and work well in European populations may work less well in the presence of greater heterogeneity in African populations. Consequently, we advocate for methodological development that will accelerate studies important for all populations, especially those currently underrepresented in genetics.
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Affiliation(s)
- Alicia R Martin
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA; Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA.
| | - Solomon Teferra
- Department of Psychiatry, School of Medicine, College of Health Sciences, Addis Ababa University, Addis Ababa, Ethiopia; Department of Epidemiology, Harvard T. H. Chan School of Public Health, Harvard University, Boston, USA
| | - Marlo Möller
- DST-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, Cape Town, South Africa
| | - Eileen G Hoal
- DST-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, Cape Town, South Africa
| | - Mark J Daly
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA; Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
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10
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O'Connell KS, Swart M, McGregor NW, Dandara C, Warnich L. Pharmacogenetics of Antiretroviral Drug Response and Pharmacokinetic Variations in Indigenous South African Populations. OMICS : A JOURNAL OF INTEGRATIVE BIOLOGY 2018; 22:589-597. [PMID: 30235109 DOI: 10.1089/omi.2018.0117] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Interindividual and interethnic differences in response to antiretroviral drugs (ARVs) are influenced by genetic variation. The few genomic studies conducted among African-Americans and African ethnic groups do not reflect the extensive genetic diversity within African populations. ARVs are widely used in Africa. Therefore, genomic characterization of African populations is required before genotype-guided dosing becomes possible. The aim of this study was to determine and report on the frequency of genetic variants in genes implicated in metabolism and transport of ARVs in South African populations. The study comprised 48 self-reported South African Colored (SAC) and 296 self-reported Black African (BA) individuals. Allele and genotype frequency distributions for 93 variants contributing to metabolism and transport of ARVs were compared between groups, and other global populations. Fifty-three variants had significant differences in allele and genotype frequencies when comparing SAC and BA groups. Thirteen of these have strong clinical annotations, affecting efavirenz and tenofovir pharmacokinetics. This study provides a summary of the genetic variation within genes implicated in metabolism and transport of ARVs in indigenous South African populations. The observed differences between indigenous population groups, and between these groups and global populations, demonstrate that data generated from specific African populations cannot be used to infer genetic diversity within other populations on the continent. These results highlight the need for comprehensive characterization of genetic variation within indigenous African populations, and the clinical utility of these variants in ARV dosing for global precision medicine. Population pharmacogenetics is a nascent field of global health and warrants further research and education.
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Affiliation(s)
- Kevin S O'Connell
- 1 Systems Genetics Working Group, Department of Genetics, Stellenbosch University , Stellenbosch, South Africa
| | - Marelize Swart
- 2 Pharmacogenomics and Drug Metabolism Group, Division of Human Genetics, Department of Pathology and Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town , Cape Town, South Africa
| | - Nathaniel W McGregor
- 1 Systems Genetics Working Group, Department of Genetics, Stellenbosch University , Stellenbosch, South Africa
| | - Collet Dandara
- 2 Pharmacogenomics and Drug Metabolism Group, Division of Human Genetics, Department of Pathology and Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town , Cape Town, South Africa
| | - Louise Warnich
- 1 Systems Genetics Working Group, Department of Genetics, Stellenbosch University , Stellenbosch, South Africa
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11
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Hemmings SMJ, Xulu K, Sommer J, Hinsberger M, Malan-Muller S, Tromp G, Elbert T, Weierstall R, Seedat S. Appetitive and reactive aggression are differentially associated with the STin2 genetic variant in the serotonin transporter gene. Sci Rep 2018; 8:6714. [PMID: 29712944 PMCID: PMC5928100 DOI: 10.1038/s41598-018-25066-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Accepted: 04/09/2018] [Indexed: 12/16/2022] Open
Abstract
Appetitive aggression is a sub-category of instrumental aggression, characterised by the primary intrinsic enjoyment of aggressive activity. Aggression is heritable, and serotonergic and monoaminergic neurotransmitter systems have been found to contribute to the underlying molecular mechanisms. The aim of this study was to investigate the role that genetic variants in the serotonin transporter (SLC6A4) and monoamine oxidase A (MAOA) genes play in the aetiology of appetitive aggression in South African Xhosa males (n = 290). SLC6A4 5-HTTLPR, rs25531, and STin2 variants, as well as MAOA-uVNTR were investigated for their association with levels of appetitive aggression using Poisson regression analysis. The STin2 VNTR12 allele was found to be associated with increased levels of appetitive aggression (p = 0.003), but with decreased levels of reactive aggression (p = 7 × 10-5). This study is the first to investigate genetic underpinnings of appetitive aggression in a South African population, with preliminary evidence suggesting that SCL6A4 STin2 variants play a role in its aetiology, and may also be important in differentiating between appetitive and reactive aggression. Although the results require replication, they shed some preliminary light on the molecular dichotomy that may underlie the two forms of aggression.
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Affiliation(s)
- Sian Megan Joanna Hemmings
- Department of Psychiatry, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, South Africa.
| | - Khethelo Xulu
- Department of Psychiatry, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, South Africa
| | - Jessica Sommer
- Department of Psychology, University of Konstanz, Konstanz, Germany
| | | | - Stefanie Malan-Muller
- Department of Psychiatry, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, South Africa
| | - Gerard Tromp
- Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, South Africa
| | - Thomas Elbert
- Department of Psychology, University of Konstanz, Konstanz, Germany
| | - Roland Weierstall
- Department of Psychology, University of Konstanz, Konstanz, Germany.,Clinical Psychology and Psychotherapy, Medical School Hamburg, Hamburg, Germany
| | - Soraya Seedat
- Department of Psychiatry, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, South Africa
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12
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Hiratsuka M, Hirasawa N, Oshima Y, Kodama S, Miyata T, Dan T, Takatoku H, Kuribayashi H, Nakamura R, Saito Y. Points-to-consider documents: Scientific information on the evaluation of genetic polymorphisms during non-clinical studies and phase I clinical trials in the Japanese population. Drug Metab Pharmacokinet 2018; 33:141-149. [PMID: 29703433 DOI: 10.1016/j.dmpk.2018.01.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Revised: 12/05/2017] [Accepted: 01/15/2018] [Indexed: 01/11/2023]
Abstract
Pharmacotherapy shows striking individual differences in pharmacokinetics and pharmacodynamics, involving drug efficacy and adverse reactions. Recent genetic research has revealed that genetic polymorphisms are important intrinsic factors for these inter-individual differences. This pharmacogenomic information could help develop safer and more effective precision pharmacotherapies and thus, regulatory guidance/guidelines were developed in this area, especially in the EU and US. The Project for the Promotion of Progressive Medicine, Medical Devices, and Regenerative Medicine by the Ministry of Health, Labour and Welfare, performed by Tohoku University, reported scientific information on the evaluation of genetic polymorphisms, mainly on drug metabolizing enzymes and transporters, during non-clinical studies and phase I clinical trials in Japanese subjects/patients. We anticipate that this paper will be helpful in drug development for the regulatory usage of pharmacogenomic information, most notably pharmacokinetics.
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Affiliation(s)
- Masahiro Hiratsuka
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Japan.
| | - Noriyasu Hirasawa
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Japan
| | - Yoshiteru Oshima
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Japan
| | - Susumu Kodama
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Japan; National Institute of Health Sciences (NIHS), Tokyo, Japan; Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama, Japan
| | - Toshio Miyata
- Graduate School of Medicine, Tohoku University, Sendai, Japan
| | - Takashi Dan
- Graduate School of Medicine, Tohoku University, Sendai, Japan
| | | | | | - Ryosuke Nakamura
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Japan; National Institute of Health Sciences (NIHS), Tokyo, Japan
| | - Yoshiro Saito
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Japan; National Institute of Health Sciences (NIHS), Tokyo, Japan
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Pharmacogenomic Impact of CYP2C19 Variation on Clopidogrel Therapy in Precision Cardiovascular Medicine. J Pers Med 2018; 8:jpm8010008. [PMID: 29385765 PMCID: PMC5872082 DOI: 10.3390/jpm8010008] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Revised: 01/20/2018] [Accepted: 01/22/2018] [Indexed: 12/21/2022] Open
Abstract
Variability in response to antiplatelet therapy can be explained in part by pharmacogenomics, particularly of the CYP450 enzyme encoded by CYP2C19. Loss-of-function and gain-of-function variants help explain these interindividual differences. Individuals may carry multiple variants, with linkage disequilibrium noted among some alleles. In the current pharmacogenomics era, genomic variation in CYP2C19 has led to the definition of pharmacokinetic phenotypes for response to antiplatelet therapy, in particular, clopidogrel. Individuals may be classified as poor, intermediate, extensive, or ultrarapid metabolizers, based on whether they carry wild type or polymorphic CYP2C19 alleles. Variant alleles differentially impact platelet reactivity, concentration of plasma clopidogrel metabolites, and clinical outcomes. Interestingly, response to clopidogrel appears to be modulated by additional factors, such as sociodemographic characteristics, risk factors for ischemic heart disease, and drug-drug interactions. Furthermore, systems medicine studies suggest that a broader approach may be required to adequately assess, predict, preempt, and manage variation in antiplatelet response. Transcriptomics, epigenomics, exposomics, miRNAomics, proteomics, metabolomics, microbiomics, and mathematical, computational, and molecular modeling should be integrated with pharmacogenomics for enhanced prediction and individualized care. In this review of pharmacogenomic variation of CYP450, a systems medicine approach is described for tailoring antiplatelet therapy in clinical practice of precision cardiovascular medicine.
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Pearce B, Jacobs C, Hoosain N, Benjeddou M. SLC22A2 - mapping genomic variations within South African indigenous and admixed populations. Drug Metab Pers Ther 2017; 31:213-220. [PMID: 27828777 DOI: 10.1515/dmpt-2016-0022] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Accepted: 09/26/2016] [Indexed: 11/15/2022]
Abstract
BACKGROUND The SLC22A2 gene is a polyspecific transporter that mediates the electrogenic transport of small organic cations with different molecular structures. Furthermore, single-nucleotide polymorphisms (SNPs) of SLC22A2 are clinically significant because they can alter the transport of substrate drugs and may, thus, influence the efficacy and toxicity thereof. Additionally, further studies have reported that SLC22A2 is responsible for 80% of the total metformin clearance. Therefore, loss-of-function variants of SLC22A2 could affect the pharmacokinetic and pharmacodynamic characteristics of metformin. Although it is widely accepted that African populations harbor a greater amount of genomic diversity compared to other populations, limited information is available regarding genetic polymorphisms in SLC genes among African populations, specifically those related to impaired functional activity of hOCT2. Therefore, the aim of this study was to map known impaired function variants in the SLC22A2 gene. METHODS Development of multiplex SNaPshot™ genotyping assay for 20 previously reported SLC22A2 nonsynonymous SNPs and the assessment of baseline allele frequencies of these variants in 140 Cape Admixed, 148 Xhosa and 152 Zulu individuals residing in Cape Town, South Africa. RESULTS We identified three nonsynonymous SNPs, namely, A270S, R400C and K432Q in the population studied at minor allele frequencies of 6.1%, 3.4% and 0.7%, respectively. The most frequently observed haplotypes across all three populations were CATAATGCGTACGCGCGACG (~85%), CATAATGATTACGCGCGACG (~7%) and CATAATGAGTACGCGCGACG (~4.5%). CONCLUSIONS In addition to SNPs, the haplotypes identified in this study can in future also aid in identifying associations between causative genetic variants and drug response. This study contributes in filling the gap that exists with regards to genetic information about important variations in organic cation transporter genes for the indigenous populations of South Africa.
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African Genetic Diversity: Implications for Cytochrome P450-mediated Drug Metabolism and Drug Development. EBioMedicine 2017; 17:67-74. [PMID: 28237373 PMCID: PMC5360579 DOI: 10.1016/j.ebiom.2017.02.017] [Citation(s) in RCA: 79] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2016] [Revised: 02/17/2017] [Accepted: 02/17/2017] [Indexed: 12/17/2022] Open
Abstract
Genetic diversity is greater in Africa than in other continental populations. Genetic variability in genes encoding drug metabolizing enzymes may contribute to the high numbers of adverse drug reactions reported in Africa. We reviewed publications (1995-April 2016) reporting frequencies of known cytochrome P450 (CYP) variants in African populations. Using principal components analysis (PCA) we identified CYP alleles of potential clinical relevance with a marked difference in distribution in Africa, compared with Asian and Caucasian populations. These were CYP2B6*6, CYP2C8*2, CYP2D6*3, CYP2D6*17, CYP2D6*29, CYP3A5*6, and CYP3A5*7. We show clearly that there is greater diversity in CYP distribution in Africa than in other continental populations and identify a need for optimization of drug therapy and drug development there. Further pharmacogenetic studies are required to confirm the CYP distributions we identified using PCA, to discover uniquely African alleles and to identify populations at a potentially increased risk of drug-induced adverse events or drug inefficacy.
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Hemmings SMJ, Martin LI, van der Merwe L, Benecke R, Domschke K, Seedat S. Serotonin transporter variants play a role in anxiety sensitivity in South African adolescents. World J Biol Psychiatry 2016; 17:66-75. [PMID: 26635248 DOI: 10.3109/15622975.2015.1102324] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
OBJECTIVES Anxiety sensitivity (AS) has predictive potential for the development of anxiety disorders. We investigated the role that gene-environment (G × E) interactions, focussing on childhood trauma (CT) and selected SLC6A4 variants, play in modulating levels of AS in a South African adolescent population. METHODS All adolescents (n = 951) completed measures for AS and CT. Six SLC6A4 polymorphisms were genotyped. G × E influences on AS levels were assessed using multiple linear regression models. Relevant confounders were included in all analyses. RESULTS Xhosa (n = 634) and Coloured (n = 317) participants were analysed independently of one another. The 5-HTTLPR-rs25531 L-G haplotype associated with reduced AS among Xhosa adolescents (P = 0.010). In addition, the rs1042173 CC-genotype protected against increased levels of AS in Xhosa participants who had experienced increased levels of CT (P = 0.038). Coloured males homozygous for the S-allele had significantly increased levels of AS compared to Coloured males with at least one L-allele (P = 0.016). CONCLUSIONS This is the first study to be conducted on AS in adolescents from two ethnically diverse populations. Results indicate that the L-G haplotype confers protection against high AS levels in a Xhosa population. Furthermore, increased CT was found to protect against high levels of AS in Xhosa rs1042173 CC-carriers.
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Affiliation(s)
- Sian M J Hemmings
- a Department of Psychiatry, Faculty of Medicine and Health Sciences , Stellenbosch University , Tygerberg , South Africa
| | - Lindi I Martin
- a Department of Psychiatry, Faculty of Medicine and Health Sciences , Stellenbosch University , Tygerberg , South Africa
| | - Lize van der Merwe
- b Department of Statistics , University of the Western Cape , Bellville , South Africa
| | - Rohan Benecke
- c Department of Biomedical Sciences, Faculty of Medicine and Health Sciences , Stellenbosch University , Tygerberg , South Africa
| | - Katharina Domschke
- d Department of Psychiatry , University of Wuerzburg , Wuerzburg , Germany
| | - Soraya Seedat
- a Department of Psychiatry, Faculty of Medicine and Health Sciences , Stellenbosch University , Tygerberg , South Africa
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Jacobs C, Pearce B, Hoosain N, Benjeddou M. Lack of genomic diversity in the SLC47A1 gene within the indigenous Xhosa population. Drug Metab Pers Ther 2016; 31:107-114. [PMID: 27226103 DOI: 10.1515/dmpt-2016-0007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2016] [Accepted: 04/22/2016] [Indexed: 06/05/2023]
Abstract
BACKGROUND Multidrug and toxin extrusion 1 (MATE1) is an organic cation/H+ exchanger, localized in the apical membrane of proximal renal tubules, which mediates the cellular elimination of organic cations into the renal lumen. These organic cations include clinically important drugs such as metformin, oxaliplatin and cimetidine. Moreover, genetic polymorphisms of SLC47A1, the pharmacogenetically relevant gene encoding human MATE1, have been implicated in reduced transport or accumulation to cytotoxic levels of these drugs in vitro. However, little or no information is available on the minor allele frequency distribution of known SLC47A1 coding SNPs in the sub-Saharan African populations. METHODS Thus, the aim of this study was to determine the baseline minor allele frequency distribution of 20 known coding SNPs in the SLC47A1 gene of 148 Xhosa individuals residing in Cape Town, South Africa. RESULTS This study did not identify any of these known SLC47A1 coding SNPs in the Xhosa individuals who participated in this study. CONCLUSIONS It is anticipated that whole genome or exome sequencing may reveal novel SNPs in the Xhosa and other sub-Saharan African populations, which may have been missed with the current genotyping strategy.
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Röhrich CR, Drögemöller BI, Ikediobi O, van der Merwe L, Grobbelaar N, Wright GE, McGregor N, Warnich L. CYP2B6*6 and CYP2B6*18 Predict Long-Term Efavirenz Exposure Measured in Hair Samples in HIV-Positive South African Women. AIDS Res Hum Retroviruses 2016; 32:529-38. [PMID: 26655325 DOI: 10.1089/aid.2015.0048] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Long-term exposure to efavirenz (EFV) measured in hair samples may predict response to antiretroviral treatment (ART). Polymorphisms in CYP2B6 are known to alter EFV levels. The aim of this study was to assess the relationship between CYP2B6 genotype, EFV levels measured in hair, and virological outcomes on ART in a real-world setting. We measured EFV levels in hair from HIV-positive South African females who had been receiving EFV-based treatment for at least 3 months from the South African Black (SAB) (n = 81) and Cape Mixed Ancestry (CMA) (n = 53) populations. Common genetic variation in CYP2B6 was determined in 15 individuals from each population using bidirectional Sanger sequencing. Prioritized variants (n = 16) were subsequently genotyped in the entire patient cohort (n = 134). The predictive value of EFV levels in hair and selected variants in CYP2B6 on virological treatment outcomes was assessed. Previously described alleles (CYP2B6*2, CYP2B6*5, CYP2B6*6, CYP2B6*17, and CYP2B6*18), as well as two novel alleles (CYP2B6*31 and CYP2B6*32), were detected in this study. Compared to noncarriers, individuals homozygous for CYP2B6*6 had ∼109% increased EFV levels in hair (p = .016) and CYP2B6*18 heterozygotes demonstrated 82% higher EFV hair levels (p = .0006). This study confirmed that alleles affecting CYP2B6 metabolism and subsequent EFV exposure are present at significant frequencies in both the SAB and CMA populations. Furthermore, this study demonstrated that the use of hair samples for testing EFV concentrations may be a useful tool in determining long-term drug exposure in resource-limited countries.
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Affiliation(s)
- Carola R. Röhrich
- Department of Genetics, Stellenbosch University, Stellenbosch, South Africa
| | | | - Ogechi Ikediobi
- Departments of Pharmacy, University of California San Francisco, UCSF, San Francisco, California
| | - Lize van der Merwe
- Department of Molecular Biology and Human Genetics, Stellenbosch University, Tygerberg, South Africa
- Department of Statistics, University of Western Cape, Bellville, South Africa
| | | | - Galen E.B. Wright
- Department of Genetics, Stellenbosch University, Stellenbosch, South Africa
| | - Nathaniel McGregor
- Department of Genetics, Stellenbosch University, Stellenbosch, South Africa
- Department of Psychiatry, Stellenbosch University, Tygerberg, South Africa
| | - Louise Warnich
- Department of Genetics, Stellenbosch University, Stellenbosch, South Africa
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Jacobs C, Pearce B, Du Plessis M, Hoosain N, Benjeddou M. Single nucleotide polymorphisms of the SLC22A2 gene within the Xhosa population of South Africa. Drug Metab Pharmacokinet 2015; 30:457-60. [PMID: 26674735 DOI: 10.1016/j.dmpk.2015.11.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Revised: 11/06/2015] [Accepted: 11/11/2015] [Indexed: 01/11/2023]
Abstract
Human organic cation transporter 2 (hOCT2) is thought to play a critical role in the uptake, pharmacological effects and/or adverse effects of many cationic clinical therapeutics and xenobiotics. Moreover, genetic variations in hOCT2 gene, SLC22A2, are increasingly being recognized as a possible mechanism that can explain individual variation in drug response. To screen for variations in this gene, SLC22A2 was directly sequenced in 96 healthy Xhosa individuals. A total of 27 variations, including three novel ones, were identified in SLC22A2: eight in exons, 15 in introns, and four in the 5'-untranslated region. The minor allele frequencies (MAF) of genetic variants observed in the Xhosa population were compared both to other African and other world populations. Seventeen of the variants observed in the SLC22A2 gene of the Xhosa population were specific to/or occurred at a higher frequency in African populations or populations with a recent connection to the African continent.
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Affiliation(s)
- Clifford Jacobs
- Department of Biotechnology, University of the Western Cape, Robert Sobukwe Road, Bellville 7535, Cape Town, South Africa
| | - Brendon Pearce
- Department of Biotechnology, University of the Western Cape, Robert Sobukwe Road, Bellville 7535, Cape Town, South Africa
| | - Mornè Du Plessis
- Department of Biotechnology, University of the Western Cape, Robert Sobukwe Road, Bellville 7535, Cape Town, South Africa
| | - Nisreen Hoosain
- Department of Biotechnology, University of the Western Cape, Robert Sobukwe Road, Bellville 7535, Cape Town, South Africa
| | - Mongi Benjeddou
- Department of Biotechnology, University of the Western Cape, Robert Sobukwe Road, Bellville 7535, Cape Town, South Africa.
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Interethnic variation of CYP2C19 alleles, 'predicted' phenotypes and 'measured' metabolic phenotypes across world populations. THE PHARMACOGENOMICS JOURNAL 2015; 16:113-23. [PMID: 26503820 DOI: 10.1038/tpj.2015.70] [Citation(s) in RCA: 92] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2015] [Revised: 07/15/2015] [Accepted: 08/19/2015] [Indexed: 02/08/2023]
Abstract
The present study evaluates the worldwide frequency distribution of CYP2C19 alleles and CYP2C19 metabolic phenotypes ('predicted' from genotypes and 'measured' with a probe drug) among healthy volunteers from different ethnic groups and geographic regions, as well as the relationship between the 'predicted' and 'measured' CYP2C19 metabolic phenotypes. A total of 52 181 healthy volunteers were studied within 138 selected original research papers. CYP2C19*17 was 42- and 24-fold more frequent in Mediterranean-South Europeans and Middle Easterns than in East Asians (P<0.001, in both cases). Contrarily, CYP2C19*2 and CYP2C19*3 alleles were more frequent in East Asians (30.26% and 6.89%, respectively), and even a twofold higher frequency of these alleles was found in Native populations from Oceania (61.30% and 14.42%, respectively; P<0.001, in all cases), which may be a consequence of genetic drift process in the Pacific Islands. Regarding CYP2C19 metabolic phenotype, poor metabolizers (PMs) were more frequent among Asians than in Europeans, contrarily to the phenomenon reported for CYP2D6. A correlation has been found between the frequencies of CYP2C19 poor metabolism 'predicted' from CYP2C19 genotypes (gPMs) and the poor metabolic phenotype 'measured' with a probe drug (mPMs) when subjects are either classified by ethnicity (r=0.94, P<0.001) or geographic region (r=0.99, P=0.002). Nevertheless, further research is needed in African and Asian populations, which are under-represented, and additional CYP2C19 variants and the 'measured' phenotype should be studied.
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Dodgen TM, Drögemöller BI, Wright GEB, Warnich L, Steffens FE, Cromarty AD, Alessandrini M, Pepper MS. Evaluation of predictive CYP2C19 genotyping assays relative to measured phenotype in a South African cohort. Pharmacogenomics 2015; 16:1343-54. [PMID: 26244421 DOI: 10.2217/pgs.15.80] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
AIM To align predicted and measured CYP2C19 phenotype in a South African cohort. MATERIALS & METHODS Genotyping of CYP2C19*2, *3, *9, *15, *17, *27 and *28 was performed using PCR-RFLP, and an activity score (AS) system was used to predict phenotype. True phenotype was measured using plasma concentrations of omeprazole and its metabolite 5'-hydroxyomperazole. RESULTS Partial genotype-phenotype discrepancies were reported, and an adapted AS system was developed, which showed a marked improvement in phenotype prediction. Results highlight the need for a more comprehensive CYP2C19 genotyping approach to improve prediction of omeprazole metabolism. CONCLUSION Evidence for the utility of a CYP2C19 AS system is provided, for which the accuracy can be further improved by means of comprehensive genotyping and substrate-specific modification.
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Affiliation(s)
- Tyren M Dodgen
- Department of Pharmacology, University of Pretoria, Pretoria, South Africa.,Department of Immunology, Faculty of Health Sciences, University of Pretoria, PO Box 2034, Pretoria 0001, South Africa.,Institute for Cellular & Molecular Medicine, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa
| | - Britt I Drögemöller
- Department of Genetics, Faculty of Science, Stellenbosch University, Stellenbosch, South Africa
| | - Galen E B Wright
- Department of Genetics, Faculty of Science, Stellenbosch University, Stellenbosch, South Africa
| | - Louise Warnich
- Department of Genetics, Faculty of Science, Stellenbosch University, Stellenbosch, South Africa
| | - Francois E Steffens
- Department of Statistics, Faculty of Natural & Agricultural Sciences, University of Pretoria, Pretoria, South Africa
| | - A Duncan Cromarty
- Department of Pharmacology, University of Pretoria, Pretoria, South Africa
| | - Marco Alessandrini
- Department of Immunology, Faculty of Health Sciences, University of Pretoria, PO Box 2034, Pretoria 0001, South Africa.,Institute for Cellular & Molecular Medicine, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa
| | - Michael S Pepper
- Department of Immunology, Faculty of Health Sciences, University of Pretoria, PO Box 2034, Pretoria 0001, South Africa.,Institute for Cellular & Molecular Medicine, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa.,Department of Genetic Medicine & Development, Faculty of Medicine, University of Geneva, Switzerland
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Alessandrini M, Pepper MS. Priority pharmacogenetics for the African continent: focus on CYP450. Pharmacogenomics 2014; 15:385-400. [PMID: 24533717 DOI: 10.2217/pgs.13.252] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Countries in Africa have a high burden of communicable disease, and are experiencing an increase in noncommunicable diseases due to the effects of globalization, industrialization and urbanization. The costs incurred through adverse drug reactions and nonresponsiveness to therapy further aggravates the situation, and the application of pharmacogenetic principles is likely to provide some relief. Having undertaken an extensive evaluation of CYP450 reports in Africa, our objective was to map out areas of need based on regional disease burdens. The data confirms a paucity of CYP450 reports and illustrates large regions for which no population information exists. There is a dire need to address the health problems of Africa, and wide-scale pharmacogenetic profiling of these populations will add significantly to improving patient care on the continent. Priority pharmacogenetics for the African continent gives precedence to the profiling of clinically relevant pharmacogenetic biomarkers, and defines the immediate need in the context of disease burden.
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Affiliation(s)
- Marco Alessandrini
- Department of Immunology & The Institute for Cellular & Molecular Medicine, Faculty of Health Sciences, University of Pretoria, South Africa
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Jacobs C, Pearce B, Du Plessis M, Hoosain N, Benjeddou M. Genetic polymorphisms and haplotypes of the organic cation transporter 1 gene (SLC22A1) in the Xhosa population of South Africa. Genet Mol Biol 2014; 37:350-9. [PMID: 25071399 PMCID: PMC4094614 DOI: 10.1590/s1415-47572014005000002] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2013] [Accepted: 02/27/2014] [Indexed: 12/13/2022] Open
Abstract
Human organic cation transporter 1 is primarily expressed in hepatocytes and mediates the electrogenic transport of various endogenous and exogenous compounds, including clinically important drugs. Genetic polymorphisms in the gene coding for human organic cation transporter 1, SLC22A1, are increasingly being recognized as a possible mechanism explaining the variable response to clinical drugs, which are substrates for this transporter. The genotypic and allelic distributions of 19 nonsynonymous and one intronic SLC22A1 single nucleotide polymorphisms were determined in 148 healthy Xhosa participants from South Africa, using a SNAPshot® multiplex assay. In addition, haplotype structure for SLC22A1 was inferred from the genotypic data. The minor allele frequencies for S14F (rs34447885), P341L (rs2282143), V519F (rs78899680), and the intronic variant rs622342 were 1.7%, 8.4%, 3.0%, and 21.6%, respectively. None of the participants carried the variant allele for R61C (rs12208357), C88R (rs55918055), S189L (rs34104736), G220V (rs36103319), P283L (rs4646277), R287G (rs4646278), G401S (rs34130495), M440I (rs35956182), or G465R (rs34059508). In addition, no variant alleles were observed for A306T (COSM164365), A413V (rs144322387), M420V (rs142448543), I421F (rs139512541), C436F (rs139512541), V501E (rs143175763), or I542V (rs137928512) in the population. Eight haplotypes were inferred from the genotypic data. This study reports important genetic data that could be useful for future pharmacogenetic studies of drug transporters in the indigenous Sub-Saharan African populations.
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Affiliation(s)
- Clifford Jacobs
- Department of Biotechnology , University of the Western Cape , Cape Town , South Africa
| | - Brendon Pearce
- Department of Biotechnology , University of the Western Cape , Cape Town , South Africa
| | - Mornè Du Plessis
- Department of Biotechnology , University of the Western Cape , Cape Town , South Africa
| | - Nisreen Hoosain
- Department of Biotechnology , University of the Western Cape , Cape Town , South Africa
| | - Mongi Benjeddou
- Department of Biotechnology , University of the Western Cape , Cape Town , South Africa
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Drögemöller BI, Wright GEB, Warnich L. Considerations for rare variants in drug metabolism genes and the clinical implications. Expert Opin Drug Metab Toxicol 2014; 10:873-84. [PMID: 24673405 DOI: 10.1517/17425255.2014.903239] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
INTRODUCTION Large-scale whole genome and exome resequencing studies have revealed that humans have a high level of deleterious rare variation, which has important implications for the design of future pharmacogenetics studies. AREAS COVERED Current pharmacogenetic guidelines focus on the implementation of common variation into dosing guidelines. However, it is becoming apparent that rare variation may also play an important role in differential drug response. Current sequencing technologies offer the opportunity to examine rare variation, but there are many challenges associated with such analyses. Nonetheless, if a comprehensive picture of the role that genetic variants play in treatment outcomes is to be obtained, it will be necessary to include the entire spectrum of variation, including rare variants, into pharmacogenetic research. EXPERT OPINION In order to implement pharmacogenetics in the clinic, patients should be genotyped for clinically actionable pharmacogenetic variants and patients responding unfavourably to treatment after pharmacogenetics-based dosing should be identified and resequenced to identify additional functionally relevant variants, including rare variants. All derived information should be added to a central database to allow for the updating of existing dosing guidelines. By routinely implementing such strategies, pharmacogenetics-based treatment guidelines will continue to improve.
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Martiny VY, Miteva MA. Advances in molecular modeling of human cytochrome P450 polymorphism. J Mol Biol 2013; 425:3978-92. [PMID: 23856621 DOI: 10.1016/j.jmb.2013.07.010] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2013] [Revised: 07/01/2013] [Accepted: 07/02/2013] [Indexed: 01/08/2023]
Abstract
Cytochrome P450 (CYP) is a supergene family of metabolizing enzymes involved in the phase I metabolism of drugs and endogenous compounds. CYP oxidation often leads to inactive drug metabolites or to highly toxic or carcinogenic metabolites involved in adverse drug reactions (ADR). During the last decade, the impact of CYP polymorphism in various drug responses and ADR has been demonstrated. Of the drugs involved in ADR, 56% are metabolized by polymorphic phase I metabolizing enzymes, 86% among them being CYP. Here, we review the major CYP polymorphic forms, their impact for drug response and current advances in molecular modeling of CYP polymorphism. We focus on recent studies exploring CYP polymorphism performed by the use of sequence-based and/or protein-structure-based computational approaches. The importance of understanding the molecular mechanisms related to CYP polymorphism and drug response at the atomic level is outlined.
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Affiliation(s)
- Virginie Y Martiny
- Université Paris Diderot, Sorbonne Paris Cité, Molécules Thérapeutiques In Silico, Inserm UMR-S 973, 35 rue Helene Brion, 75013 Paris, France; Inserm, U973, F-75205 Paris, France
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26
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Yao L, Wang HC, Liu JZ, Xiong ZM. Quantitative assessment of the influence of cytochrome P450 2C19 gene polymorphisms and digestive tract cancer risk. Tumour Biol 2013; 34:3083-91. [DOI: 10.1007/s13277-013-0875-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2013] [Accepted: 05/16/2013] [Indexed: 12/14/2022] Open
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Alessandrini M, Asfaha S, Dodgen TM, Warnich L, Pepper MS. Cytochrome P450 pharmacogenetics in African populations. Drug Metab Rev 2013; 45:253-75. [PMID: 23590174 DOI: 10.3109/03602532.2013.783062] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
The Cytochrome P450 (CYP450) family of enzymes is involved in the oxidative metabolism of many therapeutic drugs, carcinogens and various endogenous substrates. These enzymes are highly polymorphic at an inter-individual and inter-ethnic level. Polymorphisms or genetic variations account for up to 30% of inter-individual differences seen in a variety of drug responses. The frequencies of the different metabolizer categories (slow, intermediate, extensive and ultra-rapid), the distribution of genetic variants, genotype-phenotype correlations and the clinical importance of the CYP450 enzymes have been extensively documented in Caucasian and Oriental populations. Limited data exists for African populations, despite the fact that this knowledge is critically important for these populations who experience a heavy burden of communicable and non-communicable diseases. In addition, the costs incurred through adverse drug reactions and non-responsiveness to therapy could be reduced through the wide-scale application of pharmacogenetics. This review provides an overview and investigation of CYP450 genotypic and phenotypic reports published from 1980 to present in African populations. Our findings confirm the high degree of variability that is expected when comparing individuals of African origin to other ethnic groups and also highlight the distribution of clinically relevant CYP450 alleles amongst the various African populations. The notable discordance in genotypic and phenotypic data amongst African populations exemplifies the need for in-depth and well-orchestrated molecular and pharmacological investigations of these populations in the future, for which whole genome sequencing and association studies will be critical.
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Affiliation(s)
- Marco Alessandrini
- Department of Immunology, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa
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Drögemöller B, Plummer M, Korkie L, Agenbag G, Dunaiski A, Niehaus D, Koen L, Gebhardt S, Schneider N, Olckers A, Wright G, Warnich L. Characterization of the genetic variation present in CYP3A4 in three South African populations. Front Genet 2013; 4:17. [PMID: 23423246 PMCID: PMC3574981 DOI: 10.3389/fgene.2013.00017] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2012] [Accepted: 02/01/2013] [Indexed: 12/26/2022] Open
Abstract
The CYP3A4 enzyme is the most abundant human cytochrome P450 (CYP) and is regarded as the most important enzyme involved in drug metabolism. Inter-individual and inter-population variability in gene expression and enzyme activity are thought to be influenced, in part, by genetic variation. Although Southern African individuals have been shown to exhibit the highest levels of genetic diversity, they have been under-represented in pharmacogenetic research to date. Therefore, the aim of this study was to identify genetic variation within CYP3A4 in three South African population groups comprising of 29 Khoisan, 65 Xhosa and 65 Mixed Ancestry (MA) individuals. To identify known and novel CYP3A4 variants, 15 individuals were randomly selected from each of the population groups for bi-directional Sanger sequencing of ~600 bp of the 5′-upstream region and all thirteen exons including flanking intronic regions. Genetic variants detected were genotyped in the rest of the cohort. In total, 24 SNPs were detected, including CYP3A4*12, CYP3A4*15, and the reportedly functional CYP3A4*1B promoter polymorphism, as well as two novel non-synonymous variants. These putatively functional variants, p.R162W and p.Q200H, were present in two of the three populations and all three populations, respectively, and in silico analysis predicted that the former would damage the protein product. Furthermore, the three populations were shown to exhibit distinct genetic profiles. These results confirm that South African populations show unique patterns of variation in the genes encoding xenobiotic metabolizing enzymes. This research suggests that population-specific genetic profiles for CYP3A4 and other drug metabolizing genes would be essential to make full use of pharmacogenetics in Southern Africa. Further investigation is needed to determine if the identified genetic variants influence CYP3A4 metabolism phenotype in these populations.
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Affiliation(s)
- Britt Drögemöller
- Department of Genetics, Stellenbosch University Stellenbosch, South Africa
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29
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Dodgen TM, Hochfeld WE, Fickl H, Asfaha SM, Durandt C, Rheeder P, Drögemöller BI, Wright GEB, Warnich L, Labuschagne CDJ, van Schalkwyk A, Gaedigk A, Pepper MS. Introduction of the AmpliChip CYP450 Test to a South African cohort: a platform comparative prospective cohort study. BMC MEDICAL GENETICS 2013; 14:20. [PMID: 23356658 PMCID: PMC3605304 DOI: 10.1186/1471-2350-14-20] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/21/2011] [Accepted: 01/18/2013] [Indexed: 02/02/2023]
Abstract
Background Adverse drug reactions and lack of therapeutic efficacy associated with currently prescribed pharmacotherapeutics may be attributed, in part, to inter-individual variability in drug metabolism. Studies on the pharmacogenetics of Cytochrome P450 (CYP) enzymes offer insight into this variability. The objective of this study was to compare the AmpliChip CYP450 Test® (AmpliChip) to alternative genotyping platforms for phenotype prediction of CYP2C19 and CYP2D6 in a representative cohort of the South African population. Methods AmpliChip was used to screen for thirty-three CYP2D6 and three CYP2C19 alleles in two different cohorts. As a comparison cohort 2 was then genotyped using a CYP2D6 specific long range PCR with sequencing (CYP2D6 XL-PCR + Sequencing) platform and a PCR-RFLP platform for seven CYP2C19 alleles. Results Even though there was a low success rate for the AmpliChip, allele frequencies for both CYP2D6 and CYP2C19 were very similar between the two different cohorts. The CYP2D6 XL-PCR + Sequencing platform detected CYP2D6*5 more reliably and could correctly distinguish between CYP2D6*2 and *41 in the Black African individuals. Alleles not covered by the AmpliChip were identified and four novel CYP2D6 alleles were also detected. CYP2C19 PCR-RFLP identified CYP2C19*9,*15, *17 and *27 in the Black African individuals, with *2, *17 and *27 being relatively frequent in the cohort. Eliminating mismatches and identifying additional alleles will contribute to improving phenotype prediction for both enzymes. Phenotype prediction differed between platforms for both genes. Conclusion Comprehensive genotyping of CYP2D6 and CYP2C19 with the platforms used in this study, would be more appropriate than AmpliChip for phenotypic prediction in the South African population. Pharmacogenetically important novel alleles may remain undiscovered when using assays that are designed according to Caucasian specific variation, unless alternate strategies are utilised.
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Affiliation(s)
- Tyren M Dodgen
- Department of Pharmacology, University of Pretoria, Pretoria, South Africa
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Helsby NA, Burns KE. Molecular mechanisms of genetic variation and transcriptional regulation of CYP2C19. Front Genet 2012; 3:206. [PMID: 23087703 PMCID: PMC3467616 DOI: 10.3389/fgene.2012.00206] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2012] [Accepted: 09/24/2012] [Indexed: 12/11/2022] Open
Abstract
Inherited variation in the function of the drug metabolizing enzyme CYP2C19 was first observed 40 years ago. The SNP variants which underpin loss of CYP2C19 function have been elucidated and extensively studied in healthy populations. However, there has been relatively meagre translation of this information into the clinic. The presence of genotype-phenotype discordance in certain patients suggests that changes in the regulation of this gene, as well as loss of function SNPs, could play a role in deficient activity of this enzyme. Knowledge of the molecular mechanisms which control transcription of this gene, reviewed in this article, may aid the challenge of delivering CYP2C19 pharmacogenetics into clinical use.
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Affiliation(s)
- Nuala Ann Helsby
- Molecular Medicine and Pathology, Faculty of Medical and Health Sciences, University of Auckland Auckland, New Zealand
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31
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PharmGKB summary: very important pharmacogene information for cytochrome P450, family 2, subfamily C, polypeptide 19. Pharmacogenet Genomics 2012; 22:159-65. [PMID: 22027650 DOI: 10.1097/fpc.0b013e32834d4962] [Citation(s) in RCA: 127] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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32
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Al-Jenoobi FI, Alkharfy KM, Alghamdi AM, Bagulb KM, Al-Mohizea AM, Al-Muhsen S, Halwani R, Parvez MK, Al-Dosari MS. CYP2C19 genetic polymorphism in Saudi Arabians. Basic Clin Pharmacol Toxicol 2012; 112:50-4. [PMID: 22747643 DOI: 10.1111/j.1742-7843.2012.00919.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2012] [Accepted: 06/21/2012] [Indexed: 11/29/2022]
Abstract
The main objective of this study was to evaluate CYP2C19 genetic polymorphism in a Saudi Arabian population by determining the frequencies of CYP2C19*2, *3, *4, *6, *7 and *17 alleles and their relevant genotypes. Genomic DNA was isolated from 192 healthy Saudi Arabians, representing different geographical regions, and genotyping of the selected CYP2C19 variants was carried out by direct sequencing after PCR amplification. The allelic frequency of heterozygous CYP2C19*2 was 8.2% with only one individual found to carry the homozygous genotype of this defective allele. None of the other investigated poor metabolizer alleles (i.e. CYP2C19*3, *4, *6 and *7) was detected in the study population. About 46% of the examined volunteers were found to carry CYP2C19*17 genotype (37.5% heterozygous and 8.1% homozygous of the defective allele) with an overall CYP2C19*17 allelic frequency of 26.9%. In addition, a novel CYP2C19 SNP (G356A) and another very rare SNP (C336T) have been identified in this study with a frequency of about 50% for each. Further studies are required to evaluate the metabolic and clinical relevance of CYP2C19*17, G356A and C336T in the Saudi Arabian population.
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Affiliation(s)
- Fahad I Al-Jenoobi
- Department of Pharmaceutics, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
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33
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Georgitsi M, Zukic B, Pavlovic S, Patrinos GP. Transcriptional regulation and pharmacogenomics. Pharmacogenomics 2012; 12:655-73. [PMID: 21619428 DOI: 10.2217/pgs.10.215] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Interindividual variable drug response is correlated with sequence alterations in genes encoding drug-metabolizing enzymes and transporters, affecting drug absorption, distribution, metabolism and excretion. This variable drug response may have an impact on disease therapeutic outcomes, tolerance to adverse drug reactions and even survival. Sequence alterations may occur not only within the coding region of a gene, but in its regulatory elements too, affecting gene transcription and gene-expression levels. Here, we provide a compilation of the current knowledge of pharmacogenomics related to transcription, with a focus on the effect of SNPs and short tandem repeats residing in cis-regulatory elements of 11 genes encoding for drug-metabolizing enzymes and drug transporters. In addition, we comment on two genes encoding enzymes that are drug targets themselves. Finally, we briefly discuss the currently available methodologies for clinically assessing pharmacogenomic profiles, which could potentially in the future facilitate drug treatment-individualization via the identification of molecular signatures in specific patient groups.
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Affiliation(s)
- Marianthi Georgitsi
- Department of Pharmacy, School of Health Sciences, University of Patras, 26504 Rion, Patras, Greece
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Drögemöller BI, Wright GEB, Niehaus DJH, Emsley RA, Warnich L. Whole-genome resequencing in pharmacogenomics: moving away from past disparities to globally representative applications. Pharmacogenomics 2012; 12:1717-28. [PMID: 22118054 DOI: 10.2217/pgs.11.119] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Africa suffers from a high burden of disease; nonetheless, it has been one of the most under-represented continents with regard to genomic research. It can be argued that this disproportionate research is related to the fact that the genome architecture of African individuals is poorly suited to SNP-based genome-wide association studies, given existing genotyping platforms. However, this argument is no longer plausible with the arrival of next-generation sequencing technologies, which allow for the analysis of entire genomes. Using pharmacogenes to critically examine the merit of next-generation sequencing technologies in pharmacogenomics, we found a substantial amount of novel/uncharacterized variation, which was predicted to alter protein function. This variation was predominantly observed in African individuals, emphasizing the benefit of next-generation sequencing technologies specifically for these individuals. We also observed an improvement in the reliability of sequencing technologies in a relatively short time. Therefore, as sequencing technologies develop and decrease in cost, the ability to reliably detect variation will improve and these technologies will begin to replace other less comprehensive genotyping assays.
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Affiliation(s)
- Britt I Drögemöller
- Department of Genetics, Stellenbosch University, Private Bag XI, Matieland 7602, South Africa
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Dandara C, Lombard Z, Du Plooy I, McLellan T, Norris SA, Ramsay M. Genetic variants in CYP (-1A2, -2C9, -2C19, -3A4 and -3A5), VKORC1 and ABCB1 genes in a black South African population: a window into diversity. Pharmacogenomics 2012; 12:1663-70. [PMID: 22118051 DOI: 10.2217/pgs.11.106] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
AIM The frequencies of variants of pharmacogenetic importance differ across populations. African populations exhibit the greatest genetic heterogeneity, cautioning against extrapolating results among African groups. The aim of this study was to genotype pharmacogenetically relevant variants in black South Africans, to expand the limited data set available for indigenous African populations. SUBJECTS & METHODS A total of 14 SNPs associated with seven genes known to influence drug metabolism or transport (CYP1A2, CYP2C19, CYP2C9, CYP3A4, CYP3A5, VKORC1 and ABCB1) were investigated in a South African black (SAB) population (n = 993) and allele frequencies were compared with populations of African, Asian and European origin. RESULTS The majority of SNPs in the SAB demonstrated significant allele frequency differences when compared with both Europeans and Asians. There was greater similarity between the SAB and the Luhya (Kenya) and the Yoruba (Nigeria), than with Maasai (Kenya) individuals. The CYP2C9 SNP (rs1799853) was not polymorphic in the SAB and two VKORC1 SNPs (rs17708472 and rs9934438) had low variant allele frequencies, limiting their relevance to warfarin dose in this population. Population differences are emphasized by the significant differences in ABCB1 and the CYP3A gene family allele frequencies, with implications for drug metabolism and transport. CONCLUSION This study highlights the importance of investigating and documenting genetic variation at loci of pharmacogenetic relevance among different populations since this information could be used to inform drug efficacy, safety and recommended dosage.
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Affiliation(s)
- Collet Dandara
- School of Molecular & Cell Biology, University of the Witwatersrand, Johannesburg, South Africa
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36
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Lee IS, Kim D. Polymorphic metabolism by functional alterations of human cytochrome P450 enzymes. Arch Pharm Res 2011; 34:1799-816. [PMID: 22139682 DOI: 10.1007/s12272-011-1103-2] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2011] [Accepted: 08/24/2011] [Indexed: 10/14/2022]
Abstract
The study of cytochrome P450 pharmacogenomics is of particular interest because of its promise in the development of rational means to optimize drug therapy with respect to patient's genotype to ensure maximum efficacy with minimal adverse effects. Drug metabolizing P450 enzymes are polymorphic and are the main phase I enzymes responsible for the metabolism of clinical drugs. Therefore, polymorphisms in the P450s have the most impact on the fate of clinical drugs in phase I metabolism since almost 80% of drugs in use today are metabolized by these enzymes. Predictive genotyping for P450 enzymes for a more effective therapy will be routine for specific drugs in the future. In this review, we discuss the current knowledge of polymorphic metabolism by functional alterations in nonsynonymous SNPs of P450 1A2, 2A6, 2C8, 2C9, 2C19, 2D6, and 3A4 enzymes.
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Affiliation(s)
- Im-Soon Lee
- Department of Biological Sciences and Center for Biotechnology Research in UBITA, Konkuk University, Seoul 143-701, Korea
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37
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Warnich L, Drögemöller BI, Pepper MS, Dandara C, Wright GEB. Pharmacogenomic Research in South Africa: Lessons Learned and Future Opportunities in the Rainbow Nation. ACTA ACUST UNITED AC 2011; 9:191-207. [PMID: 22563365 PMCID: PMC3228231 DOI: 10.2174/187569211796957575] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2011] [Revised: 05/25/2011] [Accepted: 05/28/2011] [Indexed: 12/11/2022]
Abstract
South Africa, like many other developing countries, stands to benefit from novel diagnostics and drugs developed by pharmacogenomics guidance due to high prevalence of disease burden in the region. This includes both communicable (e.g., HIV/AIDS and tuberculosis) and non-communicable (e.g., diabetes and cardiovascular) diseases. For example, although only 0.7% of the world's population lives in South Africa, the country carries 17% of the global HIV/AIDS burden and 5% of the global tuberculosis burden. Nobel Peace Prize Laureate Archbishop Emeritus Desmond Tutu has coined the term Rainbow Nation, referring to a land of wealth in its many diverse peoples and cultures. It is now timely and necessary to reflect on how best to approach new genomics biotechnologies in a manner that carefully considers the public health needs and extant disease burden in the region. The aim of this paper is to document and review the advances in pharmacogenomics in South Africa and importantly, to evaluate the direction that future research should take. Previous research has shown that the populations in South Africa exhibit unique allele frequencies and novel genetic variation in pharmacogenetically relevant genes, often differing from other African and global populations. The high level of genetic diversity, low linkage disequilibrium and the presence of rare variants in these populations question the feasibility of the use of current commercially available genotyping platforms, and may partially account for genotype-phenotype discordance observed in past studies. However, the employment of high throughput technologies for genomic research, within the context of large clinical trials, combined with interdisciplinary studies and appropriate regulatory guidelines, should aid in acceleration of pharmacogenomic discoveries in high priority therapeutic areas in South Africa. Finally, we suggest that projects such as the H3Africa Initiative, the SAHGP and PGENI should play an integral role in the coordination of genomic research in South Africa, but also other African countries, by providing infrastructure and capital to local researchers, as well as providing aid in addressing the computational and statistical bottlenecks encountered at present.
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Affiliation(s)
- Louise Warnich
- Department of Genetics, Stellenbosch University, Stellenbosch, South Africa
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38
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Abstract
Herbal usage remains popular as an alternative or complementary form of treatment, especially in Africa. However, the misconception that herbal remedies are safe due to their "natural" origins jeopardizes human safety, as many different interactions can occur with concomitant use with other pharmaceuticals on top of potential inherent toxicity. Cytochrome P450 enzymes are highly polymorphic, and pose a problem for pharmaceutical drug tailoring to meet an individual's specific metabolic activity. The influence of herbal remedies further complicates this. The plants included in this review have been mainly researched for determining their effect on cytochrome P450 enzymes and P-glycoprotein drug transporters. Usage of herbal remedies, such as Hypoxis hemerocallidea, Sutherlandia frutescens and Harpagophytum procumbensis popular in Africa. The literature suggests that there is a potential for drug-herb interactions, which could occur through alterations in metabolism and transportation of drugs. Research has primarily been conducted in vitro, whereas in vivo data are lacking. Research concerning the effect of African herbals on drug metabolism should also be approached, as specific plants are especially popular in conjunction with certain treatments. Although these interactions can be beneficial, the harm they pose is just as great.
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Affiliation(s)
- Werner Cordier
- Department of Pharmacology, University of Pretoria, Pretoria, South Africa
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39
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Wang H, Kim RA, Sun D, Gao Y, Wang H, Zhu J, Chen C. Evaluation of the effects of 18 non-synonymous single-nucleotide polymorphisms of CYP450 2C19 onin vitrodrug inhibition potential by a fluorescence-based high-throughput assay. Xenobiotica 2011; 41:826-35. [DOI: 10.3109/00498254.2011.582893] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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40
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Ikediobi O, Aouizerat B, Xiao Y, Gandhi M, Gebhardt S, Warnich L. Analysis of pharmacogenetic traits in two distinct South African populations. Hum Genomics 2011; 5:265-82. [PMID: 21712189 PMCID: PMC3525241 DOI: 10.1186/1479-7364-5-4-265] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2011] [Accepted: 03/21/2011] [Indexed: 01/11/2023] Open
Abstract
Our knowledge of pharmacogenetic variability in diverse populations is scarce, especially in sub-Saharan Africa. To bridge this gap in knowledge, we characterised population frequencies of clinically relevant pharmacogenetic traits in two distinct South African population groups. We genotyped 211 tagging single nucleotide polymorphisms (tagSNPs) in 12 genes that influence antiretroviral drug disposition, in 176 South African individuals belonging to two distinct population groups residing in the Western Cape: the Xhosa (n = 109) and Cape Mixed Ancestry (CMA) (n = 67) groups. The minor allele frequencies (MAFs) of eight tagSNPs in six genes (those encoding the ATP binding cassette sub-family B, member 1 [ABCB1], four members of the cytochrome P450 family [CYP2A7P1, CYP2C18, CYP3A4, CYP3A5] and UDP-glucuronosyltransferase 1 [UGT1A1]) were significantly different between the Xhosa and CMA populations (Bonferroni p < 0.05). Twenty-seven haplotypes were inferred in four genes (CYP2C18, CYP3A4, the gene encoding solute carrier family 22 member 6 [SLC22A6] and UGT1A1) between the two South African populations. Characterising the Xhosa and CMA population frequencies of variant alleles important for drug transport and metabolism can help to establish the clinical relevance of pharmacogenetic testing in these populations.
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Affiliation(s)
- Ogechi Ikediobi
- University of California, San Francisco, School of Pharmacy, Department of Clinical Pharmacy, CA 94143, USA.
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41
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Current world literature. Curr Opin Allergy Clin Immunol 2011; 11:269-73. [PMID: 21516010 DOI: 10.1097/aci.0b013e3283473da8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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42
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Suarez-Kurtz G. Linkage disequilibrium between the CYP2C19*17 and CYP2C8*2 alleles in populations of African descent. Eur J Clin Pharmacol 2010; 67:211-2. [DOI: 10.1007/s00228-010-0910-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2010] [Accepted: 09/21/2010] [Indexed: 10/19/2022]
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