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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: 13] [Impact Index Per Article: 6.5] [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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Zamani P, Mohammadi H, Mirhoseini SZ. Genome-wide association study and genomic heritabilities for blood protein levels in Lori-Bakhtiari sheep. Sci Rep 2021; 11:23771. [PMID: 34887490 PMCID: PMC8660901 DOI: 10.1038/s41598-021-03290-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 12/01/2021] [Indexed: 01/01/2023] Open
Abstract
Serum protein levels are related to physiological and pathological status of animals and could be affected by both genetic and environmental factors. This study aimed to evaluate genetic variation of serum protein profile in sheep. Blood samples were randomly collected from 96 Lori-Bakhtiari ewes, a heavy meat-type breed. Total protein, albumin, globulin, α1, α2, β and γ globulins and IgG levels were measured in blood serum. The samples were genotyped using the Illumina OvineSNP50 BeadChip. The studied traits adjusted for age, birth type, birth season and estimate of breeding value for body weight were considered as pseudo-phenotypes in genome-wide association analysis. In the GWAS model, the first five principal components were fitted as covariates to correct the biases due to possible population stratification. The Plink, R and GCTA software were used for genome-wide association analysis, construction of Q-Q and Manhattan plots and estimation of genetic variances, respectively. Noticeable genomic heritabilities ± SE were estimated for total and γ globulins (0.868 ± 0.262 and 0.831 ± 0.364, respectively), but other protein fractions had zero or close to zero estimates. Based on the Bonferroni adjusted p values, four QTLs located on 181.7 Mbp of OAR3, 107.7 Mbp of OAR4, 86.3 Mbp of OAR7 and 83.0 Mbp of OAR8 were significantly associated with α1, β, β and γ globulins, respectively. The results showed that the PKP2, IGF2R, SLC22A1 and SLC22A2 genes could be considered as candidate genes for blood serum proteins. The present study showed significant genetic variations of some blood protein fractions.
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Affiliation(s)
- P Zamani
- Department of Animal Science, Faculty of Agriculture, Bu-Ali Sina University, Hamedan, Iran.
| | - H Mohammadi
- Department of Animal Science, Faculty of Agriculture, Bu-Ali Sina University, Hamedan, Iran
| | - S Z Mirhoseini
- Department of Animal Science, Faculty of Agriculture, University of Guilan, Rasht, Iran
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Zazuli Z, Duin NJCB, Jansen K, Vijverberg SJH, Maitland-van der Zee AH, Masereeuw R. The Impact of Genetic Polymorphisms in Organic Cation Transporters on Renal Drug Disposition. Int J Mol Sci 2020; 21:ijms21186627. [PMID: 32927790 PMCID: PMC7554776 DOI: 10.3390/ijms21186627] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 09/05/2020] [Accepted: 09/07/2020] [Indexed: 12/18/2022] Open
Abstract
A considerable number of drugs and/or their metabolites are excreted by the kidneys through glomerular filtration and active renal tubule secretion via transporter proteins. Uptake transporters in the proximal tubule are part of the solute carrier (SLC) superfamily, and include the organic cation transporters (OCTs). Several studies have shown that specific genetic polymorphisms in OCTs alter drug disposition and may lead to nephrotoxicity. Multiple single nucleotide polymorphisms (SNPs) have been reported for the OCT genes (SLC22A1, SLC22A2 and SLC22A3), which can influence the proteins’ structure and expression levels and affect their transport function. A gain-in-function mutation may lead to accumulation of drugs in renal proximal tubule cells, eventually leading to nephrotoxicity. This review illustrates the impact of genetic polymorphisms in OCTs on renal drug disposition and kidney injury, the clinical significances and how to personalize therapies to minimize the risk of drug toxicity.
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Affiliation(s)
- Zulfan Zazuli
- Department of Respiratory Medicine, Amsterdam UMC, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands; (S.J.H.V.); (A.H.M.-v.d.Z.)
- Department of Pharmacology-Clinical Pharmacy, School of Pharmacy, Bandung Institute of Technology, Jawa Barat 40132, Indonesia
- Correspondence: (Z.Z.); (R.M.)
| | - Naut J. C. B. Duin
- Division of Pharmacology, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, 3584 CG Utrecht, The Netherlands; (N.J.C.B.D.); (K.J.)
| | - Katja Jansen
- Division of Pharmacology, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, 3584 CG Utrecht, The Netherlands; (N.J.C.B.D.); (K.J.)
| | - Susanne J. H. Vijverberg
- Department of Respiratory Medicine, Amsterdam UMC, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands; (S.J.H.V.); (A.H.M.-v.d.Z.)
| | - Anke H. Maitland-van der Zee
- Department of Respiratory Medicine, Amsterdam UMC, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands; (S.J.H.V.); (A.H.M.-v.d.Z.)
| | - Rosalinde Masereeuw
- Division of Pharmacology, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, 3584 CG Utrecht, The Netherlands; (N.J.C.B.D.); (K.J.)
- Correspondence: (Z.Z.); (R.M.)
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Rajman I, Knapp L, Hanna I. Genetic Diversity in Drug Transporters: Impact in African Populations. Clin Transl Sci 2020; 13:848-860. [PMID: 32100958 PMCID: PMC7485953 DOI: 10.1111/cts.12769] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Accepted: 01/04/2020] [Indexed: 01/18/2023] Open
Abstract
Polymorphisms in drug transporters, like the adenosine triposphate-binding cassette (ABC) and solute carrier (SLC) superfamilies, may contribute to the observed diversity in drug response in African patients. This review aims to provide a comprehensive summary and analysis of the frequencies and distributions in African populations of ABC and SLC variants that affect drug pharmacokinetics (PK) and pharmacodynamics (PD). Of polymorphisms evaluated in African populations, SLCO1B1 rs4149056 and SLC22A6 rs1158626 were found at markedly higher frequencies than in non-African populations. SLCO1B1 rs4149056 was associated with reduction in rifampin exposure, which has implications for dosing this important anti-tuberculosis therapy. SLC22A6 rs1158626 was associated with increased affinity for antiretroviral drugs. Genetic diversity in SLC and ABC transporters in African populations has implications for conventional therapies, notably in tuberculosis and HIV. More PK and PD data in African populations are needed to assess potential for a different response to drugs compared with other global populations.
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Mtisi TJ, Ndhlovu CE, Maponga CC, Morse GD. Tenofovir-associated kidney disease in Africans: a systematic review. AIDS Res Ther 2019; 16:12. [PMID: 31171021 PMCID: PMC6554992 DOI: 10.1186/s12981-019-0227-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Accepted: 05/25/2019] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Data on chronic kidney disease development in HIV infection is important towards building a comprehensive knowledge of HIV, ageing and polypharmacy in Africa. Several previous studies on tenofovir-associated kidney disease in Africa have shown conflicting results. This review summarises what is known about the development of kidney disease in HIV-positive African patients on tenofovir disoproxil fumarate (TDF)-containing ART. We set out to document the occurrence of kidney disease in HIV-positive Africans on TDF-containing ART in population-based studies and to evaluate the renal safety of TDF in Africans. METHODS We conducted a systemic review using published studies which were identified through a computerized search of original research using the Medline/PubMed database, EMBASE, EBM Reviews, Proquest Google Scholar and Global Health reported from inception until 5 October 2017. Two reviewers independently abstracted the data and performed quality assessment of the included studies. We screened 595 articles and included 31 in the qualitative analysis performed. RESULTS A total of 106 406 patients (of whom 66,681 were on Tenofovir) were involved in these 31 studies with sample sizes ranging from 30 to 62,230. Duration on tenofovir-containing ART ranged from those initiating ART at baseline to those who received TDF for up to 9 years. All but one of the studies involved only patients 16 years and older. The studies had differing definitions of kidney dysfunction and were of variable study design quality. The documented outcomes had substantial discrepancies across the studies, most likely due to methodological differences, study size and disparate outcome definitions. CONCLUSIONS Our review identified studies in Africans reporting statistically significant renal function decline associated with TDF use but the clinical significance of this effect was not enough to contraindicate its continued use in ART regimens. Consistent with studies in other populations, patients are at greater risk if they have pre-existing renal disease and are more advanced in age. More research is needed on paediatric populations under 16 years of age. Trial registration This review was registered on Prospero (registration number CRD42018078717).
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Affiliation(s)
- Takudzwa J. Mtisi
- Department of Clinical Pharmacology, University of Zimbabwe College of Health Sciences, Harare, Zimbabwe
| | - Chiratidzo E. Ndhlovu
- Department of Medicine, University of Zimbabwe College of Health Sciences, Harare, Zimbabwe
| | - Chiedza C. Maponga
- School of Pharmacy, University of Zimbabwe College of Health Sciences, Harare, Zimbabwe
| | - Gene D. Morse
- Center for Integrated Global Biomedical Sciences; School of Pharmacy and Pharmaceutical Sciences, University at Buffalo, State University of New York, Buffalo, NY USA
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Glatard A, Guidi M, Dobrinas M, Cornuz J, Csajka C, Eap CB. Influence of body weight and UGT2B7 polymorphism on varenicline exposure in a cohort of smokers from the general population. Eur J Clin Pharmacol 2019; 75:939-949. [PMID: 30868192 DOI: 10.1007/s00228-019-02662-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Accepted: 03/06/2019] [Indexed: 12/25/2022]
Abstract
PURPOSE The abstinence rate to tobacco after varenicline treatment is moderate and might be partially affected by variability in varenicline concentrations. This study aimed at characterizing the sources of variability in varenicline pharmacokinetics and to relate varenicline exposure to abstinence. METHODS The population pharmacokinetic analysis (NONMEM®) included 121 varenicline concentrations from 82 individuals and tested the influence of genetic and non-genetic characteristics on apparent clearance (CL/F) and volume of distribution (V/F). Model-based average concentrations over 24 h (Cav) were used to test the impact of varenicline exposure on the input rate (Kin) expressed as a function of the number of cigarettes per day in a turnover model of 373 expired carbon monoxide levels. RESULTS A one-compartment model with first-order absorption and elimination appropriately described varenicline concentrations. CL/F was 8.5 L/h (coefficient of variation, 26%), V/F was 228 L, and the absorption rate (ka) was fixed to 0.98 h-1. CL/F increased by 46% in 100-kg individuals compared to 60-kg individuals and was found to be 21% higher in UGT2B7 rs7439366 TT individuals. These covariates explained 14% and 9% of the interindividual variability in CL/F, respectively. No influence of varenicline Cav was found on Kin in addition to the number of cigarettes. CONCLUSIONS Body weight mostly and to a smaller extent genetic polymorphisms of UGT2B7 can influence varenicline exposure. Dose adjustment based on body weight and, if available, on UGT2B7 genotype might be useful to improve clinical efficacy and tolerability of varenicline.
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Affiliation(s)
- Anaïs Glatard
- Unit of Pharmacogenetics and Clinical Psychopharmacology, Centre for Psychiatric Neuroscience, Department of Psychiatry, Lausanne University Hospital, Hospital of Cery, University of Lausanne, Prilly, Switzerland
- Service of Clinical Pharmacology, Department of Laboratories, Lausanne University Hospital, University of Lausanne, Lausanne, Switzerland
| | - Monia Guidi
- Service of Clinical Pharmacology, Department of Laboratories, Lausanne University Hospital, University of Lausanne, Lausanne, Switzerland
- School of Pharmaceutical Sciences, University of Geneva, University of Lausanne, Geneva, Switzerland
| | - Maria Dobrinas
- Unit of Pharmacogenetics and Clinical Psychopharmacology, Centre for Psychiatric Neuroscience, Department of Psychiatry, Lausanne University Hospital, Hospital of Cery, University of Lausanne, Prilly, Switzerland
| | - Jacques Cornuz
- Department of Ambulatory Care and Community Medicine, University of Lausanne, Lausanne, Switzerland
| | - Chantal Csajka
- Service of Clinical Pharmacology, Department of Laboratories, Lausanne University Hospital, University of Lausanne, Lausanne, Switzerland.
- School of Pharmaceutical Sciences, University of Geneva, University of Lausanne, Geneva, Switzerland.
| | - Chin B Eap
- Unit of Pharmacogenetics and Clinical Psychopharmacology, Centre for Psychiatric Neuroscience, Department of Psychiatry, Lausanne University Hospital, Hospital of Cery, University of Lausanne, Prilly, Switzerland.
- School of Pharmaceutical Sciences, University of Geneva, University of Lausanne, Geneva, Switzerland.
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Cai LL, Huang WQ, Su ZY, Ye HM, Wang LS, Wu Y, Zhang ZY, Zhang W, Tzeng CM. Identification of two novel genes SLC15A2 and SLCO1B3 associated with maintenance dose variability of warfarin in a Chinese population. Sci Rep 2017; 7:17379. [PMID: 29234073 PMCID: PMC5727167 DOI: 10.1038/s41598-017-17731-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Accepted: 11/29/2017] [Indexed: 01/12/2023] Open
Abstract
Warfarin is a commonly prescribed and effective oral anticoagulant. Genetic polymorphisms associated with warfarin metabolism and sensitivity have been implicated in the wide inter-individual dose variation that is observed. Several algorithms integrating patients’ clinical characteristics and genetic polymorphism information have been explored to predict warfarin dose. However, most of these algorithms could explain only over half of the variation in a warfarin maintenance dose, suggesting that additional genetic factors may exist and need to be identified. Here, a drug absorption, distribution, metabolism and excretion (ADME) Core Panel Kit-based pharmacogenetic study was performed to screen for warfarin dose-associated SNP sites in Han-Chinese population patients taking warfarin therapy, and the screen was followed by pyrosequencing-based validation. Finally, we confirmed that the common variant rs9923231 in VKORC1 and two novel genes, SLC15A2 (rs1143671 and rs1143672) and SLCO1B3 (rs4149117 and rs7311358), are associated with the warfarin maintenance dose. As has been shown for those carriers with the variant rs9923231 in VKORC1, it was suggested that those subjects with homozygous minor alleles in those four SNPs should take a lower warfarin dose than those carrying the wild type alleles. Together with the established predictor rs9923231 in VKORC1, those four novel variants on SLC15A2 and SLCO1B3 should be considered as useful biomarkers for warfarin dose adjustment in clinical practice in Han-Chinese populations.
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Affiliation(s)
- Liang-Liang Cai
- Translational Medicine Research Center, School of Pharmaceutical Sciences, Xiamen University, Xiamen, Fujian Sheng, China
| | - Wen-Qing Huang
- Translational Medicine Research Center, School of Pharmaceutical Sciences, Xiamen University, Xiamen, Fujian Sheng, China
| | - Zhi-Ying Su
- Clinical Research Laboratory, Xiamen's Maternal and Child Health Hospital, Teaching Hospital of Xiamen University, Xiamen, Fujian Sheng, China
| | - Hui-Ming Ye
- Translational Medicine Research Center, School of Pharmaceutical Sciences, Xiamen University, Xiamen, Fujian Sheng, China.,Clinical Research Laboratory, Xiamen's Maternal and Child Health Hospital, Teaching Hospital of Xiamen University, Xiamen, Fujian Sheng, China
| | - Lian-Sheng Wang
- Department of Clinical Pharmacology, Xiangya Hospital, Institute of Clinical Pharmacology, Central South University, Changsha, Hunan Sheng, China
| | - Yuan Wu
- Department of cardiac surgery, Xiamen Cardiovascular Hospital, School of Medicine, Xiamen University, Xiamen, Fujian Sheng, China
| | - Zhong-Ying Zhang
- Department of Clinical laboratory, Zhongshan Hospital, Xiamen University, Xiamen, Fujian Sheng, China
| | - Wei Zhang
- Department of Clinical Pharmacology, Xiangya Hospital, Institute of Clinical Pharmacology, Central South University, Changsha, Hunan Sheng, China.
| | - Chi-Meng Tzeng
- Translational Medicine Research Center, School of Pharmaceutical Sciences, Xiamen University, Xiamen, Fujian Sheng, China.
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Emami Riedmaier A, Nies AT, Schaeffeler E, Schwab M. Organic Anion Transporters and Their Implications in Pharmacotherapy. Pharmacol Rev 2012; 64:421-49. [DOI: 10.1124/pr.111.004614] [Citation(s) in RCA: 91] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
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