1
|
Zhang S, Zhao M, Zhong S, Niu J, Zhou L, Zhu B, Su H, Cao W, Xing Q, Yan H, Han X, Fu Q, Li Q, Chen L, Yang F, Zhang N, Wu H, He L, Qin S. Association between CYP2C9 and VKORC1 genetic polymorphisms and efficacy and safety of warfarin in Chinese patients. Pharmacogenet Genomics 2024; 34:105-116. [PMID: 38470454 DOI: 10.1097/fpc.0000000000000526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/13/2024]
Abstract
OBJECTIVES Genetic variation has been a major contributor to interindividual variability of warfarin dosage requirement. The specific genetic factors contributing to warfarin bleeding complications are largely unknown, particularly in Chinese patients. In this study, 896 Chinese patients were enrolled to explore the effect of CYP2C9 and VKORC1 genetic variations on both the efficacy and safety of warfarin therapy. METHODS AND RESULTS Univariate analyses unveiled significant associations between two specific single nucleotide polymorphisms rs1057910 in CYP2C9 and rs9923231 in VKORC1 and stable warfarin dosage ( P < 0.001). Further, employing multivariate logistic regression analysis adjusted for age, sex and height, the investigation revealed that patients harboring at least one variant allele in CYP2C9 exhibited a heightened risk of bleeding events compared to those with the wild-type genotype (odds ratio = 2.16, P = 0.04). Moreover, a meta-analysis conducted to consolidate findings confirmed the associations of both CYP2C9 (rs1057910) and VKORC1 (rs9923231) with stable warfarin dosage. Notably, CYP2C9 variant genotypes were significantly linked to an increased risk of hemorrhagic complications ( P < 0.00001), VKORC1 did not demonstrate a similar association. CONCLUSION The associations found between specific genetic variants and both stable warfarin dosage and bleeding risk might be the potential significance of gene detection in optimizing warfarin therapy for improving patient efficacy and safety.
Collapse
Affiliation(s)
- Suli Zhang
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai
| | - Mingzhe Zhao
- Affiliated Mental Health Center & Hangzhou Seventh People's Hospital, Zhejiang University School of Medicine, Hangzhou
| | - Shilong Zhong
- Department of Pharmacy, Guangdong Provincial People's Hospital, Guangdong
| | - Jiamin Niu
- Department of Cardiology, Jinan City People's Hospital, Jinan
| | - Lijuan Zhou
- Translational Medicine Center, Zhengzhou Central Hospital Affiliated to Zhengzhou University, Zhengzhou
| | - Bin Zhu
- Shanghai Baio Technology Co., Ltd., Shanghai
| | - Haili Su
- Department of Cardiology, Huhhot First Hospital, Huhhot
| | - Wei Cao
- Translational Medicine Center, Zhengzhou Central Hospital Affiliated to Zhengzhou University, Zhengzhou
| | - Qinghe Xing
- Institutes of Biomedical Sciences, Fudan University
| | - Hongli Yan
- Reproductive, Medicine Center, Changhai Hospital, Navy Medical University, Shanghai
| | - Xia Han
- Department of Cardiology, Jinan City People's Hospital, Jinan
| | - Qihua Fu
- Pediatric Translational Medicine Institute, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai
- Shanghai Key Laboratory of Clinical Molecular Diagnostics for Pediatrics, Shanghai
| | - Qiang Li
- Department of Geriatrics, Shandong Provincial Third Hospital, Shandong
| | - Luan Chen
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai
| | - Fan Yang
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai
| | - Na Zhang
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai
| | - Hao Wu
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai
| | - Lin He
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai
| | - Shengying Qin
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai
| |
Collapse
|
2
|
Wang Y, Wang Y. Identification of drug responsive enhancers by predicting chromatin accessibility change from perturbed gene expression profiles. NPJ Syst Biol Appl 2024; 10:62. [PMID: 38816426 PMCID: PMC11139989 DOI: 10.1038/s41540-024-00388-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Accepted: 05/20/2024] [Indexed: 06/01/2024] Open
Abstract
Individual may response to drug treatment differently due to their genetic variants located in enhancers. These variants can alter transcription factor's (TF) binding strength, affect enhancer's chromatin activity or interaction, and eventually change expression level of downstream gene. Here, we propose a computational framework, PERD, to Predict the Enhancers Responsive to Drug. A machine learning model was trained to predict the genome-wide chromatin accessibility from transcriptome data using the paired expression and chromatin accessibility data collected from ENCODE and ROADMAP. Then the model was applied to the perturbed gene expression data from Connectivity Map (CMAP) and Cancer Drug-induced gene expression Signature DataBase (CDS-DB) and identify drug responsive enhancers with significantly altered chromatin accessibility. Furthermore, the drug responsive enhancers were related to the pharmacogenomics genome-wide association studies (PGx GWAS). Stepping on the traditional drug-associated gene signatures, PERD holds the promise to enhance the causality of drug perturbation by providing candidate regulatory element of those drug associated genes.
Collapse
Affiliation(s)
- Yongcui Wang
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China.
| | - Yong Wang
- CEMS, NCMIS, HCMS, MDIS, Academy of Mathematics and Systems Science, Chinese Academy of Sciences, 100190, Beijing, China.
- Key Laboratory of Systems Biology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Hangzhou, 330106, China.
| |
Collapse
|
3
|
Ingelman-Sundberg M, Pirmohamed M. Precision medicine in cardiovascular therapeutics: Evaluating the role of pharmacogenetic analysis prior to drug treatment. J Intern Med 2024; 295:583-598. [PMID: 38343077 DOI: 10.1111/joim.13772] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
Pharmacogenomics is the examination of how genetic variation influences drug metabolism and response, in terms of both efficacy and safety. In cardiovascular disease, patient-specific diplotypes determine phenotypes, thereby influencing the efficacy and safety of drug treatments, including statins, antiarrhythmics, anticoagulants and antiplatelets. Notably, polymorphisms in key genes, such as CYP2C9, CYP2C19, VKORC1 and SLCO1B1, significantly impact the outcomes of treatment with clopidogrel, warfarin and simvastatin. Furthermore, the CYP2C19 polymorphism influences the pharmacokinetics and safety of the novel hypertrophic cardiomyopathy inhibitor, mavacamten. In this review, we critically assess the clinical application of pharmacogenomics in cardiovascular disease and delineate present and future utilization of pharmacogenomics. This includes insights into identifying missing heritability, the integration of whole genome sequencing and the application of polygenic risk scores to enhance the precision of personalized drug therapy. Our discussion encompasses health economic analyses that underscore the cost benefits associated with pre-emptive genotyping for warfarin and clopidogrel treatments, albeit acknowledging the need for further research in this area. In summary, we contend that cardiovascular pharmacogenomic analyses are underpinned by a wealth of evidence, and implementation is already occurring for some of these gene-drug pairs, but as with any area of medicine, we need to continually gather more information to optimize the use of pharmacogenomics in clinical practice.
Collapse
Affiliation(s)
- Magnus Ingelman-Sundberg
- Department of Physiology and Pharmacology, Section of Pharmacogenetics, Biomedicum 5B, Karolinska Institutet, Stockholm, Sweden
| | - Munir Pirmohamed
- Wolfson Centre for Personalised Medicine, Department of Pharmacology and Therapeutics, University of Liverpool, Liverpool, UK
| |
Collapse
|
4
|
Wang X, Zhao D, Ma J, Wang X, Liu J. Correlation between Metabolic Parameters and Warfarin Dose in Patients with Heart Valve Replacement of Different Genotypes. Rev Cardiovasc Med 2024; 25:128. [PMID: 39076565 PMCID: PMC11264039 DOI: 10.31083/j.rcm2504128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 12/18/2023] [Accepted: 12/22/2023] [Indexed: 07/31/2024] Open
Abstract
Background Warfarin has become the first choice for anticoagulation in patients who need lifelong anticoagulation due to its clinical efficacy and low price. However, the anticoagulant effect of warfarin is affected by many drugs, foods, etc. accompanied by a high risk of bleeding and embolism. The Vitamin K epoxide reductase complex 1 (VKORC1) and Cytochrome P450 2C9 (CYP2C9) genotypic variation can influence the therapeutic dose of warfarin. However, it is not clear whether there is a correlation between warfarin dose and liver function, kidney function and metabolic markers such as uric acid (UA) in patients with different genotypes. We performed a single-center retrospective cohort study to evaluate the factors affecting warfarin dose and to establish a dose conversion model for warfarin patients undergoing heart valve replacement. Methods We studied 343 patients with a mechanical heart valve replacement, compared the doses of warfarin in patients with different warfarin-related genotypes (CYP2C9 and VKORC1), and analyzed the correlation between liver function, kidney function, UA and other metabolic markers and warfarin dose in patients with different genotypes following heart valve replacement. Results Genotype analysis showed that 72.01% of patients had CYP2C9*1/*1 and VKORC1 mutant AA genotypes. Univariate regression analysis revealed that the warfarin maintenance dose was significantly correlated with gender, age, body surface area (BSA), UA and genotype. There was no correlation with liver or kidney function. Multiple linear regression analysis showed that BSA, genotype and UA were the independent factors influencing warfarin dose. Conclusions There is a significant correlation between UA content and warfarin dose in patients with heart valve replacement genotypes CYP2C9*1/*1/VKORC1(GA+GG), CYP2C9*1/*1/VKORC1AA and CYP2C9*1/*1/VKORC1AA.
Collapse
Affiliation(s)
- Xiaowu Wang
- Department of Cardiovascular Surgery, Xijing Hospital, Fourth Military Medical University, 710032 Xi'an, Shaanxi, China
| | - Diancai Zhao
- Department of Cardiovascular Surgery, Xijing Hospital, Fourth Military Medical University, 710032 Xi'an, Shaanxi, China
| | - Jipeng Ma
- Department of Cardiovascular Surgery, Xijing Hospital, Fourth Military Medical University, 710032 Xi'an, Shaanxi, China
| | - Xia Wang
- Department of Health Statistics, Faculty of Preventive Medicine, Fourth Military Medical University, 710032 Xi'an, Shaanxi, China
| | - Jincheng Liu
- Department of Cardiovascular Surgery, Xijing Hospital, Fourth Military Medical University, 710032 Xi'an, Shaanxi, China
| |
Collapse
|
5
|
Sadee W, Wang D, Hartmann K, Toland AE. Pharmacogenomics: Driving Personalized Medicine. Pharmacol Rev 2023; 75:789-814. [PMID: 36927888 PMCID: PMC10289244 DOI: 10.1124/pharmrev.122.000810] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2022] [Revised: 03/09/2023] [Accepted: 03/10/2023] [Indexed: 03/18/2023] Open
Abstract
Personalized medicine tailors therapies, disease prevention, and health maintenance to the individual, with pharmacogenomics serving as a key tool to improve outcomes and prevent adverse effects. Advances in genomics have transformed pharmacogenetics, traditionally focused on single gene-drug pairs, into pharmacogenomics, encompassing all "-omics" fields (e.g., proteomics, transcriptomics, metabolomics, and metagenomics). This review summarizes basic genomics principles relevant to translation into therapies, assessing pharmacogenomics' central role in converging diverse elements of personalized medicine. We discuss genetic variations in pharmacogenes (drug-metabolizing enzymes, drug transporters, and receptors), their clinical relevance as biomarkers, and the legacy of decades of research in pharmacogenetics. All types of therapies, including proteins, nucleic acids, viruses, cells, genes, and irradiation, can benefit from genomics, expanding the role of pharmacogenomics across medicine. Food and Drug Administration approvals of personalized therapeutics involving biomarkers increase rapidly, demonstrating the growing impact of pharmacogenomics. A beacon for all therapeutic approaches, molecularly targeted cancer therapies highlight trends in drug discovery and clinical applications. To account for human complexity, multicomponent biomarker panels encompassing genetic, personal, and environmental factors can guide diagnosis and therapies, increasingly involving artificial intelligence to cope with extreme data complexities. However, clinical application encounters substantial hurdles, such as unknown validity across ethnic groups, underlying bias in health care, and real-world validation. This review address the underlying science and technologies germane to pharmacogenomics and personalized medicine, integrated with economic, ethical, and regulatory issues, providing insights into the current status and future direction of health care. SIGNIFICANCE STATEMENT: Personalized medicine aims to optimize health care for the individual patients with use of predictive biomarkers to improve outcomes and prevent adverse effects. Pharmacogenomics drives biomarker discovery and guides the development of targeted therapeutics. This review addresses basic principles and current trends in pharmacogenomics, with large-scale data repositories accelerating medical advances. The impact of pharmacogenomics is discussed, along with hurdles impeding broad clinical implementation, in the context of clinical care, ethics, economics, and regulatory affairs.
Collapse
Affiliation(s)
- Wolfgang Sadee
- Department of Cancer Biology and Genetics, College of Medicine, The Ohio State University, Columbus Ohio (W.S., A.E.T.); Department of Pharmacotherapy and Translational Research, College of Pharmacy, University of Florida, Gainesville, Florida (D.W.); Department of Radiology, Hospital of the University of Pennsylvania, Philadelphia, Pennsylvania (K.H.); Department of Bioengineering and Therapeutic Sciences, Schools of Pharmacy and Medicine, University of California San Francisco, San Francisco, California (W.S.); and Aether Therapeutics, Austin, Texas (W.S.)
| | - Danxin Wang
- Department of Cancer Biology and Genetics, College of Medicine, The Ohio State University, Columbus Ohio (W.S., A.E.T.); Department of Pharmacotherapy and Translational Research, College of Pharmacy, University of Florida, Gainesville, Florida (D.W.); Department of Radiology, Hospital of the University of Pennsylvania, Philadelphia, Pennsylvania (K.H.); Department of Bioengineering and Therapeutic Sciences, Schools of Pharmacy and Medicine, University of California San Francisco, San Francisco, California (W.S.); and Aether Therapeutics, Austin, Texas (W.S.)
| | - Katherine Hartmann
- Department of Cancer Biology and Genetics, College of Medicine, The Ohio State University, Columbus Ohio (W.S., A.E.T.); Department of Pharmacotherapy and Translational Research, College of Pharmacy, University of Florida, Gainesville, Florida (D.W.); Department of Radiology, Hospital of the University of Pennsylvania, Philadelphia, Pennsylvania (K.H.); Department of Bioengineering and Therapeutic Sciences, Schools of Pharmacy and Medicine, University of California San Francisco, San Francisco, California (W.S.); and Aether Therapeutics, Austin, Texas (W.S.)
| | - Amanda Ewart Toland
- Department of Cancer Biology and Genetics, College of Medicine, The Ohio State University, Columbus Ohio (W.S., A.E.T.); Department of Pharmacotherapy and Translational Research, College of Pharmacy, University of Florida, Gainesville, Florida (D.W.); Department of Radiology, Hospital of the University of Pennsylvania, Philadelphia, Pennsylvania (K.H.); Department of Bioengineering and Therapeutic Sciences, Schools of Pharmacy and Medicine, University of California San Francisco, San Francisco, California (W.S.); and Aether Therapeutics, Austin, Texas (W.S.)
| |
Collapse
|
6
|
Yang W, Zhao H, Dou Y, Wang P, Chang Q, Qiao X, Wang X, Xu C, Zhang Z, Zhang L. CYP3A4 and CYP3A5 Expression is Regulated by C YP3A4*1G in CRISPR/Cas9-Edited HepG2 Cells. Drug Metab Dispos 2023; 51:492-498. [PMID: 36623883 DOI: 10.1124/dmd.122.001111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2022] [Revised: 11/16/2022] [Accepted: 12/05/2022] [Indexed: 01/10/2023] Open
Abstract
Functional CYP3A4*1G (G>A, rs2242480) in cytochrome P450 3A4 (CYP3A4) regulates the drug-metabolizing enzyme CYP3A4 expression. The objective of this study was to investigate whether CYP3A4*1G regulates both basal and rifampicin (RIF)-induced expression and enzyme activity of CYP3A4 and CYP3A5 in gene-edited human HepG2 cells. CYP3A4*1G GG and AA genotype HepG2 cells were established using the clustered regularly interspaced short palindromic repeats/CRISPR-associated protein 9 (CRISPR/Cas9) single nucleotide polymorphism technology and homology-directed repair in the CYP3A4*1G GA HepG2 cell line. In CYP3A4*1G GG, GA, and AA HepG2 cells, CYP3A4*1G regulated expression of CYP3A4 and CYP3A5 mRNA and protein in an allele-dependent manner. Of note, significantly decreased expression level of CYP3A4 and CYP3A5 was observed in CYP3A4*1G AA HepG2 cells. Moreover, the results after RIF treatment showed that CYP3A4*1G decreased the induction level of CYP3A4 and CYP3A5 mRNA expression in CYP3A4*1G AA HepG2 cells. At the same time, CYP3A4*1G decreased CYP3A4 enzyme activity and tacrolimus metabolism, especially in CYP3A4*1G GA HepG2 cells. In summary, we successfully constructed CYP3A4*1G GG and AA homozygous HepG2 cell models and found that CYP3A4*1G regulates both basal and RIF-induced expression and enzyme activity of CYP3A4 and CYP3A5 in CRISPR/Cas9 CYP3A4*1G HepG2 cells. SIGNIFICANCE STATEMENT: Cytochrome P450 (CYP) 3A4*1G regulates both basal and rifampicin (RIF)-induced expression and enzyme activity of CYP3A4 and CYP3A5. This study successfully established CYP3A4*1G (G>A, rs2242480), GG, and AA HepG2 cell models using CRISPR/Cas9, thus providing a powerful tool for studying the mechanism by which CYP3A4*1G regulates the basal and RIF-induced expression of CYP3A4 and CYP3A5.
Collapse
Affiliation(s)
- Weihong Yang
- Department of Forensic Medicine (W.Y., H.Z., Y.D., X.Q., C.X.) and Department of Pharmacology (P.W., Q.C., X.W., L.Z.), School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, China; and Department of Gastroenterology, the Second Affiliated Hospital of Zhengzhou University, Zhengzhou, China (Z.Z.)
| | - Huan Zhao
- Department of Forensic Medicine (W.Y., H.Z., Y.D., X.Q., C.X.) and Department of Pharmacology (P.W., Q.C., X.W., L.Z.), School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, China; and Department of Gastroenterology, the Second Affiliated Hospital of Zhengzhou University, Zhengzhou, China (Z.Z.)
| | - Yaojie Dou
- Department of Forensic Medicine (W.Y., H.Z., Y.D., X.Q., C.X.) and Department of Pharmacology (P.W., Q.C., X.W., L.Z.), School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, China; and Department of Gastroenterology, the Second Affiliated Hospital of Zhengzhou University, Zhengzhou, China (Z.Z.)
| | - Pei Wang
- Department of Forensic Medicine (W.Y., H.Z., Y.D., X.Q., C.X.) and Department of Pharmacology (P.W., Q.C., X.W., L.Z.), School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, China; and Department of Gastroenterology, the Second Affiliated Hospital of Zhengzhou University, Zhengzhou, China (Z.Z.)
| | - Qi Chang
- Department of Forensic Medicine (W.Y., H.Z., Y.D., X.Q., C.X.) and Department of Pharmacology (P.W., Q.C., X.W., L.Z.), School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, China; and Department of Gastroenterology, the Second Affiliated Hospital of Zhengzhou University, Zhengzhou, China (Z.Z.)
| | - Xiaomeng Qiao
- Department of Forensic Medicine (W.Y., H.Z., Y.D., X.Q., C.X.) and Department of Pharmacology (P.W., Q.C., X.W., L.Z.), School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, China; and Department of Gastroenterology, the Second Affiliated Hospital of Zhengzhou University, Zhengzhou, China (Z.Z.)
| | - Xiaofei Wang
- Department of Forensic Medicine (W.Y., H.Z., Y.D., X.Q., C.X.) and Department of Pharmacology (P.W., Q.C., X.W., L.Z.), School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, China; and Department of Gastroenterology, the Second Affiliated Hospital of Zhengzhou University, Zhengzhou, China (Z.Z.)
| | - Chen Xu
- Department of Forensic Medicine (W.Y., H.Z., Y.D., X.Q., C.X.) and Department of Pharmacology (P.W., Q.C., X.W., L.Z.), School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, China; and Department of Gastroenterology, the Second Affiliated Hospital of Zhengzhou University, Zhengzhou, China (Z.Z.)
| | - Zhe Zhang
- Department of Forensic Medicine (W.Y., H.Z., Y.D., X.Q., C.X.) and Department of Pharmacology (P.W., Q.C., X.W., L.Z.), School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, China; and Department of Gastroenterology, the Second Affiliated Hospital of Zhengzhou University, Zhengzhou, China (Z.Z.)
| | - Lirong Zhang
- Department of Forensic Medicine (W.Y., H.Z., Y.D., X.Q., C.X.) and Department of Pharmacology (P.W., Q.C., X.W., L.Z.), School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, China; and Department of Gastroenterology, the Second Affiliated Hospital of Zhengzhou University, Zhengzhou, China (Z.Z.)
| |
Collapse
|
7
|
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.
Collapse
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
| |
Collapse
|
8
|
Jiang T, Ling Z, Zhou Z, Chen X, Chen L, Liu S, Sun Y, Yang J, Yang B, Huang J, Huang L. Construction of a transposase accessible chromatin landscape reveals chromatin state of repeat elements and potential causal variant for complex traits in pigs. J Anim Sci Biotechnol 2022; 13:112. [PMID: 36217153 PMCID: PMC9552403 DOI: 10.1186/s40104-022-00767-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Accepted: 08/10/2022] [Indexed: 11/13/2022] Open
Abstract
Background A comprehensive landscape of chromatin states for multiple mammalian tissues is essential for elucidating the molecular mechanism underlying regulatory variants on complex traits. However, the genome-wide chromatin accessibility has been only reported in limited tissue types in pigs. Results Here we report a genome-wide landscape of chromatin accessibility of 20 tissues in two female pigs at ages of 6 months using ATAC-seq, and identified 557,273 merged peaks, which greatly expanded the pig regulatory element repository. We revealed tissue-specific regulatory elements which were associated with tissue-relevant biological functions. We identified both positive and negative significant correlations between the regulatory elements and gene transcripts, which showed distinct distributions in terms of their strength and distances from corresponding genes. We investigated the presence of transposable elements (TEs) in open chromatin regions across all tissues, these included identifications of porcine endogenous retroviruses (PERVs) exhibiting high accessibility in liver and homology of porcine specific virus sequences to universally accessible transposable elements. Furthermore, we prioritized a potential causal variant for polyunsaturated fatty acid in the muscle. Conclusions Our data provides a novel multi-tissues accessible chromatin landscape that serve as an important resource for interpreting regulatory sequences in tissue-specific and conserved biological functions, as well as regulatory variants of loci associated with complex traits in pigs. Supplementary Information The online version contains supplementary material available at 10.1186/s40104-022-00767-3.
Collapse
Affiliation(s)
- Tao Jiang
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Ziqi Ling
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Zhimin Zhou
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Xiaoyun Chen
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Liqing Chen
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Sha Liu
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Yingchun Sun
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Jiawen Yang
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Bin Yang
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China.
| | - Jianzhen Huang
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China.
| | - Lusheng Huang
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China
| |
Collapse
|
9
|
Abrahams-October Z, Lloyd S, Pearce B, Johnson R, Benjeddou M. Promoter haplotype structure of solute carrier 22 member 2 (SLC22A2) in the Xhosa population of South Africa and their differential effect on gene expression. Gene X 2022; 820:146292. [PMID: 35143948 DOI: 10.1016/j.gene.2022.146292] [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: 11/19/2021] [Revised: 01/06/2022] [Accepted: 02/03/2022] [Indexed: 11/20/2022] Open
Abstract
SLC22A2 is abundantly expressed in the kidney and facilitates the transport of endogenous and exogenous cationic compounds. It plays a pivotal role in the transport of pharmacologically important compounds such as metformin, cisplatin, lamivudine and cimetidine. Polymorphisms within SLC22A2 could potentially contribute to the inter-individual variable response to drugs. The SLC22A2 gene is known to show polymorphism variability amongst populations of different ethnicities. The present study was undertaken to characterize the promoter haplotype structure of the SLC22A2 gene in the Xhosa population of South Africa. In addition to this, we also investigate the effects of the observed promoter haplotypes on gene expression levels in vitro. We identified six known single nucleotide polymorphisms in the promoter region, namely rs60249401 (G424A), rs113150889 (G289A), rs55920607 (C246T), rs59695691 (A195G), rs572296424 (G156A), rs150063153 (A95C/G) and one novel SNP at location 6:160258967 (A209T). While these polymorphisms appeared in other African and non-African populations, their minor allele frequencies differed considerably from the non-African populations and could be considered to be African specific. A total of nine promoter haplotypes were characterized and the functional significance of each haplotype on promoter activity was determined using a luciferase reporter assay system. Amongst the nine observed haplotypes, three haplotypes (i.e. haplotypes 7, 8 and 9) displayed a significant decrease in expression level when compared to the wild-type with p -values of: 0.0317, <0.0001 and 0.0013 respectively. The data presented here shows African specific promoter haplotypes to cause a decrease in SLC22A2 gene expression levels, which in turn may have an impact on the pharmacokinetic profiles of cationic drugs.
Collapse
Affiliation(s)
- Zainonesa Abrahams-October
- Precision Medicine Unit, Department of Biotechnology, Faculty of Natural Sciences, University of the Western Cape, Robert Sobukwe Road, Bellville 7535, South Africa.
| | - Sheridon Lloyd
- Precision Medicine Unit, Department of Biotechnology, Faculty of Natural Sciences, University of the Western Cape, Robert Sobukwe Road, Bellville 7535, South Africa
| | - Brendon Pearce
- Precision Medicine Unit, Department of Biotechnology, Faculty of Natural Sciences, University of the Western Cape, Robert Sobukwe Road, Bellville 7535, South Africa
| | - Rabia Johnson
- Biomedical Research and Innovation Platform, South African Medical Research Council, Tygerberg, 7505 Cape Town, South Africa; Division of Medical Physiology, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg 7505, South Africa
| | - Mongi Benjeddou
- Precision Medicine Unit, Department of Biotechnology, Faculty of Natural Sciences, University of the Western Cape, Robert Sobukwe Road, Bellville 7535, South Africa
| |
Collapse
|
10
|
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.
Collapse
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
| |
Collapse
|
11
|
García-González X, Salvador-Martín S. Pharmacogenetics to Avoid Adverse Reactions in Cardiology: Ready for Implementation? J Pers Med 2021; 11:jpm11111180. [PMID: 34834533 PMCID: PMC8619366 DOI: 10.3390/jpm11111180] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 11/04/2021] [Accepted: 11/05/2021] [Indexed: 01/09/2023] Open
Abstract
Cardiovascular Diseases (CVs) are one of the main causes of mortality and disability around the world. Advances in drug treatment have greatly improved survival and quality of life in the past decades, but associated adverse events remain a relevant problem. Pharmacogenetics can help individualize cardiovascular treatment, reducing associated toxicities and improving outcomes. Several scientific societies and working groups periodically review available studies and provide consensus recommendations for those gene-drug pairs with a sufficient level of evidence. However, these recommendations are rarely mandatory, and the indications on how to adjust treatment can vary between different guidelines, which limits their clinical applicability. The aim of this review is to compile, compare and discuss available guidelines and recommendations by the main Pharmacogenetics Consortiums (Clinical Pharmacogenetics Implementation Consortium (CPIC); Dutch Pharmacogenetics Working Group (DPWG); the French Network of Pharmacogenetics (Réseau national de pharmacogénétique (RNPGx) and The Canadian Pharmacogenomics Network for Drug Safety (CPNDS) regarding how to apply pharmacogenetic results to optimize pharmacotherapy in cardiology. Pharmacogenetic recommendations included in European or American drug labels, as well as those included in the European Society of Cardiology (ESC) and the American College of Cardiology (ACC) and the American Heart Association (AHA) treatment guidelines are also discussed.
Collapse
|
12
|
Abstract
Over the past decade, pharmacogenetic testing has emerged in clinical practice to guide selected cardiovascular therapies. The most common implementation in practice is CYP2C19 genotyping to predict clopidogrel response and assist in selecting antiplatelet therapy after percutaneous coronary intervention. Additional examples include genotyping to guide warfarin dosing and statin prescribing. Increasing evidence exists on outcomes with genotype-guided cardiovascular therapies from multiple randomized controlled trials and observational studies. Pharmacogenetic evidence is accumulating for additional cardiovascular medications. However, data for many of these medications are not yet sufficient to support the use of genotyping for drug prescribing. Ultimately, pharmacogenetics might provide a means to individualize drug regimens for complex diseases such as heart failure, in which the treatment armamentarium includes a growing list of medications shown to reduce morbidity and mortality. However, sophisticated analytical approaches are likely to be necessary to dissect the genetic underpinnings of responses to drug combinations. In this Review, we examine the evidence supporting pharmacogenetic testing in cardiovascular medicine, including that available from several clinical trials. In addition, we describe guidelines that support the use of cardiovascular pharmacogenetics, provide examples of clinical implementation of genotype-guided cardiovascular therapies and discuss opportunities for future growth of the field.
Collapse
Affiliation(s)
- Julio D Duarte
- Center for Pharmacogenomics and Precision Medicine and Department of Pharmacotherapy and Translational Research, University of Florida College of Pharmacy, Gainesville, FL, USA
| | - Larisa H Cavallari
- Center for Pharmacogenomics and Precision Medicine and Department of Pharmacotherapy and Translational Research, University of Florida College of Pharmacy, Gainesville, FL, USA.
| |
Collapse
|
13
|
He S, Wu Y, Yan S, Liu J, Zhao L, Xie H, Ge S, Ye H. Methylation of CYP1A1 and VKORC1 promoter associated with stable dosage of warfarin in Chinese patients. PeerJ 2021; 9:e11549. [PMID: 34221714 PMCID: PMC8231338 DOI: 10.7717/peerj.11549] [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: 01/05/2021] [Accepted: 05/11/2021] [Indexed: 01/01/2023] Open
Abstract
Objective To investigate the association between DNA methylation and the stable warfarin dose through genome-wide DNA methylation analysis and pyrosequencing assay. Method This study included 161 patients and genome-wide DNA methylation analysis was used to screen potential warfarin dose-associated CpGs through Illumina Infinium HumanMethylation 450 K BeadChip; then, the pyrosequencing assay was used to further validate the association between the stable warfarin dose and alterations in the methylation of the screened CpGs. GenomeStudio Software and R were used to analyze the differentially methylated CpGs. Results The methylation levels of CpGs surrounding the xenobiotic response element (XRE) within the CYP1A1 promoter, differed significantly between the different dose groups (P < 0.05), and these CpGs presented a positive correlation (r> 0, P < 0.05) with an increase in the stable dose of warfarin. At the VKORC1 promoter, two CpGs methylation levels were significantly different between the differential dose groups (P < 0.05), and one CpG (Chr16: 31106793) presented a significant negative correlation (r < 0, P < 0.05) among different dose (low, medium, and high) groups. Conclusion This is a novel report of the methylation levels of six CpGs surrounding the XRE within the CYP1A1 promoter and one differential CpG at the VKORC1 promoter associated with stable warfarin dosage; these methylation levels might be applied as molecular signatures for warfarin.
Collapse
Affiliation(s)
- Shiwei He
- Department of Clinical Laboratory, Women and Children's Hospital, School of Medicine, Xiamen University, Xiamen, China.,National Institute of Diagnostics and Vaccine Development in Infectious Diseases (Xiamen University), School of Public Health, Xiamen University, Xiamen, China
| | - Yuan Wu
- Xiamen Cardiovascular Hospital, School of Medicine, Xiamen University, Xiamen, China
| | - Shuidi Yan
- Department of Clinical Laboratory, Zhongshan Hospital, School of Medicine, Xiamen University, Xiamen, China
| | - Jumei Liu
- Department of Clinical Laboratory, Women and Children's Hospital, School of Medicine, Xiamen University, Xiamen, China
| | - Li Zhao
- Department of Clinical Laboratory, Women and Children's Hospital, School of Medicine, Xiamen University, Xiamen, China.,School of Medicine, Xiamen University, Xiamen, China
| | - Huabin Xie
- Xiamen Cardiovascular Hospital, School of Medicine, Xiamen University, Xiamen, China
| | - Shengxiang Ge
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases (Xiamen University), School of Public Health, Xiamen University, Xiamen, China
| | - Huiming Ye
- Department of Clinical Laboratory, Women and Children's Hospital, School of Medicine, Xiamen University, Xiamen, China.,National Institute of Diagnostics and Vaccine Development in Infectious Diseases (Xiamen University), School of Public Health, Xiamen University, Xiamen, China.,School of Medicine, Xiamen University, Xiamen, China
| |
Collapse
|
14
|
Naushad SM, Kutala VK, Hussain T, Alrokayan SA. Pharmacogenetic determinants of warfarin in the Indian population. Pharmacol Rep 2021; 73:1396-1404. [PMID: 34106453 DOI: 10.1007/s43440-021-00297-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2021] [Revised: 06/01/2021] [Accepted: 06/03/2021] [Indexed: 01/13/2023]
Abstract
BACKGROUND Several studies optimized the warfarin dose based on CYP2C9*2, CYP2C9*3, VKORC1 -1639 G > A, CYP4F2 V433M. But, the information on the rare variants is lacking. In this study, we have explored the prevalence of common and rare pharmacogenetic determinants of warfarin and determined their damaging nature. METHODS We have analyzed 2000 healthy adults using the Infinium global screening array (GSA) for 15 pharmacogenetic determinants of warfarin. In addition, we have elucidated the impact of these variants on protein function, stability, dynamics, evolutionary preservation, and ligand binding propensity. RESULTS The GSA Analysis has revealed that CYP4F2 V433M (MAF: 39.425%), VKORC1 -1639 G > A (MAF: 20.5%), CYP2C9*3 (MAF:9.925%), and CYP2C9*2 (MAF:4.575%) are common, while CYP2C9*14 (MAF: 1.475%), CYP2C9*4 (0.175%), CYP2C9*5 (0.125%), and CYP2C9*11 (0.125%) are rare. Position-specific evolutionary preservation (PSEP) analysis has revealed that CYP2C9*4 is possibly damaging, while CYP2C9*5, CYP2C9*11, and CYP2C9*14 are probably damaging. CYP2C9*4 has high thermolability (-10.14 kcal/mol). Among the rare CYP2C9 variants, CYP2C9*4 and CYP2C9*11 exert destabilizing effects and may have increased molecular flexibility, while CYP2C9*5 and CYP2C9*14 exert stabilizing effects and may have decreased molecular flexibility. DNase I footprint analysis has revealed the loss of the E-box consensus sequence due to VKORC1 -1639 G > A polymorphism. CONCLUSION CYP2C9*2, CYP2C9*3, VKORC1 -1639 G > A and CYP4F2 V433M are common; CYP2C9*4, CYP2C9*5, CYP2C9*11, and CYP2C9*14 variants are rare in Indian subjects. All the CYP2C9 variants are found to be damaging. DNase I footprint analysis provided the mechanistic rationale for the association of VKORC1 -1639 G > A with warfarin sensitivity.
Collapse
Affiliation(s)
- Shaik Mohammad Naushad
- Department of Biochemical Genetics and Pharmacogenomics, Sandor Speciality Diagnostics Pvt Ltd, Banjara Hills, Road No 3, Hyderabad, 500034, India.
| | - Vijay Kumar Kutala
- Department of Clinical Pharmacology and Therapeutics, Nizam's Institute of Medical Sciences, Hyderabad, India
| | - Tajamul Hussain
- Center of Excellence in Biotechnology Research, College of Science, King Saud University, Riyadh, 11451, Saudi Arabia
- Research Chair for Biomedical Applications of Nanomaterials, Biochemistry Department, College of Science, King Saud University, Riyadh, 11451, Saudi Arabia
| | - Salman A Alrokayan
- Research Chair for Biomedical Applications of Nanomaterials, Biochemistry Department, College of Science, King Saud University, Riyadh, 11451, Saudi Arabia
- Biochemistry Department, College of Science, King Saud University, Riyadh, 11451, Saudi Arabia
| |
Collapse
|
15
|
Holcomb D, Alexaki A, Hernandez N, Hunt R, Laurie K, Kames J, Hamasaki-Katagiri N, Komar AA, DiCuccio M, Kimchi-Sarfaty C. Gene variants of coagulation related proteins that interact with SARS-CoV-2. PLoS Comput Biol 2021; 17:e1008805. [PMID: 33730015 PMCID: PMC8007013 DOI: 10.1371/journal.pcbi.1008805] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 03/29/2021] [Accepted: 02/15/2021] [Indexed: 12/30/2022] Open
Abstract
Thrombosis is a recognized complication of Coronavirus disease of 2019 (COVID-19) and is often associated with poor prognosis. There is a well-recognized link between coagulation and inflammation, however, the extent of thrombotic events associated with COVID-19 warrants further investigation. Poly(A) Binding Protein Cytoplasmic 4 (PABPC4), Serine/Cysteine Proteinase Inhibitor Clade G Member 1 (SERPING1) and Vitamin K epOxide Reductase Complex subunit 1 (VKORC1), which are all proteins linked to coagulation, have been shown to interact with SARS proteins. We computationally examined the interaction of these with SARS-CoV-2 proteins and, in the case of VKORC1, we describe its binding to ORF7a in detail. We examined the occurrence of variants of each of these proteins across populations and interrogated their potential contribution to COVID-19 severity. Potential mechanisms, by which some of these variants may contribute to disease, are proposed. Some of these variants are prevalent in minority groups that are disproportionally affected by severe COVID-19. Therefore, we are proposing that further investigation around these variants may lead to better understanding of disease pathogenesis in minority groups and more informed therapeutic approaches.
Collapse
Affiliation(s)
- David Holcomb
- Center for Biologics Evaluation and Research, Office of Tissues and Advanced Therapies, Division of Plasma Protein Therapeutics, Food and Drug Administration, Silver Spring, Maryland, United States of America
| | - Aikaterini Alexaki
- Center for Biologics Evaluation and Research, Office of Tissues and Advanced Therapies, Division of Plasma Protein Therapeutics, Food and Drug Administration, Silver Spring, Maryland, United States of America
| | - Nancy Hernandez
- Center for Biologics Evaluation and Research, Office of Tissues and Advanced Therapies, Division of Plasma Protein Therapeutics, Food and Drug Administration, Silver Spring, Maryland, United States of America
| | - Ryan Hunt
- Center for Biologics Evaluation and Research, Office of Tissues and Advanced Therapies, Division of Plasma Protein Therapeutics, Food and Drug Administration, Silver Spring, Maryland, United States of America
| | - Kyle Laurie
- Center for Biologics Evaluation and Research, Office of Tissues and Advanced Therapies, Division of Plasma Protein Therapeutics, Food and Drug Administration, Silver Spring, Maryland, United States of America
| | - Jacob Kames
- Center for Biologics Evaluation and Research, Office of Tissues and Advanced Therapies, Division of Plasma Protein Therapeutics, Food and Drug Administration, Silver Spring, Maryland, United States of America
| | - Nobuko Hamasaki-Katagiri
- Center for Biologics Evaluation and Research, Office of Tissues and Advanced Therapies, Division of Plasma Protein Therapeutics, Food and Drug Administration, Silver Spring, Maryland, United States of America
| | - Anton A. Komar
- Center for Gene Regulation in Health and Disease, Department of Biological, Geological and Environmental Sciences, Cleveland State University, Cleveland, Ohio, United States of America
| | - Michael DiCuccio
- National Center of Biotechnology Information, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Chava Kimchi-Sarfaty
- Center for Biologics Evaluation and Research, Office of Tissues and Advanced Therapies, Division of Plasma Protein Therapeutics, Food and Drug Administration, Silver Spring, Maryland, United States of America
| |
Collapse
|
16
|
Bargal SA, Kight JN, Augusto de Oliveira F, Shahin MH, Langaee T, Gong Y, Hamadeh IS, Cooper-DeHoff RM, Cavallari LH. Implications of Polymorphisms in the BCKDK and GATA-4 Gene Regions on Stable Warfarin Dose in African Americans. Clin Transl Sci 2020; 14:492-496. [PMID: 33278335 PMCID: PMC7993290 DOI: 10.1111/cts.12939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 11/04/2020] [Indexed: 11/28/2022] Open
Abstract
VKORC1 and CYP2C9 genotypes explain less variability in warfarin dose requirements in African Americans compared with Europeans. Variants in BCKDK and GATA-4 gene regions, purported to regulate VKORC1 and CYP2C9 expression, have been shown to play an important role in warfarin dose requirements in Europeans and Asians, respectively. We sought to determine whether rs56314408 near BCKDK or GATA-4 rs2645400 influence warfarin dose requirements in 200 African Americans. Unlike the strong linkage disequilibrium (LD) between rs56314408 and VKORC1 rs9923231 in Europeans, they were not in LD in African Americans. No associations were found on univariate analysis. On multivariable analysis, rs56314408 was associated (P = 0.027) with dose in a regression model excluding VKORC1 rs9923231, and GATA-4 rs2645400 was associated (P = 0.032) with dose in a model excluding CYP2C (CYP2C9*2, *3, *5, *6, *8, and *11, CYP2C rs12777823) variants. Neither variant contributed to dose in the model that included both VKORC1 rs9923231 and CYP2C variants. Our results do not support contributions of the studied variants to warfarin dose requirements in African Americans. However, they illustrate the value of studies in African descent populations, who have low LD in their genome, in teasing out genetic variation underlying drug response associations. They also emphasize the importance of confirming associations in persons of African ancestry.
Collapse
Affiliation(s)
- Salma A Bargal
- Department of Pharmacotherapy & Translational Research, Center for Pharmacogenomics & Precision Medicine, College of Pharmacy, University of Florida, Gainesville, Florida, USA
| | - Jennifer N Kight
- Department of Pharmacotherapy & Translational Research, Center for Pharmacogenomics & Precision Medicine, College of Pharmacy, University of Florida, Gainesville, Florida, USA
| | - Felipe Augusto de Oliveira
- Department of Pharmacotherapy & Translational Research, Center for Pharmacogenomics & Precision Medicine, College of Pharmacy, University of Florida, Gainesville, Florida, USA
| | - Mohamed H Shahin
- Department of Pharmacotherapy & Translational Research, Center for Pharmacogenomics & Precision Medicine, College of Pharmacy, University of Florida, Gainesville, Florida, USA
| | - Taimour Langaee
- Department of Pharmacotherapy & Translational Research, Center for Pharmacogenomics & Precision Medicine, College of Pharmacy, University of Florida, Gainesville, Florida, USA
| | - Yan Gong
- Department of Pharmacotherapy & Translational Research, Center for Pharmacogenomics & Precision Medicine, College of Pharmacy, University of Florida, Gainesville, Florida, USA
| | - Issam S Hamadeh
- Department of Pharmacotherapy & Translational Research, Center for Pharmacogenomics & Precision Medicine, College of Pharmacy, University of Florida, Gainesville, Florida, USA
| | - Rhonda M Cooper-DeHoff
- Department of Pharmacotherapy & Translational Research, Center for Pharmacogenomics & Precision Medicine, College of Pharmacy, University of Florida, Gainesville, Florida, USA
| | - Larisa H Cavallari
- Department of Pharmacotherapy & Translational Research, Center for Pharmacogenomics & Precision Medicine, College of Pharmacy, University of Florida, Gainesville, Florida, USA
| |
Collapse
|
17
|
Holcomb D, Alexaki A, Hernandez N, Laurie K, Kames J, Hamasaki-Katagiri N, Komar AA, DiCuccio M, Kimchi-Sarfaty C. Potential impact on coagulopathy of gene variants of coagulation related proteins that interact with SARS-CoV-2. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2020. [PMID: 32935103 DOI: 10.1101/2020.09.08.272328] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Thrombosis has been one of the complications of the Coronavirus disease of 2019 (COVID-19), often associated with poor prognosis. There is a well-recognized link between coagulation and inflammation, however, the extent of thrombotic events associated with COVID-19 warrants further investigation. Poly(A) Binding Protein Cytoplasmic 4 (PABPC4), Serine/Cysteine Proteinase Inhibitor Clade G Member 1 (SERPING1) and Vitamin K epOxide Reductase Complex subunit 1 (VKORC1), which are all proteins linked to coagulation, have been shown to interact with SARS proteins. We computationally examined the interaction of these with SARS-CoV-2 proteins and, in the case of VKORC1, we describe its binding to ORF7a in detail. We examined the occurrence of variants of each of these proteins across populations and interrogated their potential contribution to COVID-19 severity. Potential mechanisms by which some of these variants may contribute to disease are proposed. Some of these variants are prevalent in minority groups that are disproportionally affected by severe COVID-19. Therefore, we are proposing that further investigation around these variants may lead to better understanding of disease pathogenesis in minority groups and more informed therapeutic approaches. Author summary Increased blood clotting, especially in the lungs, is a common complication of COVID-19. Infectious diseases cause inflammation which in turn can contribute to increased blood clotting. However, the extent of clot formation that is seen in the lungs of COVID-19 patients suggests that there may be a more direct link. We identified three human proteins that are involved indirectly in the blood clotting cascade and have been shown to interact with proteins of SARS virus, which is closely related to the novel coronavirus. We examined computationally the interaction of these human proteins with the viral proteins. We looked for genetic variants of these proteins and examined how these variants are distributed across populations. We investigated whether variants of these genes could impact severity of COVID-19. Further investigation around these variants may provide clues for the pathogenesis of COVID-19 particularly in minority groups.
Collapse
|
18
|
Mirzaev K, Abdullaev S, Akmalova K, Sozaeva J, Grishina E, Shuev G, Bolieva L, Sozaeva M, Zhuchkova S, Gimaldinova N, Sidukova E, Serebrova S, Asoskova A, Shein A, Poptsova M, Suleymanov S, Burashnikova I, Shikaleva A, Kachanova A, Fedorinov D, Sychev D. Interethnic differences in the prevalence of main cardiovascular pharmacogenetic biomarkers. Pharmacogenomics 2020; 21:677-694. [DOI: 10.2217/pgs-2020-0005] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Background: The aim of this study was to determine the prevalence of CYP2C9, VKORC1, CYP2C19, ABCB1, CYP2D6 and SLCO1B1 genes polymorphisms among residents of the Volga region (Chuvash and Mari) and northern Caucasus (Kabardins and Ossetians). Materials & methods: The study involved 845 apparently healthy volunteers of both sexes of the four different ethnic groups living in the Russian Federation: 238 from the Chuvash ethnic group, 206 Mari, 157 Kabardins and 244 Ossetians. Results: Significant differences were identified in allele frequency of CYP2C9, VKORC1, CYP2C19, ABCB1, CYP2D6 and SLCO1B1 genes polymorphisms between the Chuvash and Kabardins, Chuvash and Ossetians, Mari and Kabardians, Mari and Ossetians.
Collapse
Affiliation(s)
- Karin Mirzaev
- Federal State Budgetary Educational Institution of Further Professional Education “Russian Medical Academy of Continuous Professional Education” of The Ministry of Healthcare of The Russian Federation, Barrikadnaya Str., 2/1, Bldg. 1, Moscow, 125993, Russian Federation
| | - Sherzod Abdullaev
- Federal State Budgetary Educational Institution of Further Professional Education “Russian Medical Academy of Continuous Professional Education” of The Ministry of Healthcare of The Russian Federation, Barrikadnaya Str., 2/1, Bldg. 1, Moscow, 125993, Russian Federation
| | - Kristina Akmalova
- Federal State Budgetary Educational Institution of Further Professional Education “Russian Medical Academy of Continuous Professional Education” of The Ministry of Healthcare of The Russian Federation, Barrikadnaya Str., 2/1, Bldg. 1, Moscow, 125993, Russian Federation
| | - Jeannette Sozaeva
- Federal State Budgetary Educational Institution of Further Professional Education “Russian Medical Academy of Continuous Professional Education” of The Ministry of Healthcare of The Russian Federation, Barrikadnaya Str., 2/1, Bldg. 1, Moscow, 125993, Russian Federation
| | - Elena Grishina
- Federal State Budgetary Educational Institution of Further Professional Education “Russian Medical Academy of Continuous Professional Education” of The Ministry of Healthcare of The Russian Federation, Barrikadnaya Str., 2/1, Bldg. 1, Moscow, 125993, Russian Federation
| | - Gregory Shuev
- Federal State Budgetary Educational Institution of Further Professional Education “Russian Medical Academy of Continuous Professional Education” of The Ministry of Healthcare of The Russian Federation, Barrikadnaya Str., 2/1, Bldg. 1, Moscow, 125993, Russian Federation
| | - Laura Bolieva
- Federal State Budgetary Educational Institution of Higher Education “North Ossetia State Medical Academy” of The Ministry of Healthcare of the Russian Federation, Pushkinskaya Str., 40, Vladikavkaz, Republic of North Ossetia–Alania, 362019, Russian Federation
| | - Mariam Sozaeva
- State Budgetary Healthcare Institution “Republican Clinical Hospital” of The Ministry of Healthcare of The Russian Federation, Nogmova Str., 91, Nalchik, Kabardino–Balkarian Republic, 360003, Russian Federation
| | - Svetlana Zhuchkova
- Autonomous Institution “Republican Clinical Oncology Center” of the Ministry of Health of The Chuvash Republic, Gladkov Str., 31, Cheboksary, Chuvash Republic, 428020, Russian Federation
| | - Natalya Gimaldinova
- Federal State Budgetary Educational Institution of Higher Education “I. N. Ulianov Chuvash State University”, Moskovskiy Pr., 15, Cheboksary, Chuvash Republic, 428015, Russian Federation
| | - Elena Sidukova
- State Budgetary Institution of The Republic of Mari El ‘Kozmodemyansk interdistrict hospital”, 3rd microdistrict, 25, Kozmodemyansk, Republic of Mari El, 425350, Russian Federation
| | - Svetlana Serebrova
- Department of Clinical Pharmacology & Propaedeutic of Internal Diseases of The Faculty of General Medicine of Sechenov First Moscow State Medical University of The Ministry of Health of The Russian Federation, Trubetskaya Str., 8, bld., Moscow, 2119991, Russian Federation
| | - Anastasia Asoskova
- Federal State Budgetary Educational Institution of Further Professional Education “Russian Medical Academy of Continuous Professional Education” of The Ministry of Healthcare of The Russian Federation, Barrikadnaya Str., 2/1, Bldg. 1, Moscow, 125993, Russian Federation
| | - Alexander Shein
- Laboratory of Bioinformatics, Big Data & Information Retrieval School, Faculty of Computer Science, National Research University Higher School of Economics, 3 Kochnovsky Proezd, Moscow, 109028, Russian Federation
| | - Maria Poptsova
- Laboratory of Bioinformatics, Big Data & Information Retrieval School, Faculty of Computer Science, National Research University Higher School of Economics, 3 Kochnovsky Proezd, Moscow, 109028, Russian Federation
| | - Salavat Suleymanov
- Russian–Japanese Medical Center “SAIKO”, Komsomolskaya St., 104, Khabarovsk, Khabarovsk Territory, 680000, Russian Federation
| | - Irina Burashnikova
- Kazan State Medical Academy, Kazan State Medical University, Mushtari st., 11, Kazan, Republic of Tatarstan, 420012, Russian Federation
| | - Anastasia Shikaleva
- Kazan State Medical Academy, Kazan State Medical University, Mushtari st., 11, Kazan, Republic of Tatarstan, 420012, Russian Federation
| | - Anastasia Kachanova
- Federal State Budgetary Educational Institution of Further Professional Education “Russian Medical Academy of Continuous Professional Education” of The Ministry of Healthcare of The Russian Federation, Barrikadnaya Str., 2/1, Bldg. 1, Moscow, 125993, Russian Federation
| | - Denis Fedorinov
- Federal State Budgetary Educational Institution of Further Professional Education “Russian Medical Academy of Continuous Professional Education” of The Ministry of Healthcare of The Russian Federation, Barrikadnaya Str., 2/1, Bldg. 1, Moscow, 125993, Russian Federation
| | - Dmitry Sychev
- Federal State Budgetary Educational Institution of Further Professional Education “Russian Medical Academy of Continuous Professional Education” of The Ministry of Healthcare of The Russian Federation, Barrikadnaya Str., 2/1, Bldg. 1, Moscow, 125993, Russian Federation
| |
Collapse
|
19
|
Asiimwe IG, Zhang EJ, Osanlou R, Krause A, Dillon C, Suarez-Kurtz G, Zhang H, Perini JA, Renta JY, Duconge J, Cavallari LH, Marcatto LR, Beasly MT, Perera MA, Limdi NA, Santos PCJL, Kimmel SE, Lubitz SA, Scott SA, Kawai VK, Jorgensen AL, Pirmohamed M. Genetic Factors Influencing Warfarin Dose in Black-African Patients: A Systematic Review and Meta-Analysis. Clin Pharmacol Ther 2020; 107:1420-1433. [PMID: 31869433 PMCID: PMC7217737 DOI: 10.1002/cpt.1755] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Accepted: 12/05/2019] [Indexed: 12/20/2022]
Abstract
Warfarin is the most commonly used oral anticoagulant in sub-Saharan Africa. Dosing is challenging due to a narrow therapeutic index and high interindividual variability in dose requirements. To evaluate the genetic factors affecting warfarin dosing in black-Africans, we performed a meta-analysis of 48 studies (2,336 patients). Significant predictors for CYP2C9 and stable dose included rs1799853 (CYP2C9*2), rs1057910 (CYP2C9*3), rs28371686 (CYP2C9*5), rs9332131 (CYP2C9*6), and rs28371685 (CYP2C9*11) reducing dose by 6.8, 12.5, 13.4, 8.1, and 5.3 mg/week, respectively. VKORC1 variants rs9923231 (-1639G>A), rs9934438 (1173C>T), rs2359612 (2255C>T), rs8050894 (1542G>C), and rs2884737 (497T>G) decreased dose by 18.1, 21.6, 17.3, 11.7, and 19.6 mg/week, respectively, whereas rs7294 (3730G>A) increased dose by 6.9 mg/week. Finally, rs12777823 (CYP2C gene cluster) was associated with a dose reduction of 12.7 mg/week. Few studies were conducted in Africa, and patient numbers were small, highlighting the need for further work in black-Africans to evaluate genetic factors determining warfarin response.
Collapse
Affiliation(s)
- Innocent G. Asiimwe
- The Wolfson Centre for Personalized Medicine, MRC Centre for Drug Safety Science, Department of Molecular and Clinical Pharmacology, University of Liverpool
| | - Eunice J. Zhang
- The Wolfson Centre for Personalized Medicine, MRC Centre for Drug Safety Science, Department of Molecular and Clinical Pharmacology, University of Liverpool
| | - Rostam Osanlou
- The Wolfson Centre for Personalized Medicine, MRC Centre for Drug Safety Science, Department of Molecular and Clinical Pharmacology, University of Liverpool
| | - Amanda Krause
- Division of Human Genetics, National Health Laboratory Service and School of Pathology, Faculty of Health Sciences, The University of the Witwatersrand, Johannesburg, South Africa
| | - Chrisly Dillon
- Department of Neurology & Epidemiology, Hugh Kaul Precision Medicine Institute, The University of Alabama at Birmingham
| | | | - Honghong Zhang
- Department of Pharmacology, Center for Pharmacogenomics, Northwestern University, Chicago IL
| | - Jamila A Perini
- Research Laboratory of Pharmaceutical Sciences, West Zone State University-UEZO, Rio de Janeiro, Brazil
| | - Jessicca Y. Renta
- University of Puerto Rico School of Pharmacy, Medical Sciences Campus, PO Box 365067, San Juan, PR 00936-5067
| | - Jorge Duconge
- University of Puerto Rico School of Pharmacy, Medical Sciences Campus, PO Box 365067, San Juan, PR 00936-5067
| | - Larisa H Cavallari
- Center for Pharmacogenomics, Department of Pharmacotherapy and Translational Research, University of Florida College of Pharmacy, Gainesville, FL, USA
| | - Leiliane R. Marcatto
- Laboratory of Genetics and Molecular Cardiology, Faculdade de Medicina FMUSP, Heart Institute (InCor), Universidade de São Paulo, São Paulo, Brazil
| | - Mark T. Beasly
- Department of Neurology & Epidemiology, Hugh Kaul Precision Medicine Institute, The University of Alabama at Birmingham
| | - Minoli A Perera
- Department of Pharmacology, Center for Pharmacogenomics, Northwestern University, Chicago IL
| | - Nita A. Limdi
- Department of Neurology & Epidemiology, Hugh Kaul Precision Medicine Institute, The University of Alabama at Birmingham
| | - Paulo C. J. L. Santos
- Department of Pharmacology, Escola Paulista de Medicina, Universidade Federal de São Paulo, EPM-Unifesp, São Paulo, Brazil
| | - Stephen E. Kimmel
- Perelman School of Medicine at the University of Pennsylvania, Department of Biostatistics, Epidemiology, and Informatics
| | - Steven A. Lubitz
- Cardiac Arrhythmia Service and Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA
| | - Stuart A. Scott
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Sema4, a Mount Sinai venture, Stamford, CT 06902, USA
| | - Vivian K. Kawai
- Division of Clinical Pharmacology, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Andrea L. Jorgensen
- Department of Biostatistics, Institute of Translational Medicine, University of Liverpool
- These authors contributed equally: Andrea Jorgensen and Munir Pirmohamed
| | - Munir Pirmohamed
- The Wolfson Centre for Personalized Medicine, MRC Centre for Drug Safety Science, Department of Molecular and Clinical Pharmacology, University of Liverpool
- These authors contributed equally: Andrea Jorgensen and Munir Pirmohamed
| |
Collapse
|
20
|
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.
Collapse
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
| |
Collapse
|
21
|
Marin JJG, Serrano MA, Monte MJ, Sanchez-Martin A, Temprano AG, Briz O, Romero MR. Role of Genetic Variations in the Hepatic Handling of Drugs. Int J Mol Sci 2020; 21:E2884. [PMID: 32326111 PMCID: PMC7215464 DOI: 10.3390/ijms21082884] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 04/09/2020] [Accepted: 04/17/2020] [Indexed: 12/18/2022] Open
Abstract
The liver plays a pivotal role in drug handling due to its contribution to the processes of detoxification (phases 0 to 3). In addition, the liver is also an essential organ for the mechanism of action of many families of drugs, such as cholesterol-lowering, antidiabetic, antiviral, anticoagulant, and anticancer agents. Accordingly, the presence of genetic variants affecting a high number of genes expressed in hepatocytes has a critical clinical impact. The present review is not an exhaustive list but a general overview of the most relevant variants of genes involved in detoxification phases. The available information highlights the importance of defining the genomic profile responsible for the hepatic handling of drugs in many ways, such as (i) impaired uptake, (ii) enhanced export, (iii) altered metabolism due to decreased activation of prodrugs or enhanced inactivation of active compounds, and (iv) altered molecular targets located in the liver due to genetic changes or activation/downregulation of alternative/compensatory pathways. In conclusion, the advance in this field of modern pharmacology, which allows one to predict the outcome of the treatments and to develop more effective and selective agents able to overcome the lack of effect associated with the existence of some genetic variants, is required to step forward toward a more personalized medicine.
Collapse
Affiliation(s)
- Jose J. G. Marin
- HEVEFARM Group, Center for the Study of Liver and Gastrointestinal Diseases (CIBERehd), Carlos III National Institute of Health, University of Salamanca, IBSAL, 37007 Salamanca, Spain; (M.A.S.); (M.J.M.); (A.S.-M.); (A.G.T.); (O.B.); (M.R.R.)
| | | | | | | | | | | | | |
Collapse
|
22
|
Abstract
The CYP3A4 enzyme is the most abundant drug-metabolizing enzyme in the liver, metabolizing ~50% of commonly used medications. CYP3A4 displays large interperson variability in expression and enzyme activity with unknown causes. This study aims to identify cis-acting regulatory elements controlling the transcription of CYP3A4, using chromatin conformation capture (4C and 3C assays), chromatin immunoprecipitation followed by quantitative PCR (ChIP-qPCR), clustered regularly interspaced short palindromic repeats (CRISPR)-mediated deletions of genomic regions and reporter gene assays in primary culture human hepatocytes and hepatic cell lines. 4C assays identified four regions (R1-R4) interacting with the CYP3A4 promoter, one of which overlaps with the previously identified upstream enhancers CLEM4/XREM (R2) while the other three are novel. ChIP-qPCR, reporter gene assays and CRISPR-mediated deletion experiments indicate regulatory roles for both R2 and R4. Interestingly, the deletion of R4 increased CYP3A4 while decreasing CYP3A43 expression, possibly due to competitive domain-domain interactions within the CYP3A cluster, supported by deletion of R4 increasing interaction between the CYP3A4 promoter and R2. We also identified a single nucleotide polymorphism rs62471956 within R4, with the variant allele A having increased transcriptional activity in a reporter gene assay. The rs62471956 A allele is associated with higher CYP3A43 expression and lower CYP3A4 expression in a cohort of 136 liver samples, further supporting the opposing effects of R4 on CYP3A4 and CYP3A43. rs62471956 is in complete linkage disequilibrium with CYP3A4*22, potentially contributing to reduced expression of CYP3A4*22. These results validate previously identified enhancers (CLEM4 and XREM) of CYP3A4 and demonstrate additional regulatory mechanisms underlying CYP3A4 transcriptional control via competitive domain-domain interactions within the CYP3A cluster.
Collapse
|
23
|
Shea MK, Booth SL. Vitamin K, Vascular Calcification, and Chronic Kidney Disease: Current Evidence and Unanswered Questions. Curr Dev Nutr 2019; 3:nzz077. [PMID: 31598579 PMCID: PMC6775440 DOI: 10.1093/cdn/nzz077] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Revised: 06/12/2019] [Accepted: 06/26/2019] [Indexed: 01/07/2023] Open
Abstract
More than 15% of the US population is currently >65 y old. As populations age there is a concomitant increase in age-related chronic diseases. One such disease is chronic kidney disease (CKD), which becomes more prevalent with age, especially over age 70 y. Individuals with CKD are at increased risk of cardiovascular disease, in part because arterial calcification increases as kidney function declines. Vitamin K is a shortfall nutrient among older adults that has been implicated in arterial calcification. Evidence suggests CKD patients have low vitamin K status, but data are equivocal because the biomarkers of vitamin K status can be influenced by CKD. Animal studies provide more compelling data on the underlying role of vitamin K in arterial calcification associated with CKD. The purpose of this review is to evaluate the strengths and limitations of the available evidence regarding the role of vitamin K in CKD.
Collapse
Affiliation(s)
- M Kyla Shea
- Jean Mayer USDA Human Nutrition Research Center on Aging at Tufts University, Boston, MA, USA
| | - Sarah L Booth
- Jean Mayer USDA Human Nutrition Research Center on Aging at Tufts University, Boston, MA, USA
| |
Collapse
|
24
|
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.
Collapse
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
| |
Collapse
|
25
|
Benincasa G, Costa D, Infante T, Lucchese R, Donatelli F, Napoli C. Interplay between genetics and epigenetics in modulating the risk of venous thromboembolism: A new challenge for personalized therapy. Thromb Res 2019; 177:145-153. [DOI: 10.1016/j.thromres.2019.03.008] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2018] [Revised: 02/12/2019] [Accepted: 03/13/2019] [Indexed: 02/09/2023]
|
26
|
Tian Z, Yang Y, Feng Z, Wu D, Yang W, Liu D. Genetic variant in the promoter region of microRNA‑137 reduces the warfarin maintenance dose in patients with atrial fibrillation. Mol Med Rep 2019; 19:5361-5367. [PMID: 31059093 DOI: 10.3892/mmr.2019.10205] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 11/11/2018] [Indexed: 11/06/2022] Open
Abstract
A substantial body of research has confirmed that Vitamin K epoxide reductase complex subunit 1 (VKORC1) plays a role in contributing to the high interpatient variability in the warfarin maintenance dose. The aim of the present study was to examine the impact of SNPs of miR‑137 on the warfarin maintenance dose. Computational analysis and luciferase assay were used to search the targets of miR‑137, and luciferase assay was also used to confirm the effect of the polymorphisms on the transcription of the promoter. The regulatory relationship between miR‑137 and VKORC1 was detected using real‑time PCR. We then performed statistical analysis to find the warfarin maintenance dose in the different groups. A total of 155 subjects were enrolled in our research, and the characteristics of the patients were collected. Using computational analysis, we identified that miR‑137 binds to the VKORC1 3'untranslated region (3'UTR) and regulates the expression of VKORC1. This hypothesis was confirmed by luciferase reporter assay as miR‑137 significantly reduced the VKORC1 3'UTR luciferase activity, while the luciferase activity of mutant VKORC1 3'UTR was similar to the scramble control. According to the result of the luciferase reporter assay, we found that miR‑137 SNP with the presence of the A allele apparently reduced the luciferase activity. Using real‑time PCR, we revealed that miR‑137 negatively regulated the expression of VKORC1 in a concentration‑dependent manner in liver cells. Furthermore, no difference was noted regarding the warfarin maintenance dose between the different age or gender groups, and furthermore AC + AA carriers showed a markedly higher warfarin maintenance dose than CC carriers. These findings collectively provide support that VKORC1 is a direct target of miR‑137 and the miR‑137 rs2660304 polymorphism is associated with warfarin maintenance dose in patients with atrial fibrillation. The rs2660304 polymorphism is a potential biomarker for predicting the clinical efficacy of warfarin in these patients.
Collapse
Affiliation(s)
- Zhen Tian
- Department of Cardiology, China‑Japan Union Hospital of Jilin University, Changchun, Jilin 130033, P.R. China
| | - Yushuang Yang
- Department of Cardiology, China‑Japan Union Hospital of Jilin University, Changchun, Jilin 130033, P.R. China
| | - Zhaohui Feng
- Department of Cardiology, China‑Japan Union Hospital of Jilin University, Changchun, Jilin 130033, P.R. China
| | - Donghui Wu
- Department of Orthopedics, People's Hospital of Jilin Province, Changchun, Jilin 130033, P.R. China
| | - Wei Yang
- Department of Psychology, Changchun Sixth Hospital, Changchun, Jilin 130033, P.R. China
| | - Dongna Liu
- Department of Cardiology, China‑Japan Union Hospital of Jilin University, Changchun, Jilin 130033, P.R. China
| |
Collapse
|
27
|
Lam YWF. Principles of Pharmacogenomics. Pharmacogenomics 2019. [DOI: 10.1016/b978-0-12-812626-4.00001-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
|
28
|
|
29
|
Galvez JM, Restrepo CM, Contreras NC, Alvarado C, Calderón-Ospina CA, Peña N, Cifuentes RA, Duarte D, Laissue P, Fonseca DJ. Creating and validating a warfarin pharmacogenetic dosing algorithm for Colombian patients. PHARMACOGENOMICS & PERSONALIZED MEDICINE 2018; 11:169-178. [PMID: 30410385 PMCID: PMC6198877 DOI: 10.2147/pgpm.s170515] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Purpose Warfarin is an oral anticoagulant associated with adverse reaction to drugs due to wide inter- and intra-individual dosage variability. Warfarin dosage has been related to non-genetic and genetic factors. CYP2C9 and VKORC1 gene polymorphisms affect warfarin metabolism and dosage. Due to the central role of populations’ ethnical and genetic origin on warfarin dosage variability, novel algorithms for Latin American subgroups are necessary to establish safe anticoagulation therapy. Patients and methods We genotyped CYP2C9*2 (c.430C > T), CYP2C9*3 (c.1075A > C), CYP4F2 (c.1297G > A), and VKORC1 (−1639 G > A) polymorphisms in 152 Colombian patients who received warfarin. We evaluated the impact on the variability of patients’ warfarin dose requirements. Multiple linear regression analysis, using genetic and non-genetic variables, was used for creating an algorithm for optimal warfarin maintenance dose. Results Median weekly prescribed warfarin dosage was significantly lower in patients having the VKORC1-1639 AA genotype and poor CYP2C9*2/*2,*2/*3 metabolizers than their wild-type counterparts. We found a 2.3-fold increase in mean dose for normal sensitivity patients (wild-type VKORC1/CYP2C9 genotypes) compared to the other groups (moderate and high sensitivity); 31.5% of the patients in our study group had warfarin sensitivity-related genotypes. The estimated regression equation accounted for 44.4% of overall variability in regard to warfarin maintenance dose. The algorithm was validated, giving 45.9% correlation (R2=0.459). Conclusion Our results describe and validate the first algorithm for predicting warfarin maintenance in a Colombian mestizo population and have contributed toward the understanding of pharmacogenetics in a Latin American population subgroup.
Collapse
Affiliation(s)
- Jubby Marcela Galvez
- GENIUROS Research Group, Center For Research in Genetics and Genomics - CIGGUR, School of Medicine and Health Sciences, Universidad del Rosario, Bogotá, Colombia,
| | - Carlos Martin Restrepo
- GENIUROS Research Group, Center For Research in Genetics and Genomics - CIGGUR, School of Medicine and Health Sciences, Universidad del Rosario, Bogotá, Colombia,
| | - Nora Constanza Contreras
- GENIUROS Research Group, Center For Research in Genetics and Genomics - CIGGUR, School of Medicine and Health Sciences, Universidad del Rosario, Bogotá, Colombia,
| | - Clara Alvarado
- GENIUROS Research Group, Center For Research in Genetics and Genomics - CIGGUR, School of Medicine and Health Sciences, Universidad del Rosario, Bogotá, Colombia,
| | - Carlos-Alberto Calderón-Ospina
- GENIUROS Research Group, Center For Research in Genetics and Genomics - CIGGUR, School of Medicine and Health Sciences, Universidad del Rosario, Bogotá, Colombia,
| | - Nidia Peña
- GENIUROS Research Group, Center For Research in Genetics and Genomics - CIGGUR, School of Medicine and Health Sciences, Universidad del Rosario, Bogotá, Colombia,
| | - Ricardo A Cifuentes
- Area of Basic Sciences, College of Medicine, Universidad Militar Nueva Granada, Bogotá, Colombia
| | - Daniela Duarte
- GENIUROS Research Group, Center For Research in Genetics and Genomics - CIGGUR, School of Medicine and Health Sciences, Universidad del Rosario, Bogotá, Colombia,
| | - Paul Laissue
- GENIUROS Research Group, Center For Research in Genetics and Genomics - CIGGUR, School of Medicine and Health Sciences, Universidad del Rosario, Bogotá, Colombia,
| | - Dora Janeth Fonseca
- GENIUROS Research Group, Center For Research in Genetics and Genomics - CIGGUR, School of Medicine and Health Sciences, Universidad del Rosario, Bogotá, Colombia,
| |
Collapse
|
30
|
Frequency of vitamin K oxidoreductase complex subunit-1 (VKORC1) polymorphisms and warfarin dose management in patients with venous thromboembolism. THE PHARMACOGENOMICS JOURNAL 2018; 18:646-651. [DOI: 10.1038/s41397-018-0037-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2017] [Revised: 04/14/2018] [Accepted: 06/19/2018] [Indexed: 12/25/2022]
|
31
|
Abstract
Considerable interindividual variability in response to cardiovascular pharmacotherapy exists with drug responses varying from being efficacious to inadequate to induce severe adverse events. Fueled by advancements and multidisciplinary collaboration across disciplines such as genetics, bioinformatics, and basic research, the vision of personalized medicine, rather than a one-size-fits-all approach, may be within reach. Pharmacogenetics offers the potential to optimize the benefit-risk profile of drugs by tailoring diagnostic and treatment strategies according to the individual patient. To date, a multitude of studies has tried to delineate the effects of gene-drug interactions for drugs commonly used to treat cardiovascular-related disease. The focus of this review is on how genetic variability may modify drug responsiveness and patient outcomes following therapy with commonly used cardiovascular drugs including clopidogrel, warfarin, statins, and β-blockers. Also included are examples of how genetic studies can be used to guide drug discovery and examples of how genetic information may be deployed in clinical decision making.
Collapse
Affiliation(s)
- Peter E Weeke
- Department of Cardiology, Copenhagen University Hospital, Bispebjerg and Frederiksberg, Denmark.
| |
Collapse
|
32
|
Elkhazraji A, Bouaiti EA, Boulahyaoui H, Nahmtchougli CP, Zahid H, Bensaid M, Ibrahimi A, Messaoudi N. Effect of CYP2C9, VKORC1, CYP4F2, and GGCX gene variants and patient characteristics on acenocoumarol maintenance dose: Proposal for a dosing algorithm for Moroccan patients. Drug Discov Ther 2018; 12:68-76. [PMID: 29760340 DOI: 10.5582/ddt.2017.01063] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
We investigated the impact of non-genetics factors, and single nucleotide polymorphisms (SNPs) in VKORC1, CYP2C9, CYP4F2, and GGCX on acenocoumarol dosage in Moroccan adult's patients, in order to develop an algorithm to predict acenocoumarol dose for Moroccan patients. Our study consisted of 217 Moroccan patients taking a maintenance dose of acenocoumarol for various indications. The patients were genotyped for VKORC1 -1639 G>A, VKORC1 1173 C>T, CYP2C9*2, CYP2C9*3, CYP4F2 1347 G>A and GGCX 12970 C>G SNPs. The statistical analysis was performed using the SPSS software. The age and SNPs in VKORC1 and CYP2C9 were significantly associated with the weekly acenocoumarol dose requirement (p = 0.023, p = 0.0001 and p = 0.001 respectively). There was no association found between the weekly acenocoumarol dose and the CYP4F2 or GGCX variants (p-value > 0.05). Non-parametric analysis confirmed the accumulate effect of variant alleles at VKORC1 -1639 G>A, VKORC1 1173 C>T and CYP2C9 SNPs on the acenocoumarol dose requirement. With 90.24% less dose required for one patient carrying homozygote variant at VKORC1 -1173 (TT) and CYP2C9 *x/*x haplotype. The multiple linear regression analysis showed that mutation in VKORC1 -1639, VKORC1 1173 SNPs, or in CYP2C9 haplotype reduces the mean acenocoumarol weekly dose to 25.4%, 23.4% and 6.2%, respectively. The R2 for multiple regression analysis final model was found to be 35.9%. In this work we were able to establish the factors influencing interindividual sensitivity to the anticoagulant therapy that can help physicians to predict optimal dose requirement for long term therapy.
Collapse
Affiliation(s)
- Abdelhak Elkhazraji
- Laboratory of Medical Biotechnology (Med Biotech), Faculty of Medicine and Pharmacy, Mohamed V University
| | - El Arbi Bouaiti
- Epidemiological and Clinical Research Laboratory, Faculty of Medicine and Pharmacy, Mohamed V University
| | - Hassan Boulahyaoui
- Research Team in Molecular Virology and Onco-Biology, Faculty of Medicine and Pharmacy, Mohamed V University
| | | | - Hafid Zahid
- Hematology and Immuno-Hematology Service, Military Teaching Hospital Mohamed V, Rabat
| | - Mounia Bensaid
- Laboratory of Medical Biotechnology (Med Biotech), Faculty of Medicine and Pharmacy, Mohamed V University.,Military Teaching Hospital Mohamed V
| | - Azeddine Ibrahimi
- Laboratory of Medical Biotechnology (Med Biotech), Faculty of Medicine and Pharmacy, Mohamed V University
| | - Nezha Messaoudi
- Hematology and Immuno-Hematology Service, Military Teaching Hospital Mohamed V, Rabat
| |
Collapse
|
33
|
Hu H, Li H, Li J, Yu J, Tan L. Genome-wide association study identified ATP6V1H locus influencing cerebrospinal fluid BACE activity. BMC MEDICAL GENETICS 2018; 19:75. [PMID: 29751835 PMCID: PMC5948839 DOI: 10.1186/s12881-018-0603-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Accepted: 05/02/2018] [Indexed: 12/13/2022]
Abstract
Background The activity of cerebrospinal fluid (CSF) β-site APP cleaving enzyme (BACE) is a potential diagnostic biomarker for Alzheimer disease (AD). Methods A total of 340 non-Hispanic Caucasian participants from the Alzheimer’s Disease Neuroimaging Initiative cohort (ADNI) database were included in this study with quality-controlled CSF BACE and genotype data. Association of CSF BACE with the genetic variants of single nucleotide polymorphisms (SNPs) was assessed using PLINK under the additive genetic model. The P values of all SNPs for CSF BACE were adjusted for multiple comparisons. Results One SNP (rs1481950) in the ATP6V1H gene reached genome-wide significance for associations with CSF BACE (P = 4.88 × 10− 9). The minor allele (G) of rs1481950 was associated with higher CSF BACE activity. Although seven SNPs in SNX31, RORA, CDH23, RGS20, LRRC4C, MAPK6PS1 and LOC105378355 did not reach genome-wide significance (P < 10− 8), they were identified as suggestive loci (P < 10− 5). Conclusion This study identified rs1481950 within ATP6V1H influencing human CSF BACE activity, which indicated that ATP6V1H gene may play some roles in the pathogenesis of neurodegenerative diseases such as AD. Electronic supplementary material The online version of this article (10.1186/s12881-018-0603-z) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Hao Hu
- Department of Neurology, Qingdao Municipal Hospital, School of Medicine, Qingdao University, No.5 Donghai Middle Road, Qingdao, 266071, Shandong Province, China
| | - Haiyan Li
- Department of Neurology, Weihai Wei People's Hospital, Weihai, China
| | - Jieqiong Li
- Department of Neurology, Qingdao Municipal Hospital, School of Medicine, Qingdao University, No.5 Donghai Middle Road, Qingdao, 266071, Shandong Province, China
| | - Jintai Yu
- Department of Neurology, Qingdao Municipal Hospital, School of Medicine, Qingdao University, No.5 Donghai Middle Road, Qingdao, 266071, Shandong Province, China. .,Clinical Research Center, Qingdao Municipal Hospital, Qingdao University, Qingdao, China. .,Department of Neurology, University of California, San Francisco, 675 Nelson Rising Lane, Suite 190, Box 1207, San Francisco, CA, 94158, USA.
| | - Lan Tan
- Department of Neurology, Qingdao Municipal Hospital, School of Medicine, Qingdao University, No.5 Donghai Middle Road, Qingdao, 266071, Shandong Province, China. .,Clinical Research Center, Qingdao Municipal Hospital, Qingdao University, Qingdao, China.
| | | |
Collapse
|
34
|
Eclov RJ, Kim MJ, Smith R, Ahituv N, Kroetz DL. Rare Variants in the ABCG2 Promoter Modulate In Vivo Activity. Drug Metab Dispos 2018; 46:636-642. [PMID: 29467213 PMCID: PMC5896364 DOI: 10.1124/dmd.117.079541] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Accepted: 02/15/2018] [Indexed: 11/22/2022] Open
Abstract
ABCG2 encodes the breast cancer resistance protein (BCRP), an efflux membrane transporter important in the detoxification of xenobiotics. In the present study, the basal activity of the ABCG2 promoter in liver, kidney, intestine, and breast cell lines was examined using luciferase reporter assays. The promoter activities of reference and variant ABCG2 sequences were compared in human hepatocellular carcinoma cell (HepG2), human embryonic kidney cell (HEK293T), human colorectal carcinoma cell (HCT116), and human breast adenocarcinoma cell (MCF-7) lines. The ABCG2 promoter activity was strongest in the kidney and intestine cell lines. Four variants in the basal ABCG2 promoter (rs76656413, rs66664036, rs139256004, and rs59370292) decreased the promoter activity by 25%-50% in at least three of the four cell lines. The activity of these four variants was also examined in vivo using the hydrodynamic tail vein assay, and two single nucleotide polymorphisms (rs76656413 and rs59370292) significantly decreased in vivo liver promoter activity by 50%-80%. Electrophoretic mobility shift assays confirmed a reduction in nuclear protein binding to the rs59370292 variant probe, whereas the rs76656413 probe had a shift in transcription factor binding specificity. Although both rs59370292 and rs76656413 are rare variants in all populations, they could contribute to patient-level variation in ABCG2 expression in the kidney, liver, and intestine.
Collapse
Affiliation(s)
- Rachel J Eclov
- Department of Bioengineering and Therapeutic Sciences (R.J.E., M.J.K., R.S., N.A., D.L.K.) and Institute for Human Genetics (N.A., M.J.K., R.S., D.L.K.), University of California San Francisco, San Francisco, California
| | - Mee J Kim
- Department of Bioengineering and Therapeutic Sciences (R.J.E., M.J.K., R.S., N.A., D.L.K.) and Institute for Human Genetics (N.A., M.J.K., R.S., D.L.K.), University of California San Francisco, San Francisco, California
| | - Robin Smith
- Department of Bioengineering and Therapeutic Sciences (R.J.E., M.J.K., R.S., N.A., D.L.K.) and Institute for Human Genetics (N.A., M.J.K., R.S., D.L.K.), University of California San Francisco, San Francisco, California
| | - Nadav Ahituv
- Department of Bioengineering and Therapeutic Sciences (R.J.E., M.J.K., R.S., N.A., D.L.K.) and Institute for Human Genetics (N.A., M.J.K., R.S., D.L.K.), University of California San Francisco, San Francisco, California
| | - Deanna L Kroetz
- Department of Bioengineering and Therapeutic Sciences (R.J.E., M.J.K., R.S., N.A., D.L.K.) and Institute for Human Genetics (N.A., M.J.K., R.S., D.L.K.), University of California San Francisco, San Francisco, California
| |
Collapse
|
35
|
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.
Collapse
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
| |
Collapse
|
36
|
Bedewy AML, Sheweita SA, Mostafa MH, Kandil LS. The Influence of CYP2C9 and VKORC1 Gene Polymorphisms on the Response to Warfarin in Egyptians. Indian J Hematol Blood Transfus 2018; 34:328-336. [PMID: 29622878 DOI: 10.1007/s12288-016-0725-4] [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: 06/25/2016] [Accepted: 09/19/2016] [Indexed: 10/20/2022] Open
Abstract
Warfarin is the most commonly used drug for chronic prevention of thromboembolic events, it also ranks high among drugs that cause serious adverse events. The variability in dose requirements has been attributed to inter-individual differences in medical, personal, and genetic factor. Cytochrome P-450 2C9 is the principle enzyme that terminates the anticoagulant effect of warfarin by catalyzing the conversion of the pharmacologically more potent S-enantiomer to its inactive metabolites. Warfarin exerts its effect by inhibition of vitamin K epoxide reductase. This protein is encoded by vitamin K epoxide reductase complex subunit 1 gene (VKORC1). The current study aimed to investigate the pharmacogenetic effect of CYP2C9 and VKORC1 gene polymorphisms on the patients response to warfarin. One hundred cases starting warfarin treatment and 20 healthy controls were enrolled. The mean daily dose of warfarin was calculated from patient's medical records. For each patient, less than 10 % variability in warfarin dose and a target international normalized ratio (INR) within the therapeutic target range were required for at least 3 months for one of the following indications (deep vein thrombosis, pulmonary embolism, cerebrovascular stroke and myocardial infarction) prior to inclusion in the study. Tetraprimer amplification refractory mutation system PCR was performed to determine CYP2C9*2, CYP2C9*3, and the VKORC1 1639 G > A genetic polymorphisms. Plasma warfarin determination was performed using rapid fluorometric assay. Plasma warfarin concentration ranged from 2.19 to 10.98 μg/ml with a median 3.52 μg/ml. Supratherpeutic INR was observed in 11 % of the cases. Thromboembolic complications occurred in 7 % of the cases and 8 % of cases experienced major bleeding. High maintenance dose (>7 mg/day) was associated with the combined non VKORC1*2 and homozygous wild type CYP2C9 (CYP2C9*1*1) alleles, while low maintenance dose was associated with the Variant (AG + AA)/Wild (*1/*1). (p value <0.001). CYP2C9 variant was a risk factor for supratherapeutic INR in the multivariate logistic regression model. Thromboembolic complication and incidence of supratherapeutic INR were observed in patients carrying combined VKORC1 Variant (AG + AA) and CYP2C9 Variant (*2/*3). Data from our study suggest that together with clinical factors, VKORC1 and CYP2C9 polymorphisms are important contributors to warfarin dosing and may help predict adverse effects in Egyptian patients.
Collapse
Affiliation(s)
- Ahmed M L Bedewy
- 1Hematology Department, Medical Research Institute, Alexandria University, Alexandria, Egypt.,Abraj Al-Shaker, Zaky Ragab Street, Smouha, Alexandria, 21615 Egypt
| | - Salah A Sheweita
- 2Biotechnology Department, Institute of Graduate Studies and Research, Alexandria University, Alexandria, Egypt
| | - Mostafa Hasan Mostafa
- 2Biotechnology Department, Institute of Graduate Studies and Research, Alexandria University, Alexandria, Egypt
| | - Lamia Saeed Kandil
- 3Biochemistry Department, Pharos University in Alexandria, Alexandria, Egypt
| |
Collapse
|
37
|
Evaluation of CYP2C9- and VKORC1-based pharmacogenetic algorithm for warfarin dose in Gaza-Palestine. Future Sci OA 2018; 4:FSO276. [PMID: 29568565 PMCID: PMC5859345 DOI: 10.4155/fsoa-2017-0112] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Accepted: 11/22/2017] [Indexed: 12/13/2022] Open
Abstract
Aim To evaluate applicability of CYP2C9*2, *3 and VKORC1-1639G > A based algorithm to predict warfarin stable dose (WSD) in a group of Palestinian patients. Patients & methods Warfarin doses were retrospectively calculated for 101 Palestinian patients under warfarin therapy using three models. Performance of the three models was assessed in 47 patients found to take WSD. Results Frequency of CYP2C9*2, *3 and VKORC1-1639G > A alleles is 13.6, 0.0 and 46.5% respectively. The international warfarin pharmacogenetics consortium algorithm was more reliable (MAE = 8.9 ± 1.4; R2 = 0.350) than both the clinical algorithm (MAE = 10.4 ± 1.4; R2 = 0.128;) and the fixed-dose algorithm (MAE = 11.1 ± 1.7). Conclusion The international warfarin pharmacogenetics consortium algorithm can be reliably applied for predicting the WSD in Palestinian population.
Collapse
|
38
|
Berny P, Esther A, Jacob J, Prescott C. Development of Resistance to Anticoagulant Rodenticides in Rodents. EMERGING TOPICS IN ECOTOXICOLOGY 2018. [DOI: 10.1007/978-3-319-64377-9_10] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
|
39
|
Mili FD, Allen T, Wadell PW, Hooper WC, Staercke CD, Bean CJ, Lally C, Austin H, Wenger NK. VKORC1-1639A allele influences warfarin maintenance dosage among Blacks receiving warfarin anticoagulation: a retrospective cohort study. Future Cardiol 2017; 14:15-26. [PMID: 29218998 DOI: 10.2217/fca-2017-0025] [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: 12/21/2022] Open
Abstract
AIM The study objectives were to investigate the association between selected CYP2C9 and VKORC1 single nucleotide polymorphisms with serious bleeding or thrombotic risk, and to estimate mean daily maintenance dose of warfarin and international normalized ratio measurements among Blacks receiving warfarin anticoagulation. METHODS We conducted a retrospective cohort study among 230 Black adults receiving warfarin for a minimum of three consecutive months with a confirmed date of first dosage. RESULTS A lower mean daily maintenance dosage of warfarin was required to maintain an international normalized ratio measurement within the therapeutic range among Blacks with the VKORC1-1639G>A variant alleles ([G/A vs G/G, p = 0.02], [A/A vs G/A, p = 0.008] and [A/A vs G/G, p = 0.001]). CONCLUSION Data indicated that VKORC1-1639A variant allele influenced warfarin daily maintenance dosage among our small, likely admixed Black patient population.
Collapse
Affiliation(s)
- Fatima Donia Mili
- Hemostasis Laboratory Branch, Division of Blood Disorders, Centers for Disease Control & Prevention, Atlanta, GA 30329, USA
| | - Tenecia Allen
- Emory Heart & Vascular Center, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Paula Weinstein Wadell
- Hemostasis Laboratory Branch, Division of Blood Disorders, Centers for Disease Control & Prevention, Atlanta, GA 30329, USA
| | - W Craig Hooper
- Hemostasis Laboratory Branch, Division of Blood Disorders, Centers for Disease Control & Prevention, Atlanta, GA 30329, USA
| | - Christine De Staercke
- Hemostasis Laboratory Branch, Division of Blood Disorders, Centers for Disease Control & Prevention, Atlanta, GA 30329, USA
| | - Christopher J Bean
- Hemostasis Laboratory Branch, Division of Blood Disorders, Centers for Disease Control & Prevention, Atlanta, GA 30329, USA
| | - Cathy Lally
- Department of Epidemiology, Emory University Rollins School of Public Health, Atlanta, GA 30322, USA
| | - Harland Austin
- Department of Epidemiology, Emory University Rollins School of Public Health, Atlanta, GA 30322, USA
| | - Nanette K Wenger
- Emory Heart & Vascular Center, Emory University School of Medicine, Atlanta, GA 30322, USA
| |
Collapse
|
40
|
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.
Collapse
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
| |
Collapse
|
41
|
Li L, Zhang L, Binkley PF, Sadee W, Wang D. Regulatory Variants Modulate Protein Kinase C α (PRKCA) Gene Expression in Human Heart. Pharm Res 2017; 34:1648-1657. [PMID: 28120175 PMCID: PMC7315374 DOI: 10.1007/s11095-017-2102-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Accepted: 01/06/2017] [Indexed: 11/26/2022]
Abstract
PURPOSE Protein kinase C α (PRKCA) is involved in multiple functions and has been implicated in heart failure risks and treatment outcomes. This study aims to identify regulatory variants affecting PRKCA expression in human heart, and evaluate attributable risk of heart disease. METHODS mRNA expression quantitative trait loci (eQTLs) were extracted from the Genotype and Tissue Expression Project (GTEx). Allelic mRNA ratios were measured in 51 human heart tissues to identify cis-acting regulatory variants. Potential regulatory regions were tested with luciferase reporter gene assays and further evaluated in GTEx and genome-wide association studies. RESULTS Located in a region with robust enhancer activity in luciferase reporter assays, rs9909004 (T > C, minor allele frequency =0.47) resides in a haplotype displaying strong eQTLs for PRKCA in heart (p = 1.2 × 10-23). The minor C allele is associated with both decreased PRKCA mRNA expression and decreased risk of phenotypes characteristic of heart failure in GWAS analyses (QT interval p = 3.0 × 10-14). While rs9909004 is the likely regulatory variant, other variants in high linkage disequilibrium cannot be excluded. Distinct regulatory variants appear to affect expression in other tissues. CONCLUSIONS The haplotype carrying rs9909004 influences PRKCA expression in the heart and is associated with traits linked to heart failure, potentially affecting therapy of heart failure.
Collapse
Affiliation(s)
- Liang Li
- Center for Pharmacogenomics and Department of Cancer Biology and Genetics, College of Medicine, The Ohio State University, 1005 BRT, 460 West 12th Ave, Columbus, Ohio, 43210, USA
| | - Lizhi Zhang
- Center for Pharmacogenomics and Department of Cancer Biology and Genetics, College of Medicine, The Ohio State University, 1005 BRT, 460 West 12th Ave, Columbus, Ohio, 43210, USA
| | - Philip F Binkley
- Department of Internal Medicine, College of Medicine, The Ohio State University, Columbus, Ohio, 43210, USA
| | - Wolfgang Sadee
- Center for Pharmacogenomics and Department of Cancer Biology and Genetics, College of Medicine, The Ohio State University, 1005 BRT, 460 West 12th Ave, Columbus, Ohio, 43210, USA
| | - Danxin Wang
- Center for Pharmacogenomics and Department of Cancer Biology and Genetics, College of Medicine, The Ohio State University, 1005 BRT, 460 West 12th Ave, Columbus, Ohio, 43210, USA.
- Center for Pharmacogenomics and Department of Cancer Biology and Genetics, College of Medicine, The Ohio State University, 1005 BRT, 460 W 12th Avenue, Columbus, Ohio, 43210, USA.
| |
Collapse
|
42
|
Claudio-Campos K, Labastida A, Ramos A, Gaedigk A, Renta-Torres J, Padilla D, Rivera-Miranda G, Scott SA, Ruaño G, Cadilla CL, Duconge-Soler J. Warfarin Anticoagulation Therapy in Caribbean Hispanics of Puerto Rico: A Candidate Gene Association Study. Front Pharmacol 2017; 8:347. [PMID: 28638342 PMCID: PMC5461284 DOI: 10.3389/fphar.2017.00347] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2017] [Accepted: 05/22/2017] [Indexed: 12/14/2022] Open
Abstract
Existing algorithms account for ~50% of observed variance in warfarin dose requirements after including common polymorphisms. However, they do not perform as well in populations other than Caucasians, in part because some ethno-specific genetic variants are overlooked. The objective of the present study was to identify genetic polymorphisms that can explain variability in warfarin dose requirements among Caribbean Hispanics of Puerto Rico. Next-Generation Sequencing of candidate genes CYP2C9 and VKORC1 and genotyping by DMET® Plus Assay of cardiovascular patients were performed. We also aimed at characterizing the genomic structure and admixture pattern of this study cohort. Our study used the Extreme Discordant Phenotype approach to perform a case-control association analysis. The CYP2C9 variant rs2860905, which was found in all the major haplotypes occurring in the Puerto Rican population, showed stronger association with warfarin sensitivity (<4 mg/day) than common variants CYP2C9*2 and CYP2C9*3. Although, CYP2C9*2 and CYP2C9*3 are separately contained within two of the haplotypes, 10 subjects with the sensitive phenotype were carriers of only the CYP2C9 rs2860905 variant. Other polymorphisms in CES2 and ABCB1 were found to be associated with warfarin resistance. Incorporation of rs2860905 in a regression model (R2 = 0.63, MSE = 0.37) that also includes additional genetics (i.e., VKORC1-1639 G>A; CYP2C9 rs1856908; ABCB1 c.IVS9-44A>G/ rs10276036; CES2 c.269-965A>G/ rs4783745) and non-genetic factors (i.e., hypertension, diabetes and age) showed better prediction of warfarin dose requirements than CYP2C9*2 and CYP2C9*3 combined (partial R2 = 0.132 vs. 0.023 and 0.007, respectively, p < 0.001). The genetic background of Puerto Ricans in the study cohort showed a tri-hybrid admixture pattern, with a slightly higher than expected contribution of Native American ancestry (25%). The genomic diversity of Puerto Ricans is highlighted by the presence of four different major haplotype blocks in the CYP2C9 locus. Although, our findings need further replication, this study contributes to the field by identifying novel genetic variants that increase predictability of stable warfarin dosing among Caribbean Hispanics.
Collapse
Affiliation(s)
- Karla Claudio-Campos
- Department of Pharmacology and Toxicology, School of Medicine, University of Puerto RicoSan Juan, PR, United States
| | - Aurora Labastida
- Independent Researcher, Primera Cerrada de Camino al Amalillo 4Mexico City, Mexico
| | - Alga Ramos
- Miami VA Healthcare System, Health System Administration Pharmacy, Clinical ServicesMiami, FL, United States
| | - Andrea Gaedigk
- Division of Clinical Pharmacology, Toxicology and Therapeutic Innovation, Children's Mercy Kansas CityKansas City, MO, United States
| | - Jessicca Renta-Torres
- Department of Biochemistry, School of Medicine, University of Puerto RicoSan Juan, PR, United States
| | - Dariana Padilla
- Department of Biology, University of Puerto Rico at Rio PiedrasSan Juan, PR, United States
| | - Giselle Rivera-Miranda
- Veterans Affairs Caribbean Healthcare Systems, Pharmacy ServiceSan Juan, PR, United States
| | - Stuart A. Scott
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount SinaiNew York, NY, United States
- Icahn School of Medicine at Mount Sinai, The Charles Bronfman Institute for Personalized MedicineNew York, NY, United States
| | | | - Carmen L. Cadilla
- Department of Biochemistry, School of Medicine, University of Puerto RicoSan Juan, PR, United States
| | - Jorge Duconge-Soler
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Puerto RicoSan Juan, PR, United States
| |
Collapse
|
43
|
Liu Y, Du J. Precision Medicine in Cardiovascular Diseases. CARDIOVASCULAR INNOVATIONS AND APPLICATIONS 2017. [DOI: 10.15212/cvia.2017.0003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
|
44
|
Friede K, Li J, Voora D. Use of Pharmacogenetic Information in the Treatment of Cardiovascular Disease. Clin Chem 2017; 63:177-185. [DOI: 10.1373/clinchem.2016.255232] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Accepted: 10/31/2016] [Indexed: 01/26/2023]
Abstract
Abstract
BACKGROUND
In 1964, Robert A. O'Reilly's research group identified members of a family who required remarkably high warfarin doses (up to 145 mg/day, 20 times the average dose) to achieve appropriate anticoagulation. Since this time, pharmacogenetics has become a mainstay of cardiovascular science, and genetic variants have been implicated in several fundamental classes of medications used in cardiovascular medicine.
CONTENT
In this review, we discuss genetic variants that affect drug response to 3 classes of cardiovascular drugs: statins, platelet P2Y12 inhibitors, and anticoagulants. These genetic variations have pharmacodynamic and pharmacokinetic effects and have been shown to explain differences in drug response such as lipid lowering, prevention of cardiovascular disease, and prevention of stroke, as well as incidence of adverse events such as musculoskeletal side effects and bleeding. Several groups have begun to implement pharmacogenetics testing as part of routine clinical care with the goal of improving health outcomes. Such strategies identify both patients at increased risk of adverse outcomes and alternative strategies to mitigate this risk as well as patients with “normal” genotypes, who, armed with this information, may have increased confidence and adherence to prescribed medications. While much is known about the genetic variants that underlie these effects, translation of this knowledge into clinical practice has been hampered by difficulty in implementing cost-effective, point-of-care tools to improve physician decision-making as well as a lack of data, as of yet, demonstrating the efficacy of using genetic information to improve health.
SUMMARY
Many genetic variants that affect individual responses to drugs used in cardiovascular disease prevention and treatment have been described. Further study of these variants is needed before successful implementation into clinical practice.
Collapse
Affiliation(s)
| | - Josephine Li
- Duke Center for Applied Genomics & Precision Medicine, Duke University, Durham, NC
| | - Deepak Voora
- Department of Medicine and and
- Duke Center for Applied Genomics & Precision Medicine, Duke University, Durham, NC
| |
Collapse
|
45
|
Prasad B, Vrana M, Mehrotra A, Johnson K, Bhatt DK. The Promises of Quantitative Proteomics in Precision Medicine. J Pharm Sci 2016; 106:738-744. [PMID: 27939376 DOI: 10.1016/j.xphs.2016.11.017] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Revised: 11/07/2016] [Accepted: 11/29/2016] [Indexed: 01/01/2023]
Abstract
Precision medicine approach has a potential to ensure optimum efficacy and safety of drugs at individual patient level. Physiologically based pharmacokinetic and pharmacodynamic (PBPK/PD) models could play a significant role in precision medicine by predicting interindividual variability in drug disposition and response. In order to develop robust PBPK/PD models, it is imperative that the critical physiological parameters affecting drug disposition and response and their variability are precisely characterized. Currently used PBPK/PD modeling software, for example, Simcyp and Gastroplus, encompass information such as organ volumes, blood flows to organs, body fat composition, glomerular filtration rate, etc. However, the information on the interindividual variability of the majority of the proteins associated with PK and PD, for example, drug metabolizing enzymes, transporters, and receptors, are not fully incorporated into these PBPK modeling platforms. Such information is significant because the population factors such as age, genotype, disease, and gender can affect abundance or activity of these proteins. To fill this critical knowledge gap, mass spectrometry-based quantitative proteomics has emerged as an important technique to characterize interindividual variability in the protein abundance of drug metabolizing enzymes, transporters, and receptors. Integration of these quantitative proteomics data into in silico PBPK/PD modeling tools will be crucial toward precision medicine.
Collapse
Affiliation(s)
- Bhagwat Prasad
- Department of Pharmaceutics, University of Washington, Seattle, P.O. Box 357610, Washington 98195.
| | - Marc Vrana
- Department of Pharmaceutics, University of Washington, Seattle, P.O. Box 357610, Washington 98195
| | - Aanchal Mehrotra
- Department of Pharmaceutics, University of Washington, Seattle, P.O. Box 357610, Washington 98195
| | - Katherine Johnson
- Department of Pharmaceutics, University of Washington, Seattle, P.O. Box 357610, Washington 98195
| | - Deepak Kumar Bhatt
- Department of Pharmaceutics, University of Washington, Seattle, P.O. Box 357610, Washington 98195
| |
Collapse
|
46
|
Abstract
Cytochrome P450 3A4 (CYP3A4) metabolizes 30-50% of clinically used drugs. Large interperson variability in CYP3A4 activity affects response to CYP3A4 substrate drugs. We had demonstrated that an intronic single nucleotide polymorphism rs35599367 (CYP3A4*22, located in intron 6) reduces mRNA/protein expression; however, the underlying mechanism remained unknown. Here we show that CYP3A4*22 is associated with a two-fold or greater increase in formation of a nonfunctional CYP3A4 alternative splice variant with partial intron 6 retention in human liver (P=0.006), but not in small intestines. Consistent with this observation, in-vitro transfection experiments with a CYP3A4 minigene (spanning from intron 5 to intron 7) demonstrated that plasmids carrying the rs35599367 minor T allele caused significantly greater intron 6 retention than the C allele in liver derived HepG2 cells, but not in intestine-derived LS-174T cells. These results indicate that tissue-specific increased formation of nonfunctional alternative splice variant causes reduced CYP3A4 mRNA/protein expression in CYP3A4*22 carriers.
Collapse
|
47
|
Alessandrini M, Chaudhry M, Dodgen TM, Pepper MS. Pharmacogenomics and Global Precision Medicine in the Context of Adverse Drug Reactions: Top 10 Opportunities and Challenges for the Next Decade. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2016; 20:593-603. [PMID: 27643672 PMCID: PMC5072285 DOI: 10.1089/omi.2016.0122] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
In a move indicative of the enthusiastic support of precision medicine, the U.S. President Barack Obama announced the Precision Medicine Initiative in January 2015. The global precision medicine ecosystem is, thus, receiving generous support from the United States ($215 million), and numerous other governments have followed suit. In the context of precision medicine, drug treatment and prediction of its outcomes have been important for nearly six decades in the field of pharmacogenomics. The field offers an elegant solution for minimizing the effects and occurrence of adverse drug reactions (ADRs). The Clinical Pharmacogenetics Implementation Consortium (CPIC) plays an important role in this context, and it aims at specifically guiding the translation of clinically relevant and evidence-based pharmacogenomics research. In this forward-looking analysis, we make particular reference to several of the CPIC guidelines and their role in guiding the treatment of highly relevant diseases, namely cardiovascular disease, major depressive disorder, cancer, and human immunodeficiency virus, with a view to predicting and managing ADRs. In addition, we provide a list of the top 10 crosscutting opportunities and challenges facing the fields of precision medicine and pharmacogenomics, which have broad applicability independent of the drug class involved. Many of these opportunities and challenges pertain to infrastructure, study design, policy, and science culture in the early 21st century. Ultimately, rational pharmacogenomics study design and the acquisition of comprehensive phenotypic data that proportionately match the genomics data should be an imperative as we move forward toward global precision medicine.
Collapse
Affiliation(s)
- Marco Alessandrini
- Department of Immunology, Faculty of Health Sciences, and Institute for Cellular and Molecular Medicine, South African Medical Research Council Extramural Unit for Stem Cell Research and Therapy, University of Pretoria , Pretoria, South Africa
| | - Mamoonah Chaudhry
- Department of Immunology, Faculty of Health Sciences, and Institute for Cellular and Molecular Medicine, South African Medical Research Council Extramural Unit for Stem Cell Research and Therapy, University of Pretoria , Pretoria, South Africa
| | - Tyren M Dodgen
- Department of Immunology, Faculty of Health Sciences, and Institute for Cellular and Molecular Medicine, South African Medical Research Council Extramural Unit for Stem Cell Research and Therapy, University of Pretoria , Pretoria, South Africa
| | - Michael S Pepper
- Department of Immunology, Faculty of Health Sciences, and Institute for Cellular and Molecular Medicine, South African Medical Research Council Extramural Unit for Stem Cell Research and Therapy, University of Pretoria , Pretoria, South Africa
| |
Collapse
|
48
|
G-1639A but Not C1173T VKORC1 Gene Polymorphism Is Related to Ischemic Stroke and Its Various Risk Factors in Ukrainian Population. BIOMED RESEARCH INTERNATIONAL 2016; 2016:1298198. [PMID: 27703968 PMCID: PMC5040782 DOI: 10.1155/2016/1298198] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 05/28/2016] [Revised: 07/25/2016] [Accepted: 08/17/2016] [Indexed: 11/18/2022]
Abstract
Vitamin K epoxide reductase complex subunit 1 (VKORC1) is integral 163-amino acid long transmembrane protein which mediates recycling of vitamin K 2,3-epoxide to vitamin K hydroquinone and it is necessary for activation of vitamin K-dependent proteins (VKDPs). Herein, the association between G-1639A (rs9923231) and C1173T (rs9934438) single-nucleotide polymorphisms (SNPs) of the VKORC1 gene and ischemic stroke (IS) was tested in Ukrainian population. Genotyping was performed in 170 IS patients and 124 control subjects (total 294 DNA samples) using PCR-RFLP (polymerase chain reaction with following restriction fragment length polymorphism analysis) method. Our data showed that G-1639A but not C1173T polymorphism was related to IS, regardless of adjustment for age, sex, body mass index, smoking status, and arterial hypertension. The risk for IS in -1639A allele carriers (OR = 2.138, P = 0.015) was higher than in individuals with G/G genotype. Haplotype analysis demonstrated that -1639G/1173T and -1639A/1173C were related to increased risk for IS (OR = 3.813, P = 0.010, and OR = 2.189, P = 0.011, resp.), while -1639G/1173C was a protective factor for IS (OR = 0.548, P < 0.001). Obtained results suggested that -1639A allele can be a possible genetic risk factor for IS in Ukrainian population.
Collapse
|
49
|
Nutescu EA, Burnett A, Fanikos J, Spinler S, Wittkowsky A. Erratum to: Pharmacology of anticoagulants used in the treatment of venous thromboembolism. J Thromb Thrombolysis 2016; 42:296-311. [PMID: 27145758 PMCID: PMC4969935 DOI: 10.1007/s11239-016-1363-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Anticoagulant drugs are the foundation of therapy for patients with VTE. While effective therapeutic agents, anticoagulants can also result in hemorrhage and other side effects. Thus, anticoagulant therapy selection should be guided by the risks, benefits and pharmacologic characteristics of each agent for each patient. Safe use of anticoagulants requires not only an in-depth knowledge of their pharmacologic properties but also a comprehensive approach to patient management and education. This paper will summarize the key pharmacologic properties of the anticoagulant agents used in the treatment of patients with VTE.
Collapse
Affiliation(s)
- Edith A Nutescu
- Department of Pharmacy Systems Outcomes and Policy and Center for Pharmacoepidemiology & Pharmacoeconomic Research, College of Pharmacy, University of Illinois at Chicago, Chicago, IL, USA.
| | - Allison Burnett
- Inpatient Antithrombosis Services, University of New Mexico Hospital, University of New Mexico College of Pharmacy, Albuquerque, NM, USA
| | - John Fanikos
- Brigham and Women's Hospital, Massachusetts College of Pharmacy, Boston, MA, USA
| | - Sarah Spinler
- Philadelphia College of Pharmacy and Science, Philadelphia, PA, USA
| | - Ann Wittkowsky
- University of Washington School of Pharmacy, Seattle, WA, USA
| |
Collapse
|
50
|
PGRNseq: a targeted capture sequencing panel for pharmacogenetic research and implementation. Pharmacogenet Genomics 2016; 26:161-168. [PMID: 26736087 DOI: 10.1097/fpc.0000000000000202] [Citation(s) in RCA: 83] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
OBJECTIVES Although the costs associated with whole-genome and whole-exome next-generation sequencing continue to decline, they remain prohibitively expensive for large-scale studies of genetic variation. As an alternative, custom-target sequencing has become a common methodology on the basis of its favorable balance between cost, throughput, and deep coverage. METHODS We have developed PGRNseq, a custom-capture panel of 84 genes with associations to pharmacogenetic phenotypes, as a tool to explore the relationship between drug response and genetic variation, both common and rare. We utilized a set of 32 diverse HapMap trios and two clinical cohorts to assess platform performance, accuracy, and ability to discover novel variation. RESULTS We found that PGRNseq generates ultra-deep coverage data (mean=496x) that are over 99.8% concordant with orthogonal datasets. In addition, in our testing sets, PGRNseq identified many novel, rare variants of interest, underscoring its value in both research and clinical settings. CONCLUSION PGRNseq is an ideal platform for carrying out sequencing-based analyses of pharmacogenetic variation in large cohorts. In addition, the high accuracy associated with genotypes from PGRNseq highlight its utility as a clinical test.
Collapse
|