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Lusiki Z, Blom D, Soko ND, Malema S, Jones E, Rayner B, Blackburn J, Sinxadi P, Dandara MT, Dandara C. Major Genetic Drivers of Statin Treatment Response in African Populations and Pharmacogenetics of Dyslipidemia Through a One Health Lens. OMICS : A JOURNAL OF INTEGRATIVE BIOLOGY 2024; 28:261-279. [PMID: 37956269 DOI: 10.1089/omi.2023.0122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
A One Health lens is increasingly significant to address the intertwined challenges in planetary health concerned with the health of humans, nonhuman animals, plants, and ecosystems. A One Health approach can benefit the public health systems in Africa that are overburdened by noncommunicable, infectious, and environmental diseases. Notably, the COVID-19 pandemic revealed the previously overlooked two-fold importance of pharmacogenetics (PGx), for individually tailored treatment of noncommunicable diseases and environmental pathogens. For example, dyslipidemia, a common cardiometabolic risk factor, has been identified as an independent COVID-19 severity risk factor. Observational data suggest that patients with COVID-19 infection receiving lipid-lowering therapy may have better outcomes. However, among African patients, the response to these drugs varies from patient to patient, pointing to the possible contribution of genetic variation in important pharmacogenes. The PGx of lipid-lowering therapies may underlie differences in treatment responses observed among dyslipidemia patients as well as patients comorbid with COVID-19 and dyslipidemia. Genetic variations in APOE, ABCB1, CETP, CYP2C9, CYP3A4, CYP3A5, HMGCR, LDLR, NPC1L1, and SLCO1B1 genes affect the pharmacogenomics of statins, and they have individually been linked to differential responses to dyslipidemia and COVID-19 treatment. African populations are underrepresented in PGx research. This leads to poor accounting of additional diverse genetic variants that could be important in understanding interindividual and between-population variations in therapeutic responses to dyslipidemia and COVID-19. This expert review examines and synthesizes the salient and priority PGx variations, as seen through a One Health lens in Africa, to improve and inform personalized medicine in both dyslipidemia and COVID-19.
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Affiliation(s)
- Zizo Lusiki
- Division of Human Genetics, Department of Pathology, Institute of Infectious Diseases and Molecular Medicine (IDM), University of Cape Town, Cape Town, South Africa
- Platform for Pharmacogenomics Research and Translation (PREMED) Unit, South African Medical Research Council (SAMRC), Cape Town, South Africa
| | - Dirk Blom
- Platform for Pharmacogenomics Research and Translation (PREMED) Unit, South African Medical Research Council (SAMRC), Cape Town, South Africa
- Division of Lipidology and Cape Heart Institute, Department of Medicine, University of Cape Town, Cape Town, South Africa
| | - Nyarai D Soko
- Division of Human Genetics, Department of Pathology, Institute of Infectious Diseases and Molecular Medicine (IDM), University of Cape Town, Cape Town, South Africa
- Platform for Pharmacogenomics Research and Translation (PREMED) Unit, South African Medical Research Council (SAMRC), Cape Town, South Africa
| | - Smangele Malema
- Platform for Pharmacogenomics Research and Translation (PREMED) Unit, South African Medical Research Council (SAMRC), Cape Town, South Africa
| | - Erika Jones
- Platform for Pharmacogenomics Research and Translation (PREMED) Unit, South African Medical Research Council (SAMRC), Cape Town, South Africa
- Division of Nephrology and Hypertension, Department of Medicine, University of Cape Town, Cape Town, South Africa
| | - Brian Rayner
- Platform for Pharmacogenomics Research and Translation (PREMED) Unit, South African Medical Research Council (SAMRC), Cape Town, South Africa
- Division of Nephrology and Hypertension, Department of Medicine, University of Cape Town, Cape Town, South Africa
| | - Jonathan Blackburn
- Division of Chemical and Systems Biology, Department of Integrative Biomedical Sciences, University of Cape Town, Cape Town, South Africa
| | - Phumla Sinxadi
- Platform for Pharmacogenomics Research and Translation (PREMED) Unit, South African Medical Research Council (SAMRC), Cape Town, South Africa
- Division of Clinical Pharmacology, Department of Medicine, University of Cape Town, Cape Town, South Africa
| | - Michelle T Dandara
- Platform for Pharmacogenomics Research and Translation (PREMED) Unit, South African Medical Research Council (SAMRC), Cape Town, South Africa
| | - Collet Dandara
- Division of Human Genetics, Department of Pathology, Institute of Infectious Diseases and Molecular Medicine (IDM), University of Cape Town, Cape Town, South Africa
- Platform for Pharmacogenomics Research and Translation (PREMED) Unit, South African Medical Research Council (SAMRC), Cape Town, South Africa
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2
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Richard-St-Hilaire A, Gamache I, Pelletier J, Grenier JC, Poujol R, Hussin JG. Signatures of Co-evolution and Co-regulation in the CYP3A and CYP4F Genes in Humans. Genome Biol Evol 2024; 16:evad236. [PMID: 38207129 PMCID: PMC10805436 DOI: 10.1093/gbe/evad236] [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: 03/14/2023] [Revised: 12/19/2023] [Accepted: 12/22/2023] [Indexed: 01/13/2024] Open
Abstract
Cytochromes P450 (CYP450) are hemoproteins generally involved in the detoxification of the body of xenobiotic molecules. They participate in the metabolism of many drugs and genetic polymorphisms in humans have been found to impact drug responses and metabolic functions. In this study, we investigate the genetic diversity of CYP450 genes. We found that two clusters, CYP3A and CYP4F, are notably differentiated across human populations with evidence for selective pressures acting on both clusters: we found signals of recent positive selection in CYP3A and CYP4F genes and signals of balancing selection in CYP4F genes. Furthermore, an extensive amount of unusual linkage disequilibrium is detected in this latter cluster, indicating co-evolution signatures among CYP4F genes. Several of the selective signals uncovered co-localize with expression quantitative trait loci (eQTL), which could suggest epistasis acting on co-regulation in these gene families. In particular, we detected a potential co-regulation event between CYP3A5 and CYP3A43, a gene whose function remains poorly characterized. We further identified a causal relationship between CYP3A5 expression and reticulocyte count through Mendelian randomization analyses, potentially involving a regulatory region displaying a selective signal specific to African populations. Our findings linking natural selection and gene expression in CYP3A and CYP4F subfamilies are of importance in understanding population differences in metabolism of nutrients and drugs.
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Affiliation(s)
- Alex Richard-St-Hilaire
- Département de biochimie et médecine moléculaire, Université de Montréal, Montreal, QC, Canada
- Sainte-Justine Hospital, Research Center, Montreal, QC, Canada
| | - Isabel Gamache
- Département de biochimie et médecine moléculaire, Université de Montréal, Montreal, QC, Canada
- Montreal Heart Institute, Research Center, Montreal, QC, Canada
| | - Justin Pelletier
- Département de biochimie et médecine moléculaire, Université de Montréal, Montreal, QC, Canada
- McGill CERC in Genomic Medicine, McGill University, Montreal, Canada
| | | | - Raphaël Poujol
- Montreal Heart Institute, Research Center, Montreal, QC, Canada
| | - Julie G Hussin
- Montreal Heart Institute, Research Center, Montreal, QC, Canada
- Département de médecine, Université de Montréal, Montreal, QC, Canada
- Mila-Quebec AI institute, Montreal, QC, Canada
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3
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Soko ND, Muyambo S, Dandara MTL, Kampira E, Blom D, Jones ESW, Rayner B, Shamley D, Sinxadi P, Dandara C. Towards Evidence-Based Implementation of Pharmacogenomics in Southern Africa: Comorbidities and Polypharmacy Profiles across Diseases. J Pers Med 2023; 13:1185. [PMID: 37623436 PMCID: PMC10455498 DOI: 10.3390/jpm13081185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 07/21/2023] [Accepted: 07/23/2023] [Indexed: 08/26/2023] Open
Abstract
Pharmacogenomics may improve patient care by guiding drug selection and dosing; however, this requires prior knowledge of the pharmacogenomics of drugs commonly used in a specific setting. The aim of this study was to identify a preliminary set of pharmacogenetic variants important in Southern Africa. We describe comorbidities in 3997 patients from Malawi, South Africa, and Zimbabwe. These patient cohorts were included in pharmacogenomic studies of anticoagulation, dyslipidemia, hypertension, HIV and breast cancer. The 20 topmost prescribed drugs in this population were identified. Using the literature, a list of pharmacogenes vital in the response to the top 20 drugs was constructed leading to drug-gene pairs potentially informative in translation of pharmacogenomics. The most reported morbidity was hypertension (58.4%), making antihypertensives the most prescribed drugs, particularly amlodipine. Dyslipidemia occurred in 31.5% of the participants, and statins were the most frequently prescribed as cholesterol-lowering drugs. HIV was reported in 20.3% of the study participants, with lamivudine/stavudine/efavirenz being the most prescribed antiretroviral combination. Based on these data, pharmacogenes of immediate interest in Southern African populations include ABCB1, CYP2B6, CYP2C9, CYP2C19, CYP2D6, CYP3A4, CYP3A5, SLC22A1, SLCO1B1 and UGT1A1. Variants in these genes are a good starting point for pharmacogenomic translation programs in Southern Africa.
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Affiliation(s)
- Nyarai Desiree Soko
- Platform for Pharmacogenomics Research and Translation (PREMED), University of Cape Town, South African Medical Research Council, Cape Town 7935, South Africa
- Department of Pharmaceutical Technology, School of Allied Health Sciences, Harare Institute of Technology, Harare, Zimbabwe
- Pharmacogenomics and Drug Metabolism Research Group, Division of Human Genetics, Department of Pathology and Institute of Infectious Diseases and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town 7935, South Africa
| | - Sarudzai Muyambo
- Department of Biological Sciences and Ecology, Faculty of Science, University of Zimbabwe, Harare, Zimbabwe
| | - Michelle T. L. Dandara
- Platform for Pharmacogenomics Research and Translation (PREMED), University of Cape Town, South African Medical Research Council, Cape Town 7935, South Africa
| | - Elizabeth Kampira
- Medical Laboratory Sciences, School of Life Sciences and Health Professionals, Kamuzu University of Health Sciences (KUHES), Blantyre, Malawi
| | - Dirk Blom
- Platform for Pharmacogenomics Research and Translation (PREMED), University of Cape Town, South African Medical Research Council, Cape Town 7935, South Africa
- Division of Lipidology and Cape Heart Institute, Department of Medicine, Groote Schuur Hospital and Faculty of Health Sciences, University of Cape Town, Cape Town 7935, South Africa
| | - Erika S. W. Jones
- Platform for Pharmacogenomics Research and Translation (PREMED), University of Cape Town, South African Medical Research Council, Cape Town 7935, South Africa
- Division of Nephrology and Hypertension, Department of Medicine, Groote Schuur Hospital and Faculty of Health Sciences, University of Cape Town, Cape Town 7935, South Africa
| | - Brian Rayner
- Platform for Pharmacogenomics Research and Translation (PREMED), University of Cape Town, South African Medical Research Council, Cape Town 7935, South Africa
| | - Delva Shamley
- Division of Clinical Anatomy and Biological Anthropology, Department of Human Biology, Faculty of Health Sciences, University of Cape Town, Cape Town 7935, South Africa
| | - Phumla Sinxadi
- Platform for Pharmacogenomics Research and Translation (PREMED), University of Cape Town, South African Medical Research Council, Cape Town 7935, South Africa
- Division of Clinical Pharmacology, Department of Medicine, Groote Schuur Hospital and Faculty of Health Sciences, University of Cape Town, Cape Town 7935, South Africa
| | - Collet Dandara
- Department of Pharmaceutical Technology, School of Allied Health Sciences, Harare Institute of Technology, Harare, Zimbabwe
- Pharmacogenomics and Drug Metabolism Research Group, Division of Human Genetics, Department of Pathology and Institute of Infectious Diseases and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town 7935, South Africa
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Edinur HA, Mat-Ghani SNA, Chambers GK. Ethnicity-based classifications and medical genetics: One Health approaches from a Western Pacific perspective. Front Genet 2022; 13:970549. [PMID: 36147511 PMCID: PMC9485872 DOI: 10.3389/fgene.2022.970549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 08/18/2022] [Indexed: 11/29/2022] Open
Abstract
A new era presently dawns for medical genetics featuring individualised whole genome sequencing and promising personalised medical genetics. Accordingly, we direct readers attention to the continuing value of allele frequency data from Genome-Wide Association Surveys (GWAS) and single gene surveys in well-defined ethnic populations as a guide for best practice in diagnosis, therapy, and prescription. Supporting evidence is drawn from our experiences working with Austronesian volunteer subjects across the Western Pacific. In general, these studies show that their gene pool has been shaped by natural selection and become highly diverged from those of Europeans and Asians. These uniquely evolved patterns of genetic variation underlie contrasting schedules of disease incidence and drug response. Thus, recognition of historical bonds of kinship among Austronesian population groups across the Asia Pacific has distinct public health advantages from a One Health perspective. Other than diseases that are common among them like gout and diabetes, Austronesian populations face a wide range of climate-dependent infectious diseases including vector-borne pathogens as they are now scattered across the Pacific and Indian Oceans. However, we caution that the value of genetic survey data in Austronesians (and other groups too) is critically dependent on the accuracy of attached descriptive information in associated metadata, including ethnicity and admixture.
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Affiliation(s)
- Hisham A. Edinur
- School of Health Sciences, Universiti Sains Malaysia, Kelantan, Malaysia
- *Correspondence: Hisham A. Edinur,
| | | | - Geoffrey K. Chambers
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
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Eapen-John D, Mohiuddin AG, Kennedy JL. A potential paradigm shift in opioid crisis management: The role of pharmacogenomics. World J Biol Psychiatry 2022; 23:411-423. [PMID: 34854362 DOI: 10.1080/15622975.2021.2012397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Pharmacogenetic investigations into the opioid crisis suggest genetic variation could be a significant cause of opioid-related morbidity and mortality. Variability in opioid system genes, including single nucleotide polymorphisms, manifest after pharmacogenetic testing, as previously invisible risk factors for addiction and overdose. Pharmacodynamic genes regulate opioid-sensitive brain networks and neural reward circuitry. Pharmacokinetic genes expressed in drug metabolic pathways regulate blood levels of active vs. inactive opioid metabolites. Elucidating the complex interplay of genetic variations in pharmacokinetic and pharmacodynamic pathways will shed new light on the addictive and toxic properties of opioids. This narrative review serves to promote understanding of key genetic mechanisms affecting the metabolism and actions of opioids, and to explore causes of the recent surge in opioid-related mortality associated with COVID-19. Personalised treatment plans centred around an individual's genetic makeup could make opioid-based pain management and opioid use disorder (OUD) treatments safer and more effective at both the individual and system levels.
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Affiliation(s)
- David Eapen-John
- Molecular Brain Science, Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Canada.,Institute of Medical Science, University of Toronto, Toronto, Canada
| | - Ayeshah G Mohiuddin
- Molecular Brain Science, Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Canada.,Institute of Medical Science, University of Toronto, Toronto, Canada
| | - James L Kennedy
- Molecular Brain Science, Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Canada.,Institute of Medical Science, University of Toronto, Toronto, Canada.,Department of Psychiatry, University of Toronto, Toronto, Canada
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6
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Muyambo S, Ndadza A, Soko ND, Kruger B, Kadzirange G, Chimusa E, Masimirembwa CM, Ntsekhe M, Nhachi CF, Dandara C. Warfarin Pharmacogenomics for Precision Medicine in Real-Life Clinical Practice in Southern Africa: Harnessing 73 Variants in 29 Pharmacogenes. OMICS : A JOURNAL OF INTEGRATIVE BIOLOGY 2022; 26:35-50. [PMID: 34958284 PMCID: PMC8792494 DOI: 10.1089/omi.2021.0199] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Pharmacogenomics is universally relevant for worldwide modern therapeutics and yet needs further development in resource-limited countries. While there is an abundance of genetic association studies in controlled medical settings, there is a paucity of studies with a naturalistic design in real-life clinical practice in patients with comorbidities and under multiple drug treatment regimens. African patients are often burdened with communicable and noncommunicable comorbidities, yet the application of pharmacogenomics in African clinical settings remains limited. Using warfarin as a model, this study aims at minimizing gaps in precision/personalized medicine research in African clinical practice. We present, therefore, pharmacogenomic profiles of a cohort of 503 black Africans (n = 252) and Mixed Ancestry (n = 251) patients from Southern Africa, on warfarin and co-prescribed drugs in a naturalized noncontrolled environment. Seventy-three (n = 73) single nucleotide polymorphisms (SNPs) in 29 pharmacogenes were characterized using a combination of allelic discrimination, Sanger sequencing, restriction fragment length polymorphism, and Sequenom Mass Array. The common comorbidities were hypertension (43-46%), heart failure (39-45%), diabetes mellitus (18%), arrhythmia (25%), and HIV infection (15%). Accordingly, the most common co-prescribed drugs were antihypertensives, antiarrhythmic drugs, antidiabetics, and antiretroviral therapy. We observed marked variation in major pharmacogenes both at interethnic levels and within African subpopulations. The Mixed Ancestry group presented a profile of genetic variants reflecting their European, Asian, and African admixture. Precision medicine requires that African populations begin to capture their own pharmacogenetic SNPs as they cannot always infer with absolute certainty from Asian and European populations. In the current historical moment of the COVID-19 pandemic, we also underscore that the spectrum of drugs interacting with warfarin will likely increase, given the systemic and cardiovascular effects of COVID-19, and the anticipated influx of COVID-19 medicines in the near future. This observational clinical pharmacogenomics study of warfarin, together with past precision medicine research, collectively, lends strong support for incorporation of pharmacogenetic profiling in clinical settings in African patients for effective and safe administration of therapeutics.
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Affiliation(s)
- Sarudzai Muyambo
- Department of Clinical Pharmacology, Faculty of Medicine and Health Sciences, University of Zimbabwe, Harare, Zimbabwe
- Department of Biological Sciences, Faculty of Science and Engineering, Bindura University of Science Education, Bindura, Zimbabwe
| | - Arinao Ndadza
- Pharmacogenomics and Drug Metabolism Research Group, Division of Human Genetics, Department of Pathology, Institute of Infectious Diseases and Molecular Medicine (IIDMM), Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Nyarai D. Soko
- Pharmacogenomics and Drug Metabolism Research Group, Division of Human Genetics, Department of Pathology, Institute of Infectious Diseases and Molecular Medicine (IIDMM), Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Bianca Kruger
- Pharmacogenomics and Drug Metabolism Research Group, Division of Human Genetics, Department of Pathology, Institute of Infectious Diseases and Molecular Medicine (IIDMM), Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Gerard Kadzirange
- Department of Medicine, Faculty of Medicine and Health Sciences, University of Zimbabwe, Harare, Zimbabwe
| | - Emile Chimusa
- Pharmacogenomics and Drug Metabolism Research Group, Division of Human Genetics, Department of Pathology, Institute of Infectious Diseases and Molecular Medicine (IIDMM), Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Collen M. Masimirembwa
- Department of Drug Metabolism and Pharmacokinetics (DMPK), African Institute of Biomedical Sciences and Technology (AiBST), Harare, Zimbabwe
| | - Mpiko Ntsekhe
- Division of Cardiology, Department of Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Charles F.B. Nhachi
- Department of Clinical Pharmacology, Faculty of Medicine and Health Sciences, University of Zimbabwe, Harare, Zimbabwe
| | - Collet Dandara
- Pharmacogenomics and Drug Metabolism Research Group, Division of Human Genetics, Department of Pathology, Institute of Infectious Diseases and Molecular Medicine (IIDMM), Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
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7
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Huynh C, Brussee JM, Pouzol L, Fonseca M, Meyer Zu Schwabedissen HE, Dingemanse J, Sidharta PN. Target engagement of the first-in-class CXCR7 antagonist ACT-1004-1239 following multiple-dose administration in mice and humans. Biomed Pharmacother 2021; 144:112363. [PMID: 34794236 DOI: 10.1016/j.biopha.2021.112363] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 10/06/2021] [Accepted: 10/19/2021] [Indexed: 10/20/2022] Open
Abstract
Antagonism of the chemokine receptor CXCR7 has shown promising effects in diverse disease areas through modulation of its ligands, CXCL11 and CXCL12. Preclinical data of the first-in-class CXCR7 antagonist, ACT-1004-1239, showed efficacy in animal models of multiple sclerosis and acute lung injury. In healthy humans, single-dose administration of ACT-1004-1239 revealed a favorable clinical profile. Here, we report the target engagement of ACT-1004-1239 in healthy mice and humans after multiple doses using CXCL11 and CXCL12 as biomarkers. In addition, safety/tolerability, concentration-QTc relationship, and pharmacokinetics (PK) were assessed in a randomized, double-blind, placebo-controlled Phase 1 clinical study. Multiple-dose ACT-1004-1239 dose-dependently increased CXCL12 plasma concentration across the investigated dose range in mice and humans (mice: 1-100 mg/kg b.i.d.; humans: 30-200 mg o.d.) when compared to vehicle/placebo demonstrating target engagement. Mouse and human PK/PD models predicted that CXCL12 concentration approached a plateau within these dose ranges. In humans, ACT-1004-1239 was rapidly absorbed (tmax: 1.75-3.01 h) and the terminal t1/2 was approximately 19 h. Steady-state conditions were reached by Day 3 with an accumulation index of 1.2. Female subjects had overall higher exposure compared to males. Multiple-dose ACT-1004-1239 was well tolerated up to 200 mg once daily in humans. There was no evidence of ACT-1004-1239-mediated QTc interval prolongation. Overall, multiple oral doses of ACT-1004-1239 showed target engagement with CXCR7 in healthy mice and humans, therefore, assessment of CXCL12 as translational tool for further investigations in patients is warranted. Favorable safety/tolerability and PK profiles allow for further clinical development.
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Affiliation(s)
- Christine Huynh
- Idorsia Pharmaceuticals Ltd, Department of Clinical Pharmacology, 4123 Allschwil, Switzerland; Biopharmacy, Department of Pharmaceutical Sciences, University of Basel, 4056 Basel, Switzerland.
| | - Janneke M Brussee
- Idorsia Pharmaceuticals Ltd, Department of Clinical Pharmacology, 4123 Allschwil, Switzerland
| | - Laetitia Pouzol
- Idorsia Pharmaceuticals Ltd, Department of Pharmacology Immunology, 4123 Allschwil, Switzerland
| | - Marlene Fonseca
- BlueClinical Phase 1, Hospital de Prelada, 4250-449 Porto, Portugal
| | | | - Jasper Dingemanse
- Idorsia Pharmaceuticals Ltd, Department of Clinical Pharmacology, 4123 Allschwil, Switzerland
| | - Patricia N Sidharta
- Idorsia Pharmaceuticals Ltd, Department of Clinical Pharmacology, 4123 Allschwil, Switzerland
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8
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Türk D, Fuhr LM, Marok FZ, Rüdesheim S, Kühn A, Selzer D, Schwab M, Lehr T. Novel models for the prediction of drug-gene interactions. Expert Opin Drug Metab Toxicol 2021; 17:1293-1310. [PMID: 34727800 DOI: 10.1080/17425255.2021.1998455] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
INTRODUCTION Adverse drug reactions (ADRs) are among the leading causes of death, and frequently associated with drug-gene interactions (DGIs). In addition to pharmacogenomic programs for implementation of genetic preemptive testing into clinical practice, mathematical modeling can help to understand, quantify and predict the effects of DGIs in vivo. Moreover, modeling can contribute to optimize prospective clinical drug trial activities and to reduce DGI-related ADRs. AREAS COVERED Approaches and challenges of mechanistical DGI implementation and model parameterization are discussed for population pharmacokinetic and physiologically based pharmacokinetic models. The broad spectrum of published DGI models and their applications is presented, focusing on the investigation of DGI effects on pharmacology and model-based dose adaptations. EXPERT OPINION Mathematical modeling provides an opportunity to investigate complex DGI scenarios and can facilitate the development process of safe and efficient personalized dosing regimens. However, reliable DGI model input data from in vivo and in vitro measurements are crucial. For this, collaboration among pharmacometricians, laboratory scientists and clinicians is important to provide homogeneous datasets and unambiguous model parameters. For a broad adaptation of validated DGI models in clinical practice, interdisciplinary cooperation should be promoted and qualification toolchains must be established.
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Affiliation(s)
- Denise Türk
- Clinical Pharmacy, Saarland University, Saarbrücken, Germany
| | | | | | - Simeon Rüdesheim
- Clinical Pharmacy, Saarland University, Saarbrücken, Germany.,Dr. Margarete Fischer-Bosch-Institute of Clinical Pharmacology, Stuttgart, Germany
| | - Anna Kühn
- Clinical Pharmacy, Saarland University, Saarbrücken, Germany
| | - Dominik Selzer
- Clinical Pharmacy, Saarland University, Saarbrücken, Germany
| | - Matthias Schwab
- Dr. Margarete Fischer-Bosch-Institute of Clinical Pharmacology, Stuttgart, Germany.,Departments of Clinical Pharmacology, Pharmacy and Biochemistry, University of Tübingen, Tübingen, Germany.,Cluster of Excellence iFIT (EXC2180) "Image-guided and Functionally Instructed Tumor Therapies," University of Tübingen, Tübingen, Germany
| | - Thorsten Lehr
- Clinical Pharmacy, Saarland University, Saarbrücken, Germany
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9
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Ibrahim ME. Genetic diversity of the Sudanese: insights on origin and implications for health. Hum Mol Genet 2021; 30:R37-R41. [PMID: 33864377 PMCID: PMC8223596 DOI: 10.1093/hmg/ddab028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 01/14/2021] [Accepted: 01/14/2021] [Indexed: 11/21/2022] Open
Abstract
By virtue of their cultural, linguistic and genetic legacies, many populations from Sudan have deep histories in the region and retain high genetic diversities. Sudan’s location in north east Africa, a unique spot believed to act as a climatic refuge during periods of climate extremes, might have dictated that fate. Among the marked consequences of this diversity is the potential to provide information on the origin and structure of human populations within and outside the continent, as well as migration patterns towards various parts of the African continent, and out of Africa. The diverse Sudanese gene pool further has the potential to inform on genetic adaptations driven by culture and the environment resulting in unique and interesting traits, some of which are yet to be investigated. In addition, these genomes could offer clues to complex issues of causation amidst the challenge of new paradigms in biology underpinned by the genomic revolution.
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Wojtyniak J, Selzer D, Schwab M, Lehr T. Physiologically Based Precision Dosing Approach for Drug‐Drug‐Gene Interactions: A Simvastatin Network Analysis. Clin Pharmacol Ther 2020; 109:201-211. [DOI: 10.1002/cpt.2111] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Accepted: 11/07/2020] [Indexed: 12/25/2022]
Affiliation(s)
- Jan‐Georg Wojtyniak
- Clinical Pharmacy Saarland University Saarbrücken Germany
- Dr. Margarete Fischer‐Bosch‐Institute of Clinical Pharmacology Stuttgart Germany
| | - Dominik Selzer
- Clinical Pharmacy Saarland University Saarbrücken Germany
| | - Matthias Schwab
- Dr. Margarete Fischer‐Bosch‐Institute of Clinical Pharmacology Stuttgart Germany
- Departments of Clinical Pharmacology and Pharmacy and Biochemistry University of Tübingen Tübingen Germany
- Cluster of Excellence iFIT (EXC2180) "Image‐guided and Functionally Instructed Tumor Therapies" University of Tübingen Tübingen Germany
| | - Thorsten Lehr
- Clinical Pharmacy Saarland University Saarbrücken Germany
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11
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Huddart R, Fohner AE, Whirl-Carrillo M, Wojcik GL, Gignoux CR, Popejoy AB, Bustamante CD, Altman RB, Klein TE. Standardized Biogeographic Grouping System for Annotating Populations in Pharmacogenetic Research. Clin Pharmacol Ther 2019; 105:1256-1262. [PMID: 30506572 DOI: 10.1002/cpt.1322] [Citation(s) in RCA: 75] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Accepted: 11/16/2018] [Indexed: 12/19/2022]
Abstract
The varying frequencies of pharmacogenetic alleles among populations have important implications for the impact of these alleles in different populations. Current population grouping methods to communicate these patterns are insufficient as they are inconsistent and fail to reflect the global distribution of genetic variability. To facilitate and standardize the reporting of variability in pharmacogenetic allele frequencies, we present seven geographically defined groups: American, Central/South Asian, East Asian, European, Near Eastern, Oceanian, and Sub-Saharan African, and two admixed groups: African American/Afro-Caribbean and Latino. These nine groups are defined by global autosomal genetic structure and based on data from large-scale sequencing initiatives. We recognize that broadly grouping global populations is an oversimplification of human diversity and does not capture complex social and cultural identity. However, these groups meet a key need in pharmacogenetics research by enabling consistent communication of the scale of variability in global allele frequencies and are now used by Pharmacogenomics Knowledgebase (PharmGKB).
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Affiliation(s)
- Rachel Huddart
- Department of Biomedical Data Science, Stanford University, Stanford, California, USA
| | - Alison E Fohner
- Department of Biomedical Data Science, Stanford University, Stanford, California, USA.,Department of Epidemiology, University of Washington, Seattle, Washington, USA
| | | | - Genevieve L Wojcik
- Department of Biomedical Data Science, Stanford University, Stanford, California, USA
| | - Christopher R Gignoux
- Department of Biostatistics, Division of Bioinformatics and Personalized Medicine, University of Colorado, Aurora, Colorado, USA
| | - Alice B Popejoy
- Department of Biomedical Data Science, Stanford University, Stanford, California, USA.,Stanford Center for Integration of Research on Genetics and Ethics, Stanford, California, USA
| | - Carlos D Bustamante
- Department of Biomedical Data Science, Stanford University, Stanford, California, USA.,Department of Genetics, Stanford University, Stanford, California, USA
| | - Russ B Altman
- Department of Biomedical Data Science, Stanford University, Stanford, California, USA.,Department of Genetics, Stanford University, Stanford, California, USA.,Department of Biomedical Engineering, Stanford University, Stanford, California, USA.,Department of Medicine, Stanford University, Stanford, California, USA
| | - Teri E Klein
- Department of Biomedical Data Science, Stanford University, Stanford, California, USA.,Department of Medicine, Stanford University, Stanford, California, USA.,Shriram Center for BioE & ChemE, Stanford, California, USA
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12
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Campagne O, Mager DE, Brazeau D, Venuto RC, Tornatore KM. Tacrolimus Population Pharmacokinetics and Multiple CYP3A5 Genotypes in Black and White Renal Transplant Recipients. J Clin Pharmacol 2018; 58:1184-1195. [PMID: 29775201 DOI: 10.1002/jcph.1118] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Accepted: 02/13/2018] [Indexed: 01/08/2023]
Abstract
Tacrolimus exhibits inter-patient pharmacokinetic variability attributed to CYP3A5 isoenzymes and the efflux transporter, P-glycoprotein. Most black renal transplant recipients require higher tacrolimus doses compared to whites to achieve similar troughs when race-adjusted recommendations are used. An established guideline provides tacrolimus genotype dosing recommendations based on CYP3A5*1(W/T) and loss of protein function variants: CYP3A5*3 (rs776746), CYP3A5*6 (rs10264272), CYP3A5*7 (rs41303343) and may provide more comprehensive race-adjusted dosing recommendations. Our objective was to develop a tacrolimus population pharmacokinetic model evaluating demographic, clinical, and genomic factors in stable black and white renal transplant recipients. A secondary objective investigated race-based tacrolimus regimens and genotype-specific dosing. Sixty-seven recipients receiving oral tacrolimus and mycophenolic acid ≥6 months completed a 12-hour pharmacokinetic study. CYP3A5*3,*6,*7 and ABCB1 1236C>T, 2677G>T/A, 3435C>T polymorphisms were characterized. Patients were classified as extensive, intermediate, and poor metabolizers using a novel CYP3A5*3*6*7 metabolic composite. Modeling and simulation was performed with computer software (NONMEM 7.3, ICON Development Solutions; Ellicott City, Maryland). A 2-compartment model with first-order elimination and absorption with lag time best described the data. The CYP3A5*3*6*7 metabolic composite was significantly associated with tacrolimus clearance (P value < .05), which was faster in extensive (mean: 45.0 L/hr) and intermediate (29.5 L/hr) metabolizers than poor metabolizers (19.8 L/hr). Simulations support CYP3A5*3*6*7 genotype-based tacrolimus dosing to enhance general race-adjusted regimens, with dose increases of 1.5-fold and 2-fold, respectively, in intermediate and extensive metabolizers for comparable exposures to poor metabolizers. This model offers a novel approach to determine tacrolimus dosing adjustments that maintain comparable therapeutic exposure between black and white recipients with different CYP3A5 genotypes.
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Affiliation(s)
- Olivia Campagne
- Department of Pharmaceutical Sciences, University at Buffalo, SUNY, Buffalo, NY, USA.,Faculty of Pharmacy, Universités Paris Descartes-Paris Diderot, Paris, France
| | - Donald E Mager
- Department of Pharmaceutical Sciences, University at Buffalo, SUNY, Buffalo, NY, USA
| | - Daniel Brazeau
- Department of Pharmaceutical Sciences, College of Pharmacy, University of New England, Portland, ME, USA
| | - Rocco C Venuto
- Erie County Medical Center, Division of Nephrology, Department of Medicine, School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY, USA
| | - Kathleen M Tornatore
- Erie County Medical Center, Division of Nephrology, Department of Medicine, School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY, USA.,Department of Pharmacy Practice, School of Pharmacy and Pharmaceutical Sciences, Immunosuppressive Pharmacology Research Program, Translational Pharmacology Research Core, NYS Center of Excellence in Bioinformatics and Life Sciences, University at Buffalo, Buffalo, NY, USA
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13
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Jmel H, Romdhane L, Ben Halima Y, Hechmi M, Naouali C, Dallali H, Hamdi Y, Shan J, Abid A, Jamoussi H, Trabelsi S, Chouchane L, Luiselli D, Abdelhak S, Kefi R. Pharmacogenetic landscape of Metabolic Syndrome components drug response in Tunisia and comparison with worldwide populations. PLoS One 2018; 13:e0194842. [PMID: 29652911 PMCID: PMC5898725 DOI: 10.1371/journal.pone.0194842] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Accepted: 03/09/2018] [Indexed: 12/12/2022] Open
Abstract
Genetic variation is an important determinant affecting either drug response or susceptibility to adverse drug reactions. Several studies have highlighted the importance of ethnicity in influencing drug response variability that should be considered during drug development. Our objective is to characterize the genetic variability of some pharmacogenes involved in the response to drugs used for the treatment of Metabolic Syndrome (MetS) in Tunisia and to compare our results to the worldwide populations. A set of 135 Tunisians was genotyped using the Affymetrix Chip 6.0 genotyping array. Variants located in 24 Very Important Pharmacogenes (VIP) involved in MetS drug response were extracted from the genotyping data. Analysis of variant distribution in Tunisian population compared to 20 worldwide populations publicly available was performed using R software packages. Common variants between Tunisians and the 20 investigated populations were extracted from genotyping data. Multidimensional screening showed that Tunisian population is clustered with North African and European populations. The greatest divergence was observed with the African and Asian population. In addition, we performed Inter-ethnic comparison based on the genotype frequencies of five VIP biomarkers. The genotype frequencies of the biomarkers rs3846662, rs1045642, rs7294 and rs12255372 located respectively in HMGCR, ABCB1, VKORC1 and TCF7L2 are similar between Tunisian, Tuscan (TSI) and European (CEU). The genotype frequency of the variant rs776746 located in CYP3A5 gene is similar between Tunisian and African populations and different from CEU and TSI. The present study shows that the genetic make up of the Tunisian population is relatively complex in regard to pharmacogenes and reflects previous historical events. It is important to consider this ethnic difference in drug prescription in order to optimize drug response to avoid serious adverse drug reactions. Taking into account similarities with other neighboring populations, our study has an impact not only on the Tunisian population but also on North African population which are underrepresented in pharmacogenomic studies.
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Affiliation(s)
- Haifa Jmel
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, Tunis, Tunisia
- University of Carthage, Tunis, Tunisia
| | - Lilia Romdhane
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, Tunis, Tunisia
- University of Carthage, Tunis, Tunisia
| | - Yosra Ben Halima
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, Tunis, Tunisia
- University of Tunis El Manar, Tunis, Tunisia
| | - Meriem Hechmi
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, Tunis, Tunisia
- University of Carthage, Tunis, Tunisia
| | - Chokri Naouali
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, Tunis, Tunisia
- University of Tunis El Manar, Tunis, Tunisia
| | - Hamza Dallali
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, Tunis, Tunisia
- University of Carthage, Tunis, Tunisia
| | - Yosr Hamdi
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, Tunis, Tunisia
| | - Jingxuan Shan
- Laboratory of Genetic Medicine and Immunology, Weill Cornell Medical College in Qatar, Qatar Foundation, Doha, Qatar
| | - Abdelmajid Abid
- Department of external consultation, National Institute of Nutrition and Food Technology, Tunis, Tunisia
| | - Henda Jamoussi
- Department of external consultation, National Institute of Nutrition and Food Technology, Tunis, Tunisia
| | - Sameh Trabelsi
- Clinical Pharmacology Service, National Pharmacovigilance Center, Tunis, Tunisia
| | - Lotfi Chouchane
- Laboratory of Genetic Medicine and Immunology, Weill Cornell Medical College in Qatar, Qatar Foundation, Doha, Qatar
| | - Donata Luiselli
- Laboratory of Molecular Anthropology, Department of Biological, Geological and Environmental Sciences (BiGeA), University of Bologna, Bologna, Italy
| | - Sonia Abdelhak
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, Tunis, Tunisia
- University of Tunis El Manar, Tunis, Tunisia
| | - Rym Kefi
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, Tunis, Tunisia
- University of Tunis El Manar, Tunis, Tunisia
- * E-mail: ,
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14
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Cascorbi I. The Pharmacogenetics of Immune-Modulating Therapy. ADVANCES IN PHARMACOLOGY (SAN DIEGO, CALIF.) 2018; 83:275-296. [PMID: 29801578 DOI: 10.1016/bs.apha.2018.02.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Immunosuppressive drugs are a prerequisite in organ transplantation to prevent rejection and are also widely used in inflammatory diseases such as inflammatory bowel disease (IBD) or also in some hematologic malignancies-depending on the mode of action. For thiopurine analogs the polymorphic thiopurine S-methyltransferase (TPMT) was early detected to be associated with thiopurine-induced leukopenia; recent studies identified also NUDT15 to be related to this severe side effect. For drugs like methotrexate and mycophenolate mofetil a number of ADME genes like UDP-glucuronosyltransferases (UGTs) and ABC efflux transporters were investigated, however, with partly contradicting results. For calcineurin inhibitors like cyclosporine and in particular tacrolimus however, cytochrome P450 3A4 and 3A5 variants were found to significantly affect the pharmacokinetics. Genetic variants in genes encoding relevant pharmacodynamic proteins, however, lacked compelling evidence to affect the clinical outcome. This chapter reviews the current evidence on the association of pharmacogenetic traits to dose finding and clinical outcome of small-molecule immunosuppressants. Moreover this chapter critically summarizes suitability to apply pharmacogenetics in clinical practice in order to optimize immunosuppressant therapy.
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Affiliation(s)
- Ingolf Cascorbi
- Institute of Experimental and Clinical Pharmacology, University Hospital Schleswig-Holstein, Kiel, Germany.
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15
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Trofe-Clark J, Brennan DC, West-Thielke P, Milone MC, Lim MA, Neubauer R, Nigro V, Bloom RD. Results of ASERTAA, a Randomized Prospective Crossover Pharmacogenetic Study of Immediate-Release Versus Extended-Release Tacrolimus in African American Kidney Transplant Recipients. Am J Kidney Dis 2017; 71:315-326. [PMID: 29162334 DOI: 10.1053/j.ajkd.2017.07.018] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Accepted: 07/20/2017] [Indexed: 12/23/2022]
Abstract
BACKGROUND Differences in tacrolimus dosing across ancestries is partly attributable to polymorphisms in CYP3A5 genes that encode tacrolimus-metabolizing cytochrome P450 3A5 enzymes. The CYP3A5*1 allele, preponderant in African Americans, is associated with rapid metabolism, subtherapeutic concentrations, and higher dose requirements for tacrolimus, all contributing to worse outcomes. Little is known about the relationship between CYP3A5 genotype and the tacrolimus pharmacokinetic area under the curve (AUC) profile in African Americans or whether pharmacogenetic differences exist between conventional twice-daily, rapidly absorbed, immediate-release tacrolimus (IR-Tac) and once-daily extended-release tacrolimus (LifeCycle Pharma Tac [LCPT]) with a delayed absorption profile. STUDY DESIGN Randomized prospective crossover study. SETTING & PARTICIPANTS 50 African American maintenance kidney recipients on stable IR-Tac dosing. INTERVENTION Recipients were randomly assigned to continue IR-Tac on days 1 to 7 and then switch to LCPT on day 8 or receive LCPT on days 1 to 7 and then switch to IR-Tac on day 8. The LCPT dose was 85% of the IR-Tac total daily dose. OUTCOMES Tacrolimus 24-hour AUC (AUC0-24), peak and trough concentrations (Cmax and Cmin), time to peak concentration, and bioavailability of LCPT versus IR-Tac, according to CYP3A5 genotype. MEASUREMENTS CYP3A5 genotype, 24-hour tacrolimus pharmacokinetic profiles. RESULTS ∼80% of participants carried the CYP3A5*1 allele (CYP3A5 expressers). There were no significant differences in AUC0-24 or Cmin between CYP3A5 expressers and nonexpressers during administration of either IR-Tac or LCPT. With IR-Tac, tacrolimus Cmax was 33% higher in CYP3A5 expressers compared with nonexpressers (P=0.04): With LCPT, this difference was 11% (P=0.4). LIMITATIONS This was primarily a pharmacogenetic study rather than an efficacy study; the follow-up period was too short to capture clinical outcomes. CONCLUSIONS Achieving therapeutic tacrolimus trough concentrations with IR-Tac in most African Americans results in significantly higher peak concentrations, potentially magnifying the risk for toxicity and adverse outcomes. This pharmacogenetic effect is attenuated by delayed tacrolimus absorption with LCPT. TRIAL REGISTRATION Registered at ClinicalTrials.gov, with study number NCT01962922.
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Affiliation(s)
- Jennifer Trofe-Clark
- Department of Pharmacy Services, Hospital of the University of Pennsylvania, Philadelphia, PA; Renal Division, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | | | | | - Michael C Milone
- Perelman School of Medicine, University of Pennsylvania, Penn Institute for Immunology, Philadelphia, PA
| | - Mary Ann Lim
- Renal Division, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Robin Neubauer
- Renal Division, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | | | - Roy D Bloom
- Renal Division, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA.
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16
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Abstract
Purpose of review Identification of genetic variants to aid in individualized treatment of solid organ allograft recipients would improve graft survival. We will review the current state of knowledge for associations of variants with transplant outcomes. Recent findings Many studies have yet to exhibit robust and reproducible results, however, pharmacogenomic studies focusing on cytochrome P450 (CYP) enzymes, transporters and HLA variants have shown strong associations with outcomes and have relevance towards drugs used in transplant. Genome wide association study data for the immunosuppressant tacrolimus have identified multiple variants in the CYP3A5 gene associated with trough concentrations. Additionally, APOL1 variants had been shown to confer risk to the development of end stage renal disease in African Americans. Summary The field is rapidly evolving and new technology such as next generation sequencing, along with larger cohorts, will soon be commonly applied in transplantation to understand genetic association with outcomes and personalized medicine.
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17
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Dorr CR, Remmel RP, Muthusamy A, Fisher J, Moriarity BS, Yasuda K, Wu B, Guan W, Schuetz EG, Oetting WS, Jacobson PA, Israni AK. CRISPR/Cas9 Genetic Modification of CYP3A5 *3 in HuH-7 Human Hepatocyte Cell Line Leads to Cell Lines with Increased Midazolam and Tacrolimus Metabolism. Drug Metab Dispos 2017; 45:957-965. [PMID: 28533324 PMCID: PMC5518718 DOI: 10.1124/dmd.117.076307] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Accepted: 05/18/2017] [Indexed: 02/06/2023] Open
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 engineering of the CYP3A5 *3 locus (rs776746) in human liver cell line HuH-7 (CYP3A5 *3/*3) has led to three CYP3A5 *1 cell lines by deletion of the exon 3B splice junction or point mutation. Cell lines CYP3A5 *1/*3 sd (single deletion), CYP3A5 *1/*1 dd (double deletion), or CYP3A5 *1/*3 pm (point mutation) expressed the CYP3A5 *1 mRNA and had elevated CYP3A5 mRNA (P < 0.0005 for all engineered cell lines) and protein expression compared with HuH-7. In metabolism assays, HuH-7 had less tacrolimus (all P < 0.05) or midazolam (MDZ) (all P < 0.005) disappearance than all engineered cell lines. HuH-7 had less 1-OH MDZ (all P < 0.0005) or 4-OH (all P < 0.005) production in metabolism assays than all bioengineered cell lines. We confirmed CYP3A5 metabolic activity with the CYP3A4 selective inhibitor CYP3CIDE. This is the first report of genomic CYP3A5 bioengineering in human cell lines with drug metabolism analysis.
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Affiliation(s)
- Casey R Dorr
- Molecular Epidemiology Laboratory, Minneapolis Medical Research Foundation, Minneapolis, Minnesota
| | - Rory P Remmel
- Molecular Epidemiology Laboratory, Minneapolis Medical Research Foundation, Minneapolis, Minnesota
| | - Amutha Muthusamy
- Molecular Epidemiology Laboratory, Minneapolis Medical Research Foundation, Minneapolis, Minnesota
| | - James Fisher
- Molecular Epidemiology Laboratory, Minneapolis Medical Research Foundation, Minneapolis, Minnesota
| | - Branden S Moriarity
- Molecular Epidemiology Laboratory, Minneapolis Medical Research Foundation, Minneapolis, Minnesota
| | - Kazuto Yasuda
- Molecular Epidemiology Laboratory, Minneapolis Medical Research Foundation, Minneapolis, Minnesota
| | - Baolin Wu
- Molecular Epidemiology Laboratory, Minneapolis Medical Research Foundation, Minneapolis, Minnesota
| | - Weihua Guan
- Molecular Epidemiology Laboratory, Minneapolis Medical Research Foundation, Minneapolis, Minnesota
| | - Erin G Schuetz
- Molecular Epidemiology Laboratory, Minneapolis Medical Research Foundation, Minneapolis, Minnesota
| | - William S Oetting
- Molecular Epidemiology Laboratory, Minneapolis Medical Research Foundation, Minneapolis, Minnesota
| | - Pamala A Jacobson
- Molecular Epidemiology Laboratory, Minneapolis Medical Research Foundation, Minneapolis, Minnesota
| | - Ajay K Israni
- Molecular Epidemiology Laboratory, Minneapolis Medical Research Foundation, Minneapolis, Minnesota
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18
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Adeagbo BA, Olugbade TA, Durosinmi MA, Bolarinwa RA, Ogungbenro K, Bolaji OO. Population Pharmacokinetics of Imatinib in Nigerians With Chronic Myeloid Leukemia: Clinical Implications for Dosing and Resistance. J Clin Pharmacol 2017; 57:1554-1563. [PMID: 28618035 DOI: 10.1002/jcph.953] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Accepted: 05/05/2017] [Indexed: 01/03/2023]
Abstract
Imatinib, a tyrosine kinase inhibitor, is the drug of choice for the treatment of chronic myeloid leukemia in Nigeria. Several studies have established interindividual and interpopulation variations in imatinib disposition although no pharmacokinetic study have been conducted in an African population since the introduction of the drug. This study explored a population pharmacokinetic approach to investigate the disposition of imatinib in Nigerians and examined the involvement of some covariates including genetic factors in the variability of the drug disposition with a view to optimize the use of the drug in this population. A total of 250 plasma concentrations from 126 chronic myeloid leukemia patients were quantified using a validated method. A population pharmacokinetic model was fitted to the data using NONMEM VII software, and the influences of 12 covariates were investigated. The mean population-derived apparent steady-state clearance, elimination half-life, area under the concentration-time curve over 24 hours, and volume of distribution were 17.2 ± 1.8 L/h., 12.05 ± 2.1 hours, 23.26 ± 0.6 μg·h/mL, and 299 ± 20.4 L, respectively. Whole blood count, ethnicity, CYP3A5*3, and ABCB1 C3435T were found to have significant influence on the apparent clearance, while the interindividual variability in clearance and interoccasion variability in bioavailability were 17.4% and 20.4%, respectively. There was a wide variability in apparent clearance and area under the curve compared to those reported in other populations. Thus, treatment with a standard dose of imatinib in this population may not produce the desired effect in most of the patients, whereas continuous exposure to a low drug concentration could lead to pharmacokinetic-derived resistance. The authors suggest the need for therapeutic drug monitoring-guided dose individualization in this population.
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Affiliation(s)
| | | | | | | | - Kayode Ogungbenro
- Cancer Pharmacometrics, Centre for Applied Pharmacokinetic Research, School of Pharmacy and Pharmaceutical Sciences, University of Manchester, UK
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19
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Adehin A, Bolaji OO, Kennedy MA. Polymorphisms in CYP2C8 and CYP3A5 genes in the Nigerian population. Drug Metab Pharmacokinet 2017; 32:189-191. [DOI: 10.1016/j.dmpk.2016.09.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Revised: 09/05/2016] [Accepted: 09/05/2016] [Indexed: 02/09/2023]
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20
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Zhou Y, Ingelman-Sundberg M, Lauschke VM. Worldwide Distribution of Cytochrome P450 Alleles: A Meta-analysis of Population-scale Sequencing Projects. Clin Pharmacol Ther 2017; 102:688-700. [PMID: 28378927 PMCID: PMC5600063 DOI: 10.1002/cpt.690] [Citation(s) in RCA: 380] [Impact Index Per Article: 54.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2017] [Revised: 02/28/2017] [Accepted: 03/11/2017] [Indexed: 12/23/2022]
Abstract
Genetic polymorphisms in cytochrome P450 (CYP) genes can result in altered metabolic activity toward a plethora of clinically important medications. Thus, single nucleotide variants and copy number variations in CYP genes are major determinants of drug pharmacokinetics and toxicity and constitute pharmacogenetic biomarkers for drug dosing, efficacy, and safety. Strikingly, the distribution of CYP alleles differs considerably between populations with important implications for personalized drug therapy and healthcare programs. To provide a global distribution map of CYP alleles with clinical importance, we integrated whole‐genome and exome sequencing data from 56,945 unrelated individuals of five major human populations. By combining this dataset with population‐specific linkage information, we derive the frequencies of 176 CYP haplotypes, providing an extensive resource for major genetic determinants of drug metabolism. Furthermore, we aggregated this dataset into spectra of predicted functional variability in the respective populations and discuss the implications for population‐adjusted pharmacological treatment strategies.
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Affiliation(s)
- Y Zhou
- Department of Physiology and Pharmacology, Section of Pharmacogenetics, Karolinska Institutet, Stockholm, Sweden
| | - M Ingelman-Sundberg
- Department of Physiology and Pharmacology, Section of Pharmacogenetics, Karolinska Institutet, Stockholm, Sweden
| | - V M Lauschke
- Department of Physiology and Pharmacology, Section of Pharmacogenetics, Karolinska Institutet, Stockholm, Sweden
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21
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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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22
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Disease burden and the role of pharmacogenomics in African populations. GLOBAL HEALTH EPIDEMIOLOGY AND GENOMICS 2017; 2:e1. [PMID: 29868213 PMCID: PMC5870420 DOI: 10.1017/gheg.2016.21] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Revised: 11/22/2016] [Accepted: 11/24/2016] [Indexed: 12/15/2022]
Abstract
Background The burden of communicable and non-communicable diseases in Sub-Saharan Africa poses a challenge in achieving quality healthcare. Although therapeutic drugs have generally improved health, their efficacy differs from individual to individual. Variability in treatment response is mainly because of genetic variants that affect the pharmacokinetics and pharmacodynamics of drugs. Method The intersection of disease burden and therapeutic intervention is reviewed, and the status of pharmacogenomics knowledge in African populations is explored. Results The most commonly studied variants with pharmacogenomics relevance are discussed, especially in genes coding for enzymes that affect the response to drugs used for HIV, malaria, sickle cell disease and cardiovascular diseases. Conclusions The genetically diverse African population is likely to benefit from a pharmacogenomics-based healthcare approach, especially with respect to reduction of drug side effects, and separation of responders and non-responders leading to optimized drug choices and doses for each patient.
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23
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Broushaki F, Thomas MG, Link V, López S, van Dorp L, Kirsanow K, Hofmanová Z, Diekmann Y, Cassidy LM, Díez-del-Molino D, Kousathanas A, Sell C, Robson HK, Martiniano R, Blöcher J, Scheu A, Kreutzer S, Bollongino R, Bobo D, Davudi H, Munoz O, Currat M, Abdi K, Biglari F, Craig OE, Bradley DG, Shennan S, Veeramah K, Mashkour M, Wegmann D, Hellenthal G, Burger J. Early Neolithic genomes from the eastern Fertile Crescent. Science 2016; 353:499-503. [PMID: 27417496 PMCID: PMC5113750 DOI: 10.1126/science.aaf7943] [Citation(s) in RCA: 144] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2016] [Accepted: 07/05/2016] [Indexed: 01/06/2023]
Abstract
We sequenced Early Neolithic genomes from the Zagros region of Iran (eastern Fertile Crescent), where some of the earliest evidence for farming is found, and identify a previously uncharacterized population that is neither ancestral to the first European farmers nor has contributed substantially to the ancestry of modern Europeans. These people are estimated to have separated from Early Neolithic farmers in Anatolia some 46,000 to 77,000 years ago and show affinities to modern-day Pakistani and Afghan populations, but particularly to Iranian Zoroastrians. We conclude that multiple, genetically differentiated hunter-gatherer populations adopted farming in southwestern Asia, that components of pre-Neolithic population structure were preserved as farming spread into neighboring regions, and that the Zagros region was the cradle of eastward expansion.
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Affiliation(s)
- Farnaz Broushaki
- Palaeogenetics Group, Johannes Gutenberg University Mainz, 55099 Mainz, Germany
| | - Mark G Thomas
- Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK
| | - Vivian Link
- Department of Biology, University of Fribourg, 1700 Fribourg, Switzerland
- Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Saioa López
- Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK
| | - Lucy van Dorp
- Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK
| | - Karola Kirsanow
- Palaeogenetics Group, Johannes Gutenberg University Mainz, 55099 Mainz, Germany
| | - Zuzana Hofmanová
- Palaeogenetics Group, Johannes Gutenberg University Mainz, 55099 Mainz, Germany
| | - Yoan Diekmann
- Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK
| | - Lara M. Cassidy
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | - David Díez-del-Molino
- Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, SE-10405, Stockholm, Sweden
| | - Athanasios Kousathanas
- Department of Biology, University of Fribourg, 1700 Fribourg, Switzerland
- Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
- Unit of Human Evolutionary Genetics, Institut Pasteur, 75015 Paris, France
| | - Christian Sell
- Palaeogenetics Group, Johannes Gutenberg University Mainz, 55099 Mainz, Germany
| | - Harry K. Robson
- BioArCh, Department of Archaeology, University of York, York, YO10 5YW, UK
| | - Rui Martiniano
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | - Jens Blöcher
- Palaeogenetics Group, Johannes Gutenberg University Mainz, 55099 Mainz, Germany
| | - Amelie Scheu
- Palaeogenetics Group, Johannes Gutenberg University Mainz, 55099 Mainz, Germany
| | - Susanne Kreutzer
- Palaeogenetics Group, Johannes Gutenberg University Mainz, 55099 Mainz, Germany
| | - Ruth Bollongino
- Palaeogenetics Group, Johannes Gutenberg University Mainz, 55099 Mainz, Germany
| | - Dean Bobo
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, New York, 11794- 5245, USA
| | - Hossein Davudi
- Department of Archaeology, Faculty of Humanities, Tarbiat Modares University, Tehran, Iran
| | - Olivia Munoz
- UMR 7041 ArScAn -VEPMO, Maison de l’Archéologie et de l’Ethnologie, 21 allée de l’Université, 92023 Nanterre, France
| | - Mathias Currat
- Department of Genetics & Evolution-Anthropology Unit, University of Geneva, 1211 Geneva, Switzerland
| | - Kamyar Abdi
- Samuel Jordan Center for Persian Studies and Culture, University of California-lrvine, Irvine, CA 92697-3370, USA
| | - Fereidoun Biglari
- Paleolithic Department, National Museum of Iran, 113617111, Tehran, Iran
| | - Oliver E. Craig
- BioArCh, Department of Archaeology, University of York, York, YO10 5YW, UK
| | - Daniel G Bradley
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | - Stephen Shennan
- Institute of Archaeology, University College London, London WC1H 0PY, UK
| | - Krishna Veeramah
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, New York, 11794- 5245, USA
| | - Marjan Mashkour
- CNRS/MNHN/SUs – UMR 7209, Archéozoologie et Archéobotanique, Sociétés, Pratiques et Environnements, Département Ecologie et Gestion de la Biodiversité, 55 rue Buffon, 75005 Paris, France
| | - Daniel Wegmann
- Department of Biology, University of Fribourg, 1700 Fribourg, Switzerland
- Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Garrett Hellenthal
- Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK
| | - Joachim Burger
- Palaeogenetics Group, Johannes Gutenberg University Mainz, 55099 Mainz, Germany
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Adeagbo BA, Bolaji OO, Olugbade TA, Durosinmi MA, Bolarinwa RA, Masimirembwa C. Influence of CYP3A5*3 and ABCB1 C3435T on clinical outcomes and trough plasma concentrations of imatinib in Nigerians with chronic myeloid leukaemia. J Clin Pharm Ther 2016; 41:546-51. [DOI: 10.1111/jcpt.12424] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2016] [Accepted: 06/16/2016] [Indexed: 12/22/2022]
Affiliation(s)
- B. A. Adeagbo
- Department of Pharmaceutical Chemistry; Obafemi Awolowo University; Ile-Ife Nigeria
| | - O. O. Bolaji
- Department of Pharmaceutical Chemistry; Obafemi Awolowo University; Ile-Ife Nigeria
| | - T. A. Olugbade
- Department of Pharmaceutical Chemistry; Obafemi Awolowo University; Ile-Ife Nigeria
| | - M. A. Durosinmi
- Department of Haematology & Immunology; Obafemi Awolowo University; Ile-Ife Nigeria
| | - R. A. Bolarinwa
- Department of Haematology & Immunology; Obafemi Awolowo University; Ile-Ife Nigeria
| | - C. Masimirembwa
- African Institute of Biomedical Science and Technology; Harare Zimbabwe
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Mhandire D, Lacerda M, Castel S, Mhandire K, Zhou D, Swart M, Shamu T, Smith P, Musingwini T, Wiesner L, Stray-Pedersen B, Dandara C. Effects of CYP2B6 and CYP1A2 Genetic Variation on Nevirapine Plasma Concentration and Pharmacodynamics as Measured by CD4 Cell Count in Zimbabwean HIV-Infected Patients. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2016; 19:553-62. [PMID: 26348712 DOI: 10.1089/omi.2015.0104] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The extremely high prevalence of HIV/AIDS in sub-Saharan Africa and limitations of current antiretroviral medicines demand new tools to optimize therapy such as pharmacogenomics for person-to-person variations. African populations exhibit greater genetic diversity than other world populations, thus making it difficult to extrapolate findings from one population to another. Nevirapine, an antiretroviral medicine, displays large plasma concentration variability which adversely impacts therapeutic virological response. This study, therefore, aimed to identify sources of variability in nevirapine pharmacokinetics and pharmacodynamics, focusing on genetic variation in CYP2B6 and CYP1A2. Using a cross-sectional study design, 118 HIV-infected adult Zimbabwean patients on nevirapine-containing highly active antiretroviral therapy (HAART) were characterized for three key functional single nucleotide polymorphisms (SNPs), CYP2B6 c.516G>T (rs3745274), CYP2B6 c.983T>C (rs28399499), and CYP1A2 g.-163C>A (rs762551). We investigated whether genotypes at these loci were associated with nevirapine plasma concentration, a therapeutic biomarker, and CD4 cell count, a biomarker of disease progression. CYP2B6 and CYP1A2 were chosen as the candidate genes based on reports in literature, as well as their prominence in the metabolism of efavirenz, a drug in the same class with nevirapine. Nevirapine plasma concentration was determined using LC-MS/MS. The mean nevirapine concentration for CYP2B6 c.516T/T genotype differed significantly from that of 516G/G (p < 0.001) and 516G/T (p < 0.01) genotypes, respectively. There were also significant differences in mean nevirapine concentration between CYP2B6 c.983T > C genotypes (p = 0.04). Importantly, the CYP1A2 g.-163C>A SNP was significantly associated with the pharmacodynamics endpoint, the CD4 cell count (p = 0.012). Variant allele frequencies for the three SNPs observed in this Zimbabwean group were similar to other African population groups but different to observations among Caucasian and Asian populations. We conclude that CYP2B6 c.516G>T and CYP2B6 c.983T>C could be important sources of nevirapine pharmacokinetic variability that could be considered for dosage optimization, while CYP1A2 g.-163C>A seems to be associated with HIV disease progression. These inter- and intra-population pharmacokinetic and pharmacodynamics differences suggest that a single prescribed dosage may not be appropriate for the treatment of disease. Further research into a personalized nevirapine regimen is required.
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Affiliation(s)
- Doreen Mhandire
- 1 Department of Chemical Pathology, College of Health Sciences, University of Zimbabwe , Harare, Zimbabwe
| | - Miguel Lacerda
- 2 Department of Statistical Sciences, Faculty of Science, University of Cape Town , Cape Town, South Africa
| | - Sandra Castel
- 3 Division of Clinical Pharmacology, Department of Medicine, Faculty of Health Sciences, University of Cape Town , Cape Town, South Africa
| | - Kudakwashe Mhandire
- 1 Department of Chemical Pathology, College of Health Sciences, University of Zimbabwe , Harare, Zimbabwe
| | - Danai Zhou
- 4 Department of Medical Laboratory Sciences, College of Health Sciences, University of Zimbabwe , Harare, Zimbabwe .,7 Institute of Clinical Medicine, University of Oslo , Oslo, Norway
| | - Marelize Swart
- 5 Division of Human Genetics, Department of Clinical Laboratory Sciences and Institute for Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town , Cape Town, South Africa
| | | | - Peter Smith
- 3 Division of Clinical Pharmacology, Department of Medicine, Faculty of Health Sciences, University of Cape Town , Cape Town, South Africa
| | - Tutsirai Musingwini
- 4 Department of Medical Laboratory Sciences, College of Health Sciences, University of Zimbabwe , Harare, Zimbabwe
| | - Lubbe Wiesner
- 3 Division of Clinical Pharmacology, Department of Medicine, Faculty of Health Sciences, University of Cape Town , Cape Town, South Africa
| | | | - Collet Dandara
- 5 Division of Human Genetics, Department of Clinical Laboratory Sciences and Institute for Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town , Cape Town, South Africa
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26
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Kuang J, Zhao M, Li H, Dang W, Li W. Identification of potential therapeutic target genes and mechanisms in head and neck squamous cell carcinoma by bioinformatics analysis. Oncol Lett 2016; 11:3009-3014. [PMID: 27123054 PMCID: PMC4840659 DOI: 10.3892/ol.2016.4358] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2015] [Accepted: 03/08/2016] [Indexed: 02/07/2023] Open
Abstract
The present study aimed to identify the potential target genes and underlying molecular mechanisms involved in head and neck squamous cell carcinoma (HNSCC) by bioinformatics analysis. Microarray data of a Gene Expression Omnibus series GSE6631 was downloaded from the Gene Expression Omnibus database, which was generated from paired samples of HNSCC and normal tissue from 22 patients, and was used to identify differentially expressed genes (DEGs). Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes enrichment analyses were performed to investigate the functions of the identified DEGs. Furthermore, the protein-protein interaction (PPI) network of these DEGs was constructed using Cytoscape software. Between HNSCC and normal samples there was a difference in 419 DEGs, including 196 upregulated and 223 downregulated genes. The upregulated DEGs were mainly enriched in GO terms of cell adhesion, extracellular matrix (ECM) organization and collagen metabolic process, while the downregulated DEGs were mainly associated with epidermis development and epidermal cell differentiation. The DEGs were enriched in pathways such as ECM-receptor interaction, focal adhesion and drug metabolism. Fibronectin 1 (FN1), epidermal growth factor receptor (EGFR), collagen type I alpha 1 (COL1A1) and matrix metallopeptidase-9 (MMP-9) were hub nodes in the PPI network. These results suggested that cell adhesion and drug metabolism may be associated with HNSCC development, and genes such as FN1, EGFR, COL4A1 and MMP-9 may be potential therapeutic target genes in HNSCC.
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Affiliation(s)
- Jing Kuang
- Department of Plastic Surgery, Jinan Central Hospital Affiliated to Shandong University, Jinan, Shandong 250013, P.R. China
| | - Mei Zhao
- Department of News Office, Jinan Central Hospital Affiliated to Shandong University, Jinan, Shandong 250013, P.R. China
| | - Huilian Li
- Department of Plastic Surgery, Jinan Central Hospital Affiliated to Shandong University, Jinan, Shandong 250013, P.R. China
| | - Wei Dang
- Department of Plastic Surgery, Jinan Central Hospital Affiliated to Shandong University, Jinan, Shandong 250013, P.R. China
| | - Wei Li
- Department of Healthcare, Jinan Central Hospital Affiliated to Shandong University, Jinan, Shandong 250013, P.R. China
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Maglo KN, Mersha TB, Martin LJ. Population Genomics and the Statistical Values of Race: An Interdisciplinary Perspective on the Biological Classification of Human Populations and Implications for Clinical Genetic Epidemiological Research. Front Genet 2016; 7:22. [PMID: 26925096 PMCID: PMC4756148 DOI: 10.3389/fgene.2016.00022] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2015] [Accepted: 02/02/2016] [Indexed: 01/14/2023] Open
Abstract
The biological status and biomedical significance of the concept of race as applied to humans continue to be contentious issues despite the use of advanced statistical and clustering methods to determine continental ancestry. It is thus imperative for researchers to understand the limitations as well as potential uses of the concept of race in biology and biomedicine. This paper deals with the theoretical assumptions behind cluster analysis in human population genomics. Adopting an interdisciplinary approach, it demonstrates that the hypothesis that attributes the clustering of human populations to "frictional" effects of landform barriers at continental boundaries is empirically incoherent. It then contrasts the scientific status of the "cluster" and "cline" constructs in human population genomics, and shows how cluster may be instrumentally produced. It also shows how statistical values of race vindicate Darwin's argument that race is evolutionarily meaningless. Finally, the paper explains why, due to spatiotemporal parameters, evolutionary forces, and socio-cultural factors influencing population structure, continental ancestry may be pragmatically relevant to global and public health genomics. Overall, this work demonstrates that, from a biological systematic and evolutionary taxonomical perspective, human races/continental groups or clusters have no natural meaning or objective biological reality. In fact, the utility of racial categorizations in research and in clinics can be explained by spatiotemporal parameters, socio-cultural factors, and evolutionary forces affecting disease causation and treatment response.
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Affiliation(s)
- Koffi N Maglo
- Department of Philosophy, Center for Clinical and Translational Science and Training, University of Cincinnati Cincinnati, OH, USA
| | - Tesfaye B Mersha
- Department of Pediatrics, Cincinnati Children's Hospital Medical Center, University of Cincinnati Cincinnati, OH, USA
| | - Lisa J Martin
- Department of Pediatrics, Cincinnati Children's Hospital Medical Center, University of Cincinnati Cincinnati, OH, USA
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Oetting WS, Schladt DP, Guan W, Miller MB, Remmel RP, Dorr C, Sanghavi K, Mannon RB, Herrera B, Matas AJ, Salomon DR, Kwok PY, Keating BJ, Israni AK, Jacobson PA. Genomewide Association Study of Tacrolimus Concentrations in African American Kidney Transplant Recipients Identifies Multiple CYP3A5 Alleles. Am J Transplant 2016; 16:574-82. [PMID: 26485092 PMCID: PMC4733408 DOI: 10.1111/ajt.13495] [Citation(s) in RCA: 85] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2015] [Revised: 08/05/2015] [Accepted: 08/15/2015] [Indexed: 01/25/2023]
Abstract
We previously reported that tacrolimus (TAC) trough blood concentrations for African American (AA) kidney allograft recipients were lower than those observed in white patients. Subtherapeutic TAC troughs may be associated with acute rejection (AR) and AR-associated allograft failure. This variation in TAC troughs is due, in part, to differences in the frequency of the cytochrome P450 CYP3A5*3 allele (rs776746, expresses nonfunctional enzyme) between white and AA recipients; however, even after accounting for this variant, variability in AA-associated troughs is significant. We conducted a genomewide association study of TAC troughs in AA kidney allograft recipients to search for additional genetic variation. We identified two additional CYP3A5 variants in AA recipients independently associated with TAC troughs: CYP3A5*6 (rs10264272) and CYP3A5*7 (rs41303343). All three variants and clinical factors account for 53.9% of the observed variance in troughs, with 19.8% of the variance coming from demographic and clinical factors including recipient age, glomerular filtration rate, anticytomegalovirus drug use, simultaneous pancreas-kidney transplant and antibody induction. There was no evidence of common genetic variants in AA recipients significantly influencing TAC troughs aside from the CYP3A gene. These results reveal that additional and possibly rare functional variants exist that account for the additional variation.
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Affiliation(s)
- W. S. Oetting
- University of Minnesota, Experimental and Clinical Pharmacology, Minneapolis, MN,Corresponding author: William S. Oetting,
| | - D. P. Schladt
- Minneapolis Medical Research Foundation, Minneapolis, MN
| | - W. Guan
- University of Minnesota, Department of Biostatistics, Minneapolis, MN
| | - M. B. Miller
- University of Minnesota, Experimental and Clinical Pharmacology, Minneapolis, MN
| | - R. P. Remmel
- University of Minnesota, Experimental and Clinical Pharmacology, Minneapolis, MN
| | - C. Dorr
- Minneapolis Medical Research Foundation, Minneapolis, MN
| | - K. Sanghavi
- University of Minnesota, Experimental and Clinical Pharmacology, Minneapolis, MN
| | - R. B. Mannon
- University of Alabama, Division of Nephrology, Birmingham, AL
| | - B. Herrera
- University of California, San Francisco, CA
| | - A. J. Matas
- University of Minnesota, Department of Surgery, Minneapolis, MN
| | | | - P.-Y. Kwok
- University of California, San Francisco, CA
| | - B. J. Keating
- Children's Hospital of Philadelphia, Philadelphia, PA
| | - A. K. Israni
- Minneapolis Medical Research Foundation, Minneapolis, MN,University of Minnesota, Department of Medicine, Hennepin County Medical Center, Minneapolis, MN,University of Minnesota, Department of Epidemiology and Community Health, Minneapolis, MN
| | - P. A. Jacobson
- University of Minnesota, Experimental and Clinical Pharmacology, Minneapolis, MN
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Chen Z, Li J, Chen P, Wang F, Zhang N, Yang M, Jin T, Chen C. Genetic polymorphisms of the drug-metabolizing enzyme cytochrome P450 3A5 in a Uyghur Chinese population. Xenobiotica 2016; 46:850-6. [PMID: 26739429 DOI: 10.3109/00498254.2015.1128012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
1. Detection of CYP3A5 variant alleles, and knowledge about their allelic frequency in Uyghur ethnic groups, is important to establish the clinical relevance of screening for these polymorphisms to optimize pharmacotherapy. 2. We used DNA sequencing to investigate the promoter, exons and surrounding introns, and 3'-untranslated region of the CYP3A5 gene in 96 unrelated healthy Uyghur individuals. We also used SIFT and PolyPhen-2 to predict the protein function of the novel non-synonymous mutation in CYP3A5 coding regions. 3. We found 24 different CYP3A5 polymorphisms in the Uyghur population, three of which were novel: the synonymous mutation 43C > T in exon 1, two mutations 32120C > G and 32245T > C in 3'-untranslated region, and we detected the allele frequencies of CYP3A5*1 and *3 as 64.58% and 35.42%, respectively. While no subjects with CYP3A5*6 were identified. Other identified genotypes included the heterozygous genotype 1A/3A (59.38%) and 1A/3E (11.46%), which lead to decreased enzyme activity. In addition, the frequency of haplotype "TTAGGT" was the most prevalent with 0.781. 4. Our data provide new information regarding CYP3A5 genetic polymorphisms in Uyghur individuals, which may help to improve individualization of drug therapy and offer a preliminary basis for more rational use of drugs.
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Affiliation(s)
- Zhengshuai Chen
- a School of Life Sciences, Northwest University , Xi'an , China .,b National Engineering Research Center for Miniaturized Detection Systems , Xi'an , China
| | - Jingjie Li
- a School of Life Sciences, Northwest University , Xi'an , China .,b National Engineering Research Center for Miniaturized Detection Systems , Xi'an , China
| | - Peng Chen
- a School of Life Sciences, Northwest University , Xi'an , China .,b National Engineering Research Center for Miniaturized Detection Systems , Xi'an , China
| | - Fengjiao Wang
- b National Engineering Research Center for Miniaturized Detection Systems , Xi'an , China
| | - Ning Zhang
- b National Engineering Research Center for Miniaturized Detection Systems , Xi'an , China
| | - Min Yang
- b National Engineering Research Center for Miniaturized Detection Systems , Xi'an , China
| | - Tianbo Jin
- a School of Life Sciences, Northwest University , Xi'an , China .,b National Engineering Research Center for Miniaturized Detection Systems , Xi'an , China .,c Key Laboratory of High Altitude Environment and Genes Related to Diseases of Tibet Autonomous Region, School of Medicine, Xizang Minzu University , Xianyang , China , and.,d Key Laboratory for Basic Life Science Research of Tibet Autonomous Region, School of Medicine, Xizang Minzu University , Xianyang , China
| | - Chao Chen
- a School of Life Sciences, Northwest University , Xi'an , China .,b National Engineering Research Center for Miniaturized Detection Systems , Xi'an , China
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30
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Sanghavi K, Brundage RC, Miller MB, Schladt DP, Israni AK, Guan W, Oetting WS, Mannon RB, Remmel RP, Matas AJ, Jacobson PA. Genotype-guided tacrolimus dosing in African-American kidney transplant recipients. THE PHARMACOGENOMICS JOURNAL 2015; 17:61-68. [PMID: 26667830 PMCID: PMC4909584 DOI: 10.1038/tpj.2015.87] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/28/2015] [Revised: 10/07/2015] [Accepted: 11/02/2015] [Indexed: 12/11/2022]
Abstract
Tacrolimus is dependent on CYP3A5 enzyme for metabolism. Expression of the CYP3A5 enzyme is controlled by several alleles including CYP3A5*1, CYP3A5*3, CYP3A5*6 and CYP3A5*7. African Americans (AAs) have on average higher tacrolimus dose requirements than Caucasians; however, some have requirements similar to Caucasians. Studies in AAs have primarily evaluated the CYP3A5*3 variant; however, there are other common nonfunctional variants in AAs (CYP3A5*6 and CYP3A5*7) that do not occur in Caucasians. These variants are associated with lower dose requirements and may explain why some AAs are metabolically similar to Caucasians. We created a tacrolimus clearance model in 354 AAs using a development and validation cohort. Time after transplant, steroid and antiviral use, age and CYP3A5*1, *3, *6 and *7 alleles were significant toward clearance. This study is the first to develop an AA-specific genotype-guided tacrolimus dosing model to personalize therapy.
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Affiliation(s)
- K Sanghavi
- Department of Experimental and Clinical Pharmacology, College of Pharmacy, University of Minnesota, Minneapolis, MN, USA
| | - R C Brundage
- Department of Experimental and Clinical Pharmacology, College of Pharmacy, University of Minnesota, Minneapolis, MN, USA
| | - M B Miller
- Department of Psychology, University of Minnesota, Minneapolis, MN, USA
| | - D P Schladt
- Department of Nephrology and Chronic Disease Research Group, Minneapolis Medical Research Foundation, Hennepin County Medical Center, Minneapolis, MN, USA
| | - A K Israni
- Department of Surgery, University of Minnesota, Minneapolis, MN, USA
| | - W Guan
- Department of Biostatistics, University of Minnesota, Minneapolis, MN, USA
| | - W S Oetting
- Department of Experimental and Clinical Pharmacology, College of Pharmacy, University of Minnesota, Minneapolis, MN, USA
| | - R B Mannon
- Department of Nephrology, University of Alabama, Birmingham, AL, USA
| | - R P Remmel
- Department of Medicinal Chemistry, College of Pharmacy, University of Minnesota, Minneapolis, MN, USA
| | - A J Matas
- Department of Surgery, University of Minnesota, Minneapolis, MN, USA
| | - P A Jacobson
- Department of Experimental and Clinical Pharmacology, College of Pharmacy, University of Minnesota, Minneapolis, MN, USA
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Efectos de los inductores antiepilépticos en la neuropsicofarmacología: una cuestión ignorada. Parte II: cuestiones farmacológicas y comprensión adicional. REVISTA DE PSIQUIATRIA Y SALUD MENTAL 2015; 8:167-88. [DOI: 10.1016/j.rpsm.2014.10.005] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2014] [Accepted: 10/23/2014] [Indexed: 12/19/2022]
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Genetic diversity of CYP3A4 and CYP3A5 polymorphisms in North African populations from Morocco and Tunisia. Int J Biol Markers 2015; 30:e148-51. [PMID: 25385241 DOI: 10.5301/jbm.5000118] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/23/2014] [Indexed: 02/04/2023]
Abstract
The genes CYP3A4 and CYP3A5 form part of a cluster of cytochrome P450 genes involved in drug metabolism reactions. The allelic variants of these genes CYP3A4*1B, CYP3A4*3, CYP3A4*17 and CYP3A5*3 have been linked both to the reduced catalytic activity of cytochromes and to prostate cancer risk in whites, though scarce data exist for North African populations. The main objective of this study was to describe CYP3A4*3, CYP3A4*17, CYP3A4*1B and CYP3A5*3 allele frequencies and haplotype variation in Moroccan Berbers and the general Tunisian population. The data obtained for the Tunisian participants were consistent with the European allele frequency ranges described, while Moroccan Berbers showed high frequencies of CYP3A4*17 (1.8%), CYP3A4*3 (8.5%) and the CYP3A4*1B/CYP3A5*3 haplotype (18.4%). This haplotype, linked to an increased risk of prostate cancer, was detected at a much higher frequency compared with the present Tunisian population (8.4%) or with reported frequencies for populations such as whites (0.6%) or African Americans (5.3%).
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Marwa KJ, Schmidt T, Sjögren M, Minzi OMS, Kamugisha E, Swedberg G. Cytochrome P450 single nucleotide polymorphisms in an indigenous Tanzanian population: a concern about the metabolism of artemisinin-based combinations. Malar J 2014; 13:420. [PMID: 25363545 PMCID: PMC4228099 DOI: 10.1186/1475-2875-13-420] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2014] [Accepted: 10/25/2014] [Indexed: 01/24/2023] Open
Abstract
BACKGROUND Artemisinin-based combinations currently recommended for treatment of uncomplicated Plasmodium falciparum malaria in many countries of sub-Saharan Africa are substrates of CYP enzymes. The cytochrome enzyme system is responsible for metabolism of about 80-90% of clinically used drugs. It is, therefore, important to obtain the pharmacogenetics of the population in the region with respect to these combinations and thereby enable practitioners to predict treatment outcomes. The aim of this study was to detect and determine allelic frequencies of CYP2C8*2, CYP2C8*3, CYP3A4*1B, CYP3A5*3 and CYP2B6*6 variant alleles in a Tanzanian indigenous population. METHODS Genomic DNA extraction from blood obtained from 256 participants who escorted patients at Karume Health Centre in Mwanza Tanzania, was carried out using the Gene JET™ Genomic DNA purification kit (Thermo Scientific). Genotyping for the cytochrome P450 variant alleles was performed using predesigned primers. Amplification was done by PCR while differentiation between alleles was done by restriction fragment length polymorphism (PCR-RFLP) (for CYP2C8*2, CYP2C8*3) and sequencing (for CYP2B6*6, CYP3A5*3 and CYP3A4*1B). RESULTS CYP2C8*2, CYP2C8*3, CYP3A5*3, CYP3A4*1B and CYP2B6*6 variant allelic frequencies were found to be 19,10,16,78 and 36% respectively. CONCLUSION Prevalence of CYP2C8*2, CYP3A5*3, CYP3A4*1B and CYP2B6*6 mutations in a Tanzanian population/subjects are common. The impact of these point mutations on the metabolism of anti-malarial drugs, particularly artemisinin-based combinations, and their potential drug-drug interactions (DDIs) needs to be further evaluated.
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Affiliation(s)
- Karol J Marwa
- Department of Pharmacology, Catholic University of Health and Allied Sciences, Mwanza, Tanzania.
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Parnell LD, Blokker BA, Dashti HS, Nesbeth PD, Cooper BE, Ma Y, Lee YC, Hou R, Lai CQ, Richardson K, Ordovás JM. CardioGxE, a catalog of gene-environment interactions for cardiometabolic traits. BioData Min 2014; 7:21. [PMID: 25368670 PMCID: PMC4217104 DOI: 10.1186/1756-0381-7-21] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2014] [Accepted: 10/18/2014] [Indexed: 12/29/2022] Open
Abstract
Background Genetic understanding of complex traits has developed immensely over the past decade but remains hampered by incomplete descriptions of contribution to phenotypic variance. Gene-environment (GxE) interactions are one of these contributors and in the guise of diet and physical activity are important modulators of cardiometabolic phenotypes and ensuing diseases. Results We mined the scientific literature to collect GxE interactions from 386 publications for blood lipids, glycemic traits, obesity anthropometrics, vascular measures, inflammation and metabolic syndrome, and introduce CardioGxE, a gene-environment interaction resource. We then analyzed the genes and SNPs supporting cardiometabolic GxEs in order to demonstrate utility of GxE SNPs and to discern characteristics of these important genetic variants. We were able to draw many observations from our extensive analysis of GxEs. 1) The CardioGxE SNPs showed little overlap with variants identified by main effect GWAS, indicating the importance of environmental interactions with genetic factors on cardiometabolic traits. 2) These GxE SNPs were enriched in adaptation to climatic and geographical features, with implications on energy homeostasis and response to physical activity. 3) Comparison to gene networks responding to plasma cholesterol-lowering or regression of atherosclerotic plaques showed that GxE genes have a greater role in those responses, particularly through high-energy diets and fat intake, than do GWAS-identified genes for the same traits. Other aspects of the CardioGxE dataset were explored. Conclusions Overall, we demonstrate that SNPs supporting cardiometabolic GxE interactions often exhibit transcriptional effects or are under positive selection. Still, not all such SNPs can be assigned potential functional or regulatory roles often because data are lacking in specific cell types or from treatments that approximate the environmental factor of the GxE. With research on metabolic related complex disease risk embarking on genome-wide GxE interaction tests, CardioGxE will be a useful resource.
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Affiliation(s)
- Laurence D Parnell
- JM-USDA Human Nutrition Research Center on Aging at Tufts University, 711 Washington Street, Boston, MA 02111, USA
| | - Britt A Blokker
- JM-USDA Human Nutrition Research Center on Aging at Tufts University, 711 Washington Street, Boston, MA 02111, USA
| | - Hassan S Dashti
- JM-USDA Human Nutrition Research Center on Aging at Tufts University, 711 Washington Street, Boston, MA 02111, USA
| | - Paula-Dene Nesbeth
- JM-USDA Human Nutrition Research Center on Aging at Tufts University, 711 Washington Street, Boston, MA 02111, USA
| | - Brittany Elle Cooper
- JM-USDA Human Nutrition Research Center on Aging at Tufts University, 711 Washington Street, Boston, MA 02111, USA
| | - Yiyi Ma
- JM-USDA Human Nutrition Research Center on Aging at Tufts University, 711 Washington Street, Boston, MA 02111, USA
| | - Yu-Chi Lee
- JM-USDA Human Nutrition Research Center on Aging at Tufts University, 711 Washington Street, Boston, MA 02111, USA
| | - Ruixue Hou
- JM-USDA Human Nutrition Research Center on Aging at Tufts University, 711 Washington Street, Boston, MA 02111, USA
| | - Chao-Qiang Lai
- JM-USDA Human Nutrition Research Center on Aging at Tufts University, 711 Washington Street, Boston, MA 02111, USA
| | - Kris Richardson
- JM-USDA Human Nutrition Research Center on Aging at Tufts University, 711 Washington Street, Boston, MA 02111, USA
| | - José M Ordovás
- JM-USDA Human Nutrition Research Center on Aging at Tufts University, 711 Washington Street, Boston, MA 02111, USA
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Maglo KN, Rubinstein J, Huang B, Ittenbach RF. BiDil in the Clinic: An Interdisciplinary Investigation of Physicians' Prescription Patterns of a Race-Based Therapy. AJOB Empir Bioeth 2014; 5:37-52. [PMID: 25177710 DOI: 10.1080/23294515.2014.907371] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
BACKGROUND The African American Heart Failure Trial (A-HeFT) and the FDA approval of BiDil for race-specific prescription have stirred the debate about the scientific and medical status of race. Yet there is no assessment of the potential fallouts of this dispute on physicians' willingness to prescribe the drug. We present here an analysis of the factors influencing physicians' prescription of BiDil and investigate whether exposure to the controversy has an impact on their therapeutic judgments about the drug. METHODS We conducted an electronic survey with physicians in the department of internal medicine at the University of Cincinnati. Participants were randomly assigned to two groups, with one group receiving information about the controversy over BiDil. We used various statistical tests, including a linear mixed effects model, to analyze the results. RESULTS 27% of the participants reported using patients' race as a major factor in making treatment decisions. 33% reported the inefficacy of standard therapies, 25% the severity of the disease, and 15% other unspecified factors as primary determining criteria in prescribing BiDil. With respect to the controversy, 68% of physicians reported that they were not aware of any controversy surrounding BiDil. Physicians' willingness to prescribe BiDil as a therapy was associated with their awareness of the controversy surrounding A-HeFT (p < 0.003). But their willingness to prescribe the therapy along racial lines did not vary significantly with exposure to the controversy. CONCLUSIONS Overall, physicians prescribe and are willing to prescribe BiDil more to black patients than to white patients. However, physicians' lack of awareness about the controversial scientific status of A-HeFT suggests the need for more efficient ways to convey scientific information about BiDil to clinicians. Furthermore, the uncertainties about the determination of clinical utility of BiDil for the individual patient raise questions about whether this specific race-based therapy is in patients' best interest.
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Affiliation(s)
- Koffi N Maglo
- Department of Philosophy, 206 McMicken Hall, PO Box 210374, University of Cincinnati, Cincinnati, OH 45221-0374, Tel (513) 556-6337,
| | | | - Bin Huang
- University of Cincinnati and Cincinnati Children's Hospital Medical Center
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Petersen KE, Prows CA, Martin LJ, Maglo KN. Personalized medicine, availability, and group disparity: an inquiry into how physicians perceive and rate the elements and barriers of personalized medicine. Public Health Genomics 2014; 17:209-20. [PMID: 24852571 DOI: 10.1159/000362359] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2013] [Accepted: 03/20/2014] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND The success of personalized medicine depends on factors influencing the availability and implementation of its new tools to individualize clinical care. However, little is known about physicians' views of the availability of personalized medicine across racial/ethnic groups and the relationship between perceived availability and clinical implementation. This study examines physicians' perceptions of key elements/tools and potential barriers to personalized medicine in connection with their perceptions of the availability of the latter across subpopulations. METHODS Study subjects consisted of physicians recruited from Cincinnati Children's Hospital Medical Center and UC Health. An electronic survey conducted from September 2012 to November 2012 recruited 104 physicians. Wilcoxon rank sum analysis compared groups. RESULTS Physicians were divided about whether personalized medicine contributes to health equality, as 37.4% of them believe that personalized medicine is currently available only for some subpopulations. They also rated the importance of racial/ethnic background almost as high as the importance of genetic information in the delivery of personalized medicine. Actual elements of personalized medicine rated highest include family history, drug-drug interaction alerts in medical records, and biomarker measurements to guide therapy. Costs of gene-based therapies and genetic testing were rated the most significant barriers. The ratings of several elements and barriers were associated with perceived availability of personalized medicine across subpopulations. CONCLUSION While physicians hold differing views about the availability and implementation of personalized medicine, they likewise establish complex relationships between race/ethnicity and personalized medicine that may carry serious implications for its clinical success.
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Affiliation(s)
- Katelin E Petersen
- Department of Pediatrics, University of Cincinnati School of Medicine, Cincinnati, Ohio, USA
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Dandara C, Swart M, Mpeta B, Wonkam A, Masimirembwa C. Cytochrome P450 pharmacogenetics in African populations: implications for public health. Expert Opin Drug Metab Toxicol 2014; 10:769-85. [PMID: 24588448 DOI: 10.1517/17425255.2014.894020] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
INTRODUCTION Africa harbors a disproportionate burden of disease when taking into account the triple challenge caused by HIV/AIDS, tuberculosis (TB) and malaria, against a backdrop of an increasing burden of noncommunicable diseases. More than 80% of therapeutic drugs used in the management of these diseases/conditions are metabolized by CYP enzymes that exhibit genetic polymorphisms. AREAS COVERED There is variability in the expression and activities of CYPs resulting in interindividual differences in the response to standard doses of therapeutic drugs, due to genetic polymorphisms, which exhibit both quantitative and qualitative differences between racial and between ethnic groups. The review aims to evaluate the implications of the genetic variation in CYPs on the public health of Africans. The CYPs reviewed here metabolize most of the commonly used therapeutic drugs and include CYP1A2, 2A6, 2B6, 2C8, 2C9, 2C19, 2D6, 3A4 and 3A5. Allele frequencies are compared between African ethnic groups and among populations of African, Asian and European origin. Data are obtained from our own studies and literature. EXPERT OPINION The variability in the pattern of genetic variation between populations translates into differences in drug response. Understanding CYP variability improves rational drug use and has public health significance.
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Affiliation(s)
- Collet Dandara
- University of Cape Town, Faculty of Health Sciences, Pharmacogenetics and Cancer Research Group, Division of Human Genetics, Department of Clinical Laboratory Sciences , Anzio Road Observatory, 7925, Cape Town , South Africa +27 21 406 6506 ;
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Fu LJ, Wang B. Investigation of the hub genes and related mechanism in ovarian cancer via bioinformatics analysis. J Ovarian Res 2013; 6:92. [PMID: 24341673 PMCID: PMC3892009 DOI: 10.1186/1757-2215-6-92] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2013] [Accepted: 11/23/2013] [Indexed: 11/25/2022] Open
Abstract
Background Ovarian cancer is a cancerous growth arising from the ovary. Objective This study was aimed to explore the molecular mechanism of the development and progression of the ovarian cancer. Methods We first identified the differentially expressed genes (DEGs) between the ovarian cancer samples and the healthy controls by analyzing the GSE14407 affymetrix microarray data, and then the functional enrichments of the DEGs were investigated. Furthermore, we constructed the protein-protein interaction network of the DEGs using the STRING online tools to find the genes which might play important roles in the progression of ovarian cancer. In addition, we performed the enrichment analysis to the PPI network. Results Our study screened 659 DEGs, including 77 up- and 582 down-regulated genes. These DEGs were enriched in pathways such as Cell cycle, p53 signaling pathway, Pathways in cancer and Drug metabolism. CCNE1, CCNB2 and CYP3A5 were the significant genes identified from these pathways. Protein-protein interaction (PPI) network was constructed and network Module A was found closely associated with ovarian cancer. Hub nodes such as VEGFA, CALM1, BIRC5 and POLD1 were found in the PPI network. Module A was related to biological processes such as mitotic cell cycle, cell cycle, nuclear division, and pathways namely Cell cycle, Oocyte meiosis and p53 signaling pathway. Conclusions It indicated that ovarian cancer was closely associated to the dysregulation of p53 signaling pathway, drug metabolism, tyrosine metabolism and cell cycle. Besides, we also predicted genes such as CCNE1, CCNB2, CYP3A5 and VEGFA might be target genes for diagnosing the ovarian cancer.
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Affiliation(s)
- Ling-Jie Fu
- Department of gynaecology and obstetrics, Shengjing hospital of China Medical University, No,36 Sanhao Street, Shenyang City 110004, China.
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Philips BJ, Lane K, Dixon J, MacPhee I. The effects of acute renal failure on drug metabolism. Expert Opin Drug Metab Toxicol 2013; 10:11-23. [DOI: 10.1517/17425255.2013.835802] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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Bains RK. African variation at Cytochrome P450 genes: Evolutionary aspects and the implications for the treatment of infectious diseases. EVOLUTION MEDICINE AND PUBLIC HEALTH 2013; 2013:118-34. [PMID: 24481193 PMCID: PMC3868406 DOI: 10.1093/emph/eot010] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The genomics revolution has provided a plethora of data from many previously uncharacterized populations. The increase in the amount of genetic data has improved our understanding of why individuals and populations differ in their susceptibility to multiple diseases. It has also enabled researchers to identify how genomic variation, including at the Cytochrome P450 (CYP450) super-family, affects the safety and efficacy of therapeutic drugs. CYP450 metabolize ∼90% of clinically administered drugs. Variability in CYP450 expression is known to affect the safety and efficacy of therapeutic drugs, including many used in the treatment and control of infectious diseases. There are inter-ethnic differences in the frequencies of clinically relevant CYP450 variants which affect CYP450 expression. Comparative studies of African populations have identified population structuring at CYP450 genes. This is associated with intra-African differences in the success of drug therapies used in the treatment of infectious diseases. Therapeutic drugs dominate control strategies for infectious diseases and are widely administered through mass drug administration campaigns. However, resistance to chemotherapy is spreading across endemic regions. The most common response has been to increase chemotherapeutic dosages, and administer combination therapies. However, there are few pharmacovigilance data examining how these changes influence adverse drug reactions. This review provides an overview of current knowledge of intra-Africa CYP450 variation, and the known associations with sub-optimal clinical outcomes in the treatment of infectious diseases. In addition, the potential for evolutionary approaches in the study of CYP450 variation is discussed to examine their potential in preventative medicine and intervention strategies within Africa.
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Affiliation(s)
- Ripudaman K Bains
- Research Department of Genetics, Evolution and Environment, Darwin Building, University College London, London WC1E 6BT, UK
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