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Altawil Y, Youssef LA. Frequencies of VKORC1-1639G>A and rs397509427 in Patients on Warfarin and Healthy Syrian Subjects. Cardiovasc Ther 2023; 2023:8898922. [PMID: 38045109 PMCID: PMC10689069 DOI: 10.1155/2023/8898922] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/29/2023] [Revised: 11/03/2023] [Accepted: 11/13/2023] [Indexed: 12/05/2023] Open
Abstract
Background Vitamin K epoxide reductase complex subunit 1 (VKORC1) gene encodes a key enzyme with multiple cellular activities, namely, the reduction of vitamin K to its active form. VKORC1-1639G>A (rs9923231) is a common single nucleotide polymorphism with a crucial impact on warfarin dosing and possibly other physiological functions. This study aimed at investigating the frequencies of VKORC1-1639G>A alleles and genotypes in Syrian healthy subjects and patients on warfarin for different indications. Methods A total of 138 individuals were enrolled in this cross-sectional study. Genomic DNA was extracted from both patients on warfarin and healthy subjects, and polymerase chain reaction (PCR) specific amplicons were genotyped via standard sequencing which also allowed the detection of rs397509427. Comparisons of -1639G>A frequency with other populations were drawn. Results Of 94 patients on warfarin, 53 (56.38%) were with idiopathic venous thromboembolism (VTE). Despite comparable frequencies of the -1639A allele (47% and 50%), the AA and GA genotypes were at disparate frequencies of 93.2% versus 79.8% in the healthy subjects (n = 44) versus patients on warfarin, respectively. Carriers of the GG genotype were at a four-fold increased risk of VTE in comparison with those of the AA and GA genotypes (odds ratio (OR) = 4, 95% CI = 1.105 - 13.6, P = 0.0469). All study subjects were wild-type for the rs397509427 variant. Conclusions Our results prove a high -1639A prevalence in Syrian healthy subjects and patients on warfarin at frequencies comparable to other Mediterranean and Middle Eastern populations. The A allele carriers are at a lower VTE risk, whereas a global prevalence gradient of the G allele is suggested to be associated with VTE risk.
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Affiliation(s)
- Yara Altawil
- Department of Pharmaceutics and Pharmaceutical Technology, Program of Clinical and Hospital Pharmacy, Faculty of Pharmacy, Damascus University, Damascus, Syria
| | - Lama A. Youssef
- Department of Pharmaceutics and Pharmaceutical Technology, Program of Clinical and Hospital Pharmacy, Faculty of Pharmacy, Damascus University, Damascus, Syria
- National Commission for Biotechnology, Damascus, Syria
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2
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Wang D, Wu H, Zhang Q, Zhou X, An Y, Zhao A, Chong J, Wang S, Wang F, Yang J, Dai D, Chen H. Optimisation of warfarin-dosing algorithms for Han Chinese patients with CYP2C9*13 variants. Eur J Clin Pharmacol 2023; 79:1315-1320. [PMID: 37458773 DOI: 10.1007/s00228-023-03540-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2023] [Accepted: 07/13/2023] [Indexed: 09/16/2023]
Abstract
BACKGROUND Existing pharmacogenetic algorithms cannot fully explain warfarin dose variability in all patients. CYP2C9*13 is an important allelic variant in the Han Chinese population. However, adjustment of warfarin dosing in CYP2C9*13 variant carriers remains unclear. To the best of our knowledge, this study is the first to assess the effects of adjusting warfarin dosages in Han Chinese patients harbouring CYP2C9*13 variants. METHODS In total, 971 warfarin-treated Han Chinese patients with atrial fibrillation were enrolled in this study. Clinical data were collected, and CYP2C9*2, *3, *13 and VKORC1-1639 G > A variants were genotyped. We quantitatively analysed the effect of CYP2C9*13 on warfarin maintenance dose and provided multiplicative adjustments for CYP2C9*13 using validated pharmacogenetic algorithms. RESULTS Approximately 0.6% of the Han Chinese population carried CYP2C9*13 variant, and the genotype frequency was between those of CYP2C9*2 and CYP2C9*3. The warfarin maintenance doses were significantly reduced in CYP2C9*13 carriers. When CYP2C9*13 variants were not considered, the pharmacogenetic algorithms overestimated warfarin maintenance doses by 1.03-1.16 mg/d on average. The actual warfarin dose in CYP2C9*13 variant carriers was approximately 40% lower than the algorithm-predicted dose. Adjusting the warfarin-dosing algorithm according to the CYP2C9*13 allele could reduce the dose prediction error. CONCLUSION Our study showed that the algorithm-predicted doses should be lowered for CYP2C9*13 carriers. Inclusion of the CYP2C9*13 variant in the warfarin-dosing algorithm tends to predict the warfarin maintenance dose more accurately and improves the efficacy and safety of warfarin administration in Han Chinese patients.
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Affiliation(s)
- Dongxu Wang
- Cardiovascular Department, Beijing Hospital, National Centre of Gerontology, Beijing, 100730, China
- Fuwai Hospital, Arrhythmia Center, Chinese Academy of Medical Sciences, National Center for Cardiovascular Diseases, 100037, Beijing, China
| | - Hualan Wu
- Cardiovascular Department, Beijing Hospital, National Centre of Gerontology, Beijing, 100730, China
| | - Qing Zhang
- Cardiovascular Department, Beijing Hospital, National Centre of Gerontology, Beijing, 100730, China
| | - Xiaoyue Zhou
- Cardiovascular Department, Beijing Hospital, National Centre of Gerontology, Beijing, 100730, China
| | - Yang An
- Cardiovascular Department, Beijing Hospital, National Centre of Gerontology, Beijing, 100730, China
| | - Anxu Zhao
- Cardiovascular Department, Beijing Hospital, National Centre of Gerontology, Beijing, 100730, China
| | - Jia Chong
- Cardiovascular Department, Beijing Hospital, National Centre of Gerontology, Beijing, 100730, China
| | - Shuanghu Wang
- Laboratory of Clinical Pharmacy, The Sixth Affiliated Hospital of Wenzhou Medical University, The People's Hospital of Lishui, Lishui, 323020, China
| | - Fang Wang
- Cardiovascular Department, Beijing Hospital, National Centre of Gerontology, Beijing, 100730, China
| | - Jiefu Yang
- Cardiovascular Department, Beijing Hospital, National Centre of Gerontology, Beijing, 100730, China
| | - Dapeng Dai
- The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Beijing Hospital, National Centre of Gerontology, Beijing, 100730, China
| | - Hao Chen
- Cardiovascular Department, Beijing Hospital, National Centre of Gerontology, Beijing, 100730, China.
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Shamsuzzaman M, Ahsan T, Rahman H, Das KC, Salimullah. Integration of pharmacogenomic and pharmacomicrobiomic data for personalized medicine. PRECISION MEDICAL SCIENCES 2023. [DOI: 10.1002/prm2.12095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/06/2023] Open
Affiliation(s)
- Muhammad Shamsuzzaman
- Molecular Biotechnology Division National Institute of Biotechnology (NIB) Dhaka Bangladesh
| | - Tamim Ahsan
- Molecular Biotechnology Division National Institute of Biotechnology (NIB) Dhaka Bangladesh
| | - Hadisur Rahman
- Molecular Biotechnology Division National Institute of Biotechnology (NIB) Dhaka Bangladesh
| | - Keshob Chandra Das
- Molecular Biotechnology Division National Institute of Biotechnology (NIB) Dhaka Bangladesh
| | - Salimullah
- Molecular Biotechnology Division National Institute of Biotechnology (NIB) Dhaka Bangladesh
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Forgerini M, Urbano G, De Nadai TR, Batah SS, Fabro AT, De Carvalho Mastroianni P. The role of CYP2C9*2, CYP2C9*3 and VKORC1-1639 variants on the susceptibility of upper gastrointestinal bleeding: A full case-control study. JOURNAL OF PHARMACY & PHARMACEUTICAL SCIENCES : A PUBLICATION OF THE CANADIAN SOCIETY FOR PHARMACEUTICAL SCIENCES, SOCIETE CANADIENNE DES SCIENCES PHARMACEUTIQUES 2023; 26:11136. [PMID: 36942299 PMCID: PMC9990631 DOI: 10.3389/jpps.2023.11136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 01/06/2023] [Indexed: 01/31/2023]
Abstract
Purpose: To investigate whether interindividual variability in the CYP2C9 (*2 and *3 alleles) and VKORC1 (rs9923231) genes is associated with increased risk of upper gastrointestinal bleeding (UGIB) in users of non-steroidal anti-inflammatory drugs (NSAIDs) or low-dose aspirin (LDA). Methods: A full case-control study including 200 cases of patients diagnosed with UGIB and 706 controls was conducted in a Brazilian hospital complex. To perform an analysis of NSAIDs dose-effect, the defined daily dose (DDD) for NSAIDs was calculated in the 7-day etiologic window preceding the data index. Three categories of DDD, considering the genotypes of the genetic variants, were established: non-users of NSAIDs (DDD = 0), DDD ≤0.5, and DDD >0.5. Genetic variants and LDA or NSAIDs use synergism was estimated through Synergism Index (SI) and Relative Excess Risk Due To Interaction (RERI). Results: For DDDs of NSAIDs upward of 0.50, a risk of UGIB was identified in carriers of the *3 allele (OR: 15,650, 95% CI: 1.41-174.10) and in carriers of the variant homozygous genotype (TT) of rs9923231 (OR: 38,850, 95% CI: 2.70-556.00). In LDA users, the risk of UGIB was observed to be similar between carriers of the wild type homozygous genotype and carriers of the variant alleles for the CYP2C9 and VKORC1 genes. No synergism was identified. Conclusion: Our findings suggest an increased risk of UGIB in carriers of the variant allele of rs9923231 and in carriers of the *3 allele associated with doses of NSAIDs greater than 0.5. Hence, the assessment of these variants might reduce the incidence of NSAIDs-related UGIB and contribute to the safety of the NSAIDs user.
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Affiliation(s)
- Marcela Forgerini
- Department of Drugs and Medicines, School of Pharmaceutical Sciences, São Paulo State University (UNESP), Araraquara, São Paulo, Brazil
| | - Gustavo Urbano
- Department of Surgery, School of Medicine, University of São Paulo (USP), Ribeirão Preto, São Paulo, Brazil
| | - Tales Rubens De Nadai
- Department of Public Health, Bauru School of Dentistry, University of São Paulo (USP), Bauru, São Paulo, Brazil
| | - Sabrina Setembre Batah
- Department of Pathology and Legal Medicine, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Alexandre Todorovic Fabro
- Department of Pathology and Legal Medicine, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Patrícia De Carvalho Mastroianni
- Department of Drugs and Medicines, School of Pharmaceutical Sciences, São Paulo State University (UNESP), Araraquara, São Paulo, Brazil
- *Correspondence: Patrícia De Carvalho Mastroianni,
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Holail J, Mobarak R, Al-Ghamdi B, Aljada A, Fakhoury H. Association of VKORC1 and CYP2C9 single-nucleotide polymorphisms with warfarin dose adjustment in Saudi patients. Drug Metab Pers Ther 2022; 37:353-359. [PMID: 36476275 DOI: 10.1515/dmpt-2022-0108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 02/14/2022] [Indexed: 12/13/2022]
Abstract
OBJECTIVES Despite its wide usage, warfarin therapy remains challenging due to its narrow therapeutic index, inter-individual response variability, and risk of bleeding. Previous reports have suggested that polymorphisms in VKORC1 and CYP2C9 genes could influence warfarin therapy. Herein, we investigated whether VKORC1 -1173C>T, CYP2C9*2, and CYP2C9*3 gene polymorphisms are associated with warfarin dose adjustment and related bleeding events. METHODS This cross-sectional study was conducted on Saudi adults receiving warfarin for more than 1 month. Their demographics and relevant clinical data were obtained. Genotyping for VKORC1 -1173C>T, CYP2C9*2, and CYP2C9*2 genotypes was performed. RESULTS Patients who are homozygous for the mutant T allele VKORC1 T/T required the lowest warfarin daily maintenance dose, compared to VKORC1 C/T and VKORC1 C/C. Similarly, there was a significant reduction in warfarin daily maintenance dose among CYP2C9*1/*3 and CYP2C9*1/*2 groups compared to CYP2C9*1/*1. However, we found no significant correlation between the studied polymorphisms and warfarin-associated bleeding. CONCLUSIONS Similar to other populations, the VKORC1 and CYP2C9 gene polymorphisms are significantly associated with warfarin dosage in Saudi patients. The presence of at least one copy of the mutant alleles for VKORC1 -1173C>T, CYP2C9*2, and CYP2C9*3 is associated with a significant reduction in warfarin maintenance dose.
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Affiliation(s)
- Jasmine Holail
- Department of Biochemistry and Molecular Medicine, College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
| | - Reem Mobarak
- Department of Biochemistry and Molecular Medicine, College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
| | - Bandar Al-Ghamdi
- Heart Center, King Faisal Specialist Hospital and Research Center (KFSH&RC), Riyadh, Saudi Arabia
| | - Ahmad Aljada
- Department of Biochemistry and Molecular Medicine, College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
| | - Hana Fakhoury
- Department of Biochemistry and Molecular Medicine, College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
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Aldiban W, Altawil Y, Hussein S, Aljamali M, Youssef LA. Hyper-responsiveness to warfarin in a young patient with the VKORC1 -1639GA/CYP2C9*1*46 genotype: a case report. Thromb J 2022; 20:65. [PMID: 36303140 PMCID: PMC9608913 DOI: 10.1186/s12959-022-00425-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 10/17/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Warfarin is the most widely used oral anticoagulant; nevertheless, dosing of warfarin is problematic for clinicians worldwide. Inter-individual variability in response to warfarin is attributed to genetic as well as non-genetic factors. Pharmacogenomics studies have identified variants in CYP2C9 and VKORC1 genes as significant predictors of warfarin dose, however, phenotypes of rare variants are not well characterized. CASE PRESENTATION We report a case of hyper-responsiveness to warfarin in a 22-year-old outpatient with Crohn's disease who presented with a swollen, red, and painful left calf. Deep venous thrombosis (DVT) in the left lower extremity was confirmed via ultrasonography, and hence, anticoagulation therapy of heparin and concomitant warfarin was initiated. Warfarin dose of 7.5 mg/day was estimated by the physician based on clinical factors. Higher than the expected international normalized ratio (INR) value of 4.5 necessitated the reduction of the warfarin dose to 5 and eventually to 2.5 mg/day to reach a therapeutic INR value of 2.6. Pharmacogenetic profiling of the VKORC1 -1639G > A and CYP2C9 *2, *3, *4, *5, *8, *14, *20, *24, *26, *33, *40, *41, *42, *43, *45, *46, *55, *62, *63, *66, *68, *72, *73 and *78 revealed a VKORC1-1639GA/CYP2C9*1*46 genotype. The lower catalytic activity of the CYP2C9*46 (A149T) variant was previously reported in in vitro settings. CONCLUSIONS This is the first report on a case of warfarin hyper-responsive phenotype of a patient with the heterozygous CYP2C9*1*46 polymorphism.
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Affiliation(s)
- Weam Aldiban
- Program of Clinical and Hospital Pharmacy, Department of Pharmaceutics and Pharmaceutical Technology, Faculty of Pharmacy, Damascus University, Damascus, Syrian Arab Republic
- Faculty of Pharmacy, International University for Science and Technology (IUST), Daraa, Syrian Arab Republic
| | - Yara Altawil
- Program of Clinical and Hospital Pharmacy, Department of Pharmaceutics and Pharmaceutical Technology, Faculty of Pharmacy, Damascus University, Damascus, Syrian Arab Republic
| | | | - Majd Aljamali
- Department of Biochemistry and Microbiology, Faculty of Pharmacy, Damascus University, Damascus, Syrian Arab Republic
- National Commission for Biotechnology, Damascus, Syrian Arab Republic
| | - Lama A. Youssef
- Program of Clinical and Hospital Pharmacy, Department of Pharmaceutics and Pharmaceutical Technology, Faculty of Pharmacy, Damascus University, Damascus, Syrian Arab Republic
- Faculty of Pharmacy, International University for Science and Technology (IUST), Daraa, Syrian Arab Republic
- National Commission for Biotechnology, Damascus, Syrian Arab Republic
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Mendes M, Jonnalagadda M, Ozarkar S, Lima Torres FC, Borda Pua V, Kendall C, Tarazona-Santos E, Parra EJ. Identifying signatures of natural selection in Indian populations. PLoS One 2022; 17:e0271767. [PMID: 35925921 PMCID: PMC9352006 DOI: 10.1371/journal.pone.0271767] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 07/06/2022] [Indexed: 11/18/2022] Open
Abstract
In this study, we present the results of a genome-wide scan for signatures of positive selection using data from four tribal groups (Kokana, Warli, Bhil, and Pawara) and two caste groups (Deshastha Brahmin and Kunbi Maratha) from West of the Maharashtra State In India, as well as two samples of South Asian ancestry from the 1KG project (Gujarati Indian from Houston, Texas and Indian Telugu from UK). We used an outlier approach based on different statistics, including PBS, xpEHH, iHS, CLR, Tajima's D, as well as two recently developed methods: Graph-aware Retrieval of Selective Sweeps (GRoSS) and Ascertained Sequentially Markovian Coalescent (ASMC). In order to minimize the risk of false positives, we selected regions that are outliers in all the samples included in the study using more than one method. We identified putative selection signals in 107 regions encompassing 434 genes. Many of the regions overlap with only one gene. The signals observed using microarray-based data are very consistent with our analyses using high-coverage sequencing data, as well as those identified with a novel coalescence-based method (ASMC). Importantly, at least 24 of these genomic regions have been identified in previous selection scans in South Asian populations or in other population groups. Our study highlights genomic regions that may have played a role in the adaptation of anatomically modern humans to novel environmental conditions after the out of Africa migration.
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Affiliation(s)
- Marla Mendes
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
- Department of Anthropology, University of Toronto—Mississauga Campus, Mississauga, ON, Canada
| | - Manjari Jonnalagadda
- Symbiosis School for Liberal Arts (SSLA), Symbiosis International University (SIU), Pune, India
| | - Shantanu Ozarkar
- Department of Anthropology, Savitribai Phule Pune University, Pune, India
| | - Flávia Carolina Lima Torres
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Victor Borda Pua
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, United States of America
| | - Christopher Kendall
- Department of Anthropology, University of Toronto—Mississauga Campus, Mississauga, ON, Canada
| | - Eduardo Tarazona-Santos
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Esteban J. Parra
- Department of Anthropology, University of Toronto—Mississauga Campus, Mississauga, ON, Canada
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Tron C, Bouvet R, Verdier MC, Lamoureux F, Hennart B, Dubourg C, Bellissant E, Galibert MD. A Robust and Fast/Multiplex Pharmacogenetics Assay to Simultaneously Analyze 17 Clinically Relevant Genetic Polymorphisms in CYP3A4, CYP3A5, CYP1A2, CYP2C9, CYP2C19, CYP2D6, ABCB1, and VKORC1 Genes. Pharmaceuticals (Basel) 2022; 15:ph15050637. [PMID: 35631462 PMCID: PMC9145594 DOI: 10.3390/ph15050637] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 05/11/2022] [Accepted: 05/13/2022] [Indexed: 11/16/2022] Open
Abstract
In the field of pharmacogenetics, the trend is to analyze a panel of several actionable genetic polymorphisms. It may require the use of high-throughput sequencing which demands expensive reagents/instruments and specific skills to interpret results. As an alternative, the aim of this work was to validate an easy, fast, and inexpensive multiplex pharmacogenetics assay to simultaneously genotype a panel of 17 clinically actionable variants involved in drug pharmacokinetics/pharmacodynamics. We designed primers to perform a multiplex PCR assay using a single mix. Primers were labeled by two fluorescent dye markers to discriminate alleles, while the size of the PCR fragments analyzed by electrophoresis allowed identifying amplicon. Polymorphisms of interest were CYP3A4*22, CYP3A5*3, CYP1A2*1F, CYP2C9*2-*3, CYP2C19*2-*3-*17, VKORC1-1639G > A, ABCB1 rs1045642-rs1128503-rs2229109-rs2032582, and CYP2D6*3-*4-*6-*9. The assay was repeatable and a minimum quantity of 10 ng of DNA/ sample was needed to obtain accurate results. The method was applied to a validation cohort of 121 samples and genotyping results were consistent with those obtained with reference methods. The assay was fast and cost-effective with results being available within one working-day. This robust assay can easily be implemented in laboratories as an alternative to cumbersome simplex assays or expensive multiplex approaches. Together it should widespread access to pharmacogenetics in clinical routine practice.
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Affiliation(s)
- Camille Tron
- Pharmacology Department, CHU Rennes, Inserm, EHESP, Irset (Institut de Recherche en Santé, Environnement et Travail)-UMR_S 1085, Univ Rennes, F-35000 Rennes, France; (M.-C.V.); (E.B.)
- Correspondence: ; Tel.: +33-2-99-28-42-80
| | - Régis Bouvet
- Department of Molecular Genetics and Genomics, Rennes Hospital University, F-35000 Rennes, France; (R.B.); (C.D.); (M.-D.G.)
| | - Marie-Clémence Verdier
- Pharmacology Department, CHU Rennes, Inserm, EHESP, Irset (Institut de Recherche en Santé, Environnement et Travail)-UMR_S 1085, Univ Rennes, F-35000 Rennes, France; (M.-C.V.); (E.B.)
| | | | - Benjamin Hennart
- CHU Lille, Service de Toxicologie et Génopathies, F-59000 Lille, France;
| | - Christèle Dubourg
- Department of Molecular Genetics and Genomics, Rennes Hospital University, F-35000 Rennes, France; (R.B.); (C.D.); (M.-D.G.)
- CNRS, IGDR (Institut de Génétique et Développement de Rennes)-UMR 6290, Univ Rennes, F-35000 Rennes, France
| | - Eric Bellissant
- Pharmacology Department, CHU Rennes, Inserm, EHESP, Irset (Institut de Recherche en Santé, Environnement et Travail)-UMR_S 1085, Univ Rennes, F-35000 Rennes, France; (M.-C.V.); (E.B.)
| | - Marie-Dominique Galibert
- Department of Molecular Genetics and Genomics, Rennes Hospital University, F-35000 Rennes, France; (R.B.); (C.D.); (M.-D.G.)
- CNRS, IGDR (Institut de Génétique et Développement de Rennes)-UMR 6290, Univ Rennes, F-35000 Rennes, France
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Anjum F, Mohammad T, Asrani P, Shafie A, Singh S, Yadav DK, Uversky VN, Hassan MI. Identification of intrinsically disorder regions in non-structural proteins of SARS-CoV-2: New insights into drug and vaccine resistance. Mol Cell Biochem 2022; 477:1607-1619. [PMID: 35211823 PMCID: PMC8869350 DOI: 10.1007/s11010-022-04393-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 02/10/2022] [Indexed: 02/06/2023]
Abstract
The outbreak of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) emerged in December 2019 and caused coronavirus disease 2019 (COVID-19), which causes pneumonia and severe acute respiratory distress syndrome. It is a highly infectious pathogen that promptly spread. Like other beta coronaviruses, SARS-CoV-2 encodes some non-structural proteins (NSPs), playing crucial roles in viral transcription and replication. NSPs likely have essential roles in viral pathogenesis by manipulating many cellular processes. We performed a sequence-based analysis of NSPs to get insights into their intrinsic disorders, and their functions in viral replication were annotated and discussed in detail. Here, we provide newer insights into the structurally disordered regions of SARS-CoV-2 NSPs. Our analysis reveals that the SARS-CoV-2 proteome has a chunk of the disordered region that might be responsible for increasing its virulence. In addition, mutations in these regions are presumably responsible for drug and vaccine resistance. These findings suggested that the structurally disordered regions of SARS-CoV-2 NSPs might be invulnerable in COVID-19.
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Affiliation(s)
- Farah Anjum
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Taif University, P.O. Box 11099, Taif, 21944, Saudi Arabia
| | - Taj Mohammad
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, 110025, India
| | - Purva Asrani
- Department of Microbiology, University of Delhi, New Delhi, 110021, India
| | - Alaa Shafie
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Taif University, P.O. Box 11099, Taif, 21944, Saudi Arabia
| | - Shailza Singh
- National Centre for Cell Science, NCCS Complex, Ganeshkhind, SP, Pune University Campus, Pune, 411007, India
| | - Dharmendra Kumar Yadav
- College of Pharmacy, Gachon University of Medicine and Science, Hambakmoeiro, Yeonsu-gu, Incheon City, 21924, South Korea.
| | - Vladimir N Uversky
- Department of Molecular Medicine and USF Health Byrd Alzheimer's Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, 33612, USA
| | - Md Imtaiyaz Hassan
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, 110025, India.
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10
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Holail J, Mobarak R, Al-Ghamdi B, Aljada A, Fakhoury H. Association of VKORC1 and CYP2C9 single-nucleotide polymorphisms with warfarin dose adjustment in Saudi patients. Drug Metab Pers Ther 2022; 0:dmdi-2022-0108. [PMID: 35365981 DOI: 10.1515/dmdi-2022-0108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 02/14/2022] [Indexed: 11/15/2022]
Abstract
OBJECTIVES Despite its wide usage, warfarin therapy remains challenging due to its narrow therapeutic index, inter-individual response variability, and risk of bleeding. Previous reports have suggested that polymorphisms in VKORC1 and CYP2C9 genes could influence warfarin therapy. Herein, we investigated whether VKORC1 -1173C>T, CYP2C9*2, and CYP2C9*3 gene polymorphisms are associated with warfarin dose adjustment and related bleeding events. METHODS This cross-sectional study was conducted on Saudi adults receiving warfarin for more than 1 month. Their demographics and relevant clinical data were obtained. Genotyping for VKORC1 -1173C>T, CYP2C9*2, and CYP2C9*2 genotypes was performed. RESULTS Patients who are homozygous for the mutant T allele VKORC1 T/T required the lowest warfarin daily maintenance dose, compared to VKORC1 C/T and VKORC1 C/C. Similarly, there was a significant reduction in warfarin daily maintenance dose among CYP2C9*1/*3 and CYP2C9*1/*2 groups compared to CYP2C9*1/*1. However, we found no significant correlation between the studied polymorphisms and warfarin-associated bleeding. CONCLUSIONS Similar to other populations, the VKORC1 and CYP2C9 gene polymorphisms are significantly associated with warfarin dosage in Saudi patients. The presence of at least one copy of the mutant alleles for VKORC1 -1173C>T, CYP2C9*2, and CYP2C9*3 is associated with a significant reduction in warfarin maintenance dose.
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Affiliation(s)
- Jasmine Holail
- Department of Biochemistry and Molecular Medicine, College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
| | - Reem Mobarak
- Department of Biochemistry and Molecular Medicine, College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
| | - Bandar Al-Ghamdi
- Heart Center, King Faisal Specialist Hospital and Research Center (KFSH&RC), Riyadh, Saudi Arabia
| | - Ahmad Aljada
- Department of Biochemistry and Molecular Medicine, College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
| | - Hana Fakhoury
- Department of Biochemistry and Molecular Medicine, College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
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11
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Sahana S, Bhoyar RC, Sivadas A, Jain A, Imran M, Rophina M, Senthivel V, Kumar Diwakar M, Sharma D, Mishra A, Sivasubbu S, Scaria V. Pharmacogenomic landscape of Indian population using whole genomes. Clin Transl Sci 2022; 15:866-877. [PMID: 35338580 PMCID: PMC9010271 DOI: 10.1111/cts.13153] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 08/01/2021] [Accepted: 08/18/2021] [Indexed: 12/17/2022] Open
Abstract
Ethnic differences in pharmacogenomic (PGx) variants have been well documented in literature and could significantly impact variability in response and adverse events to therapeutics. India is a large country with diverse ethnic populations of distinct genetic architecture. India's national genome sequencing initiative (IndiGen) provides a unique opportunity to explore the landscape of PGx variants using population-scale whole genome sequences. We have analyzed the IndiGen variation dataset (N = 1029 genomes) along with global population scale databases to map the most prevalent clinically actionable and potentially deleterious PGx variants among Indians. Differential frequencies for the known and novel variants were studied and interaction of the disrupted PGx genes affecting drug responses were analyzed by performing a pathway analysis. We have highlighted significant differences in the allele frequencies of clinically actionable PGx variants in Indians when compared to the global populations. We identified 134 mostly common (allele frequency [AF] > 0.1) potentially deleterious PGx variants that could alter or inhibit the function of 102 pharmacogenes in Indians. We also estimate that on, an average, each Indian individual carried eight PGx variants (single nucleotide variants) that have a direct impact on the choice of treatment or drug dosing. We have also highlighted clinically actionable PGx variants and genes for which preemptive genotyping is most recommended for the Indian population. The study has put forward the most comprehensive PGx landscape of the Indian population from whole genomes that could enable optimized drug selection and genotype-guided prescriptions for improved therapeutic outcomes and minimizing adverse events.
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Affiliation(s)
- S Sahana
- CSIR Institute of Genomics and Integrative Biology, New Delhi, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Rahul C Bhoyar
- CSIR Institute of Genomics and Integrative Biology, New Delhi, India
| | - Ambily Sivadas
- Division of Nutrition, St. John's Research Institute, St. John's National Academy of Health Sciences, Bangalore, India
| | - Abhinav Jain
- CSIR Institute of Genomics and Integrative Biology, New Delhi, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Mohamed Imran
- CSIR Institute of Genomics and Integrative Biology, New Delhi, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Mercy Rophina
- CSIR Institute of Genomics and Integrative Biology, New Delhi, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Vigneshwar Senthivel
- CSIR Institute of Genomics and Integrative Biology, New Delhi, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Mohit Kumar Diwakar
- CSIR Institute of Genomics and Integrative Biology, New Delhi, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Disha Sharma
- CSIR Institute of Genomics and Integrative Biology, New Delhi, India
| | - Anushree Mishra
- CSIR Institute of Genomics and Integrative Biology, New Delhi, India
| | - Sridhar Sivasubbu
- CSIR Institute of Genomics and Integrative Biology, New Delhi, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Vinod Scaria
- CSIR Institute of Genomics and Integrative Biology, New Delhi, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
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12
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Pharmacogenomic analysis of a genetically distinct Indigenous population. THE PHARMACOGENOMICS JOURNAL 2022; 22:100-108. [PMID: 34824386 DOI: 10.1038/s41397-021-00262-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 11/08/2021] [Accepted: 11/10/2021] [Indexed: 11/09/2022]
Abstract
Indigenous Australians face a disproportionately severe burden of chronic disease relative to other Australians, with elevated rates of morbidity and mortality. While genomics technologies are slowly gaining momentum in personalised treatments for many, a lack of pharmacogenomic research in Indigenous peoples could delay adoption. Appropriately implementing pharmacogenomics in clinical care necessitates an understanding of the frequencies of pharmacologically relevant genetic variants within Indigenous populations. We analysed whole-genome sequence data from 187 individuals from the Tiwi Islands and characterised the pharmacogenomic landscape of this population. Specifically, we compared variant profiles and allelic distributions of previously described pharmacologically significant genes and variants with other population groups. We identified 22 translationally relevant pharmacogenomic variants and 18 clinically actionable guidelines with implications for drug dosing and treatment of conditions including heart disease, diabetes and cancer. We specifically observed increased poor and intermediate metabolizer phenotypes in the CYP2C9 (PM:19%, IM:44%) and CYP2C19 (PM:18%, IM:44%) genes.
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13
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Suwanawiboon B, Rotchanapanya W, Mahaprom K, Thongnoppakhun W, Lalerd Y, Limwongse C, Sermsathanasawadi N, Owattanapanich W. The efficacy of low-dose warfarin initiation (3 mg versus 5 mg) in newly diagnosed venous thromboembolism patients among a population with a high prevalence of warfarin-sensitive haplotype of the VKORC1 gene: a randomized controlled trial. Hematology 2022; 27:95-104. [DOI: 10.1080/16078454.2021.2019891] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Affiliation(s)
- Bundarika Suwanawiboon
- Division of Hematology, Department of Medicine, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Wannaphorn Rotchanapanya
- Division of Hematology, Department of Medicine, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Komkrit Mahaprom
- Division of Hematology, Department of Medicine, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Wanna Thongnoppakhun
- Division of Molecular Genetics, Department of Research and Development, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Yupaporn Lalerd
- Division of Medical Genetics, Department of Medicine, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Chanin Limwongse
- Division of Medical Genetics, Department of Medicine, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Nuttawut Sermsathanasawadi
- Division of Vascular Surgery, Department of Surgery, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Weerapat Owattanapanich
- Division of Hematology, Department of Medicine, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
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14
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Kim B, Yoon DY, Lee S, Jang IJ, Yu KS, Cho JY, Oh J. Comprehensive analysis of important pharmacogenes in Koreans using the DMET™ platform. Transl Clin Pharmacol 2021; 29:135-149. [PMID: 34621706 PMCID: PMC8492395 DOI: 10.12793/tcp.2021.29.e14] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 07/29/2021] [Accepted: 08/25/2021] [Indexed: 11/29/2022] Open
Abstract
Genetic polymorphisms of enzymes and transporters associated with the absorption, distribution, metabolism, and elimination (ADME) of drugs are one of the major factors that contribute to interindividual variations in drug response. In the present study, we aimed to elucidate the pharmacogenetic profiles of the Korean population using the Affymetrix Drug Metabolizing Enzyme and Transporters (DMET™) platform. A total of 1,012 whole blood samples collected from Korean subjects were genotyped using the DMET™ plus microarray. In total, 1,785 single nucleotide polymorphism (SNP) markers for 231 ADME genes were identified. The genotype and phenotype of 13 clinically important ADME genes implemented in the Clinical Pharmacogenetics Implementation Consortium guidelines were compared among different ethnic groups. Overall, the genotype frequencies of the Korean population were similar to those of the East Asian population. Several genes, notably CYP2C19 and VKORC1, showed marked differences in Koreans compared to Europeans (EURs) or Africans (AFRs). The percentage of CYP2C19 poor metabolizers was 15% in Koreans and less than 3% in EURs or AFRs. The frequencies of causative SNPs of the VKORC1 gene for the low warfarin dose phenotype were 90%, 60%, and 10% in Koreans, EURs and AFRs, respectively. Our findings can be utilized for optimal pharmacotherapy in Korean patients.
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Affiliation(s)
- Byungwook Kim
- Department of Clinical Pharmacology and Therapeutics, Seoul National University College of Medicine and Hospital, Seoul 03080, Korea
| | - Deok Yong Yoon
- Department of Clinical Pharmacology and Therapeutics, Seoul National University College of Medicine and Hospital, Seoul 03080, Korea
| | - SeungHwan Lee
- Department of Clinical Pharmacology and Therapeutics, Seoul National University College of Medicine and Hospital, Seoul 03080, Korea
| | - In-Jin Jang
- Department of Clinical Pharmacology and Therapeutics, Seoul National University College of Medicine and Hospital, Seoul 03080, Korea
| | - Kyung-Sang Yu
- Department of Clinical Pharmacology and Therapeutics, Seoul National University College of Medicine and Hospital, Seoul 03080, Korea
| | - Joo-Youn Cho
- Department of Clinical Pharmacology and Therapeutics, Seoul National University College of Medicine and Hospital, Seoul 03080, Korea
| | - Jaeseong Oh
- Department of Clinical Pharmacology and Therapeutics, Seoul National University College of Medicine and Hospital, Seoul 03080, Korea
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15
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Cavieres M, Suárez M, Verón G, Quiñones LA, Varela NM. Retrospective pharmacogenetic analysis of a pediatric patient under anticoagulant treatment: Clinical case. BIOMEDICA : REVISTA DEL INSTITUTO NACIONAL DE SALUD 2021; 41:403-408. [PMID: 34559488 PMCID: PMC8519589 DOI: 10.7705/biomedica.5840] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 05/28/2021] [Indexed: 06/13/2023]
Abstract
We present the clinical case of a 10-year-old patient diagnosed with dilated cardiomyopathy who registered INR values above 10 upon receiving standard doses of acenocoumarol, as well as other values reported as uncoagulable, forcing the discontinuation and restart of treatment more than once. Expected and stable INR levels were achieved after more than 30 days of treatment, surprisingly with half the recommended dose for a patient of her age and weight. We decided to conduct a retrospective pharmacogenomic analysis including nucleotide genetic polymorphisms (SNPs) with different degrees of association with the dose/response to antivitamin K (AVK) drugs: rs2108622 (gene CYP4F2), rs9923231, rs7294 (gene VKORC1), rs1799853, and rs1057910 (CYP2C9 gene) using TaqMan® RT-PCR. The patient was homozygous for rs9923231 (VKORC1) and heterozygous for rs2108622 (CYP4F2),a genetic profile strongly associated with a requirement of lower AVK doses as shown by national and international evidence. In conclusion, the pharmacogenetic analysis confirmed that this patient’s genetic conditions, involving low expression of the VKA therapeutic target, required a lower dose than that established in clinical protocols as recommended by the Food and Drug Administration (FDA) and the PharmGKB® for coumarin drugs. A previous genotypic analysis of the patient would have allowed reaching the therapeutic range sooner, thus avoiding potential bleeding risks. This shows the importance of pharmacogenetic analyses for highly variable treatments with a narrow therapeutic range.
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Affiliation(s)
- Mirta Cavieres
- Laboratorio Clínico, Hospital Dr. Luis Calvo Mackenna, Santiago, Chile.
| | - Marcelo Suárez
- Laboratorio de Carcinogénesis Química y Farmacogenética, Departamento de Oncología Básico-Clínico, Facultad de Medicina, Universidad de Chile, Santiago, Chile; Servicio de Farmacia, Hospital Clínico Red de Salud UC-Christus, Santiago, Chile.
| | - Gabriel Verón
- Laboratorio de Carcinogénesis Química y Farmacogenética, Departamento de Oncología Básico-Clínico, Facultad de Medicina, Universidad de Chile, Santiago, Chile; Red Latinoamericana para la Implementación y Validación de Guías Clínicas Farmacogenómicas (RELIVAF-CYTED), Santiago, Chile.
| | - Luis Abel Quiñones
- Laboratorio de Carcinogénesis Química y Farmacogenética, Departamento de Oncología Básico-Clínico, Facultad de Medicina, Universidad de Chile, Santiago, Chile; Red Latinoamericana para la Implementación y Validación de Guías Clínicas Farmacogenómicas (RELIVAF-CYTED), Santiago, Chile.
| | - Nelson Miguel Varela
- Laboratorio de Carcinogénesis Química y Farmacogenética, Departamento de Oncología Básico-Clínico, Facultad de Medicina, Universidad de Chile, Santiago, Chile; Red Latinoamericana para la Implementación y Validación de Guías Clínicas Farmacogenómicas (RELIVAF-CYTED), Santiago, Chile.
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16
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Geck RC, Boyle G, Amorosi CJ, Fowler DM, Dunham MJ. Measuring Pharmacogene Variant Function at Scale Using Multiplexed Assays. Annu Rev Pharmacol Toxicol 2021; 62:531-550. [PMID: 34516287 DOI: 10.1146/annurev-pharmtox-032221-085807] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
As costs of next-generation sequencing decrease, identification of genetic variants has far outpaced our ability to understand their functional consequences. This lack of understanding is a central challenge to a key promise of pharmacogenomics: using genetic information to guide drug selection and dosing. Recently developed multiplexed assays of variant effect enable experimental measurement of the function of thousands of variants simultaneously. Here, we describe multiplexed assays that have been performed on nearly 25,000 variants in eight key pharmacogenes (ADRB2, CYP2C9, CYP2C19, NUDT15, SLCO1B1, TMPT, VKORC1, and the LDLR promoter), discuss advances in experimental design, and explore key challenges that must be overcome to maximize the utility of multiplexed functional data. Expected final online publication date for the Annual Review of Pharmacology and Toxicology, Volume 62 is January 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Renee C Geck
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA; ,
| | - Gabriel Boyle
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA; ,
| | - Clara J Amorosi
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA; ,
| | - Douglas M Fowler
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA; , .,Department of Bioengineering, University of Washington, Seattle, Washington 98195, USA
| | - Maitreya J Dunham
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA; ,
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17
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Tafazoli A, Guchelaar HJ, Miltyk W, Kretowski AJ, Swen JJ. Applying Next-Generation Sequencing Platforms for Pharmacogenomic Testing in Clinical Practice. Front Pharmacol 2021; 12:693453. [PMID: 34512329 PMCID: PMC8424415 DOI: 10.3389/fphar.2021.693453] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2021] [Accepted: 07/26/2021] [Indexed: 11/13/2022] Open
Abstract
Pharmacogenomics (PGx) studies the use of genetic data to optimize drug therapy. Numerous clinical centers have commenced implementing pharmacogenetic tests in clinical routines. Next-generation sequencing (NGS) technologies are emerging as a more comprehensive and time- and cost-effective approach in PGx. This review presents the main considerations for applying NGS in guiding drug treatment in clinical practice. It discusses both the advantages and the challenges of implementing NGS-based tests in PGx. Moreover, the limitations of each NGS platform are revealed, and the solutions for setting up and management of these technologies in clinical practice are addressed.
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Affiliation(s)
- Alireza Tafazoli
- Department of Analysis and Bioanalysis of Medicines, Faculty of Pharmacy with the Division of Laboratory Medicine, Medical University of Bialystok, Bialystok, Poland
- Clinical Research Centre, Medical University of Bialystok, Bialystok, Poland
| | - Henk-Jan Guchelaar
- Department of Clinical Pharmacy and Toxicology, Leiden University Medical Center, Leiden, Netherlands
- Leiden Network of Personalized Therapeutics, Leiden, Netherlands
| | - Wojciech Miltyk
- Department of Analysis and Bioanalysis of Medicines, Faculty of Pharmacy with the Division of Laboratory Medicine, Medical University of Bialystok, Bialystok, Poland
| | - Adam J. Kretowski
- Clinical Research Centre, Medical University of Bialystok, Bialystok, Poland
- Department of Endocrinology, Diabetology and Internal Medicine, Medical University of Bialystok, Bialystok, Poland
| | - Jesse J. Swen
- Department of Clinical Pharmacy and Toxicology, Leiden University Medical Center, Leiden, Netherlands
- Leiden Network of Personalized Therapeutics, Leiden, Netherlands
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18
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Kaesler N, Schurgers LJ, Floege J. Vitamin K and cardiovascular complications in CKD patients. Kidney Int 2021; 100:1023-1036. [PMID: 34310988 DOI: 10.1016/j.kint.2021.06.037] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 06/08/2021] [Accepted: 06/11/2021] [Indexed: 01/07/2023]
Abstract
Vitamin K, well known for its role in coagulation, encompasses two major subgroups: Vitamin K1 is exclusively synthesized by plants, whereas vitamin K2 mostly originates from bacterial synthesis. Vitamin K serves as a cofactor for the enzyme γ-glutamyl carboxylase, which carboxylates and thereby activates various vitamin K dependent proteins. Several vitamin K-dependent proteins are synthesized in bone but the role of vitamin K for bone health in CKD patients, in particular the prevention of osteoporosis is still not firmly established. Here we focus on another prominent action of vitamin K, in particular vitamin K2, namely the activation of matrix Gla protein (MGP), the most potent inhibitor of cardiovascular calcifications. Multiple observational studies link relative vitamin K deficiency or low intake to cardiovascular calcification progress, morbidity and mortality. Patients with advanced chronic kidney disease (CKD) are particularly vitamin K deficient, in part because of dietary restrictions but possibly also due to impaired endogenous recycling of vitamin K. At the same time this population is characterized by markedly accelerated cardiovascular calcifications and mortality. High dose dietary supplementation with vitamin K2, in particular the most potent form menaquinone-7 (MK7), can potently reduce circulating levels of dephosphorylated uncarboxylated, i.e. inactive MGP in patients with end stage kidney disease. However, despite this compelling data basis, several randomized controlled trials with high dose MK7 supplements in patients with advanced CKD have failed to confirm cardiovascular benefits. Here we discuss potential reasons and solutions for this.
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Affiliation(s)
- Nadine Kaesler
- Division of Nephrology and Rheumatology, University Hospital, Rheinisch Westfälische Technische Hochschule, Aachen, Germany
| | - Leon J Schurgers
- Department of Biochemistry and Cardiovascular Research Institute Maastricht, School for Cardiovascular Diseases, Maastricht University, Maastricht, the Netherlands; Institute of Experimental Medicine and Systems Biology, Rheinisch Westfälische Technische Hochschule, Aachen University, Aachen, Germany
| | - Jürgen Floege
- Division of Nephrology and Rheumatology, University Hospital, Rheinisch Westfälische Technische Hochschule, Aachen, Germany.
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19
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Competitive tight-binding inhibition of VKORC1 underlies warfarin dosage variation and antidotal efficacy. Blood Adv 2021; 4:2202-2212. [PMID: 32433747 DOI: 10.1182/bloodadvances.2020001750] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Accepted: 04/24/2020] [Indexed: 11/20/2022] Open
Abstract
Dose control of warfarin is a major complication in anticoagulation therapy and overdose is reversed by the vitamin K antidote. Improving the dosage management and antidotal efficacy requires mechanistic understanding. Here we find that effects of the major predictor of warfarin dosage, SNP -1639 G>A, follow a general correlation that warfarin 50% inhibitory concentration decreases with cellular level of vitamin K epoxide reductase (VKORC1), suggesting stoichiometric inhibition. Characterization of the inhibition kinetics required the use of microsomal VKORC1 with a native reductant, glutathione, that enables effective warfarin inhibition in vitro. The kinetics data can be fitted with the Morrison equation, giving a nanomolar inhibition constant and demonstrating that warfarin is a tight-binding inhibitor. However, warfarin is released from purified VKORC1-warfarin complex with increasing amount of vitamin K, indicating competitive inhibition. The competition occurs also in cells, resulting in rescued VKORC1 activity that augments the antidotal effects of vitamin K. Taken together, warfarin is a competitive inhibitor that binds VKORC1 tightly and inhibits at a stoichiometric (1:1) concentration, whereas exceeding the VKORC1 level results in warfarin overdose. Thus, warfarin dosage control should use VKORC1 level as a major indicator, and improved antidotes may be designed based on their competition with warfarin.
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20
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Panahi L, Udeani G, Horseman M, Weston J, Samuel N, Joseph M, Mora A, Bazan D. Review of Medical Therapies for the Management of Pulmonary Embolism. MEDICINA (KAUNAS, LITHUANIA) 2021; 57:110. [PMID: 33530544 PMCID: PMC7912594 DOI: 10.3390/medicina57020110] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 01/11/2021] [Accepted: 01/13/2021] [Indexed: 12/12/2022]
Abstract
Traditionally, the management of patients with pulmonary embolism has been accomplished with anticoagulant treatment with parenteral heparins and oral vitamin K antagonists. Although the administration of heparins and oral vitamin K antagonists still plays a role in pulmonary embolism management, the use of these therapies are limited due to other options now available. This is due to their toxicity profile, clearance limitations, and many interactions with other medications and nutrients. The emergence of direct oral anticoagulation therapies has led to more options now being available to manage pulmonary embolism in inpatient and outpatient settings conveniently. These oral therapeutic options have opened up opportunities for safe and effective pulmonary embolism management, as more evidence and research is now available about reversal agents and monitoring parameters. The evolution of the pharmacological management of pulmonary embolism has provided us with better understanding regarding the selection of anticoagulants. There is also a better understanding and employment of anticoagulants in pulmonary embolism in special populations, such as patients with liver failure, renal failure, malignancy, and COVID-19.
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Affiliation(s)
- Ladan Panahi
- Department of Pharmacy Practice, Texas A&M Rangel College of Pharmacy, 1010 W Ave B, Kingsville, TX 78363, USA; (M.H.); (J.W.); (N.S.); (M.J.); (A.M.); (D.B.)
| | - George Udeani
- Department of Pharmacy Practice, Texas A&M Rangel College of Pharmacy, 1010 W Ave B, Kingsville, TX 78363, USA; (M.H.); (J.W.); (N.S.); (M.J.); (A.M.); (D.B.)
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21
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Eghbali M, Fatemi KS, Salehpour S, Abiri M, Saei H, Talebi S, Olyaei NA, Yassaee VR, Modarressi MH. Whole-Exome Sequencing Uncovers Novel Causative Variants and Additional Findings in Three Patients Affected by Glycogen Storage Disease Type VI and Fanconi-Bickel Syndrome. Front Genet 2021; 11:601566. [PMID: 33505429 PMCID: PMC7831547 DOI: 10.3389/fgene.2020.601566] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 12/07/2020] [Indexed: 01/08/2023] Open
Abstract
Glycogen storage diseases (GSDs) are the heterogeneous group of disorders caused by mutations in at least 30 different genes. Different types of GSDs, especially liver GSDs, take overlapping symptoms and can be clinically indistinguishable. This survey evaluated the use of whole-exome sequencing (WES) for the genetic analysis of the liver GSD-suspected patients in three unrelated families. An in-house filtering pipeline was used to assess rare pathogenic variants in GSD-associated genes, autosomal recessive/mendelian disorder genes (carrier status for genetic counseling subjects), and the ACMG's list of 59 actionable genes. For the interpretation of the causative variants and the incidental/secondary findings, ACMG guidelines were applied. Additionally, we have explored PharmGKB class IA/IB pharmacogenetic variants. The segregation analysis was performed using Sanger sequencing for the novel causative variants. Bioinformatics analysis of the exome data in three individuals revealed three novel homozygous causative variants in the GSD-associated genes. The first variant, c.298_307delATGATCAACC in PYGL gene has related to HERS disease (GSD VI). Both variants of c.1043dupT and c.613-1G > C in SLC2A2 gene have been associated with Fanconi-Bickel syndrome (GSDXI). Eight pathogenic/likely pathogenic medical actionable findings in Mendelian disease genes and 10 pharmacogenetic variants with underlying drug response phenotypes have been identified. No known/expected pathogenic variants were detected in the ACMG's list of 59 actionable genes. The logical filtering steps can help in finding other medical actionable secondary/incidental findings as well as effectively identifying the causative variants in heterogeneous conditions such as GSDs. Three novel variants related to GSD genes recognized in liver GSD-suspected patients with early infantile and childhood-age onset.
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Affiliation(s)
- Maryam Eghbali
- Department of Medical Genetics, Faculty of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Kiyana Sadat Fatemi
- Dr. Zenali's Medical Genetics Laboratory, Kawsar Human Genetics Research Center, Tehran, Iran
| | - Shadab Salehpour
- Genomic Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran.,Department of Pediatric Endocrinology and Metabolism, Mofid Children's Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Maryam Abiri
- Shahid Akbarabadi Clinical Research Development Unit, Iran University of Medical Sciences, Tehran, Iran.,Department of Medical Genetics and Molecular Biology, Faculty of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Hassan Saei
- Department of Medical Genetics and Molecular Biology, Faculty of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Saeed Talebi
- Department of Medical Genetics and Molecular Biology, Faculty of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Nasrin Alipour Olyaei
- Genomic Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Vahid Reza Yassaee
- Genomic Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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22
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Han N, Oh JM, Kim IW. Combination of Genome-Wide Polymorphisms and Copy Number Variations of Pharmacogenes in Koreans. J Pers Med 2021; 11:33. [PMID: 33430289 PMCID: PMC7825650 DOI: 10.3390/jpm11010033] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 12/16/2020] [Accepted: 01/04/2021] [Indexed: 12/12/2022] Open
Abstract
For predicting phenotypes and executing precision medicine, combination analysis of single nucleotide variants (SNVs) genotyping with copy number variations (CNVs) is required. The aim of this study was to discover SNVs or common copy CNVs and examine the combined frequencies of SNVs and CNVs in pharmacogenes using the Korean genome and epidemiology study (KoGES), a consortium project. The genotypes (N = 72,299) and CNV data (N = 1000) were provided by the Korean National Institute of Health, Korea Centers for Disease Control and Prevention. The allele frequencies of SNVs, CNVs, and combined SNVs with CNVs were calculated and haplotype analysis was performed. CYP2D6 rs1065852 (c.100C>T, p.P34S) was the most common variant allele (48.23%). A total of 8454 haplotype blocks in 18 pharmacogenes were estimated. DMD ranked the highest in frequency for gene gain (64.52%), while TPMT ranked the highest in frequency for gene loss (51.80%). Copy number gain of CYP4F2 was observed in 22 subjects; 13 of those subjects were carriers with CYP4F2*3 gain. In the case of TPMT, approximately one-half of the participants (N = 308) had loss of the TPMT*1*1 diplotype. The frequencies of SNVs and CNVs in pharmacogenes were determined using the Korean cohort-based genome-wide association study.
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Affiliation(s)
| | | | - In-Wha Kim
- College of Pharmacy and Research Institute of Pharmaceutical Sciences, Seoul National University, Seoul 08826, Korea; (N.H.); (J.M.O.)
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Davies JP, Almasy KM, McDonald EF, Plate L. Comparative Multiplexed Interactomics of SARS-CoV-2 and Homologous Coronavirus Nonstructural Proteins Identifies Unique and Shared Host-Cell Dependencies. ACS Infect Dis 2020; 6:3174-3189. [PMID: 33263384 PMCID: PMC7724760 DOI: 10.1021/acsinfecdis.0c00500] [Citation(s) in RCA: 68] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Indexed: 12/15/2022]
Abstract
Human coronaviruses (hCoVs) have become a threat to global health and society, as evident from the SARS outbreak in 2002 caused by SARS-CoV-1 and the most recent COVID-19 pandemic caused by SARS-CoV-2. Despite a high sequence similarity between SARS-CoV-1 and -2, each strain has a distinctive virulence. A better understanding of the basic molecular mechanisms mediating changes in virulence is needed. Here, we profile the virus-host protein-protein interactions of two hCoV nonstructural proteins (nsps) that are critical for virus replication. We use tandem mass tag-multiplexed quantitative proteomics to sensitively compare and contrast the interactomes of nsp2 and nsp4 from three betacoronavirus strains: SARS-CoV-1, SARS-CoV-2, and hCoV-OC43-an endemic strain associated with the common cold. This approach enables the identification of both unique and shared host cell protein binding partners and the ability to further compare the enrichment of common interactions across homologues from related strains. We identify common nsp2 interactors involved in endoplasmic reticulum (ER) Ca2+ signaling and mitochondria biogenesis. We also identify nsp4 interactors unique to each strain, such as E3 ubiquitin ligase complexes for SARS-CoV-1 and ER homeostasis factors for SARS-CoV-2. Common nsp4 interactors include N-linked glycosylation machinery, unfolded protein response associated proteins, and antiviral innate immune signaling factors. Both nsp2 and nsp4 interactors are strongly enriched in proteins localized at mitochondria-associated ER membranes suggesting a new functional role for modulating host processes, such as calcium homeostasis, at these organelle contact sites. Our results shed light on the role these hCoV proteins play in the infection cycle, as well as host factors that may mediate the divergent pathogenesis of OC43 from SARS strains. Our mass spectrometry workflow enables rapid and robust comparisons of multiple bait proteins, which can be applied to additional viral proteins. Furthermore, the identified common interactions may present new targets for exploration by host-directed antiviral therapeutics.
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Affiliation(s)
- Jonathan P. Davies
- Department of Biological Sciences, Immunology and Inflammation, Nashville, TN, USA
- Vanderbilt Institute for Infection, Immunology and Inflammation, Nashville, TN, USA
| | - Katherine M. Almasy
- Department of Chemistry, Vanderbilt University, Immunology and Inflammation, Nashville, TN, USA
- Vanderbilt Institute for Infection, Immunology and Inflammation, Nashville, TN, USA
| | - Eli F. McDonald
- Department of Chemistry, Vanderbilt University, Immunology and Inflammation, Nashville, TN, USA
| | - Lars Plate
- Department of Biological Sciences, Immunology and Inflammation, Nashville, TN, USA
- Department of Chemistry, Vanderbilt University, Immunology and Inflammation, Nashville, TN, USA
- Vanderbilt Institute for Infection, Immunology and Inflammation, Nashville, TN, USA
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Rollinson V, Turner R, Pirmohamed M. Pharmacogenomics for Primary Care: An Overview. Genes (Basel) 2020; 11:E1337. [PMID: 33198260 PMCID: PMC7696803 DOI: 10.3390/genes11111337] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 11/02/2020] [Accepted: 11/04/2020] [Indexed: 12/11/2022] Open
Abstract
Most of the prescribing and dispensing of medicines happens in primary care. Pharmacogenomics (PGx) is the study and clinical application of the role of genetic variation on drug response. Mounting evidence suggests PGx can improve the safety and/or efficacy of several medications commonly prescribed in primary care. However, implementation of PGx has generally been limited to a relatively few academic hospital centres, with little adoption in primary care. Despite this, many primary healthcare providers are optimistic about the role of PGx in their future practice. The increasing prevalence of direct-to-consumer genetic testing and primary care PGx studies herald the plausible gradual introduction of PGx into primary care and highlight the changes needed for optimal translation. In this article, the potential utility of PGx in primary care will be explored and on-going barriers to implementation discussed. The evidence base of several drug-gene pairs relevant to primary care will be outlined with a focus on antidepressants, codeine and tramadol, statins, clopidogrel, warfarin, metoprolol and allopurinol. This review is intended to provide both a general introduction to PGx with a more in-depth overview of elements relevant to primary care.
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25
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Wang D, Dai DP, Wu H, Chong J, Lü Y, Yin R, Zhao X, Zhao A, Yang J, Chen H. Effects of rare CYP2C9 alleles on stable warfarin doses in Chinese Han patients with atrial fibrillation. Pharmacogenomics 2020; 21:1021-1031. [PMID: 32893731 DOI: 10.2217/pgs-2020-0051] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Aim: Gene polymorphisms are critical in warfarin dosing variation. Here, the role of rare CYP2C9 alleles on warfarin doses in Chinese Han patients was investigated. Methods: A retrospective study recruited 681 warfarin treated atrial fibrillation patients. The genetic and clinical data were collected. Dose-related variables were selected by univariate analyses and the warfarin-dosing algorithm was derived by multivariate regression analysis. Results: Three rare CYP2C9 alleles (CYP2C9*13, *16 and *60) were associated with lower stable doses. Inclusion of the rare CYP2C9 alleles in the prediction model added an extra 3.7% warfarin dose predictive power. Conclusion: CYP2C9*13, *16 and *60 was associated with lower stable warfarin doses in Chinese patients. The algorithm including rare CYP2C9 alleles tends to more accurately predict stable warfarin doses.
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Affiliation(s)
- Dongxu Wang
- Cardiovascular Department, Beijing Hospital, National Centre of Gerontology, Beijing, 100730, China
| | - Da-Peng Dai
- The Key Laboratory of Geriatrics, Beijing Hospital, National Centre of Gerontology, Beijing, 100730, China
| | - Hualan Wu
- Cardiovascular Department, Beijing Hospital, National Centre of Gerontology, Beijing, 100730, China
| | - Jia Chong
- Cardiovascular Department, Beijing Hospital, National Centre of Gerontology, Beijing, 100730, China
| | - You Lü
- Cardiovascular Department, Beijing Hospital, National Centre of Gerontology, Beijing, 100730, China
| | - Ruoyun Yin
- Cardiovascular Department, Beijing Hospital, National Centre of Gerontology, Beijing, 100730, China
| | - Xinlong Zhao
- Cardiovascular Department, Beijing Hospital, National Centre of Gerontology, Beijing, 100730, China
| | - Anxu Zhao
- Cardiovascular Department, Beijing Hospital, National Centre of Gerontology, Beijing, 100730, China
| | - Jiefu Yang
- Cardiovascular Department, Beijing Hospital, National Centre of Gerontology, Beijing, 100730, China
| | - Hao Chen
- Cardiovascular Department, Beijing Hospital, National Centre of Gerontology, Beijing, 100730, China
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26
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Chiasson MA, Rollins NJ, Stephany JJ, Sitko KA, Matreyek KA, Verby M, Sun S, Roth FP, DeSloover D, Marks DS, Rettie AE, Fowler DM. Multiplexed measurement of variant abundance and activity reveals VKOR topology, active site and human variant impact. eLife 2020; 9:e58026. [PMID: 32870157 PMCID: PMC7462613 DOI: 10.7554/elife.58026] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Accepted: 07/28/2020] [Indexed: 01/05/2023] Open
Abstract
Vitamin K epoxide reductase (VKOR) drives the vitamin K cycle, activating vitamin K-dependent blood clotting factors. VKOR is also the target of the widely used anticoagulant drug, warfarin. Despite VKOR's pivotal role in coagulation, its structure and active site remain poorly understood. In addition, VKOR variants can cause vitamin K-dependent clotting factor deficiency or alter warfarin response. Here, we used multiplexed, sequencing-based assays to measure the effects of 2,695 VKOR missense variants on abundance and 697 variants on activity in cultured human cells. The large-scale functional data, along with an evolutionary coupling analysis, supports a four transmembrane domain topology, with variants in transmembrane domains exhibiting strongly deleterious effects on abundance and activity. Functionally constrained regions of the protein define the active site, and we find that, of four conserved cysteines putatively critical for function, only three are absolutely required. Finally, 25% of human VKOR missense variants show reduced abundance or activity, possibly conferring warfarin sensitivity or causing disease.
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Affiliation(s)
- Melissa A Chiasson
- Department of Genome Sciences, University of WashingtonSeattleUnited States
| | - Nathan J Rollins
- Department of Systems Biology, Harvard Medical SchoolBostonUnited States
| | - Jason J Stephany
- Department of Genome Sciences, University of WashingtonSeattleUnited States
| | - Katherine A Sitko
- Department of Genome Sciences, University of WashingtonSeattleUnited States
| | - Kenneth A Matreyek
- Department of Genome Sciences, University of WashingtonSeattleUnited States
| | - Marta Verby
- Donnelly Centre and Departments of Molecular Genetics and Computer Science, University of Toronto, and Lunenfeld-Tanenbaum Research Institute, Sinai Health SystemTorontoCanada
| | - Song Sun
- Donnelly Centre and Departments of Molecular Genetics and Computer Science, University of Toronto, and Lunenfeld-Tanenbaum Research Institute, Sinai Health SystemTorontoCanada
| | - Frederick P Roth
- Donnelly Centre and Departments of Molecular Genetics and Computer Science, University of Toronto, and Lunenfeld-Tanenbaum Research Institute, Sinai Health SystemTorontoCanada
| | | | - Debora S Marks
- Department of Systems Biology, Harvard Medical SchoolBostonUnited States
| | - Allan E Rettie
- Department of Medicinal Chemistry, University of WashingtonSeattleUnited States
| | - Douglas M Fowler
- Department of Genome Sciences, University of WashingtonSeattleUnited States
- Department of Bioengineering, University of WashingtonSeattleUnited States
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27
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Davies JP, Almasy KM, McDonald EF, Plate L. Comparative multiplexed interactomics of SARS-CoV-2 and homologous coronavirus non-structural proteins identifies unique and shared host-cell dependencies. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2020:2020.07.13.201517. [PMID: 32699849 PMCID: PMC7373130 DOI: 10.1101/2020.07.13.201517] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Human coronaviruses (hCoV) have become a threat to global health and society, as evident from the SARS outbreak in 2002 caused by SARS-CoV-1 and the most recent COVID-19 pandemic caused by SARS-CoV-2. Despite high sequence similarity between SARS-CoV-1 and -2, each strain has distinctive virulence. A better understanding of the basic molecular mechanisms mediating changes in virulence is needed. Here, we profile the virus-host protein-protein interactions of two hCoV non-structural proteins (nsps) that are critical for virus replication. We use tandem mass tag-multiplexed quantitative proteomics to sensitively compare and contrast the interactomes of nsp2 and nsp4 from three betacoronavirus strains: SARS-CoV-1, SARS-CoV-2, and hCoV-OC43 - an endemic strain associated with the common cold. This approach enables the identification of both unique and shared host cell protein binding partners and the ability to further compare the enrichment of common interactions across homologs from related strains. We identify common nsp2 interactors involved in endoplasmic reticulum (ER) Ca 2+ signaling and mitochondria biogenesis. We also identifiy nsp4 interactors unique to each strain, such as E3 ubiquitin ligase complexes for SARS-CoV-1 and ER homeostasis factors for SARS-CoV-2. Common nsp4 interactors include N -linked glycosylation machinery, unfolded protein response (UPR) associated proteins, and anti-viral innate immune signaling factors. Both nsp2 and nsp4 interactors are strongly enriched in proteins localized at mitochondrial-associated ER membranes suggesting a new functional role for modulating host processes, such as calcium homeostasis, at these organelle contact sites. Our results shed light on the role these hCoV proteins play in the infection cycle, as well as host factors that may mediate the divergent pathogenesis of OC43 from SARS strains. Our mass spectrometry workflow enables rapid and robust comparisons of multiple bait proteins, which can be applied to additional viral proteins. Furthermore, the identified common interactions may present new targets for exploration by host-directed anti-viral therapeutics.
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Affiliation(s)
- Jonathan P. Davies
- Department of Biological Sciences, Immunology and Inflammation, Nashville, TN, USA
- Vanderbilt Institute for Infection, Immunology and Inflammation, Nashville, TN, USA
| | - Katherine M. Almasy
- Department of Chemistry, Vanderbilt University, Immunology and Inflammation, Nashville, TN, USA
- Vanderbilt Institute for Infection, Immunology and Inflammation, Nashville, TN, USA
| | - Eli F. McDonald
- Department of Chemistry, Vanderbilt University, Immunology and Inflammation, Nashville, TN, USA
| | - Lars Plate
- Department of Biological Sciences, Immunology and Inflammation, Nashville, TN, USA
- Department of Chemistry, Vanderbilt University, Immunology and Inflammation, Nashville, TN, USA
- Vanderbilt Institute for Infection, Immunology and Inflammation, Nashville, TN, USA
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28
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Pratt VM, Cavallari LH, Del Tredici AL, Hachad H, Ji Y, Kalman LV, Ly RC, Moyer AM, Scott SA, Whirl-Carrillo M, Weck KE. Recommendations for Clinical Warfarin Genotyping Allele Selection: A Report of the Association for Molecular Pathology and the College of American Pathologists. J Mol Diagn 2020; 22:847-859. [PMID: 32380173 DOI: 10.1016/j.jmoldx.2020.04.204] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Revised: 03/18/2020] [Accepted: 04/01/2020] [Indexed: 11/19/2022] Open
Abstract
The goal of the Association for Molecular Pathology (AMP) Clinical Practice Committee's AMP Pharmacogenomics (PGx) Working Group is to define the key attributes of PGx alleles recommended for clinical testing and a minimum set of variants that should be included in clinical PGx genotyping assays. This document series provides recommendations for a minimum panel of variant alleles (tier 1) and an extended panel of variant alleles (tier 2) that will aid clinical laboratories when designing assays for PGx testing. The AMP PGx Working Group considered functional impact of the variants, allele frequencies in multiethnic populations, the availability of reference materials, as well as other technical considerations for PGx testing when developing these recommendations. The ultimate goal is to promote standardization of PGx gene/allele testing across clinical laboratories. These recommendations are not to be interpreted as prescriptive but to provide a reference guide. Of note, a separate article with recommendations for CYP2C9 allele selection was previously developed by the PGx Working Group that can be applied broadly to CYP2C9-related medications. The warfarin allele recommendations in this report incorporate the previous CYP2C9 allele recommendations and additional genes and alleles that are specific to warfarin testing.
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Affiliation(s)
- Victoria M Pratt
- The Pharmacogenomics Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana.
| | - Larisa H Cavallari
- The Pharmacogenomics Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pharmacotherapy and Translational Research and Center for Pharmacogenomics and Precision Medicine, University of Florida, Gainesville, Florida
| | - Andria L Del Tredici
- The Pharmacogenomics Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Millennium Health, LLC, San Diego, California
| | - Houda Hachad
- The Pharmacogenomics Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Translational Software, Bellevue, Washington
| | - Yuan Ji
- The Pharmacogenomics Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology and ARUP Laboratories, University of Utah School of Medicine, Salt Lake City, Utah
| | - Lisa V Kalman
- Division of Laboratory Systems, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Reynold C Ly
- The Pharmacogenomics Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Medicine, Indiana University School of Medicine, Indianapolis, Indiana
| | - Ann M Moyer
- The Pharmacogenomics Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Stuart A Scott
- The Pharmacogenomics Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York; Sema4, a Mount Sinai venture, Stamford, Connecticut
| | - Michelle Whirl-Carrillo
- The Pharmacogenomics Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Biomedical Data Science, Stanford University, Stanford, California
| | - Karen E Weck
- The Pharmacogenomics Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Departments of Pathology and Laboratory Medicine and Genetics, University of North Carolina, Chapel Hill, North Carolina
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29
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Zhong Y, De T, Alarcon C, Park CS, Lec B, Perera MA. Discovery of novel hepatocyte eQTLs in African Americans. PLoS Genet 2020; 16:e1008662. [PMID: 32310939 PMCID: PMC7192504 DOI: 10.1371/journal.pgen.1008662] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Revised: 04/30/2020] [Accepted: 02/11/2020] [Indexed: 12/21/2022] Open
Abstract
African Americans (AAs) are disproportionately affected by metabolic diseases and adverse drug events, with limited publicly available genomic and transcriptomic data to advance the knowledge of the molecular underpinnings or genetic associations to these diseases or drug response phenotypes. To fill this gap, we obtained 60 primary hepatocyte cultures from AA liver donors for genome-wide mapping of expression quantitative trait loci (eQTL) using LAMatrix. We identified 277 eGenes and 19,770 eQTLs, of which 67 eGenes and 7,415 eQTLs are not observed in the Genotype-Tissue Expression Project (GTEx) liver eQTL analysis. Of the eGenes found in GTEx only 25 share the same lead eQTL. These AA-specific eQTLs are less correlated to GTEx eQTLs. in effect sizes and have larger Fst values compared to eQTLs found in both cohorts (overlapping eQTLs). We assessed the overlap between GWAS variants and their tagging variants with AA hepatocyte eQTLs and demonstrated that AA hepatocyte eQTLs can decrease the number of potential causal variants at GWAS loci. Additionally, we identified 75,002 exon QTLs of which 48.8% are not eQTLs in AA hepatocytes. Our analysis provides the first comprehensive characterization of AA hepatocyte eQTLs and highlights the unique discoveries that are made possible due to the increased genetic diversity within the African ancestry genome.
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Affiliation(s)
- Yizhen Zhong
- Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, United States of America
| | - Tanima De
- Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, United States of America
| | - Cristina Alarcon
- Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, United States of America
| | - C. Sehwan Park
- Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, United States of America
| | - Bianca Lec
- Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, United States of America
| | - Minoli A. Perera
- Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, United States of America
- * E-mail:
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30
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Caspar SM, Dubacher N, Kopps AM, Meienberg J, Henggeler C, Matyas G. Clinical sequencing: From raw data to diagnosis with lifetime value. Clin Genet 2019; 93:508-519. [PMID: 29206278 DOI: 10.1111/cge.13190] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Revised: 11/28/2017] [Accepted: 11/30/2017] [Indexed: 12/22/2022]
Abstract
High-throughput sequencing (HTS) has revolutionized genetics by enabling the detection of sequence variants at hitherto unprecedented large scale. Despite these advances, however, there are still remaining challenges in the complete coverage of targeted regions (genes, exome or genome) as well as in HTS data analysis and interpretation. Moreover, it is easy to get overwhelmed by the plethora of available methods and tools for HTS. Here, we review the step-by-step process from the generation of sequence data to molecular diagnosis of Mendelian diseases. Highlighting advantages and limitations, this review addresses the current state of (1) HTS technologies, considering targeted, whole-exome, and whole-genome sequencing on short- and long-read platforms; (2) read alignment, variant calling and interpretation; as well as (3) regulatory issues related to genetic counseling, reimbursement, and data storage.
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Affiliation(s)
- S M Caspar
- Center for Cardiovascular Genetics and Gene Diagnostics, Foundation for People with Rare Diseases, Schlieren-Zurich, Switzerland
| | - N Dubacher
- Center for Cardiovascular Genetics and Gene Diagnostics, Foundation for People with Rare Diseases, Schlieren-Zurich, Switzerland
| | - A M Kopps
- Center for Cardiovascular Genetics and Gene Diagnostics, Foundation for People with Rare Diseases, Schlieren-Zurich, Switzerland
| | - J Meienberg
- Center for Cardiovascular Genetics and Gene Diagnostics, Foundation for People with Rare Diseases, Schlieren-Zurich, Switzerland
| | - C Henggeler
- Center for Cardiovascular Genetics and Gene Diagnostics, Foundation for People with Rare Diseases, Schlieren-Zurich, Switzerland
| | - G Matyas
- Center for Cardiovascular Genetics and Gene Diagnostics, Foundation for People with Rare Diseases, Schlieren-Zurich, Switzerland.,Zurich Center for Integrative Human Physiology, University of Zurich, Zurich, Switzerland
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31
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Helin TA, Joutsi-Korhonen L, Asmundela H, Niemi M, Orpana A, Lassila R. Warfarin dose requirement in patients having severe thrombosis or thrombophilia. Br J Clin Pharmacol 2019; 85:1684-1691. [PMID: 30933373 DOI: 10.1111/bcp.13948] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Revised: 03/12/2019] [Accepted: 03/23/2019] [Indexed: 12/17/2022] Open
Abstract
AIMS Warfarin dose requirement varies significantly. We compared the clinically established doses based on international normalized ratio (INR) among patients with severe thrombosis and/or thrombophilia with estimates from genetic dosing algorithms. METHODS Fifty patients with severe thrombosis and/or thrombophilia requiring permanent anticoagulation, referred to the Helsinki University Hospital Coagulation Center, were screened for thrombophilias and genotyped for CYP2C9*2 (c.430C>T, rs1799853), CYP2C9*3 (c.1075A>C, rs1057910) and VKORC1 c.-1639G>A (rs9923231) variants. The warfarin maintenance doses (target INR 2.0-3.0 in 94%, 2.5-3.5 in 6%) were estimated by the Gage and the International Warfarin Pharmacogenetics Consortium (IWPC) algorithms. The individual warfarin maintenance dose was tailored, supplementing estimates with comprehensive clinical evaluation and INR data. RESULTS Mean patient age was 47 years (range 20-76), and BMI 27 (SD 6), 68% being women. Forty-six (92%) had previous venous or arterial thrombosis, and 26 (52%) had a thrombophilia, with 22% having concurrent aspirin. A total of 40% carried the CYP2C9*2 or *3 allele and 54% carried the VKORC1-1639A allele. The daily mean maintenance dose of warfarin estimated by the Gage algorithm was 5.4 mg (95% CI 4.9-5.9 mg), and by the IWPC algorithm was 5.2 mg (95% CI 4.7-5.7 mg). The daily warfarin maintenance dose after clinical visits and follow-up was higher than the estimates, mean 6.9 mg (95% CI 5.6-8.2 mg, P < 0.006), with highest dose in patients having multiple thrombophilic factors (P < 0.03). CONCLUSIONS In severe thrombosis and/or thrombophilia, variation in thrombin generation and pharmacodynamics influences warfarin response. Pharmacogenetic dosing algorithms seem to underestimate dose requirement.
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Affiliation(s)
- Tuukka A Helin
- Coagulation Disorders Unit, Clinical Chemistry, University of Helsinki and HUSLAB, Helsinki University Hospital, Helsinki, Finland
| | - Lotta Joutsi-Korhonen
- Coagulation Disorders Unit, Clinical Chemistry, University of Helsinki and HUSLAB, Helsinki University Hospital, Helsinki, Finland
| | - Heidi Asmundela
- Coagulation Disorders Unit, Hematology, University of Helsinki, Helsinki University Hospital, Helsinki, Finland
| | - Mikko Niemi
- Department of Clinical Pharmacology, Individualized Drug Therapy Research Program, Faculty of Medicine, University of Helsinki and HUSLAB, Helsinki University Hospital, Helsinki, Finland
| | - Arto Orpana
- Genetics and Clinical Chemistry, University of Helsinki and HUSLAB, Helsinki University Hospital, Helsinki, Finland
| | - Riitta Lassila
- Coagulation Disorders Unit, Clinical Chemistry, University of Helsinki and HUSLAB, Helsinki University Hospital, Helsinki, Finland.,Coagulation Disorders Unit, Hematology, University of Helsinki, Helsinki University Hospital, Helsinki, Finland
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32
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Kampouraki E, Kamali F. Pharmacogenetics of anticoagulants used for stroke prevention in patients with atrial fibrillation. Expert Opin Drug Metab Toxicol 2019; 15:449-458. [PMID: 31120800 DOI: 10.1080/17425255.2019.1623878] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Introduction: The inclusion of pharmacogenetics alongside clinical information in anticoagulant therapy offers the opportunity for a tailored approach to treatment according to individual patient characteristics. Areas covered: Literature was searched using PubMed database, focusing on pharmacogenetics of oral anticoagulants. Original research articles and review articles in English language were included in the literature reviewed. This article includes all information available for the genetic cause of inter-individual variability in anticoagulation response to oral anticoagulant drugs. The pharmacogenetics of VKAs and NOACs are described in detail. Expert opinion: There have been numerous studies focusing on the pharmacogenetics of VKAs, particularly warfarin. Current evidence suggests that known genetic and clinical factors explain a large proportion of the inter-individual variability in response to warfarin. Pharmacogenetic-based algorithms have been validated to determine their clinical utility with equivocal results. To date, only a limited number of mostly small studies on the pharmacogenetics of NOACs exists. The latter have highlighted genetic polymorphisms in specific genes that may affect clinical outcomes. Further evaluations of these polymorphisms are needed before firm conclusions can be drawn about the significance of pharmacogenetics on NOAC therapy.
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Affiliation(s)
- Emmanouela Kampouraki
- a Institute of Cellular Medicine within Faculty of Medical Sciences , Newcastle University , Newcastle upon Tyne , UK
| | - Farhad Kamali
- b Newcastle upon Tyne Hospitals, NHS Foundation Trust , Newcastle upon Tyne , UK
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Al-Mahayri ZN, Al Jaibeji HS, Saab Y, Soliman K, Al-Gazali L, Patrinos GP, Ali BR. VKORC1 variants as significant predictors of warfarin dose in Emiratis. Pharmgenomics Pers Med 2019; 12:47-57. [PMID: 31114289 PMCID: PMC6489578 DOI: 10.2147/pgpm.s187350] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Accepted: 12/22/2018] [Indexed: 02/05/2023] Open
Abstract
Purpose: Variability in response to warfarin is one of the main obstacles challenging its use in clinical practice. Vitamin K epoxide reductase complex (VKORC) is the target enzyme of warfarin, and variations in the form of single nucleotide polymorphisms (SNPs) in VKORC1, coding for this enzyme, are known to cause resistance to warfarin treatment. This study aimed to explore VKORC1 variants in Emirati patients receiving warfarin treatment and to correlate their genotypes at the studied SNPs to their maintenance warfarin dose. Patients and methods: Sanger sequencing of the majority of the VKORC1 gene was applied to samples from 90 patients and 117 normal individuals recruited from Tawam Hospital, Al-Ain, UAE. Genotypes at the following variants were determined (rs9923231, rs188009042, rs61742245, rs17708472, rs9934438, rs8050894, rs2359612, rs7294). Statistical analysis was applied, including ANOVA, cross-tabulation, and multiple linear regression analysis, to determine the ability of nongenetic factors (age and gender) and genetic factors (VKORC1 genotypes) to explain variability in warfarin dose in patients. Results: Different frequencies of minor alleles were detected in the selected SNPs. Significant variation among genotypes at six VKORC1 variants were identified (rs9923231, rs9934438, rs8050894, rs2359612, rs7294). The main predictors for warfarin dose were rs9923231, age, and rs61742245 with 50.7% of the average warfarin dose in our sample could be explained by a regression model built on these three factors. Conclusion: This is the first report of the explanatory power of VKORC1 genotypes and nongenetic factors (age and gender) on warfarin dose among Emiratis. Also, this study highlighted the positive effect of considering rare pharmacogenomic variants on explaining warfarin dose variability.
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Affiliation(s)
- Zeina N Al-Mahayri
- Department of Pathology, College of Medicine and Health Sciences, United Arab Emirates University, Al-Ain, United Arab Emirates
| | - Hayat S Al Jaibeji
- Sharjah Institute for Medical Research, College of Medicine, University of Sharjah, Sharjah, United Arab Emirates
| | - Yolande Saab
- School of Pharmacy, Lebanese American University, Byblos, Lebanon
| | - Karem Soliman
- INR Clinic, Tawam Hospital, Al-Ain, United Arab Emirates
| | - Lihadh Al-Gazali
- Department of Pediatrics, College of Medicine and Health Sciences, United Arab Emirates University, Al-Ain, United Arab Emirates
| | - George P Patrinos
- Department of Pathology, College of Medicine and Health Sciences, United Arab Emirates University, Al-Ain, United Arab Emirates.,Department of Pharmacy, School of Health Sciences, University of Patras, Patras, Greece.,Zayed Center for Health Sciences, United Arab Emirates University, Al-Ain, United Arab Emirates
| | - Bassam R Ali
- Department of Pathology, College of Medicine and Health Sciences, United Arab Emirates University, Al-Ain, United Arab Emirates.,Zayed Center for Health Sciences, United Arab Emirates University, Al-Ain, United Arab Emirates
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Ozgen M, Cosan DT, Doganer F, Soyocak A, Armagan O, Kuzgun S, Aydogan AM, Gunes HV, Degirmenci I, Mutlu F. Is there any association between osteoporotic vertebral fracture and vitamin K epoxide reductase complex subunit-1 polymorphism in Turkish society? A pilot study. Clinics (Sao Paulo) 2019; 74:e739. [PMID: 30892416 PMCID: PMC6399659 DOI: 10.6061/clinics/2019/e739] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Accepted: 11/28/2018] [Indexed: 11/21/2022] Open
Abstract
OBJECTIVE In this study, the relationship between osteoporotic vertebral fractures and 9041 Guanine/Adenine and 3673 Guanine/Adenine polymorphisms related to the vitamin K epoxide reductase complex subunit-1 (VKORC1) gene in postmenopausal women with osteoporosis was investigated. METHOD DNA was isolated from blood samples collected from 150 women with postmenopausal osteoporosis. Genotyping of the two polymorphic regions (9041 Guanine/Adenine and 3673 Guanine/Adenine) in VKORC1 was performed using polymerase chain reaction-restriction fragment length polymorphism analysis. The presence of radiographic fractures among the 150 patients was ascertained by using the Genant method. RESULT At least one fracture was detected in 98 patients, and no fracture was observed in 52 patients on radiological images. We found no association between the 9041 Guanine/Adenine (p=0.283) and 3673 Guanine/Adenine (p=0.232) polymorphisms of the VKORC1 gene and the development of secondary postosteoporotic fractures in our study. CONCLUSION There was no relationship between osteoporotic vertebral fracture and VKORC1 gene polymorphism in a postmenopausal Turkish population.
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Affiliation(s)
- Merih Ozgen
- Department of Physical Medicine and Rehabilitation, Faculty of Medicine, Eskisehir Osmangazi University, Eskisehir, Turkey
- Corresponding author: E-mail: /
| | - Didem Turgut Cosan
- Department of Medical Biology, Faculty of Medicine, Eskisehir Osmangazi University, Eskisehir, Turkey
| | - Fulya Doganer
- Department of Biotechnology and Molecular Biology, Faculty of Arts and Sciences, Aksaray University, Aksaray, Turkey
| | - Ahu Soyocak
- Department of Medical Biology and Genetics, Faculty of Medicine, Istanbul Aydin University, Istanbul, Turkey
| | - Onur Armagan
- Department of Physical Medicine and Rehabilitation, Faculty of Medicine, Eskisehir Osmangazi University, Eskisehir, Turkey
| | - Selen Kuzgun
- Department of Physical Medicine and Rehabilitation, Zübeyde Hanım Campus, Eskişehir State Hospital, Eskisehir, Turkey
| | - Ayse Merve Aydogan
- Department of Physical Medicine and Rehabilitation, Faculty of Medicine, Eskisehir Osmangazi University, Eskisehir, Turkey
| | - Hasan Veysi Gunes
- Department of Medical Biology, Faculty of Medicine, Eskisehir Osmangazi University, Eskisehir, Turkey
| | - Irfan Degirmenci
- Department of Medical Biology, Faculty of Medicine, Kutahya Health Sciences University, Kutahya, Turkey
| | - Fezan Mutlu
- Department of Biostatistics and Medical Informatics, Faculty of Medicine, Eskisehir Osmangazi University, Eskisehir, Turkey
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Jain N, Reilly RF. Clinical Pharmacology of Oral Anticoagulants in Patients with Kidney Disease. Clin J Am Soc Nephrol 2019; 14:278-287. [PMID: 29802125 PMCID: PMC6390909 DOI: 10.2215/cjn.02170218] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Oral anticoagulants are commonly used drugs in patients with CKD and patients with ESKD to treat atrial fibrillation to reduce stroke and systemic embolism. Some of these drugs are used to treat or prevent deep venous thrombosis and pulmonary embolism in patients with CKD who undergo knee and hip replacement surgeries. Warfarin is the only anticoagulant that is approved for use by the Food and Drug Administration in individuals with mechanical heart valves. Each oral anticoagulant affects the coagulation profile in the laboratory uniquely. Warfarin and apixaban are the only anticoagulants that are Food and Drug Administration approved for use in patients with CKD and patients with ESKD. However, other oral anticoagulants are commonly used off label in this patient population. Given the acquired risk of bleeding from uremia, these drugs are known to cause increased bleeding events, hospitalization, and overall morbidity. Each anticoagulant has unique pharmacologic properties of which nephrologists need to be aware to optimally manage patients. In addition, nephrologists are increasingly asked to aid in the management of adverse bleeding events related to oral anticoagulant use in patients with CKD and patients with ESKD. This article summarizes the clinical pharmacology of these drugs and identifies knowledge gaps in the literature related to their use.
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Affiliation(s)
- Nishank Jain
- Division of Nephrology, Department of Internal Medicine, University of Arkansas for Medical Sciences, Little Rock, Arkansas
- Medicine Service, Central Arkansas Veterans Affairs Health Care System, Little Rock, Arkansas
| | - Robert F. Reilly
- Division of Nephrology, Department of Internal Medicine, University of Alabama at Birmingham School of Medicine, Birmingham, Alabama; and
- Division of Nephrology, Department of Medicine, Birmingham Veterans Affairs Medical Center, Birmingham, Alabama
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Michaux A, Matagrin B, Debaux JV, Schurgers LJ, Benoit E, Lattard V. Missense mutation of VKORC1 leads to medial arterial calcification in rats. Sci Rep 2018; 8:13733. [PMID: 30214074 PMCID: PMC6137107 DOI: 10.1038/s41598-018-31788-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Accepted: 08/21/2018] [Indexed: 01/22/2023] Open
Abstract
Vitamin K plays a crucial role in the regulation of vascular calcifications by allowing activation of matrix Gla protein. The dietary requirement for vitamin K is low because of an efficient recycling of vitamin K by vitamin K epoxide reductase (VKORC1). However, decreased VKORC1 activity may result in vascular calcification. More than 30 coding mutations of VKORC1 have been described. While these mutations have been suspected of causing anticoagulant resistance, their association with an increase in the risk of vascular calcification has never been considered. We thus investigated functional cardiovascular characteristics in a rat model mutated in VKORC1. This study revealed that limited intake in vitamin K in mutated rat induced massive calcified areas in the media of arteries of lung, aortic arch, kidneys and testis. Development of calcifications could be inhibited by vitamin K supplementation. In calcified areas, inactive Matrix Gla protein expression increased, while corresponding mRNA expression was not modified. Mutation in VKORC1 associated with a limited vitamin K intake is thus a major risk for cardiovascular disease. Our model is the first non-invasive rat model that shows spontaneous medial calcifications and would be useful for studying physiological function of vitamin K.
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Affiliation(s)
- Arnaud Michaux
- USC 1233 RS2GP, INRA, VetAgro Sup, Univ Lyon, F-69280, Marcy l'Etoile, France
| | - Benjamin Matagrin
- USC 1233 RS2GP, INRA, VetAgro Sup, Univ Lyon, F-69280, Marcy l'Etoile, France
| | - Jean-Valéry Debaux
- USC 1233 RS2GP, INRA, VetAgro Sup, Univ Lyon, F-69280, Marcy l'Etoile, France
| | - Leon J Schurgers
- Department of Biochemistry, Cardiovascular Research Institute Maastricht (CARIM), Maastricht University, Maastricht, The Netherlands
| | - Etienne Benoit
- USC 1233 RS2GP, INRA, VetAgro Sup, Univ Lyon, F-69280, Marcy l'Etoile, France
| | - Virginie Lattard
- USC 1233 RS2GP, INRA, VetAgro Sup, Univ Lyon, F-69280, Marcy l'Etoile, France.
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Abstract
Pharmacogenetics is an emerging area of medicine, and more work is needed to fully integrate it into a clinical setting for the benefit of patients. Genetic markers can influence the action of many drugs, including those that prevent and treat cardiovascular conditions. Genotyping is not yet commonplace, but guidelines are being put in place to help practitioners determine the effect a genetic marker may have on certain drugs. With advancements in genetic technology and falling costs, genotyping could be available to all patients via a simple saliva test. This would be a cost-effective way for practitioners to determine the most effective treatment for individuals, reducing "trial and error," adverse effects, and rehospitalization rates and increasing patient compliance. Cardiovascular diseases are the leading causes of death worldwide, so using the most effective medication to treat or prevent them is of utmost importance in reducing incidence and mortality.
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38
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Dong AN, Tan BH, Pan Y, Ong CE. Cytochrome P450 genotype-guided drug therapies: An update on current states. Clin Exp Pharmacol Physiol 2018; 45:991-1001. [PMID: 29858511 DOI: 10.1111/1440-1681.12978] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2018] [Revised: 05/30/2018] [Accepted: 05/30/2018] [Indexed: 01/07/2023]
Abstract
Over the past 2 decades, knowledge of the role and clinical value of pharmacogenetic markers has expanded so that individualized pre-emptive therapy based on genetic background of patients could be within reach for clinical implementation. This is evidenced from the frequent updating of drug labels that incorporates pharmacogenetic information (where compelling data become available) by the regulatory agencies (such as the US FDA), and the periodical publication of guidelines of specific therapeutic recommendations based on the results of pharmacogenetic tests by the pharmacogenetics working groups or consortiums of professional bodies. Clinical relevance of the cytochrome P450 (CYP) polymorphism related to dose, effectiveness and/or toxicity of key drugs are presented in this review, including that of warfarin, clopidogrel, tricyclic antidepressants, and proton pump inhibitors. Prospect for routine clinical application of CYP genotyping before prescribing drugs is still currently unclear due to challenges and barriers associated with availability of well-defined and validated pharmacogenetic studies, the interpretation, result reporting and potential error of genotype testing, involvement of non-genetic factors, and other patient's demographic and disease conditions. Further studies to provide additional supporting clinical data and acceleration of pharmacogenetic testing standards and techniques should help improve the evidence base needed for clinical utility and hence move the implementation of genotype-guided therapy in clinical practice a step closer to reality.
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Affiliation(s)
- Amelia Nathania Dong
- School of Pharmacy, Monash University Malaysia, Bandar Sunway, Selangor, Malaysia
| | - Boon Hooi Tan
- Division of Applied Biomedical Sciences and Biotechnology, International Medical University, Kuala Lumpur, Malaysia
| | - Yan Pan
- Department of Biomedical Science, University of Nottingham Malaysia Campus, Semenyih, Selangor, Malaysia
| | - Chin Eng Ong
- School of Pharmacy, International Medical University, Kuala Lumpur, Malaysia
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Warfarin Dosing According to the Genotype-guided Algorithm is Most Beneficial in Patients With Atrial Fibrillation: A Randomized Parallel Group Trial. Ther Drug Monit 2018; 40:362-368. [DOI: 10.1097/ftd.0000000000000501] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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40
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Serna MJ, Rivera-Caravaca JM, Gonzalez-Conejero R, Esteve-Pastor MA, Valdés M, Vicente V, Lip GYH, Roldán V, Marín F. Pharmacogenetics of vitamin K antagonists and bleeding risk prediction in atrial fibrillation. Eur J Clin Invest 2018; 48:e12929. [PMID: 29577257 DOI: 10.1111/eci.12929] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Accepted: 03/19/2018] [Indexed: 12/16/2022]
Abstract
BACKGROUND Polymorphisms in the vitamin K epoxide reductase complex 1 (VKORC1) and cytochrome P450 2C9 (CYP2C9) genes increase the bleeding risk in anticoagulated atrial fibrillation (AF) patients. Here, we aimed to investigate whether VKORC1 and CYP2C9 polymorphisms improved the predictive performance for major bleeding using the HAS-BLED score. MATERIAL AND METHODS We recruited 652 consecutive AF patients stable on vitamin K antagonist (INR 2.0-3.0) during at least the previous 6 months. A baseline venous blood sample was obtained for DNA extraction. We gave an extra point to the HAS-BLED score if the patient was a simultaneous carrier of the VKORC1 and CYP2C9 polymorphisms related to bleeding, and we called this modified score "GEN|HAS-BLED." During a median follow-up of 7.6 years (IQR 5.6-8.0), all major bleeding events were recorded. RESULTS During follow-up, 106 (16.2%) patients experienced a major bleeding (2.81%/y; 42 intracranial haemorrhages and 44 gastrointestinal bleeding) and 24 (3.7%) died from major bleeding (0.48%/y). Cox regression analyses demonstrated a significant association between HAS-BLED or GEN|HAS-BLED and major bleeds, both as continuous or categorical scores. Comparison of receiver operating characteristic (ROC) curves shows that original HAS-BLED clinical score had better predictive ability than GEN|HAS-BLED (0.660, 95% CI 0.622-0.696 vs 0.645, 95% CI 0.607-0.682; P = .030). Discrimination and reclassification analyses showed that GEN|HAS-BLED did not improve sensitivity compared with the original score and even showed significant negative reclassification. CONCLUSION Adding pharmacogenetic factors (ie polymorphisms of the VKORC1 and CYP2C9 genes) to the HAS-BLED score does not improve the prediction or discrimination performance for major bleeding.
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Affiliation(s)
- María José Serna
- Department of Hematology and Clinical Oncology, Hospital General Universitario Morales Meseguer, Instituto Murciano de Investigación Biosanitaria (IMIB-Arrixaca), Murcia, Spain
| | - José Miguel Rivera-Caravaca
- Department of Hematology and Clinical Oncology, Hospital General Universitario Morales Meseguer, Instituto Murciano de Investigación Biosanitaria (IMIB-Arrixaca), Murcia, Spain
| | - Rocío Gonzalez-Conejero
- Centro Regional de Hemodonación, Universidad de Murcia, CIBERER, Instituto Murciano de Investigación Biosanitaria (IMIB-Arrixaca), Murcia, Spain
| | - María Asunción Esteve-Pastor
- Department of Cardiology, Hospital Clínico Universitario Virgen de la Arrixaca, Instituto Murciano de Investigación Biosanitaria (IMIB-Arrixaca), CIBER-CV, Murcia, Spain
| | - Mariano Valdés
- Department of Cardiology, Hospital Clínico Universitario Virgen de la Arrixaca, Instituto Murciano de Investigación Biosanitaria (IMIB-Arrixaca), CIBER-CV, Murcia, Spain
| | - Vicente Vicente
- Department of Hematology and Clinical Oncology, Hospital General Universitario Morales Meseguer, Instituto Murciano de Investigación Biosanitaria (IMIB-Arrixaca), Murcia, Spain.,Centro Regional de Hemodonación, Universidad de Murcia, CIBERER, Instituto Murciano de Investigación Biosanitaria (IMIB-Arrixaca), Murcia, Spain
| | - Gregory Y H Lip
- Institute of Cardiovascular Sciences, University of Birmingham, Birmingham, UK.,Aalborg Thrombosis Research Unit, Department of Clinical Medicine, Aalborg University, Aalborg, Denmark
| | - Vanessa Roldán
- Department of Hematology and Clinical Oncology, Hospital General Universitario Morales Meseguer, Instituto Murciano de Investigación Biosanitaria (IMIB-Arrixaca), Murcia, Spain
| | - Francisco Marín
- Department of Cardiology, Hospital Clínico Universitario Virgen de la Arrixaca, Instituto Murciano de Investigación Biosanitaria (IMIB-Arrixaca), CIBER-CV, Murcia, Spain
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Tavares LC, Marcatto LR, Santos PCJL. Genotype-guided warfarin therapy: current status. Pharmacogenomics 2018; 19:667-685. [PMID: 29701078 DOI: 10.2217/pgs-2017-0207] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Warfarin pharmacogenomics has been an extensively studied field in the last decades as it is focused on personalized therapy to overcome the wide interpatient warfarin response variability and decrease the risk of side effects. In this expert review, besides briefly summarizing the current knowledge about warfarin pharmacogenetics, we also present an overview of recent studies that aimed to assess the efficacy, safety and economic issues related to genotype-based dosing algorithms used to guide warfarin therapy, including randomized and controlled clinical trials, meta-analyses and cost-effectiveness studies. To date, the findings still present disparities, mostly because of standard limitations. Thus, further studies should be encouraged to try to demonstrate the benefits of the application of warfarin pharmacogenomic dosing algorithms in clinical practice.
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Affiliation(s)
- Letícia C Tavares
- Laboratory of Genetics & Molecular Cardiology, Heart Institute (InCor), Faculdade de Medicina FMUSP, Universidade de Sao Paulo, SP 05403-900, Brazil
| | - Leiliane R Marcatto
- Laboratory of Genetics & Molecular Cardiology, Heart Institute (InCor), Faculdade de Medicina FMUSP, Universidade de Sao Paulo, SP 05403-900, Brazil
| | - Paulo C J L Santos
- Department of Pharmacology, Universidade Federal de Sao Paulo UNIFESP, SP 04044-020, Brazil
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Zanger UM, Klein K, Kugler N, Petrikat T, Ryu CS. Epigenetics and MicroRNAs in Pharmacogenetics. ADVANCES IN PHARMACOLOGY (SAN DIEGO, CALIF.) 2018; 83:33-64. [PMID: 29801581 DOI: 10.1016/bs.apha.2018.02.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Germline pharmacogenetics has so far mainly studied common variants in "pharmacogenes," i.e., genes encoding drug metabolizing enzymes and transporters (DMET genes), certain auxiliary and regulatory genes, and drug target genes. Despite remarkable progress in understanding genetically determined differences in pharmacokinetics and pharmacodynamics of drugs, currently known common variants even in important pharmacogenes explain genetic variability only partially. This suggests "missing heritability" that may in part be due to rare variants in the classical pharmacogenes, but current evidence suggests that largely unexplored resources with potential for pharmacogenetics exist, both within already known pharmacogenes and in entirely new areas. In particular, recent studies suggest that epigenetic processes and noncoding RNAs, including mostly microRNAs (miRNAs), represent important and largely unexplored layers of DMET gene regulation that may fill some of the gaps in understanding interindividual variability and lead to new biomarkers. In this chapter we summarize recent advances in the understanding of genetic variability in epigenetic and miRNA-mediated processes with focus on their significance for DMET regulation and pharmacokinetic or pharmacological endpoints.
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Affiliation(s)
- Ulrich M Zanger
- Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart, Germany; University Hospital Tübingen, Tübingen, Germany.
| | - Kathrin Klein
- Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart, Germany
| | - Nicole Kugler
- Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart, Germany
| | - Tamara Petrikat
- Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart, Germany
| | - Chang S Ryu
- Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart, Germany
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43
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44
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Abstract
Since the human genome project in 2003, the view of personalized medicine to improve diagnosis and cure diseases at the molecular level became more real. Sequencing the human genome brought some benefits in medicine such as early detection of diseases with a genetic predisposition, treating patients with rare diseases, the design of gene therapy and the understanding of pharmacogenetics in the metabolism of drugs. This review explains the concepts of pharmacogenetics, polymorphisms, mutations, variations, and alleles, and how this information has helped us better understand the metabolism of drugs. Multiple resources are presented to promote reducing the gap between scientists, physicians, and patients in understanding the use and benefits of pharmacogenetics. Some of the most common clinical examples of genetic variants and how pharmacogenetics was used to determine treatment options for patients having these variants were discussed. Finally, we evaluated some of the challenges of implementing pharmacogenetics in a clinical setting and proposed actions to be taken to make pharmacogenetics a standard diagnostic tool in personalized medicine.
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Affiliation(s)
- J T Oates
- Department of Pharmaceutical Sciences, Biomanufacturing Research Institute and Technology Enterprise (BRITE), College of Arts and Sciences, North Carolina Central University, USA
| | - D Lopez
- Department of Pharmaceutical Sciences, Biomanufacturing Research Institute and Technology Enterprise (BRITE), College of Arts and Sciences, North Carolina Central University, USA
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45
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Schärfe CPI, Tremmel R, Schwab M, Kohlbacher O, Marks DS. Genetic variation in human drug-related genes. Genome Med 2017; 9:117. [PMID: 29273096 PMCID: PMC5740940 DOI: 10.1186/s13073-017-0502-5] [Citation(s) in RCA: 80] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Accepted: 11/24/2017] [Indexed: 12/17/2022] Open
Abstract
Background Variability in drug efficacy and adverse effects are observed in clinical practice. While the extent of genetic variability in classic pharmacokinetic genes is rather well understood, the role of genetic variation in drug targets is typically less studied. Methods Based on 60,706 human exomes from the ExAC dataset, we performed an in-depth computational analysis of the prevalence of functional variants in 806 drug-related genes, including 628 known drug targets. We further computed the likelihood of 1236 FDA-approved drugs to be affected by functional variants in their targets in the whole ExAC population as well as different geographic sub-populations. Results We find that most genetic variants in drug-related genes are very rare (f < 0.1%) and thus will likely not be observed in clinical trials. Furthermore, we show that patient risk varies for many drugs and with respect to geographic ancestry. A focused analysis of oncological drug targets indicates that the probability of a patient carrying germline variants in oncological drug targets is, at 44%, high enough to suggest that not only somatic alterations but also germline variants carried over into the tumor genome could affect the response to antineoplastic agents. Conclusions This study indicates that even though many variants are very rare and thus likely not observed in clinical trials, four in five patients are likely to carry a variant with possibly functional effects in a target for commonly prescribed drugs. Such variants could potentially alter drug efficacy. Electronic supplementary material The online version of this article (doi:10.1186/s13073-017-0502-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Charlotta Pauline Irmgard Schärfe
- Department of Systems Biology, Harvard Medical School, Boston, 02115, Massachusetts, USA.,Center for Bioinformatics, University of Tübingen, 72076, Tübingen, Germany.,pplied Bioinformatics, Department of Computer Science, 72076, Tübingen, Germany
| | - Roman Tremmel
- Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, 70376, Stuttgart, Germany
| | - Matthias Schwab
- Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, 70376, Stuttgart, Germany.,Department of Clinical Pharmacology, University Hospital Tübingen, 72076, Tübingen, Germany.,Department of Pharmacy and Biochemistry, University of Tübingen, 72076, Tübingen, Germany.,German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
| | - Oliver Kohlbacher
- Center for Bioinformatics, University of Tübingen, 72076, Tübingen, Germany. .,pplied Bioinformatics, Department of Computer Science, 72076, Tübingen, Germany. .,Quantitative Biology Center, 72076, Tübingen, Germany. .,Faculty of Medicine, University of Tübingen, 72076, Tübingen, Germany. .,Biomolecular Interactions, Max Planck Institute for Developmental Biology, 72076, Tübingen, Germany.
| | - Debora Susan Marks
- Department of Systems Biology, Harvard Medical School, Boston, 02115, Massachusetts, USA.
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Gottlieb A, Daneshjou R, DeGorter M, Bourgeois S, Svensson PJ, Wadelius M, Deloukas P, Montgomery SB, Altman RB. Cohort-specific imputation of gene expression improves prediction of warfarin dose for African Americans. Genome Med 2017; 9:98. [PMID: 29178968 PMCID: PMC5702158 DOI: 10.1186/s13073-017-0495-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Accepted: 11/14/2017] [Indexed: 12/27/2022] Open
Abstract
Background Genome-wide association studies are useful for discovering genotype–phenotype associations but are limited because they require large cohorts to identify a signal, which can be population-specific. Mapping genetic variation to genes improves power and allows the effects of both protein-coding variation as well as variation in expression to be combined into “gene level” effects. Methods Previous work has shown that warfarin dose can be predicted using information from genetic variation that affects protein-coding regions. Here, we introduce a method that improves dose prediction by integrating tissue-specific gene expression. In particular, we use drug pathways and expression quantitative trait loci knowledge to impute gene expression—on the assumption that differential expression of key pathway genes may impact dose requirement. We focus on 116 genes from the pharmacokinetic and pharmacodynamic pathways of warfarin within training and validation sets comprising both European and African-descent individuals. Results We build gene-tissue signatures associated with warfarin dose in a cohort-specific manner and identify a signature of 11 gene-tissue pairs that significantly augments the International Warfarin Pharmacogenetics Consortium dosage-prediction algorithm in both populations. Conclusions Our results demonstrate that imputed expression can improve dose prediction and bridge population-specific compositions. MATLAB code is available at https://github.com/assafgo/warfarin-cohort Electronic supplementary material The online version of this article (doi:10.1186/s13073-017-0495-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Assaf Gottlieb
- School of Biomedical Informatics, University of Texas Health Center, 7000 Fannin St., Houston, TX, 77030, USA.
| | - Roxana Daneshjou
- Department of Genetics, Stanford University, Stanford, CA, 94305, USA
| | - Marianne DeGorter
- Department of Genetics, Stanford University, Stanford, CA, 94305, USA.,Department of Pathology, Stanford University, Stanford, CA, 94305, USA
| | - Stephane Bourgeois
- William Harvey Research Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, EC1M 6BQ, UK
| | - Peter J Svensson
- Department of Translational Medicine, University of Lund, Malmö, 205 02, Sweden
| | - Mia Wadelius
- Department of Medical Sciences and Science for Life laboratory, Uppsala University, Uppsala, 751 85, Sweden
| | - Panos Deloukas
- William Harvey Research Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, EC1M 6BQ, UK.,Princess Al-Jawhara Al-Brahim Centre of Excellence in Research of Hereditary Disorders (PACER-HD), King Abdulaziz University, Jeddah, 21589, Saudi Arabia
| | - Stephen B Montgomery
- Department of Genetics, Stanford University, Stanford, CA, 94305, USA.,Department of Pathology, Stanford University, Stanford, CA, 94305, USA
| | - Russ B Altman
- Department of Genetics, Stanford University, Stanford, CA, 94305, USA.,Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA
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47
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Lévi F, Karaboué A, Saffroy R, Desterke C, Boige V, Smith D, Hebbar M, Innominato P, Taieb J, Carvalho C, Guimbaud R, Focan C, Bouchahda M, Adam R, Ducreux M, Milano G, Lemoine A. Pharmacogenetic determinants of outcomes on triplet hepatic artery infusion and intravenous cetuximab for liver metastases from colorectal cancer (European trial OPTILIV, NCT00852228). Br J Cancer 2017; 117:965-973. [PMID: 28817838 PMCID: PMC5625679 DOI: 10.1038/bjc.2017.278] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Revised: 07/18/2017] [Accepted: 07/24/2017] [Indexed: 01/29/2023] Open
Abstract
Background: The hepatic artery infusion (HAI) of irinotecan, oxaliplatin and 5-fluorouracil with intravenous cetuximab achieved outstanding efficacy in previously treated patients with initially unresectable liver metastases from colorectal cancer. This planned study aimed at the identification of pharmacogenetic predictors of outcomes. Methods: Circulating mononuclear cells were analysed for 207 single-nucleotide polymorphisms (SNPs) from 34 pharmacology genes. Single-nucleotide polymorphisms passing stringent Hardy–Weinberg equilibrium test were tested for their association with outcomes in 52 patients (male/female, 36/16; WHO PS, 0–1). Results: VKORC1 SNPs (rs9923231 and rs9934438) were associated with early and objective responses, and survival. For rs9923231, T/T achieved more early responses than C/T (50% vs 5%, P=0.029) and greatest 4-year survival (46% vs 0%, P=0.006). N-acetyltransferase-2 (rs1041983 and rs1801280) were associated with up to seven-fold more macroscopically complete hepatectomies. Progression-free survival was largest in ABCB1 rs1045642 T/T (P=0.026) and rs2032582 T/T (P=0.035). Associations were found between toxicities and gene variants (P<0.05), including neutropenia with ABCB1 (rs1045642) and SLC0B3 (rs4149117 and rs7311358); and diarrhoea with CYP2C9 (rs1057910), CYP2C19 (rs3758581), UGT1A6 (rs4124874) and SLC22A1 (rs72552763). Conclusion: VKORC1, NAT2 and ABCB1 variants predicted for HAI efficacy. Pharmacogenetics could guide the personalisation of liver-targeted medico-surgical therapies.
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Affiliation(s)
- Francis Lévi
- INSERM, UMRS 935 Team 'Cancer Chronotherapy and Postoperative Liver Function', Campus CNRS, 7 rue Guy Môquet, and UMRS 1193 'Physiopathology and treatment of Liver diseases', Paul Brousse Hospital, 14 avenue Paul-Vaillant-Couturier, 94800 Villejuif, France.,Université Paris Sud, UFR médecine, Institut André Lwoff, Paul Brousse Hospital, 14 avenue Paul-Vaillant-Couturier, 94800 Villejuif, France.,Assistance Publique-Hopitaux de Paris, Paul Brousse Hospital, Departments of Medical Oncology, Biochemistry and Oncogenetics, and Hepatobiliary Center, 14 avenue Paul-Vaillant-Couturier, 94800 Villejuif, France.,Cancer Chronotherapy Unit, Warwick Medical School, Warwick University, Gibbet Hill Road, Coventry CV4 7AL, UK
| | - Abdoulaye Karaboué
- INSERM, UMRS 935 Team 'Cancer Chronotherapy and Postoperative Liver Function', Campus CNRS, 7 rue Guy Môquet, and UMRS 1193 'Physiopathology and treatment of Liver diseases', Paul Brousse Hospital, 14 avenue Paul-Vaillant-Couturier, 94800 Villejuif, France.,AK-SCIENCE, Research and Therapeutic Innovation, 34 Boulevard de Stalingrad, 94400 Vitry-Sur-Seine, France
| | - Raphaël Saffroy
- INSERM, UMRS 935 Team 'Cancer Chronotherapy and Postoperative Liver Function', Campus CNRS, 7 rue Guy Môquet, and UMRS 1193 'Physiopathology and treatment of Liver diseases', Paul Brousse Hospital, 14 avenue Paul-Vaillant-Couturier, 94800 Villejuif, France.,Université Paris Sud, UFR médecine, Institut André Lwoff, Paul Brousse Hospital, 14 avenue Paul-Vaillant-Couturier, 94800 Villejuif, France.,Assistance Publique-Hopitaux de Paris, Paul Brousse Hospital, Departments of Medical Oncology, Biochemistry and Oncogenetics, and Hepatobiliary Center, 14 avenue Paul-Vaillant-Couturier, 94800 Villejuif, France
| | - Christophe Desterke
- INSERM, UMRS 935 Team 'Cancer Chronotherapy and Postoperative Liver Function', Campus CNRS, 7 rue Guy Môquet, and UMRS 1193 'Physiopathology and treatment of Liver diseases', Paul Brousse Hospital, 14 avenue Paul-Vaillant-Couturier, 94800 Villejuif, France.,Université Paris Sud, UFR médecine, Institut André Lwoff, Paul Brousse Hospital, 14 avenue Paul-Vaillant-Couturier, 94800 Villejuif, France
| | - Valerie Boige
- Gustave-Roussy Institute, 114 Rue Edouard Vaillant, 94400 Villejuif, France
| | - Denis Smith
- Saint André Hospital, 1 Rue Jean Burguet, 33000 Bordeaux, France
| | - Mohamed Hebbar
- Medical Oncology Unit, Huriez Hospital, 1 rue Polonovski, 59037 Lille, France
| | - Pasquale Innominato
- INSERM, UMRS 935 Team 'Cancer Chronotherapy and Postoperative Liver Function', Campus CNRS, 7 rue Guy Môquet, and UMRS 1193 'Physiopathology and treatment of Liver diseases', Paul Brousse Hospital, 14 avenue Paul-Vaillant-Couturier, 94800 Villejuif, France.,Cancer Chronotherapy Unit, Warwick Medical School, Warwick University, Gibbet Hill Road, Coventry CV4 7AL, UK
| | - Julien Taieb
- Georges Pompidou European Hospital, 20 Rue Leblanc, 75015 Paris, France
| | - Carlos Carvalho
- Champalimaud Clinical Centre, Medical Oncology Department, Avenida Brasília, 1400-038 Lisbon, Portugal
| | - Rosine Guimbaud
- Digestive Medical Oncology Unit, Toulouse University Hospital, 170 avenue de Casselardit, 31059 Toulouse, France
| | - Christian Focan
- CHC Saint Joseph Clinics, rue de Hesbaye 75, 4000 Liège, Belgium
| | - Mohamed Bouchahda
- INSERM, UMRS 935 Team 'Cancer Chronotherapy and Postoperative Liver Function', Campus CNRS, 7 rue Guy Môquet, and UMRS 1193 'Physiopathology and treatment of Liver diseases', Paul Brousse Hospital, 14 avenue Paul-Vaillant-Couturier, 94800 Villejuif, France.,Assistance Publique-Hopitaux de Paris, Paul Brousse Hospital, Departments of Medical Oncology, Biochemistry and Oncogenetics, and Hepatobiliary Center, 14 avenue Paul-Vaillant-Couturier, 94800 Villejuif, France.,Ramsay GDS Mousseau Clinics, 2 Avenue de Mousseau, 91035 Evry, France
| | - René Adam
- INSERM, UMRS 935 Team 'Cancer Chronotherapy and Postoperative Liver Function', Campus CNRS, 7 rue Guy Môquet, and UMRS 1193 'Physiopathology and treatment of Liver diseases', Paul Brousse Hospital, 14 avenue Paul-Vaillant-Couturier, 94800 Villejuif, France.,Université Paris Sud, UFR médecine, Institut André Lwoff, Paul Brousse Hospital, 14 avenue Paul-Vaillant-Couturier, 94800 Villejuif, France.,Assistance Publique-Hopitaux de Paris, Paul Brousse Hospital, Departments of Medical Oncology, Biochemistry and Oncogenetics, and Hepatobiliary Center, 14 avenue Paul-Vaillant-Couturier, 94800 Villejuif, France
| | - Michel Ducreux
- Gustave-Roussy Institute, 114 Rue Edouard Vaillant, 94400 Villejuif, France
| | - Gérard Milano
- Oncopharmacology Laboratory, EA 3836, Antoine Lacassagne Center, 33, Avenue de Valombrose, 06189 Nice, France
| | - Antoinette Lemoine
- INSERM, UMRS 935 Team 'Cancer Chronotherapy and Postoperative Liver Function', Campus CNRS, 7 rue Guy Môquet, and UMRS 1193 'Physiopathology and treatment of Liver diseases', Paul Brousse Hospital, 14 avenue Paul-Vaillant-Couturier, 94800 Villejuif, France.,Université Paris Sud, UFR médecine, Institut André Lwoff, Paul Brousse Hospital, 14 avenue Paul-Vaillant-Couturier, 94800 Villejuif, France.,Assistance Publique-Hopitaux de Paris, Paul Brousse Hospital, Departments of Medical Oncology, Biochemistry and Oncogenetics, and Hepatobiliary Center, 14 avenue Paul-Vaillant-Couturier, 94800 Villejuif, France
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48
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John SE, Antony D, Eaaswarkhanth M, Hebbar P, Alkayal F, Tuomilehto J, Alsmadi O, Thanaraj TA. Genetic variants associated with warfarin dosage in Kuwaiti population. Pharmacogenomics 2017; 18:757-764. [PMID: 28592190 DOI: 10.2217/pgs-2017-0020] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Assessing the distinct prevalence or absence of genetic variants associated with differential response to the anticoagulant medication of warfarin in different population groups is actively pursued by pharmacogenomics community. Populations from Arabian Peninsula are underrepresented in such studies. By way of examining exome- and genome-wide genotype data from 1395 Arab individuals in Kuwait, we report distinct occurrence of warfarin response-related variants rs12460590_A/CYP2A7, rs2108622_T/CYP4F2, rs2884737_C/VKORC1 and distinct absence of rs11150606_C/PRSS53 in Kuwaiti population. The presented results in conjunction with similar literature reports on Qatari population enhance the worldwide understanding on population-specific distributions of genetic variants associated with warfarin drug dosage.
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Affiliation(s)
- Sumi Elsa John
- Population Genomics & Genetic Epidemiology Unit, Dasman Diabetes Institute, P.O. Box 1180, Dasman, 15462, Kuwait
| | - Dinu Antony
- Functional Genomics Unit, Dasman Diabetes Institute, P.O. Box 1180, Dasman, 15462, Kuwait
| | - Muthukrishnan Eaaswarkhanth
- Population Genomics & Genetic Epidemiology Unit, Dasman Diabetes Institute, P.O. Box 1180, Dasman, 15462, Kuwait
| | - Prashantha Hebbar
- Population Genomics & Genetic Epidemiology Unit, Dasman Diabetes Institute, P.O. Box 1180, Dasman, 15462, Kuwait
| | - Fadi Alkayal
- Population Genomics & Genetic Epidemiology Unit, Dasman Diabetes Institute, P.O. Box 1180, Dasman, 15462, Kuwait
| | - Jaakko Tuomilehto
- Population Genomics & Genetic Epidemiology Unit, Dasman Diabetes Institute, P.O. Box 1180, Dasman, 15462, Kuwait
| | - Osama Alsmadi
- Functional Genomics Unit, Dasman Diabetes Institute, P.O. Box 1180, Dasman, 15462, Kuwait
| | - Thangavel Alphonse Thanaraj
- Population Genomics & Genetic Epidemiology Unit, Dasman Diabetes Institute, P.O. Box 1180, Dasman, 15462, Kuwait
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49
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Turck D, Bresson JL, Burlingame B, Dean T, Fairweather-Tait S, Heinonen M, Hirsch-Ernst KI, Mangelsdorf I, McArdle HJ, Naska A, Nowicka G, Pentieva K, Sanz Y, Siani A, Sjödin A, Stern M, Tomé D, Van Loveren H, Vinceti M, Willatts P, Lamberg-Allardt C, Przyrembel H, Tetens I, Dumas C, Fabiani L, Ioannidou S, Neuhäuser-Berthold M. Dietary reference values for vitamin K. EFSA J 2017; 15:e04780. [PMID: 32625486 PMCID: PMC7010012 DOI: 10.2903/j.efsa.2017.4780] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Following a request from the European Commission, the EFSA Panel on Dietetic Products, Nutrition and Allergies (NDA) derives dietary reference values (DRVs) for vitamin K. In this Opinion, the Panel considers vitamin K to comprise both phylloquinone and menaquinones. The Panel considers that none of the biomarkers of vitamin K intake or status is suitable by itself to derive DRVs for vitamin K. Several health outcomes possibly associated with vitamin K intake were also considered but data could not be used to establish DRVs. The Panel considers that average requirements and population reference intakes for vitamin K cannot be derived for adults, infants and children, and therefore sets adequate intakes (AIs). The Panel considers that available evidence on occurrence, absorption, function and content in the body or organs of menaquinones is insufficient, and, therefore, sets AIs for phylloquinone only. Having assessed additional evidence available since 1993 in particular related to biomarkers, intake data and the factorial approach, which all are associated with considerable uncertainties, the Panel maintains the reference value proposed by the Scientific Committee for Food (SCF) in 1993. An AI of 1 μg phylloquinone/kg body weight per day is set for all age and sex population groups. Considering the respective reference body weights, AIs for phylloquinone are set at 70 μg/day for all adults including pregnant and lactating women, at 10 μg/day for infants aged 7-11 months, and between 12 μg/day for children aged 1-3 years and 65 μg/day for children aged 15-17 years.
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50
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Turgut Cosan D, Yazıcı HU, Colak E, Soyocak A, Degirmenci I, Kurt H, Birdane A, Colak E, Gunes HV. Susceptiveness of Vitamin K epOxide Reductase Complex Subunit 1 Gene Polymorphism in Essential Hypertension. Genet Test Mol Biomarkers 2017; 21:292-297. [PMID: 28281786 DOI: 10.1089/gtmb.2016.0311] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
BACKGROUND Essential hypertension (EH) is defined as a worldwide public health problem and one of the important risk factors for development of human coronary artery disease. Increased peripheral arterial resistance is one of the distinguishing characteristics of EH. The extracellular deposition of calcium in the arterial wall is defined as vascular calcification, which results in aortic stiffness and elevation of blood pressure. Regulation of vascular calcification is physiologically limited by γ-carboxylated proteins that regulate mineralization. Any deficiencies related to mineralization influence vascular calcification. As a result of vitamin-K deficiency or any problem associated with the vitamin K epOxide reductase complex subunit 1 (VKORC1) gene, Glu cannot be transformed to Gla and calcification initiates in blood vessels, myocardium, and cardiac. OBJECTIVE The aim of the study was to investigate the potential association of VKORC1 polymorphisms with the risk of EH. MATERIALS AND METHODS There were 100 individuals diagnosed with EH and 100 healthy individuals involved in the study. 3673G/A (rs9923231) and 9041G/A (rs7294) polymorphisms in the VKORC1 gene were determined by the PCR-restriction fragment length polymorphism method. RESULTS A significant difference was found between the rs7294 polymorphisms ratios of the case and control groups, but significant differences weren't found in distribution of the rs9923231 alleles. Finally it was determined that the GG genotype provides a 3.97-fold increased risk for EH compared to the AA genotype for the rs7294 polymorphism. CONCLUSIONS Our results suggest that the VKORC1 gene rs7294 polymorphism is important for the development of EH.
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Affiliation(s)
- Didem Turgut Cosan
- 1 Department of Medical Biology, Faculty of Medicine, Eskisehir Osmangazi University , Eskisehir, Turkey
| | - Huseyin Ugur Yazıcı
- 2 Department of Cardiology, Faculty of Medicine, Eskisehir Osmangazi University , Eskisehir, Turkey
| | - Emine Colak
- 1 Department of Medical Biology, Faculty of Medicine, Eskisehir Osmangazi University , Eskisehir, Turkey
| | - Ahu Soyocak
- 3 Department of Medical Biology, Faculty of Medicine, Istanbul Aydın University , Istanbul, Turkey
| | - Irfan Degirmenci
- 1 Department of Medical Biology, Faculty of Medicine, Eskisehir Osmangazi University , Eskisehir, Turkey
| | - Hulyam Kurt
- 1 Department of Medical Biology, Faculty of Medicine, Eskisehir Osmangazi University , Eskisehir, Turkey
| | - Alparslan Birdane
- 2 Department of Cardiology, Faculty of Medicine, Eskisehir Osmangazi University , Eskisehir, Turkey
| | - Ertugrul Colak
- 4 Department of Biostatistics, Faculty of Medicine, Eskisehir Osmangazi University , Eskisehir, Turkey
| | - Hasan Veysi Gunes
- 1 Department of Medical Biology, Faculty of Medicine, Eskisehir Osmangazi University , Eskisehir, Turkey
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