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Maulana Y, Toro Jimenez R, Twesigomwe D, Sani L, Irwanto A, Bertin N, Gonzalez-Porta M. The variation landscape of CYP2D6 in a multi-ethnic Asian population. Sci Rep 2024; 14:16725. [PMID: 39030343 PMCID: PMC11271511 DOI: 10.1038/s41598-024-67691-6] [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: 01/24/2024] [Accepted: 07/15/2024] [Indexed: 07/21/2024] Open
Abstract
Cytochrome P450 2D6 (CYP2D6) plays a crucial role in metabolizing approximately 20% of medications prescribed clinically. This enzyme is encoded by the CYP2D6 gene, known for its extensive polymorphism with over 170 catalogued haplotypes or star alleles, which can have a profound impact on drug efficacy and safety. Despite its importance, a gap exists in the global genomic databases, which are predominantly representative of European ancestries, thereby limiting comprehensive knowledge of CYP2D6 variation in ethnically diverse populations. In an effort to bridge this knowledge gap, we focused on elucidating the CYP2D6 variation landscape within a multi-ethnic Asian cohort, encompassing individuals of Chinese, Malay, and Indian descent. Our study comprised data analysis of 1850 whole genomes from the SG10K_Health dataset using an in-house consensus algorithm, which integrates the capabilities of Cyrius, Aldy, and StellarPGx. This analysis unveiled distinct population-specific star-allele distribution trends, highlighting the unique genetic makeup of the Singaporean population. Significantly, 46% of our cohort harbored actionable CYP2D6 variants-those with direct implications for drug dosing and treatment strategies. Furthermore, we identified 14 potential novel CYP2D6 star-alleles, of which 7 were observed in multiple individuals, suggesting their broader relevance. Overall, our study contributes novel data on CYP2D6 genetic variations specific to the Southeast Asian context. The findings are instrumental for the advancement of pharmacogenomics and personalized medicine, not only in Southeast Asia but also in other regions with comparable genetic diversity.
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Affiliation(s)
| | - Rodrigo Toro Jimenez
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, Singapore
| | - David Twesigomwe
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Division of Human Genetics, Faculty of Health Sciences, National Health Laboratory Service, and School of Pathology, University of the Witwatersrand, Johannesburg, South Africa
| | | | | | - Nicolas Bertin
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, Singapore.
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2
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Hossam Abdelmonem B, Abdelaal NM, Anwer EKE, Rashwan AA, Hussein MA, Ahmed YF, Khashana R, Hanna MM, Abdelnaser A. Decoding the Role of CYP450 Enzymes in Metabolism and Disease: A Comprehensive Review. Biomedicines 2024; 12:1467. [PMID: 39062040 PMCID: PMC11275228 DOI: 10.3390/biomedicines12071467] [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: 04/16/2024] [Revised: 06/13/2024] [Accepted: 06/14/2024] [Indexed: 07/28/2024] Open
Abstract
Cytochrome P450 (CYP450) is a group of enzymes that play an essential role in Phase I metabolism, with 57 functional genes classified into 18 families in the human genome, of which the CYP1, CYP2, and CYP3 families are prominent. Beyond drug metabolism, CYP enzymes metabolize endogenous compounds such as lipids, proteins, and hormones to maintain physiological homeostasis. Thus, dysregulation of CYP450 enzymes can lead to different endocrine disorders. Moreover, CYP450 enzymes significantly contribute to fatty acid metabolism, cholesterol synthesis, and bile acid biosynthesis, impacting cellular physiology and disease pathogenesis. Their diverse functions emphasize their therapeutic potential in managing hypercholesterolemia and neurodegenerative diseases. Additionally, CYP450 enzymes are implicated in the onset and development of illnesses such as cancer, influencing chemotherapy outcomes. Assessment of CYP450 enzyme expression and activity aids in evaluating liver health state and differentiating between liver diseases, guiding therapeutic decisions, and optimizing drug efficacy. Understanding the roles of CYP450 enzymes and the clinical effect of their genetic polymorphisms is crucial for developing personalized therapeutic strategies and enhancing drug responses in diverse patient populations.
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Affiliation(s)
- Basma Hossam Abdelmonem
- Institute of Global Health and Human Ecology, School of Sciences and Engineering, The American University in Cairo, New Cairo 11835, Egypt; (B.H.A.); (M.A.H.); (Y.F.A.); (R.K.); (M.M.H.)
- Department of Microbiology and Immunology, Faculty of Pharmacy, October University for Modern Sciences & Arts (MSA), Giza 12451, Egypt
| | - Noha M. Abdelaal
- Biotechnology Graduate Program, School of Sciences and Engineering, The American University in Cairo, New Cairo 11835, Egypt; (N.M.A.); (E.K.E.A.); (A.A.R.)
| | - Eman K. E. Anwer
- Biotechnology Graduate Program, School of Sciences and Engineering, The American University in Cairo, New Cairo 11835, Egypt; (N.M.A.); (E.K.E.A.); (A.A.R.)
- Department of Microbiology and Immunology, Faculty of Pharmacy, Modern University for Technology and Information, Cairo 4411601, Egypt
| | - Alaa A. Rashwan
- Biotechnology Graduate Program, School of Sciences and Engineering, The American University in Cairo, New Cairo 11835, Egypt; (N.M.A.); (E.K.E.A.); (A.A.R.)
| | - Mohamed Ali Hussein
- Institute of Global Health and Human Ecology, School of Sciences and Engineering, The American University in Cairo, New Cairo 11835, Egypt; (B.H.A.); (M.A.H.); (Y.F.A.); (R.K.); (M.M.H.)
| | - Yasmin F. Ahmed
- Institute of Global Health and Human Ecology, School of Sciences and Engineering, The American University in Cairo, New Cairo 11835, Egypt; (B.H.A.); (M.A.H.); (Y.F.A.); (R.K.); (M.M.H.)
| | - Rana Khashana
- Institute of Global Health and Human Ecology, School of Sciences and Engineering, The American University in Cairo, New Cairo 11835, Egypt; (B.H.A.); (M.A.H.); (Y.F.A.); (R.K.); (M.M.H.)
| | - Mireille M. Hanna
- Institute of Global Health and Human Ecology, School of Sciences and Engineering, The American University in Cairo, New Cairo 11835, Egypt; (B.H.A.); (M.A.H.); (Y.F.A.); (R.K.); (M.M.H.)
| | - Anwar Abdelnaser
- Institute of Global Health and Human Ecology, School of Sciences and Engineering, The American University in Cairo, New Cairo 11835, Egypt; (B.H.A.); (M.A.H.); (Y.F.A.); (R.K.); (M.M.H.)
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3
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Carrera-Pacheco SE, Mueller A, Puente-Pineda JA, Zúñiga-Miranda J, Guamán LP. Designing cytochrome P450 enzymes for use in cancer gene therapy. Front Bioeng Biotechnol 2024; 12:1405466. [PMID: 38860140 PMCID: PMC11164052 DOI: 10.3389/fbioe.2024.1405466] [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: 03/22/2024] [Accepted: 04/30/2024] [Indexed: 06/12/2024] Open
Abstract
Cancer is a significant global socioeconomic burden, as millions of new cases and deaths occur annually. In 2020, almost 10 million cancer deaths were recorded worldwide. Advancements in cancer gene therapy have revolutionized the landscape of cancer treatment. An approach with promising potential for cancer gene therapy is introducing genes to cancer cells that encode for chemotherapy prodrug metabolizing enzymes, such as Cytochrome P450 (CYP) enzymes, which can contribute to the effective elimination of cancer cells. This can be achieved through gene-directed enzyme prodrug therapy (GDEPT). CYP enzymes can be genetically engineered to improve anticancer prodrug conversion to its active metabolites and to minimize chemotherapy side effects by reducing the prodrug dosage. Rational design, directed evolution, and phylogenetic methods are some approaches to developing tailored CYP enzymes for cancer therapy. Here, we provide a compilation of genetic modifications performed on CYP enzymes aiming to build highly efficient therapeutic genes capable of bio-activating different chemotherapeutic prodrugs. Additionally, this review summarizes promising preclinical and clinical trials highlighting engineered CYP enzymes' potential in GDEPT. Finally, the challenges, limitations, and future directions of using CYP enzymes for GDEPT in cancer gene therapy are discussed.
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Affiliation(s)
- Saskya E. Carrera-Pacheco
- Centro de Investigación Biomédica (CENBIO), Facultad de Ciencias de la Salud Eugenio Espejo, Universidad UTE, Quito, Ecuador
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Soh SPY, See Toh WY, Ten WQ, Leong KP, Goh LL. Validating two international warfarin pharmacogenetic dosing algorithms for estimating the maintenance dose for patients in Singapore. ANNALS OF THE ACADEMY OF MEDICINE, SINGAPORE 2024; 53:208-210. [PMID: 38920246 DOI: 10.47102/annals-acadmedsg.2023186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/27/2024]
Abstract
Predicting optimal warfarin dosing is difficult due to complex pharmacodynamics and pharmacokinetics, narrow therapeutic index and susceptibility to many factors.1 Genetic variations of the CYP2C9 and VKORC1 enzymes, occurring in different frequencies in different populations, play a significant role in determining warfarin dosing.1-4 Using pharmacogenetic dosing algorithms to predict warfarin doses may shorten the time to achieve target International Normalised Ratio (INR) and stable dose.2,5 The Clinical Pharmacogenetics Implementation Consortium Guidelines 2017 Update4 recommends the Gage (WarfarinDosing.org7) and International Warfarin Pharmacogenetics Consortium (IWPC)8 pharmacogenetic algorithms.
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Affiliation(s)
| | | | - Wei Qing Ten
- Department of Pharmacy, Tan Tock Seng Hospital, Singapore
| | - Khai Pang Leong
- Department of Rheumatology, Allergy and Immunology, Tan Tock Seng Hospital, Singapore
- Molecular Diagnostic Laboratory, Personalised Medicine Service, Tan Tock Seng Hospital, Singapore
| | - Liuh Ling Goh
- Molecular Diagnostic Laboratory, Personalised Medicine Service, Tan Tock Seng Hospital, Singapore
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Gan P, Hajis MIB, Yumna M, Haruman J, Matoha HK, Wahyudi DT, Silalahi S, Oktariani DR, Dela F, Annisa T, Pitaloka TDA, Adhiwijaya PK, Pauzi RY, Hertanto R, Kumaheri MA, Sani L, Irwanto A, Pradipta A, Chomchopbun K, Gonzalez-Porta M. Development and validation of a pharmacogenomics reporting workflow based on the illumina global screening array chip. Front Pharmacol 2024; 15:1349203. [PMID: 38529185 PMCID: PMC10961362 DOI: 10.3389/fphar.2024.1349203] [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: 12/04/2023] [Accepted: 02/05/2024] [Indexed: 03/27/2024] Open
Abstract
Background: Microarrays are a well-established and widely adopted technology capable of interrogating hundreds of thousands of loci across the human genome. Combined with imputation to cover common variants not included in the chip design, they offer a cost-effective solution for large-scale genetic studies. Beyond research applications, this technology can be applied for testing pharmacogenomics, nutrigenetics, and complex disease risk prediction. However, establishing clinical reporting workflows requires a thorough evaluation of the assay's performance, which is achieved through validation studies. In this study, we performed pre-clinical validation of a genetic testing workflow based on the Illumina Global Screening Array for 25 pharmacogenomic-related genes. Methods: To evaluate the accuracy of our workflow, we conducted multiple pre-clinical validation studies. Here, we present the results of accuracy and precision assessments, involving a total of 73 cell lines. These assessments encompass reference materials from the Genome-In-A-Bottle (GIAB), the Genetic Testing Reference Material Coordination Program (GeT-RM) projects, as well as additional samples from the 1000 Genomes project (1KGP). We conducted an accuracy assessment of genotype calls for target loci in each indication against established truth sets. Results: In our per-sample analysis, we observed a mean analytical sensitivity of 99.39% and specificity 99.98%. We further assessed the accuracy of star-allele calls by relying on established diplotypes in the GeT-RM catalogue or calls made based on 1KGP genotyping. On average, we detected a diplotype concordance rate of 96.47% across 14 pharmacogenomic-related genes with star allele-calls. Lastly, we evaluated the reproducibility of our findings across replicates and observed 99.48% diplotype and 100% phenotype inter-run concordance. Conclusion: Our comprehensive validation study demonstrates the robustness and reliability of the developed workflow, supporting its readiness for further development for applied testing.
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Affiliation(s)
- Pamela Gan
- Nalagenetics Pte Ltd., Singapore, Singapore
| | | | | | | | | | | | | | | | - Fitria Dela
- PT Genomik Solidaritas Indonesia, Jakarta, Indonesia
| | - Tazkia Annisa
- PT Genomik Solidaritas Indonesia, Jakarta, Indonesia
| | | | | | | | | | | | | | | | - Ariel Pradipta
- PT Genomik Solidaritas Indonesia, Jakarta, Indonesia
- Department Biochemistry and Molecular Biology, Faculty of Medicine, Universitas Indonesia, Jakarta, Indonesia
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6
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Narasimhalu K, Chan J, Ang YK, De Silva DA, Tan KB. Empiric treatment with aspirin and ticagrelor is the most cost-effective strategy in patients with minor stroke or transient ischemic attack. Int J Stroke 2024; 19:209-216. [PMID: 37679898 DOI: 10.1177/17474930231202374] [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] [Indexed: 09/09/2023]
Abstract
BACKGROUND Patients with minor ischemic stroke or transient ischemic attacks (TIAs) are often treated with dual antiplatelet therapy regimens as part of secondary stroke prevention. Clopidogrel, an antiplatelet used in these regimens, is metabolized into its active form by the CYP2C19 enzyme. Patients with loss of function (LOF) mutations in CYP2C19 are at risk for poorer secondary outcomes when prescribed clopidogrel. AIMS We aimed to determine the cost-effectiveness of three different treatment antiplatelet regimens in ischemic stroke populations with minor strokes or TIAs and how these treatment regimens are influenced by the LOF prevalence in the population. METHODS Markov models were developed to look at the cost-effectiveness of empiric treatment with aspirin and clopidogrel versus empiric treatment with aspirin and ticagrelor, versus genotype-guided therapy for either 21 or 30 days. Effect ratios were obtained from the literature, and incidence rates and costs were obtained from the national data published by the Singapore Ministry of Health. The primary endpoints were the incremental cost-effectiveness ratios (ICERs). RESULTS Empiric treatment with aspirin and ticagrelor was the most cost-effective treatment. Genotype-guided therapy was more cost-effective than empiric aspirin and clopidogrel if the LOF was above 48%. Empiric ticagrelor and aspirin was cost saving when compared to genotype-guided therapy. Results in models of dual antiplatelet therapy for 30 days were similar. CONCLUSION This study suggests that in patients with minor stroke and TIA planned for dual antiplatelet regimens, empiric ticagrelor and aspirin is the most cost-effective treatment regimen. If ticagrelor is not available, genotype-guided therapy is the most cost-effective treatment regimen if the LOF prevalence in the population is more than 48%.
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Affiliation(s)
- Kaavya Narasimhalu
- Department of Neurology (SGH Campus), National Neuroscience Institute, Singapore
| | - Jeremy Chan
- Department of Neurology (SGH Campus), National Neuroscience Institute, Singapore
| | - Yoong Kwei Ang
- Sydney Medical School, The University of Sydney, Sydney, NSW, Australia
- School of Public Health, National University of Singapore, Singapore
| | - Deidre Anne De Silva
- Department of Neurology (SGH Campus), National Neuroscience Institute, Singapore
| | - Kelvin Bryan Tan
- School of Public Health, National University of Singapore, Singapore
- Policy, Research and Evaluation Division, Ministry of Health, Singapore
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7
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Guo J, You W, Lin K, Li Q, Guo X, Wang S, Bian Y, Ren W, Zhang R, Wang Y, Li B. An extraction-free method for rapid detection of CYP2C19 * 2/3/17 polymorphisms in one tube using melting curve analysis. Biotechnol J 2023; 18:e2300207. [PMID: 37551831 DOI: 10.1002/biot.202300207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 07/11/2023] [Accepted: 08/02/2023] [Indexed: 08/09/2023]
Abstract
Drug-metabolizing enzymes play an important role in the metabolism of drugs in vivo. Their activity is an important factor affecting the rate of drug metabolism, which directly determines the intensity and persistence of drug action. Patients taking medication can be divided into different metabolic types through detection of CYP2C19 drug-metabolizing enzyme gene polymorphisms, which can then be used for medication guidance for clopidogrel. Here, we describe a detection method based on real-time polymerase chain reaction (PCR). This method uses multicolor melting curve analysis to accurately identify different mutation sites and genotypes of CYP2C19 * 2, CYP2C19 * 3, and CYP2C19 * 17. The detection limit of plasmid samples was 1 copies μL-1 ; that of genomic samples was 0.1 ng μL-1 . The system can detect nine types of CYP2C19 * 2/3/17 at three sites in one tube, quickly achieving detection within 1 h. Combined with the sample release agent, sample extraction was completed in 5 s, achieving rapid diagnosis without extraction for timely diagnosis and treatment. Furthermore, the system is not limited to blood samples and can also be applied to oropharyngeal and saliva samples, increasing sampling diversity and convenience. When using clinical blood samples (n = 93), the detection system we established was able to quickly and accurately identify different genotypes, and the accuracy and effectiveness of the detection were confirmed by Sanger sequencing. Due to its accuracy, rapidity, simple operation, and low cost, detection technology based on real-time polymerase amplification combined with melting curve analysis is expected to become a powerful tool for detecting and guiding clopidogrel use in countries with limited resources.
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Affiliation(s)
- Jianguang Guo
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling, Network and Engineering Research Center of Molecular Diagnostics of the Ministry, of Education, School of Life Sciences, Xiamen University, Xiamen, Fujian, China
| | - Weixin You
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling, Network and Engineering Research Center of Molecular Diagnostics of the Ministry, of Education, School of Life Sciences, Xiamen University, Xiamen, Fujian, China
| | - Kangfeng Lin
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling, Network and Engineering Research Center of Molecular Diagnostics of the Ministry, of Education, School of Life Sciences, Xiamen University, Xiamen, Fujian, China
| | - Qinghan Li
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling, Network and Engineering Research Center of Molecular Diagnostics of the Ministry, of Education, School of Life Sciences, Xiamen University, Xiamen, Fujian, China
| | - Xiangju Guo
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling, Network and Engineering Research Center of Molecular Diagnostics of the Ministry, of Education, School of Life Sciences, Xiamen University, Xiamen, Fujian, China
| | - Shuai Wang
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling, Network and Engineering Research Center of Molecular Diagnostics of the Ministry, of Education, School of Life Sciences, Xiamen University, Xiamen, Fujian, China
| | - Ya Bian
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling, Network and Engineering Research Center of Molecular Diagnostics of the Ministry, of Education, School of Life Sciences, Xiamen University, Xiamen, Fujian, China
| | - Wenjing Ren
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling, Network and Engineering Research Center of Molecular Diagnostics of the Ministry, of Education, School of Life Sciences, Xiamen University, Xiamen, Fujian, China
| | - Rui Zhang
- Xiamen Cell Therapy Research Center, The First Affiliated Hospital of Xiamen, University, School of Medicine, Xiamen University, Xiamen, China
| | - Yanping Wang
- Emergency Department, HuBei ProvinciaI HospitaI Of TCM, Wuhan, China
| | - Boan Li
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling, Network and Engineering Research Center of Molecular Diagnostics of the Ministry, of Education, School of Life Sciences, Xiamen University, Xiamen, Fujian, China
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8
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Oni-Orisan A, Tuteja S, Hoffecker G, Smith DM, Castrichini M, Crews KR, Murphy WA, Nguyen NHK, Huang Y, Lteif C, Friede KA, Tantisira K, Aminkeng F, Voora D, Cavallari LH, Whirl-Carrillo M, Duarte JD, Luzum JA. An Introductory Tutorial on Cardiovascular Pharmacogenetics for Healthcare Providers. Clin Pharmacol Ther 2023; 114:275-287. [PMID: 37303270 PMCID: PMC10406163 DOI: 10.1002/cpt.2957] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 05/17/2023] [Indexed: 06/13/2023]
Abstract
Pharmacogenetics can improve clinical outcomes by reducing adverse drug effects and enhancing therapeutic efficacy for commonly used drugs that treat a wide range of cardiovascular diseases. One of the major barriers to the clinical implementation of cardiovascular pharmacogenetics is limited education on this field for current healthcare providers and students. The abundance of pharmacogenetic literature underscores its promise, but it can also be challenging to learn such a wealth of information. Moreover, current clinical recommendations for cardiovascular pharmacogenetics can be confusing because they are outdated, incomplete, or inconsistent. A myriad of misconceptions about the promise and feasibility of cardiovascular pharmacogenetics among healthcare providers also has halted clinical implementation. Therefore, the main goal of this tutorial is to provide introductory education on the use of cardiovascular pharmacogenetics in clinical practice. The target audience is any healthcare provider (or student) with patients that use or have indications for cardiovascular drugs. This tutorial is organized into the following 6 steps: (1) understand basic concepts in pharmacogenetics; (2) gain foundational knowledge of cardiovascular pharmacogenetics; (3) learn the different organizations that release cardiovascular pharmacogenetic guidelines and recommendations; (4) know the current cardiovascular drugs/drug classes to focus on clinically and the supporting evidence; (5) discuss an example patient case of cardiovascular pharmacogenetics; and (6) develop an appreciation for emerging areas in cardiovascular pharmacogenetics. Ultimately, improved education among healthcare providers on cardiovascular pharmacogenetics will lead to a greater understanding for its potential in improving outcomes for a leading cause of morbidity and mortality.
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Affiliation(s)
- Akinyemi Oni-Orisan
- Department of Clinical Pharmacy, University of California San Francisco, San Francisco, California, USA
| | - Sony Tuteja
- Division of Translational Medicine and Human Genetics, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Glenda Hoffecker
- Division of Translational Medicine and Human Genetics, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - D. Max Smith
- MedStar Health, Columbia, Maryland, USA
- Department of Oncology, Georgetown University Medical Center, Washington, DC, USA
| | - Matteo Castrichini
- Department of Cardiovascular Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Kristine R. Crews
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | - William A. Murphy
- Division of Pharmacotherapy and Experimental Therapeutics, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Nam H. K. Nguyen
- Department of Pharmacotherapy and Translational Research and Center for Pharmacogenomics and Precision Medicine, University of Florida, Gainesville, Florida, USA
| | - Yimei Huang
- Department of Pharmacotherapy and Translational Research and Center for Pharmacogenomics and Precision Medicine, University of Florida, Gainesville, Florida, USA
| | - Christelle Lteif
- Department of Pharmacotherapy and Translational Research and Center for Pharmacogenomics and Precision Medicine, University of Florida, Gainesville, Florida, USA
| | - Kevin A. Friede
- Division of Cardiology, University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA
| | - Kelan Tantisira
- Division of Respiratory Medicine, Department of Pediatrics, University of California San Diego, San Diego, California, USA
| | - Folefac Aminkeng
- Departments of Medicine and Biomedical Informatics (DBMI), Yong Loo Lin School of Medicine, National University of Singapore, Singapore City, Singapore
- Centre for Precision Health (CPH), National University Health System (NUHS), Singapore City, Singapore
| | - Deepak Voora
- Precision Medicine Program, Department of Medicine, Duke University School of Medicine, Durham, North Carolina, USA
| | - Larisa H. Cavallari
- Department of Pharmacotherapy and Translational Research and Center for Pharmacogenomics and Precision Medicine, University of Florida, Gainesville, Florida, USA
| | | | - Julio D. Duarte
- Department of Pharmacotherapy and Translational Research and Center for Pharmacogenomics and Precision Medicine, University of Florida, Gainesville, Florida, USA
| | - Jasmine A. Luzum
- Department of Clinical Pharmacy, University of Michigan College of Pharmacy, Ann Arbor, Michigan, USA
- Center for Individualized and Genomic Medicine Research, Henry Ford Health System, Detroit, Michigan, USA
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Cronin JM, Yu AM. Recombinant Technologies Facilitate Drug Metabolism, Pharmacokinetics, and General Biomedical Research. Drug Metab Dispos 2023; 51:685-699. [PMID: 36948592 PMCID: PMC10197202 DOI: 10.1124/dmd.122.001008] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 03/08/2023] [Accepted: 03/09/2023] [Indexed: 03/24/2023] Open
Abstract
The development of safe and effective medications requires a profound understanding of their pharmacokinetic (PK) and pharmacodynamic properties. PK studies have been built through investigation of enzymes and transporters that drive drug absorption, distribution, metabolism, and excretion (ADME). Like many other disciplines, the study of ADME gene products and their functions has been revolutionized through the invention and widespread adoption of recombinant DNA technologies. Recombinant DNA technologies use expression vectors such as plasmids to achieve heterologous expression of a desired transgene in a specified host organism. This has enabled the purification of recombinant ADME gene products for functional and structural characterization, allowing investigators to elucidate their roles in drug metabolism and disposition. This strategy has also been used to offer recombinant or bioengineered RNA (BioRNA) agents to investigate the posttranscriptional regulation of ADME genes. Conventional research with small noncoding RNAs such as microRNAs (miRNAs) and small interfering RNAs has been dependent on synthetic RNA analogs that are known to carry a range of chemical modifications expected to improve stability and PK properties. Indeed, a novel transfer RNA fused pre-miRNA carrier-based bioengineering platform technology has been established to offer consistent and high-yield production of unparalleled BioRNA molecules from Escherichia coli fermentation. These BioRNAs are produced and processed inside living cells to better recapitulate the properties of natural RNAs, representing superior research tools to investigate regulatory mechanisms behind ADME. SIGNIFICANCE STATEMENT: This review article summarizes recombinant DNA technologies that have been an incredible boon in the study of drug metabolism and PK, providing investigators with powerful tools to express nearly any ADME gene products for functional and structural studies. It further overviews novel recombinant RNA technologies and discusses the utilities of bioengineered RNA agents for the investigation of ADME gene regulation and general biomedical research.
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Affiliation(s)
- Joseph M Cronin
- Department of Biochemistry and Molecular Medicine, UC Davis School of Medicine, Sacramento, CA (J.M.C., A.-M.Y.)
| | - Ai-Ming Yu
- Department of Biochemistry and Molecular Medicine, UC Davis School of Medicine, Sacramento, CA (J.M.C., A.-M.Y.)
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10
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Chamboko CR, Veldman W, Tata RB, Schoeberl B, Tastan Bishop Ö. Human Cytochrome P450 1, 2, 3 Families as Pharmacogenes with Emphases on Their Antimalarial and Antituberculosis Drugs and Prevalent African Alleles. Int J Mol Sci 2023; 24:ijms24043383. [PMID: 36834793 PMCID: PMC9961538 DOI: 10.3390/ijms24043383] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 01/30/2023] [Accepted: 02/06/2023] [Indexed: 02/10/2023] Open
Abstract
Precision medicine gives individuals tailored medical treatment, with the genotype determining the therapeutic strategy, the appropriate dosage, and the likelihood of benefit or toxicity. Cytochrome P450 (CYP) enzyme families 1, 2, and 3 play a pivotal role in eliminating most drugs. Factors that affect CYP function and expression have a major impact on treatment outcomes. Therefore, polymorphisms of these enzymes result in alleles with diverse enzymatic activity and drug metabolism phenotypes. Africa has the highest CYP genetic diversity and also the highest burden of malaria and tuberculosis, and this review presents current general information on CYP enzymes together with variation data concerning antimalarial and antituberculosis drugs, while focusing on the first three CYP families. Afrocentric alleles such as CYP2A6*17, CYP2A6*23, CYP2A6*25, CYP2A6*28, CYP2B6*6, CYP2B6*18, CYP2C8*2, CYP2C9*5, CYP2C9*8, CYP2C9*9, CYP2C19*9, CYP2C19*13, CYP2C19*15, CYP2D6*2, CYP2D6*17, CYP2D6*29, and CYP3A4*15 are implicated in diverse metabolic phenotypes of different antimalarials such as artesunate, mefloquine, quinine, primaquine, and chloroquine. Moreover, CYP3A4, CYP1A1, CYP2C8, CYP2C18, CYP2C19, CYP2J2, and CYP1B1 are implicated in the metabolism of some second-line antituberculosis drugs such as bedaquiline and linezolid. Drug-drug interactions, induction/inhibition, and enzyme polymorphisms that influence the metabolism of antituberculosis, antimalarial, and other drugs, are explored. Moreover, a mapping of Afrocentric missense mutations to CYP structures and a documentation of their known effects provided structural insights, as understanding the mechanism of action of these enzymes and how the different alleles influence enzyme function is invaluable to the advancement of precision medicine.
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Affiliation(s)
- Chiratidzo R Chamboko
- Research Unit in Bioinformatics (RUBi), Department of Biochemistry and Microbiology, Rhodes University, Makhanda 6139, South Africa
| | - Wayde Veldman
- Research Unit in Bioinformatics (RUBi), Department of Biochemistry and Microbiology, Rhodes University, Makhanda 6139, South Africa
| | - Rolland Bantar Tata
- Research Unit in Bioinformatics (RUBi), Department of Biochemistry and Microbiology, Rhodes University, Makhanda 6139, South Africa
| | - Birgit Schoeberl
- Translational Medicine, Novartis Institutes for BioMedical Research, 220 Massachusetts Ave, Cambridge, MA 02139, USA
| | - Özlem Tastan Bishop
- Research Unit in Bioinformatics (RUBi), Department of Biochemistry and Microbiology, Rhodes University, Makhanda 6139, South Africa
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11
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Rodieux F, Daali Y, Rollason V, Samer CF, Ing Lorenzini K. Practice of CYP450 genotyping and phenotyping in children in a real-life setting. Front Pharmacol 2023; 14:1130100. [PMID: 36937881 PMCID: PMC10022732 DOI: 10.3389/fphar.2023.1130100] [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: 12/22/2022] [Accepted: 02/14/2023] [Indexed: 03/02/2023] Open
Abstract
Pharmacokinetics varies widely between children. Many factors play an important role in this variability, such as ontogeny, pharmacogenetics, gender, comorbidities, and drug-drug interactions. Significant work has already been done in adults to understand the impact of genetic polymorphisms on drug-metabolizing enzyme activity and drug response. Data remain poor in children due to ontogeny that impacts genotyping-phenotyping correlation and the difficulty enrolling children in prospective studies. Our study aimed to describe the use of cytochromes P450 (CYP) phenotyping and/or genotyping tests in children in a real-life setting and assess the correlation between the genotype and the phenotype. We reviewed the results of tests performed between January 2005 and December 2020. Fifty-two children were genotyped and/or phenotyped. Four patients were excluded from the present analysis as they only underwent ABCB1 genotyping, without CYP testing. Of the remainder, 18 underwent simultaneous CYP genotyping and phenotyping, while 17 underwent CYP genotyping only, and 13 underwent CYP phenotyping only. In all cases, investigations were performed after the following situations: insufficient clinical response to treatment, low plasma concentrations, and adverse drug reactions (ADR). The vast majority of cases were related to immunosuppressive or antipsychotic therapy. Genotyping and/or phenotyping explained or contributed to the aforementioned clinical events in 56% of cases. The correlation between the genotype and the phenotype showed variability depending on the assessed cytochrome. In several cases, the phenotype did not correspond to the genotype because of comedications. In conclusion, there is clearly value in guiding drug based on CYP activity in children.
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Affiliation(s)
- Frédérique Rodieux
- Division of Clinical Pharmacology and Toxicology, Department of Anesthesiology, Pharmacology, Emergency Medicine and Intensive care, Geneva University Hospitals, Geneva, Switzerland
- *Correspondence: Frédérique Rodieux,
| | - Youssef Daali
- Division of Clinical Pharmacology and Toxicology, Department of Anesthesiology, Pharmacology, Emergency Medicine and Intensive care, Geneva University Hospitals, Geneva, Switzerland
- School of Pharmaceutical Sciences, University of Geneva, Geneva, Switzerland
- Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Victoria Rollason
- Division of Clinical Pharmacology and Toxicology, Department of Anesthesiology, Pharmacology, Emergency Medicine and Intensive care, Geneva University Hospitals, Geneva, Switzerland
- Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Caroline F. Samer
- Division of Clinical Pharmacology and Toxicology, Department of Anesthesiology, Pharmacology, Emergency Medicine and Intensive care, Geneva University Hospitals, Geneva, Switzerland
- School of Pharmaceutical Sciences, University of Geneva, Geneva, Switzerland
- Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Kuntheavy Ing Lorenzini
- Division of Clinical Pharmacology and Toxicology, Department of Anesthesiology, Pharmacology, Emergency Medicine and Intensive care, Geneva University Hospitals, Geneva, Switzerland
- Faculty of Medicine, University of Geneva, Geneva, Switzerland
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12
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Chan SH, Bylstra Y, Teo JX, Kuan JL, Bertin N, Gonzalez-Porta M, Hebrard M, Tirado-Magallanes R, Tan JHJ, Jeyakani J, Li Z, Chai JF, Chong YS, Davila S, Goh LL, Lee ES, Wong E, Wong TY, Prabhakar S, Liu J, Cheng CY, Eisenhaber B, Karnani N, Leong KP, Sim X, Yeo KK, Chambers JC, Tai ES, Tan P, Jamuar SS, Ngeow J, Lim WK, Gluckman PD, Goh DLM, Jain K, Kam S, Kassam I, Lakshmanan LN, Lee CG, Lee J, Lee SC, Lee YS, Li H, Lim CW, Lim TH, Loh M, Maurer-Stroh S, Mina TH, Mok SQ, Ng HK, Pua CJ, Riboli E, Rim TH, Sabanayagam C, Sim WC, Subramaniam T, Tan ES, Tan EK, Tantoso E, Tay D, Teo YY, Tham YC, Toh LXG, Tsai PK, van Dam RM, Veeravalli L, Khin-lin GW, Wilm A, Yang C, Yap F, Yew YW, Prabhakar S, Liu J, Cheng CY, Eisenhaber B, Karnani N, Leong KP, Sim X, Yeo KK, Chambers JC, Tai ES, Tan P, Jamuar SS, Ngeow J, Lim WK. Analysis of clinically relevant variants from ancestrally diverse Asian genomes. Nat Commun 2022; 13:6694. [PMID: 36335097 PMCID: PMC9637116 DOI: 10.1038/s41467-022-34116-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 10/12/2022] [Indexed: 11/06/2022] Open
Abstract
Asian populations are under-represented in human genomics research. Here, we characterize clinically significant genetic variation in 9051 genomes representing East Asian, South Asian, and severely under-represented Austronesian-speaking Southeast Asian ancestries. We observe disparate genetic risk burden attributable to ancestry-specific recurrent variants and identify individuals with variants specific to ancestries discordant to their self-reported ethnicity, mostly due to cryptic admixture. About 27% of severe recessive disorder genes with appreciable carrier frequencies in Asians are missed by carrier screening panels, and we estimate 0.5% Asian couples at-risk of having an affected child. Prevalence of medically-actionable variant carriers is 3.4% and a further 1.6% harbour variants with potential for pathogenic classification upon additional clinical/experimental evidence. We profile 23 pharmacogenes with high-confidence gene-drug associations and find 22.4% of Asians at-risk of Centers for Disease Control and Prevention Tier 1 genetic conditions concurrently harbour pharmacogenetic variants with actionable phenotypes, highlighting the benefits of pre-emptive pharmacogenomics. Our findings illuminate the diversity in genetic disease epidemiology and opportunities for precision medicine for a large, diverse Asian population.
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Affiliation(s)
- Sock Hoai Chan
- grid.410724.40000 0004 0620 9745Cancer Genetics Service, Division of Medical Oncology, National Cancer Centre Singapore, Singapore, 169610 Singapore ,grid.428397.30000 0004 0385 0924Oncology Academic Clinical Program, Duke-NUS Medical School, Singapore, 169857 Singapore ,grid.59025.3b0000 0001 2224 0361Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, 308232 Singapore
| | - Yasmin Bylstra
- grid.4280.e0000 0001 2180 6431SingHealth Duke-NUS Institute of Precision Medicine, Singapore, 169609 Singapore
| | - Jing Xian Teo
- grid.4280.e0000 0001 2180 6431SingHealth Duke-NUS Institute of Precision Medicine, Singapore, 169609 Singapore
| | - Jyn Ling Kuan
- grid.4280.e0000 0001 2180 6431SingHealth Duke-NUS Institute of Precision Medicine, Singapore, 169609 Singapore
| | - Nicolas Bertin
- grid.418377.e0000 0004 0620 715XGenome Research Informatics & Data Science Platform, Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, 138672 Singapore
| | - Mar Gonzalez-Porta
- grid.418377.e0000 0004 0620 715XGenome Research Informatics & Data Science Platform, Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, 138672 Singapore
| | - Maxime Hebrard
- grid.418377.e0000 0004 0620 715XGenome Research Informatics & Data Science Platform, Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, 138672 Singapore
| | - Roberto Tirado-Magallanes
- grid.418377.e0000 0004 0620 715XGenome Research Informatics & Data Science Platform, Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, 138672 Singapore
| | - Joanna Hui Juan Tan
- grid.418377.e0000 0004 0620 715XGenome Research Informatics & Data Science Platform, Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, 138672 Singapore
| | - Justin Jeyakani
- grid.418377.e0000 0004 0620 715XGenome Research Informatics & Data Science Platform, Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, 138672 Singapore
| | - Zhihui Li
- grid.418377.e0000 0004 0620 715XGenome Research Informatics & Data Science Platform, Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, 138672 Singapore
| | - Jin Fang Chai
- grid.4280.e0000 0001 2180 6431Saw Swee Hock School of Public Health, National University of Singapore, Singapore, 117549 Singapore
| | - Yap Seng Chong
- grid.4280.e0000 0001 2180 6431Department of Obstetrics & Gynaecology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 119228 Singapore ,grid.452264.30000 0004 0530 269XSingapore Institute for Clinical Sciences, Singapore, 117609 Singapore
| | - Sonia Davila
- grid.4280.e0000 0001 2180 6431SingHealth Duke-NUS Institute of Precision Medicine, Singapore, 169609 Singapore ,grid.428397.30000 0004 0385 0924Cardiovascular and Metabolic Disorders Program, Duke-NUS Medical School, Singapore, 169857 Singapore ,grid.4280.e0000 0001 2180 6431SingHealth Duke-NUS Genomic Medicine Centre, Singapore, 168582 Singapore
| | - Liuh Ling Goh
- grid.240988.f0000 0001 0298 8161Personalized Medicine Service, Tan Tock Seng Hospital, Singapore, 308433 Singapore
| | - Eng Sing Lee
- grid.59025.3b0000 0001 2224 0361Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, 308232 Singapore ,grid.466910.c0000 0004 0451 6215National Healthcare Group Polyclinics, Singapore, 138543 Singapore
| | - Eleanor Wong
- grid.418377.e0000 0004 0620 715XGenome Institute of Singapore, Agency for Science, Technology and Research, Singapore, 138672 Singapore
| | - Tien Yin Wong
- grid.419272.b0000 0000 9960 1711Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, 168751 Singapore
| | | | - Shyam Prabhakar
- grid.418377.e0000 0004 0620 715XLaboratory of Systems Biology and Data Analytics, Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, 138672 Singapore
| | - Jianjun Liu
- grid.418377.e0000 0004 0620 715XHuman Genomics, Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, 138672 Singapore ,grid.4280.e0000 0001 2180 6431Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 119228 Singapore
| | - Ching-Yu Cheng
- grid.419272.b0000 0000 9960 1711Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, 168751 Singapore ,grid.428397.30000 0004 0385 0924Ophthalmology & Visual Sciences Academic Clinical Program (Eye ACP), Duke-NUS Medical School, Singapore, 169857 Singapore
| | - Birgit Eisenhaber
- grid.418377.e0000 0004 0620 715XGenome Institute of Singapore, Agency for Science, Technology and Research, Singapore, 138672 Singapore ,grid.418325.90000 0000 9351 8132Bioinformatics Institute, Agency for Science, Technology and Research, Singapore, 138671 Singapore
| | - Neerja Karnani
- grid.452264.30000 0004 0530 269XHuman Development, Singapore Institute for Clinical Sciences, Singapore, 117609 Singapore ,grid.418325.90000 0000 9351 8132Clinical Data Engagement, Bioinformatics Institute, Agency for Science, Technology and Research, Singapore, 138671 Singapore ,grid.4280.e0000 0001 2180 6431Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117596 Singapore
| | - Khai Pang Leong
- grid.240988.f0000 0001 0298 8161Personalized Medicine Service, Tan Tock Seng Hospital, Singapore, 308433 Singapore ,grid.240988.f0000 0001 0298 8161Department of Rheumatology, Allergy and Immunology, Tan Tock Seng Hospital, Singapore, 308433 Singapore
| | - Xueling Sim
- grid.4280.e0000 0001 2180 6431Saw Swee Hock School of Public Health, National University of Singapore, Singapore, 117549 Singapore
| | - Khung Keong Yeo
- grid.4280.e0000 0001 2180 6431SingHealth Duke-NUS Institute of Precision Medicine, Singapore, 169609 Singapore ,grid.419385.20000 0004 0620 9905Department of Cardiology, National Heart Centre Singapore, Singapore, 169609 Singapore ,grid.428397.30000 0004 0385 0924Duke-NUS Medical School, Singapore, 169857 Singapore
| | - John C. Chambers
- grid.59025.3b0000 0001 2224 0361Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, 308232 Singapore ,Precision Health Research Singapore (PRECISE), Singapore, 139234 Singapore ,grid.7445.20000 0001 2113 8111Department of Epidemiology and Biostatistics, Imperial College London, London, W2 1PG UK
| | - E-Shyong Tai
- grid.4280.e0000 0001 2180 6431Saw Swee Hock School of Public Health, National University of Singapore, Singapore, 117549 Singapore ,grid.4280.e0000 0001 2180 6431Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 119228 Singapore ,grid.428397.30000 0004 0385 0924Duke-NUS Medical School, Singapore, 169857 Singapore ,Precision Health Research Singapore (PRECISE), Singapore, 139234 Singapore
| | - Patrick Tan
- grid.4280.e0000 0001 2180 6431SingHealth Duke-NUS Institute of Precision Medicine, Singapore, 169609 Singapore ,grid.418377.e0000 0004 0620 715XGenome Institute of Singapore, Agency for Science, Technology and Research, Singapore, 138672 Singapore ,Precision Health Research Singapore (PRECISE), Singapore, 139234 Singapore ,grid.428397.30000 0004 0385 0924Cancer & Stem Cell Biology Program, Duke-NUS Medical School, Singapore, 169857 Singapore ,grid.4280.e0000 0001 2180 6431Cancer Science Institute of Singapore, National University of Singapore, Singapore, 117599 Singapore
| | - Saumya S. Jamuar
- grid.4280.e0000 0001 2180 6431SingHealth Duke-NUS Institute of Precision Medicine, Singapore, 169609 Singapore ,grid.4280.e0000 0001 2180 6431SingHealth Duke-NUS Genomic Medicine Centre, Singapore, 168582 Singapore ,grid.414963.d0000 0000 8958 3388Genetics Service, Department of Paediatrics, KK Women’s and Children’s Hospital, Singapore, 229899 Singapore ,grid.428397.30000 0004 0385 0924Paediatric Academic Clinical Program, Duke-NUS Medical School, Singapore, 169857 Singapore
| | - Joanne Ngeow
- grid.410724.40000 0004 0620 9745Cancer Genetics Service, Division of Medical Oncology, National Cancer Centre Singapore, Singapore, 169610 Singapore ,grid.428397.30000 0004 0385 0924Oncology Academic Clinical Program, Duke-NUS Medical School, Singapore, 169857 Singapore ,grid.59025.3b0000 0001 2224 0361Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, 308232 Singapore ,grid.185448.40000 0004 0637 0221Institute of Molecular and Cellular Biology, Agency for Science, Technology and Research, Singapore, 138673 Singapore
| | - Weng Khong Lim
- grid.4280.e0000 0001 2180 6431SingHealth Duke-NUS Institute of Precision Medicine, Singapore, 169609 Singapore ,grid.4280.e0000 0001 2180 6431SingHealth Duke-NUS Genomic Medicine Centre, Singapore, 168582 Singapore ,grid.428397.30000 0004 0385 0924Cancer & Stem Cell Biology Program, Duke-NUS Medical School, Singapore, 169857 Singapore
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13
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Igumnova V, Kivrane A, Viksna A, Norvaisa I, Ranka R. Next-Generation Sequencing and Bioinformatics-Based Protocol for the Full-Length CYP2E1 Gene Polymorphism Analysis. Pharmgenomics Pers Med 2022; 15:959-965. [DOI: 10.2147/pgpm.s371709] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Accepted: 10/07/2022] [Indexed: 11/09/2022] Open
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14
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Goh LL, Lim CW, Leong KP, Ong KH. TPMT and NUDT15 testing for thiopurine therapy: A major tertiary hospital experience and lessons learned. Front Pharmacol 2022; 13:837164. [PMID: 36210828 PMCID: PMC9537458 DOI: 10.3389/fphar.2022.837164] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Accepted: 08/23/2022] [Indexed: 11/13/2022] Open
Abstract
Variants in thiopurine methyltransferase (TPMT) and nudix hydrolase 15 (NUDT15) are associated with an accumulation of cytotoxic metabolites leading to increased risk of drug-related toxicity with standard doses of thiopurine drugs. We established TPMT and NUDT15 genetic testing for clinical use and evaluated the utilization, service outcomes and potential value of multi-gene PGx testing for 210 patients that underwent pharmacogenetics (PGx) testing for thiopurine therapy with the aim to optimize service delivery for future prescribing. The test was most commonly ordered for Gastroenterology (40.0%) and Neurology (31.4%), with an average turnaround time of 2 days. Following testing, 24.3% patients were identified as intermediate or poor metabolizers, resulting in 51 recommendations for a drug or dose change in thiopurine therapy, which were implemented in 28 (54.9%) patients. In the remaining patients, 14 were not adjusted and 9 had no data available. Focusing on drug gene interactions available for testing in our laboratory, multi-gene PGx results would present opportunities for treatment optimization for at least 33.8% of these patients who were on 2 or more concurrent medications with actionable PGx guidance. However, the use of PGx panel testing in clinical practice will require the development of guidelines and education as revealed by a survey with the test providers. The evaluation demonstrated successful implementation of single gene PGx testing and this experience guides the transition to a pre-emptive multi-gene testing approach that provides the opportunity to improve clinical care.
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Affiliation(s)
- Liuh Ling Goh
- Molecular Diagnostic Laboratory, Personalized Medicine Service, Tan Tock Seng Hospital, Singapore, Singapore
- *Correspondence: Liuh Ling Goh,
| | - Chia Wei Lim
- Molecular Diagnostic Laboratory, Personalized Medicine Service, Tan Tock Seng Hospital, Singapore, Singapore
| | - Khai Pang Leong
- Molecular Diagnostic Laboratory, Personalized Medicine Service, Tan Tock Seng Hospital, Singapore, Singapore
- Department of Rheumatology, Allergy & Immunology, Tan Tock Seng Hospital, Singapore, Singapore
| | - Kiat Hoe Ong
- Molecular Diagnostic Laboratory, Personalized Medicine Service, Tan Tock Seng Hospital, Singapore, Singapore
- Department of Haematology, Tan Tock Seng Hospital, Singapore, Singapore
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15
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Narayanan V, Rodrigues AL, Dordick JS. Influence of Circadian Rhythm on Drug Metabolism in 3D Hepatic Spheroids. Biotechnol Bioeng 2022; 119:2842-2856. [PMID: 35822281 DOI: 10.1002/bit.28180] [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: 04/08/2022] [Revised: 06/29/2022] [Accepted: 07/04/2022] [Indexed: 11/10/2022]
Abstract
Circadian rhythms are characterized as oscillations that fluctuate based on a 24h cycle and are responsible for regulation of physiological functions. While the internal clock synchronizes gene expression using external cues like light, a similar synchronization can be induced in vitro by incubating the cells with an increased percentage of serum followed by its rapid removal. Previous studies have suggested that synchronization of HepG2 cell line induced the rhythmic expression of drug metabolizing enzymes (DME) most specifically the cytochrome P450 enzymes. However, there is a lack of evidence demonstrating the influence of 3D microenvironment on the rhythmicity of these genes. To understand this interplay, gene expression of the circadian machinery and CYP450s were compared using the model human hepatocarcinoma cell line, HepG2. Upon serum shock synchronization, gene and protein expression of core clock regulators was assessed and rhythmic expression of these genes was demonstrated. Further insight into the interrelations between various gene pairs was obtained using statistical analysis. Using RNA sequencing, an in-depth understanding of the widespread effects of circadian regulation on genes involved in metabolic processes in the liver was obtained. This study aids in the better understanding of chronopharmacokinetic events in humans using physiologically relevant 3D culture systems. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Vibha Narayanan
- Department of Chemical and Biological Engineering, and Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA
| | - Andre L Rodrigues
- Department of Chemical and Biological Engineering, and Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA.,Instituto Superior Técnico, University of Lisbon, Av. Rovisco Pais, 1049-001, Lisbon, Portugal
| | - Jonathan S Dordick
- Department of Chemical and Biological Engineering, and Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA.,Departments of Biological Sciences and Biomedical Engineering, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA
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16
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Mbavha BT, Kanji CR, Stadler N, Stingl J, Stanglmair A, Scholl C, Wekwete W, Masimirembwa C. Population genetic polymorphisms of pharmacogenes in Zimbabwe, a potential guide for the safe and efficacious use of medicines in people of African ancestry. Pharmacogenet Genomics 2022; 32:173-182. [PMID: 35190514 DOI: 10.1097/fpc.0000000000000467] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
OBJECTIVE Pharmacogenomics (PGx) is a clinically significant factor in the safe and efficacious use of medicines. While PGx knowledge is abundant for other populations, there are scarce PGx data on African populations and is little knowledge on drug-gene interactions for medicines used to treat diseases common in Africa. The aim of this study was to use a custom-designed open array to genotype clinically actionable variants in a Zimbabwean population. This study also identified some of the commonly used drugs in Zimbabwe and the associated genes involved in their metabolism. METHODS A custom-designed open array that covers 120 genetic variants was used to genotype 522 black Zimbabwean healthy volunteers using TaqMan-based single nucleotide polymorphism genotyping. Data were also accessed from Essential Drugs' List in Zimbabwe (EDLIZ), and the medicines were grouped into the associated biomarker groups based on their metabolism. We also estimated the national drug procurement levels for medicines that could benefit from PGx-guided use based on the data obtained from the national authorities in Zimbabwe. RESULTS The results demonstrate the applicability of an open-array chip in simultaneously determining multiple genetic variants in an individual, thus significantly reducing cost and time to generate PGx data. There were significantly high frequencies of African-specific variants, such as the CYP2D6*17 and *29 variants and the CYP2B6*18 variant. The data obtained showed that the Zimbabwean population exhibits PGx variations in genes important for the safe and efficacious use of drugs approved by the EDLIZ and are procured at significantly large amounts annually. The study has established a cohort of genotyped healthy volunteers that can be accessed and used in the conduct of clinical pharmacogenetic studies for drugs entering a market of people of predominantly African ancestry. CONCLUSION Our study demonstrated the potential benefit of integrating PGx in Zimbabwe for the safe and efficacious use of drugs that are commonly used.
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Affiliation(s)
- Bianza T Mbavha
- Department of Genomic Medicine, African Institute of Biomedical Science and Technology (AiBST), Harare, Zimbabwe
| | - Comfort R Kanji
- Department of Genomic Medicine, African Institute of Biomedical Science and Technology (AiBST), Harare, Zimbabwe
| | - Nadina Stadler
- Research Division, Federal Institute for Drugs and Medical Devices (BfArM), Bonn
| | - Julia Stingl
- Institute of Clinical Pharmacology, University Hospital RWTH Aachen, Aachen, Germany
| | - Andrea Stanglmair
- Research Division, Federal Institute for Drugs and Medical Devices (BfArM), Bonn
| | - Catharina Scholl
- Research Division, Federal Institute for Drugs and Medical Devices (BfArM), Bonn
| | - William Wekwete
- Evaluations and Registration Division, Medicines Control Authority of Zimbabwe (MCAZ), Harare, Zimbabwe
| | - Collen Masimirembwa
- Department of Genomic Medicine, African Institute of Biomedical Science and Technology (AiBST), Harare, Zimbabwe
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17
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Koo SH, Soon GH, Pruvost A, Benech H, Ang TL, Lee EJD, Ang DSW. Evaluation of a six-probe cocktail (caffeine, tolbutamide, omeprazole, dextromethorphan, midazolam, and digoxin) approach to estimate hepatic drug detoxification capability and dosage requirements after a single oral dosing in healthy Chinese volunteers. Naunyn Schmiedebergs Arch Pharmacol 2022; 395:815-826. [PMID: 35394133 DOI: 10.1007/s00210-022-02235-1] [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: 01/31/2022] [Accepted: 03/21/2022] [Indexed: 12/01/2022]
Abstract
The primary objectives of this study were to investigate the suitability of a 6-probe cocktail (caffeine, tolbutamide, omeprazole, dextromethorphan, midazolam, and digoxin) to be used as a tool for assessing the activity of drug metabolizing enzymes and transporters, and examine differences in the way drugs are handled among groups with different genetic regulation of these processes. This was a single-center, open-label, phase I clinical study involving 20 young, healthy Chinese volunteers (equal gender distribution). The subjects were administered a single, oral dose of the 6-probe cocktail and serum samples were collected to assess the disposition of the different probe substrates and produced metabolites. The serum samples were analyzed using ultra-performance liquid chromatography-electrospray ionization-tandem mass spectrometry technology. The DNA samples were subjected to whole exome sequencing. Nineteen healthy volunteers completed the study. The 6-probe cocktail was safe and well-tolerated by all the subjects. The parent substrates and metabolites-caffeine (paraxanthine), dextromethorphan (dextrorphan), digoxin, midazolam (1-hydroxy-midazolam), omeprazole (5-hydroxy-omeprazole), and tolbutamide (4-hydroxy-tolbutamide)-were within the detectable window. Genetic variations known to alter drug metabolism (CYP2D6*10, CYP2C19*2, CYP2C19*3, and CYP2C9*3) were identified and generally correlated with phenotypic status. The 6-probe cocktail appeared to be suitable for assessing drug metabolizing activities. This, in conjunction with individual genetics, will pave the way for the implementation of personalized medicine in clinical practice. This will hopefully improve efficacy and reduce the incidence of adverse drug reactions.
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Affiliation(s)
- Seok Hwee Koo
- Clinical Trials and Research Unit, Changi General Hospital, Singapore, Singapore
| | - Gaik Hong Soon
- Clinical Trials and Research Unit, Changi General Hospital, Singapore, Singapore
| | - Alain Pruvost
- Département Médicaments et Technologies pour la Santé (DMTS), Université Paris-Saclay, CEA, INRAE, SPI, 91191, Gif-sur-Yvette, France
| | - Henri Benech
- Département Médicaments et Technologies pour la Santé (DMTS), Université Paris-Saclay, CEA, INRAE, SPI, 91191, Gif-sur-Yvette, France
| | - Tiing Leong Ang
- Department of Gastroenterology and Hepatology, Changi General Hospital, 2 Simei Street 3, Singapore, 529889, Singapore
| | - Edmund Jon Deoon Lee
- Clinical Trials and Research Unit, Changi General Hospital, Singapore, Singapore.,Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Daphne Shih Wen Ang
- Department of Gastroenterology and Hepatology, Changi General Hospital, 2 Simei Street 3, Singapore, 529889, Singapore.
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18
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Zheng B, Chen L, Zheng T, Hou L, Huang X, Li C, Wang X, Fang Q, Chen J, Tang Z, Li Z, Ouyang D. A novel solid phase extraction sample preparation method for sensitively determining doxepin and N-nordoxepin in human plasma and its application in a bioequivalence study in healthy Chinese volunteers. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2022; 14:2168-2178. [PMID: 35608048 DOI: 10.1039/d2ay00129b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Doxepin, a tricyclic antidepressant (TCA), is widely used in the treatment of depressive disorder and anxiety. There are some liquid chromatography-tandem mass spectrometry (LC-MS/MS) methods that have been reported for detecting doxepin, but inadequacies in recovery and cumbersome sample preparation obstruct the pharmacokinetics study. Therefore, we aimed to develop and validate a rapid sample preparation method based on solid-phase extraction (SPE) for the precise quantification of doxepin and its metabolites. Chromatography separation was performed on a Waters ACQUITY UPLC BEH C18 column (2.1 × 100 mm, 1.7 μm) and a mobile phase consisting of 70% of mobile phase A (0.1% formic acid and 10 mM ammonium formate) and 30% mobile phase B (0.1% formic acid in acetonitrile) at a flow rate of 0.4 mL min-1 in the step gradient elution conditions. The lower limits of quantification for doxepin and N-nordoxepin were 4 pg mL-1 and 2 pg mL-1, respectively. This method was validated with satisfactory results including good precision and accuracy. A rapid, sensitive, and specific LC-MS/MS method was developed and validated for the determination of doxepin in human plasma. This method could be applied for determining doxepin and N-nordoxepin concentrations in plasma that could be useful for bioequivalence study of 3 mg doxepin.
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Affiliation(s)
- Binjie Zheng
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha 410008, P. R. China.
- Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, 110 Xiangya Road, Changsha 410078, P. R. China
- Engineering Research Center of Applied Technology of Pharmacogenomics, Ministry of Education, 110 Xiangya Road, Changsha 410078, P. R. China
| | - Lulu Chen
- Hunan Key Laboratory for Bioanalysis of Complex Matrix Samples, Changsha Duxact Biotech Co., Ltd, Changsha, China.
- Hunan Changsha Duxact Clinical Laboratory Co., Ltd, Changsha Duxact Biotech Co., Ltd, Changsha, China
- School of Pharmacy, Xiangnan University, Chenzhou 423000, China
| | - Tiandong Zheng
- Hunan Key Laboratory for Bioanalysis of Complex Matrix Samples, Changsha Duxact Biotech Co., Ltd, Changsha, China.
- Hunan Changsha Duxact Clinical Laboratory Co., Ltd, Changsha Duxact Biotech Co., Ltd, Changsha, China
| | - Liping Hou
- Hunan Key Laboratory for Bioanalysis of Complex Matrix Samples, Changsha Duxact Biotech Co., Ltd, Changsha, China.
| | - Xinyi Huang
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha 410008, P. R. China.
- Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, 110 Xiangya Road, Changsha 410078, P. R. China
- Engineering Research Center of Applied Technology of Pharmacogenomics, Ministry of Education, 110 Xiangya Road, Changsha 410078, P. R. China
| | - Chao Li
- Hunan Key Laboratory for Bioanalysis of Complex Matrix Samples, Changsha Duxact Biotech Co., Ltd, Changsha, China.
- Hunan Changsha Duxact Clinical Laboratory Co., Ltd, Changsha Duxact Biotech Co., Ltd, Changsha, China
| | - Xintong Wang
- Hunan Key Laboratory for Bioanalysis of Complex Matrix Samples, Changsha Duxact Biotech Co., Ltd, Changsha, China.
- Hunan Changsha Duxact Clinical Laboratory Co., Ltd, Changsha Duxact Biotech Co., Ltd, Changsha, China
| | - Qing Fang
- Hunan Key Laboratory for Bioanalysis of Complex Matrix Samples, Changsha Duxact Biotech Co., Ltd, Changsha, China.
- Hunan Changsha Duxact Clinical Laboratory Co., Ltd, Changsha Duxact Biotech Co., Ltd, Changsha, China
| | - Jie Chen
- Hunan Key Laboratory for Bioanalysis of Complex Matrix Samples, Changsha Duxact Biotech Co., Ltd, Changsha, China.
- Hunan Changsha Duxact Clinical Laboratory Co., Ltd, Changsha Duxact Biotech Co., Ltd, Changsha, China
| | - Zhi Tang
- Hunan Key Laboratory for Bioanalysis of Complex Matrix Samples, Changsha Duxact Biotech Co., Ltd, Changsha, China.
- Hunan Changsha Duxact Clinical Laboratory Co., Ltd, Changsha Duxact Biotech Co., Ltd, Changsha, China
| | - Zhenyu Li
- Department of Geriatric Medicine, Xiangya Hospital, Central South University, Changsha, China.
| | - Dongsheng Ouyang
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha 410008, P. R. China.
- Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, 110 Xiangya Road, Changsha 410078, P. R. China
- Engineering Research Center of Applied Technology of Pharmacogenomics, Ministry of Education, 110 Xiangya Road, Changsha 410078, P. R. China
- Hunan Key Laboratory for Bioanalysis of Complex Matrix Samples, Changsha Duxact Biotech Co., Ltd, Changsha, China.
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19
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Muyambo S, Ndadza A, Soko ND, Kruger B, Kadzirange G, Chimusa E, Masimirembwa CM, Ntsekhe M, Nhachi CF, Dandara C. Warfarin Pharmacogenomics for Precision Medicine in Real-Life Clinical Practice in Southern Africa: Harnessing 73 Variants in 29 Pharmacogenes. OMICS : A JOURNAL OF INTEGRATIVE BIOLOGY 2022; 26:35-50. [PMID: 34958284 PMCID: PMC8792494 DOI: 10.1089/omi.2021.0199] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Pharmacogenomics is universally relevant for worldwide modern therapeutics and yet needs further development in resource-limited countries. While there is an abundance of genetic association studies in controlled medical settings, there is a paucity of studies with a naturalistic design in real-life clinical practice in patients with comorbidities and under multiple drug treatment regimens. African patients are often burdened with communicable and noncommunicable comorbidities, yet the application of pharmacogenomics in African clinical settings remains limited. Using warfarin as a model, this study aims at minimizing gaps in precision/personalized medicine research in African clinical practice. We present, therefore, pharmacogenomic profiles of a cohort of 503 black Africans (n = 252) and Mixed Ancestry (n = 251) patients from Southern Africa, on warfarin and co-prescribed drugs in a naturalized noncontrolled environment. Seventy-three (n = 73) single nucleotide polymorphisms (SNPs) in 29 pharmacogenes were characterized using a combination of allelic discrimination, Sanger sequencing, restriction fragment length polymorphism, and Sequenom Mass Array. The common comorbidities were hypertension (43-46%), heart failure (39-45%), diabetes mellitus (18%), arrhythmia (25%), and HIV infection (15%). Accordingly, the most common co-prescribed drugs were antihypertensives, antiarrhythmic drugs, antidiabetics, and antiretroviral therapy. We observed marked variation in major pharmacogenes both at interethnic levels and within African subpopulations. The Mixed Ancestry group presented a profile of genetic variants reflecting their European, Asian, and African admixture. Precision medicine requires that African populations begin to capture their own pharmacogenetic SNPs as they cannot always infer with absolute certainty from Asian and European populations. In the current historical moment of the COVID-19 pandemic, we also underscore that the spectrum of drugs interacting with warfarin will likely increase, given the systemic and cardiovascular effects of COVID-19, and the anticipated influx of COVID-19 medicines in the near future. This observational clinical pharmacogenomics study of warfarin, together with past precision medicine research, collectively, lends strong support for incorporation of pharmacogenetic profiling in clinical settings in African patients for effective and safe administration of therapeutics.
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Affiliation(s)
- Sarudzai Muyambo
- Department of Clinical Pharmacology, Faculty of Medicine and Health Sciences, University of Zimbabwe, Harare, Zimbabwe
- Department of Biological Sciences, Faculty of Science and Engineering, Bindura University of Science Education, Bindura, Zimbabwe
| | - Arinao Ndadza
- Pharmacogenomics and Drug Metabolism Research Group, Division of Human Genetics, Department of Pathology, Institute of Infectious Diseases and Molecular Medicine (IIDMM), Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Nyarai D. Soko
- Pharmacogenomics and Drug Metabolism Research Group, Division of Human Genetics, Department of Pathology, Institute of Infectious Diseases and Molecular Medicine (IIDMM), Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Bianca Kruger
- Pharmacogenomics and Drug Metabolism Research Group, Division of Human Genetics, Department of Pathology, Institute of Infectious Diseases and Molecular Medicine (IIDMM), Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Gerard Kadzirange
- Department of Medicine, Faculty of Medicine and Health Sciences, University of Zimbabwe, Harare, Zimbabwe
| | - Emile Chimusa
- Pharmacogenomics and Drug Metabolism Research Group, Division of Human Genetics, Department of Pathology, Institute of Infectious Diseases and Molecular Medicine (IIDMM), Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Collen M. Masimirembwa
- Department of Drug Metabolism and Pharmacokinetics (DMPK), African Institute of Biomedical Sciences and Technology (AiBST), Harare, Zimbabwe
| | - Mpiko Ntsekhe
- Division of Cardiology, Department of Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Charles F.B. Nhachi
- Department of Clinical Pharmacology, Faculty of Medicine and Health Sciences, University of Zimbabwe, Harare, Zimbabwe
| | - Collet Dandara
- Pharmacogenomics and Drug Metabolism Research Group, Division of Human Genetics, Department of Pathology, Institute of Infectious Diseases and Molecular Medicine (IIDMM), Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
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20
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Zhou W, Jiang Y, Xu Y, Wang Y, Ma X, Zhou L, Lin Y, Wang Y, Wu Z, Li M, Yin W, Lu J. Comparison of adverse drug reactions between tamoxifen and toremifene in breast cancer patients with different CYP2D6 genotypes: a propensity-score matched cohort study. Int J Cancer 2021; 150:1664-1676. [PMID: 34957551 DOI: 10.1002/ijc.33919] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Revised: 11/18/2021] [Accepted: 12/10/2021] [Indexed: 11/06/2022]
Abstract
CYP2D6 gene polymorphism had a profound impact upon the effect of tamoxifen as adjuvant endocrine therapy in breast cancers. However, it had never been reported whether the adverse drug reactions vary by CYP2D6 metabolic status for patients treated with tamoxifen or toremifene. We conducted an retrospective study in breast cancer patients to investigate the impact of CYP2D6 metabolizers on liver dysfunction events, gynecological events, and dyslipidemia events. According to CYP2D6*10 (100C → T) genotype, the enrolled patients were further categorized into four cohorts (extensive metabolizers taking tamoxifen [EM + TAM], extensive metabolizers taking toremifene [EM + TOR], intermediate metabolizers taking tamoxifen [IM + TAM], intermediate metabolizers taking toremifene cohort [IM + TOR]). A total of 192 patients were included into the study, with a median follow-up time of 26.2 months. In EM + TAM cohort, the risks of liver dysfunction events (P = 0.004) and gynecological events (P = 0.004) were significantly higher compared with EM + TOR cohort. In IM + TAM cohort, the risks of liver dysfunction events (P = 0.14) and gynecological events (P = 0.99) were not significantly different from IM + TOR cohort. Significant decrease of total cholesterol was observed in EM + TAM cohort around 1 year after taking tamoxifen (P < 0.001). Significant interactions between CYP2D6 metabolic status and endocrine agents were observed in terms of liver dysfunction events (p-interaction = 0.007) and gynecological events (p-interaction = 0.026). These findings suggested that CYP2D6 gene polymorphism played a significant role in predicting liver dysfunction, gynecological diseases and lipid metabolism changes among patients taking tamoxifen or toremifene. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Weihang Zhou
- Department of Breast Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Yiwei Jiang
- Department of Breast Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Yaqian Xu
- Department of Breast Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,Department of General Surgery, Beijing Friendship Hospital, Capital Medical University, Beijing, China
| | - Yaohui Wang
- Department of Breast Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Xiaowei Ma
- Department of Clinical Laboratory, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Liheng Zhou
- Department of Breast Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Yanping Lin
- Department of Breast Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Yan Wang
- Department of Breast Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Ziping Wu
- Department of Breast Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Min Li
- Department of Clinical Laboratory, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Wenjin Yin
- Department of Breast Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Jinsong Lu
- Department of Breast Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
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21
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Genetic variations and epigenetic modulations in CYP genes: Implications in NSAID-treatment of arthritis patients. THE NUCLEUS 2021. [DOI: 10.1007/s13237-021-00373-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
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22
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Chou PS, Huang LC, Hour TC, Yen CW, Yang YH. Impact of the CYP2D6 single nucleotide polymorphism on the concentration of and therapeutic response to donepezil in mild-to-moderate Alzheimer's disease. J Formos Med Assoc 2021; 121:409-415. [PMID: 34120801 DOI: 10.1016/j.jfma.2021.05.026] [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: 02/12/2021] [Revised: 05/20/2021] [Accepted: 05/24/2021] [Indexed: 11/17/2022] Open
Abstract
BACKGROUND/PURPOSE Donepezil was approved for the treatment of Alzheimer's disease (AD) but causes variable therapeutic responses. Thus, identifying specific genetic polymorphisms, which can predict a therapeutic response to donepezil, would enable a development of personalized strategy to treatment for patients with AD. The research aimed to exam the impact of the cytochrome P450 2D6 (CYP2D6) single nucleotide polymorphism (SNP) rs1080985 on the concentration of and therapeutic response to donepezil in AD. METHODS In total, 40 newly diagnosed AD patients who had a clinical dementia rating (CDR) of 0.5-2 and who were on donepezil were enrolled and followed up. Plasma concentrations of donepezil were determined after 6 months of donepezil treatment. Cognitive and functional statuses were evaluated annually during follow-up. The response to therapy was defined based on the change in CDR. RESULTS At a mean of 21.8 ± 5.7 months of follow-up, 10 of 40 patients (25.0%) were nonresponders to donepezil treatment. Patients who were homozygous for the G allele exhibited a higher concentration of donepezil and concentration-to-dose ratio than those with other genotypes. Furthermore, a significantly higher proportion of patients with the G/G genotype were responders than nonresponders (90.0% vs 50.0%, P = 0.015, effect size of V: 0.457) to donepezil treatment. Conversely, patients carrying the C allele had a significantly high risk of poor responses to donepezil treatment (odds ratio: 9.00, 95% confidence interval: 1.611-50.275). CONCLUSION The CYP2D6 SNP rs1080985 might be a useful pharmacogenetic marker of the long-term therapeutic response to donepezil in patients with AD.
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Affiliation(s)
- Ping-Song Chou
- Department of Neurology, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan; Department of and Master's Program in Neurology, Faculty of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan; Neuroscience Research Center, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Ling-Chun Huang
- Department of Neurology, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan; Neuroscience Research Center, Kaohsiung Medical University, Kaohsiung, Taiwan; Department of Neurology, Kaohsiung Municipal Ta-Tung Hospital, Kaohsiung, Taiwan
| | - Tzyh-Chyuan Hour
- Division of Biochemistry and Molecular Biology, Graduate Institute of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan; Department of Medical Research, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
| | - Chen-Wen Yen
- Department of Mechanical and Electro-Mechanical Engineering, National Sun Yat-Sen University, Kaohsiung, Taiwan
| | - Yuan-Han Yang
- Department of Neurology, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan; Department of and Master's Program in Neurology, Faculty of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan; Neuroscience Research Center, Kaohsiung Medical University, Kaohsiung, Taiwan; Department of Neurology, Kaohsiung Municipal Ta-Tung Hospital, Kaohsiung, Taiwan.
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23
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Mehlotra RK, Gaedigk A, Howes RE, Rakotomanga TA, Ratsimbasoa AC, Zimmerman PA. CYP2D6 Genetic Variation and Its Implication for Vivax Malaria Treatment in Madagascar. Front Pharmacol 2021; 12:654054. [PMID: 33959023 PMCID: PMC8093859 DOI: 10.3389/fphar.2021.654054] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 03/01/2021] [Indexed: 12/19/2022] Open
Abstract
Plasmodium vivax is one of the five human malaria parasite species, which has a wide geographical distribution and can cause severe disease and fatal outcomes. It has the ability to relapse from dormant liver stages (hypnozoites), weeks to months after clearance of the acute blood-stage infection. An 8-aminoquinoline drug primaquine (PQ) can clear the hypnozoites, and thus can be used as an anti-relapse therapeutic agent. Recently, a number of studies have found that its efficacy is compromised by polymorphisms in the cytochrome P450 2D6 (CYP2D6) gene; decreased or absence of CYP2D6 activity contributes to PQ therapeutic failure. The present study sought to characterize CYP2D6 genetic variation in Madagascar, where populations originated from admixture between Asian and African populations, vivax malaria is endemic, and PQ can be deployed soon to achieve national malaria elimination. In a total of 211 samples collected from two health districts, CYP2D6 decreased function alleles CYP2D6*10, *17, *29, *36+*10, and *41 were observed at frequencies of 3.55-17.06%. In addition, nonfunctional alleles were observed, the most common of which were CYP2D6*4 (2.13%), *5 (1.66%), and the *4x2 gene duplication (1.42%). Given these frequencies, 34.6% of the individuals were predicted to be intermediate metabolizers (IM) with an enzyme activity score (AS) ≤ 1.0; both the IM phenotype and AS ≤ 1.0 have been found to be associated with PQ therapeutic failure. Furthermore, the allele and genotype frequency distributions add to the archaeological and genomic evidence of Malagasy populations constituting a unique, Asian-African admixed origin. The results from this exploratory study provide fresh insights about genomic characteristics that could affect the metabolism of PQ into its active state, and may enable optimization of PQ treatment across human genetic diversity, which is critical for achieving P. vivax elimination.
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Affiliation(s)
- Rajeev K Mehlotra
- Center for Global Health and Diseases, Case Western Reserve University School of Medicine, Cleveland, OH, United States
| | - Andrea Gaedigk
- Division of Clinical Pharmacology, Toxicology & Therapeutic Innovation, Children's Mercy Kansas City, Kanas City, MO, United States
| | - Rosalind E Howes
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, United Kingdom.,Foundation for Innovative New Diagnostics, Geneva, Switzerland
| | - Tovonahary A Rakotomanga
- The National Malaria Control Program, Ministry of Health, Antananarivo, Madagascar.,University of Fianarantsoa, Fianarantsoa, Madagascar
| | - Arsene C Ratsimbasoa
- The National Malaria Control Program, Ministry of Health, Antananarivo, Madagascar.,University of Fianarantsoa, Fianarantsoa, Madagascar
| | - Peter A Zimmerman
- Center for Global Health and Diseases, Case Western Reserve University School of Medicine, Cleveland, OH, United States
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24
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Fredrikson KM, Fasolino T. Pharmacogenetic testing: Clinical integration and application for chronic pain management. Nurse Pract 2021; 46:12-19. [PMID: 33739321 DOI: 10.1097/01.npr.0000737180.73290.1f] [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: 11/26/2022]
Abstract
ABSTRACT NPs commonly prescribe pharmaceutical therapies such as opiates, antidepressants, and/or other analgesics to improve the health and well-being of patients experiencing chronic pain. This article provides NPs with pharmacogenetic testing knowledge, such as readiness for clinical implementation, considerations for choosing a testing service, and testing costs for chronic pain management.
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25
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Bakar NS. Pharmacogenetics of common SNP affecting drug metabolizing enzymes: comparison of allele frequencies between European and Malaysian/Singaporean. Drug Metab Pers Ther 2021; 36:173-181. [PMID: 34412170 DOI: 10.1515/dmpt-2020-0153] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2020] [Accepted: 01/03/2021] [Indexed: 11/15/2022]
Abstract
Compared to Europe, data on genetic variation in genes transcribing drug metabolizing enzymes among Asian is limited due to ethnic diversity. Here we compare frequencies for clinically relevant single nucleotide polymorphism (SNP) commonly observed in drug metabolizing enzymes between European and Malaysian/Singaporean. Minor allele frequencies (MAF) for the indicated SNPs for European, South Asian and East Asian populations were obtained from the NCBI website (https://www.ncbi.nlm.nih.gov/snp). The SNP prevalence among Malaysian/Singaporean was characterized from gene association studies. Generally, some SNPs in CYP2D6 and CYP2C19 do not show good agreement between the two populations as to the MAF value obtained. CYP2D6*4 tends to be more common among European, whereas CYP2D6*10 is more common in Malays and Chinese among Singaporean. Regardless of different phenotype, MAF of CYP2D6*4 for Indians is similar to that seen by the European. Singaporeans show smaller MAF for CYP2C19*17 but higher CYP2C19*2 frequencies as opposed to European ones. Following growing attention to the contribution of CYP3A4/5, N-acetyltransferases (NAT2), thiopurine methyltransferase (TPMT) and uridine diphosphate glucuronosyltransferases (UGT)2B7 in predicting drug response across Europe, there are limited pharmacogenetics (PGx) studies examining the gene-drug interaction among Malaysian/Singaporean. To better understand the heterogeneity of the drug response, PGx studies for the abovementioned enzymes between ethnics in Malaysian/Singaporean should be identified.
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Affiliation(s)
- Nur Salwani Bakar
- School of Health Sciences, Universiti Sains Malaysia, Kubang Kerian, Kelantan, Malaysia
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26
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Bakar NS. Pharmacogenetics of common SNP affecting drug metabolizing enzymes: comparison of allele frequencies between European and Malaysian/Singaporean. Drug Metab Pers Ther 2021; 0:dmdi-2020-0153. [PMID: 33735954 DOI: 10.1515/dmdi-2020-0153] [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: 09/12/2020] [Accepted: 01/03/2021] [Indexed: 11/15/2022]
Abstract
Compared to Europe, data on genetic variation in genes transcribing drug metabolizing enzymes among Asian is limited due to ethnic diversity. Here we compare frequencies for clinically relevant single nucleotide polymorphism (SNP) commonly observed in drug metabolizing enzymes between European and Malaysian/Singaporean. Minor allele frequencies (MAF) for the indicated SNPs for European, South Asian and East Asian populations were obtained from the NCBI website (https://www.ncbi.nlm.nih.gov/snp). The SNP prevalence among Malaysian/Singaporean was characterized from gene association studies. Generally, some SNPs in CYP2D6 and CYP2C19 do not show good agreement between the two populations as to the MAF value obtained. CYP2D6*4 tends to be more common among European, whereas CYP2D6*10 is more common in Malays and Chinese among Singaporean. Regardless of different phenotype, MAF of CYP2D6*4 for Indians is similar to that seen by the European. Singaporeans show smaller MAF for CYP2C19*17 but higher CYP2C19*2 frequencies as opposed to European ones. Following growing attention to the contribution of CYP3A4/5, N-acetyltransferases (NAT2), thiopurine methyltransferase (TPMT) and uridine diphosphate glucuronosyltransferases (UGT)2B7 in predicting drug response across Europe, there are limited pharmacogenetics (PGx) studies examining the gene-drug interaction among Malaysian/Singaporean. To better understand the heterogeneity of the drug response, PGx studies for the abovementioned enzymes between ethnics in Malaysian/Singaporean should be identified.
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Affiliation(s)
- Nur Salwani Bakar
- School of Health Sciences, Universiti Sains Malaysia, Kubang Kerian, Kelantan, Malaysia
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27
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A functional polymorphism in the ATP-Binding Cassette B1 transporter predicts pharmacologic response to combination of nortriptyline and morphine in neuropathic pain patients. Pain 2021; 161:619-629. [PMID: 31738228 DOI: 10.1097/j.pain.0000000000001750] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Many genetic markers have been associated with variations in treatment response to analgesics, but none have been assessed in the context of combination therapies. In this study, the treatment effects of nortriptyline and morphine were tested for an association with genetic markers relevant to pain pathways. Treatment effects were determined for single and combination therapies. A total of 24 functional single nucleotide polymorphisms were tested within the gene loci of mu-opioid receptor (OPRM1) gene locus, ATP-Binding Cassette B1 Transporter (ABCB1), Cytochrome P450 gene family (CYP2C19 and CYP2D6), catecholamine inactivator Catechol-O-Methyl Transferase (COMT), and serotonin receptor 2A (HTR2A). Genotyping was performed in a population of neuropathic pain patients who previously participated in a clinical trial. For monotherapy, neither nortriptyline nor morphine responses were associated with single nucleotide polymorphisms. However, for nortriptyline + morphine combination therapy, the single nucleotide polymorphism rs1045642 within the drug efflux pump ABCB1 transporter significantly predicted analgesic response. The presence of the C allele accounted for 51% of pain variance in this subgroup in response to combination treatment. The T-allele homozygotes demonstrated only 20% improvement in pain scores, whereas the C-allele homozygotes 88%. There was no significant contribution of rs1045642 to the medication side effects under all treatment conditions. The UK Biobank data set was then used to validate this genetic association. Here, patients receiving similar combination therapy (opioid + tricyclic antidepressant) carrying the C allele of rs1045642 displayed 33% fewer body pain sites than patients without that allele, suggesting better pain control. In all, our results show a robust effect of the rs1045642 polymorphism in response to chronic pain treatment with a nortriptyline + morphine combination.
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Wang T, Zhou Y, Cao G. Pharmacogenetics of tamoxifen therapy in Asian populations: from genetic polymorphism to clinical outcomes. Eur J Clin Pharmacol 2021; 77:1095-1111. [PMID: 33515076 DOI: 10.1007/s00228-021-03088-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Accepted: 01/11/2021] [Indexed: 12/15/2022]
Abstract
BACKGROUND Compared with western countries, Asian breast cancer patients have unique pathological and biological characteristics. Most of them are premenopausal women with HR positive. Tamoxifen as the first-line drug for premenopausal women with HR+ is involved in multiple enzymes and transporters during metabolizing and transporting process. Variants that cause decreased or inactive gene products leading to abnormal responses in tamoxifen therapy have well been studied in western countries, whereas such information is much less reported in Asian populations. OBJECTIVE In order to elucidate the relationship between genetic variants and tamoxifen-induced individual drug reactions in different Asian populations and further identify genotypes/phenotypes with potential therapeutic significance. METHODS We reviewed the frequencies of genetic variants in major enzymes and transporter genes involved in the metabolism and transport of tamoxifen across Asian populations as well as significant correlations between genotypes/metabolic phenotypes and metabolites concentrations or BC clinical outcomes. RESULTS Significant inter-ethnic differences in allele frequencies was found among Asian populations, such as CYP2D6*4, *10, *41, CYP2C9*2, ABCB1 C3435T and SLCO1B1*5, and CYP2D6*10/*10 is the most common genotype correlated with adverse clinical outcomes. Moreover, we summarized the barriers and controversies of implementing pharmacogenetics in tamoxifen therapy and concluded that more population-specific pharmacogenetic studies are needed in the future. CONCLUSION This review revealed more systematic pharmacogenomics of genes involved in the metabolism and transport besides CYP2D6, are required to optimize the genotyping strategies and guide the personalized tamoxifen therapy in Asian populations.
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Affiliation(s)
- Tingyu Wang
- College of Pharmacy, Hubei University of Chinese Medicine, Wuhan, 430065, China
| | - Yitian Zhou
- Department of Physiology and Pharmacology, Karolinska Institutet, 17177, Stockholm, Sweden
| | - Guosheng Cao
- College of Pharmacy, Hubei University of Chinese Medicine, Wuhan, 430065, China.
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Narasimhalu K, Ang YK, Tan DSY, De Silva DA, Tan KB. Cost Effectiveness of Genotype-Guided Antiplatelet Therapy in Asian Ischemic Stroke Patients: Ticagrelor as an Alternative to Clopidogrel in Patients with CYP2C19 Loss of Function Mutations. Clin Drug Investig 2020; 40:1063-1070. [PMID: 32959334 DOI: 10.1007/s40261-020-00970-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
BACKGROUND Patients with ischemic stroke are often treated with clopidogrel monotherapy as part of secondary stroke prevention. The prevalence of loss of function (LOF) mutations in the CYP2C19 gene is higher in Asians than in Western populations. Patients with loss of function (LOF) mutations are at risk for poorer secondary outcomes when prescribed clopidogrel. OBJECTIVE We aimed to determine the cost effectiveness of genotype-guided antiplatelet therapy in an Asian population with the aim of prescribing ticagrelor as an alternative to patients with LOF mutations. METHODS Markov models were developed to look at the cost effectiveness of genetic testing of CYP2C19, with patients who screened positive for LOF alleles being switched to ticagrelor compared to universal clopidogrel treatment. Effect ratios were obtained from the literature and incidence rates and costs were obtained from the national data published by the Singapore Ministry of Health. Lifetime costs and quality-adjusted life-years (QALYs) were calculated. The primary endpoints were the incremental cost-effectiveness ratios (ICERs). RESULTS The prevalence of the LOF mutations was 61% in the population, with 65% of ethnic Chinese, 60% of ethnic Indian, and 53% of ethnic Malay patients having LOF mutations. Based on this prevalence, the overall ICER of genetic testing was S$33,839/QALY with ICERS of S$30,755/QALY, S$33,177/QALY, and S$41,470/QALY for Chinese, Indians, and Malays, respectively. CONCLUSION This study suggests that it is cost effective to screen for LOF mutations in the CYP2C19 gene in ischemic stroke populations, with ticagrelor as a substitute for clopidogrel in those with LOF mutations.
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Affiliation(s)
- Kaavya Narasimhalu
- Department of Neurology (SGH Campus), National Neuroscience Institute, Outram Road, 169608, Singapore, Singapore.
| | - Yoong Kwei Ang
- Policy, Research and Evaluation Division, Ministry of Health, Singapore, Singapore
- Sydney Medical School, University of Sydney, Sydney, NSW, Australia
| | - Doreen Su Yin Tan
- Policy, Research and Evaluation Division, Ministry of Health, Singapore, Singapore
- Khoo Teck Puat Hospital, Singapore, Singapore
| | - Deidre Anne De Silva
- Department of Neurology (SGH Campus), National Neuroscience Institute, Outram Road, 169608, Singapore, Singapore
| | - Kelvin Bryan Tan
- Policy, Research and Evaluation Division, Ministry of Health, Singapore, Singapore
- School of Public Health, National University of Singapore, Singapore, Singapore
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Kow CS, Zaihan AF, Hasan SS. CYP2C19 Genotype-Guided Antiplatelet Therapy Among Asian Patients with Ischaemic Stroke. Clin Drug Investig 2020; 41:115-116. [PMID: 33237558 DOI: 10.1007/s40261-020-00985-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/29/2020] [Indexed: 10/22/2022]
Affiliation(s)
- Chia Siang Kow
- School of Postgraduate Studies, International Medical University, Kuala Lumpur, Malaysia.
| | | | - Syed Shahzad Hasan
- Department of Pharmacy, University of Huddersfield, Huddersfield, United Kingdom.,School of Biomedical Sciences and Pharmacy, University of Newcastle, Callaghan, Australia
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31
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Moraes JCD, Nunes FDD, Coeli-Lacchini FB, Miyazaki AHL, Flória-Santos M, Lacchini R. Nurse empowerment through Pharmacogenetics. Rev Lat Am Enfermagem 2020; 28:e3265. [PMID: 32813781 PMCID: PMC7426146 DOI: 10.1590/1518-8345.3415.3265] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Accepted: 02/03/2020] [Indexed: 02/03/2023] Open
Abstract
Objective: to verify the existence of elements that justify the use of pharmacogenetics by the Brazilian nurse. Method: this is a quantitative, cross-sectional, observational, descriptive study, whose final sample was 67 individuals. The participants were healthy at the time of the study and reported a history of previous use and the occurrence of adverse effects by drugs commonly used and metabolized by CYP2C9. We collected 4 mL of venous blood for subsequent DNA extraction by salting out method and genotyping of the CYP2C9*2 and CYP2C9*3 polymorphisms, using Polymerase Chain Reaction in real time using Taqman assays. Results: the use of drugs metabolized by CYP2C9 was frequent (more than 75% of the individuals have already used between 2 or 4 of these drugs). Regarding adverse events, there were 19 perceived symptomatic occurrences associated with drugs metabolized by CYP2C9. The allele frequency of the polymorphism * 2 and * 3 in the population studied was 11.1% and 7.5%, respectively, and there was a coincidence between the presence of alleles of low enzyme activity and the occurrence of adverse effects. Conclusion: there are elements that justify the adoption of pharmacogenetics in the nursing care to reduce the occurrence of adverse reactions to drugs metabolized by CYP2C9.
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Affiliation(s)
| | | | | | | | - Milena Flória-Santos
- Escola de Enfermagem de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP, Brazil
| | - Riccardo Lacchini
- Escola de Enfermagem de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP, Brazil
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32
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Chan SL, Liew HZW, Nguyen F, Thumboo J, Chow WC, Sung C. Prescription patterns of outpatients and the potential of multiplexed pharmacogenomic testing. Br J Clin Pharmacol 2020; 87:886-894. [PMID: 32559336 DOI: 10.1111/bcp.14439] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Revised: 06/02/2020] [Accepted: 06/09/2020] [Indexed: 01/18/2023] Open
Abstract
BACKGROUND Pre-emptive pharmacogenomic (PGx) testing is potentially an efficient approach to improve drug safety and efficacy but the target population to test is unclear. OBJECTIVES We aim to describe the prescription pattern of PGx drugs among adult medical outpatients. METHODS We estimated the 5-year cumulative incidence (CI) for receiving three groups of PGx drugs using competing risks analysis: (i) all PGx drugs, (ii) PGx drugs with guidelines and (iii) PGx drugs with serious clinical effects. Comparisons of CIs were also done by patient characteristics using Gray's test. RESULTS The 5-year CIs of receiving any new PGx drug, PGx drug with guidelines and serious clinical effects were 42.6%, 37.3% and 13.7%, respectively. The 5-year CI of receiving any new PGx drug was higher for patients >40 years old (43.6% vs ≤40 years old 36.0%, P < 2.2 × 10-22 ), Malays and Indians (50.3% and 49.8% vs Chinese 31.1%, P < 2.2 × 10-22 ), those who attended one of the following four specialties at the index visit compared to other specialties (infectious diseases [46.2% vs 42.6%, P = 2.9 × 10-4 ], psychiatry [48.3% vs 42.3%, P = 7.4 × 10-13 ], renal [49.8% vs 40.9%, P < 2.2 × 10-22 ], and rheumatology and immunology [54.8% vs 41.7%, P < 2.2 × 10-22 ]) and those prescribed ≥5 drugs at index visit (51.7% vs 0-4 drugs 41.7%, P < 2.2 × 10-22 ). CONCLUSIONS Medical outpatients have a substantial probability of benefiting from pre-emptive PGx testing and this is higher in certain subgroups of patients.
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Affiliation(s)
- Sze Ling Chan
- Health Services Research Centre, SingHealth, Singapore
| | | | | | - Julian Thumboo
- Department of Rheumatology and Immunology and Health Services Research Unit, Singapore General Hospital, Singapore
| | - Wan Cheng Chow
- Department of Gastroenterology & Hepatology, Singapore General Hospital, Singapore
| | - Cynthia Sung
- Health Services and Systems Research, Duke-NUS Medical School, Singapore
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Poh BH, Lee JH, Abdul Haium AA, Choo TLJ. Complete Heart Block Secondary to Flecainide Toxicity: Is It Time for CYP2D6 Genotype Testing? Pediatrics 2020; 146:peds.2019-2608. [PMID: 32561613 DOI: 10.1542/peds.2019-2608] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 12/30/2019] [Indexed: 11/24/2022] Open
Abstract
Flecainide acetate is a Vaughan-Williams class IC antiarrhythmic drug prescribed for the treatment of supraventricular arrhythmias. It has a narrow therapeutic index and proarrhythmic effects even at therapeutic doses. Flecainide is metabolized by a CYP2D6 enzyme that exhibits polymorphism. In this case report, we present, to our best knowledge, the first case of toxicity contributed by genetic polymorphism in an infant. Our patient with recurrent supraventricular tachycardia was treated with a therapeutic dose of flecainide but developed heart block requiring extracorporeal membrane oxygenation support and subsequent treatment with lipid emulsion therapy. He was found to have supratherapeutic serum flecainide concentration, and gene testing revealed the patient to be an intermediate metabolizer. With this case report, we reinforce the importance of evaluating the CYP2D6 genotype before drug initiation in the neonatal population and recommend regular monitoring of serum flecainide levels and electrocardiograms in these patients.
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Affiliation(s)
| | - Jan Hau Lee
- Children's Intensive Care Unit, KK Women's and Children's Hospital, Singapore; and.,Medical School, Duke-National University of Singapore, Singapore
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34
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Png WY, Wong XY, Kwan YH, Lin YY, Tan DSY. Perspective on CYP2C19 genotyping test among patients with acute coronary syndrome - a qualitative study. Future Cardiol 2020; 16:655-662. [PMID: 32524842 DOI: 10.2217/fca-2020-0036] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Aim: Identify factors patients consider regarding CYP2C19 genotyping test to guide choice of antiplatelet therapy. Patients & methods: Patient's perception and attitude toward use of CYP2C19 genotyping test was gathered according to an interview guide. Thematic analysis was conducted. Results: A total of 14 patients were interviewed. The main factors found to influence uptake of CYP2C19 genotyping test are, convenience of genotyping test (n = 4), physician's recommendation (n = 11), prior explanation of genetic testing by medical personnel (n = 5) and inclination toward clopidogrel, with three sub-factors; less frequent dosing (n = 3), lower cost (n = 7) and lower risk of bleeding (n = 9). Conclusion: This study provided the information needed to develop a discrete choice experiment to empirically quantify patients' preference and willingness to pay for genetic testing and to simulate uptake.
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Affiliation(s)
- Wan Yu Png
- Department of Pharmacy, Khoo Teck Puat Hospital, 90 Yishun Central, Singapore 768828
| | - Xin Yi Wong
- Department of Pharmacy, National University of Singapore, 18 Science Drive 4, Singapore 117559
| | - Yu Heng Kwan
- Program in Health Services & Systems Research, Duke-NUS Medical School, 8 College Road, Singapore 169857
| | - Ying Ying Lin
- Department of Pharmacy, Khoo Teck Puat Hospital, 90 Yishun Central, Singapore 768828
| | - Doreen Su-Yin Tan
- Department of Pharmacy, Khoo Teck Puat Hospital, 90 Yishun Central, Singapore 768828
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35
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Wee JW, Png WY, Wong XY, Kwan YH, Lin YY, Tan DSY, Wee HL. Measuring preferences for CYP2C19 genotyping in patients with acute coronary syndrome - a discrete choice experiment. Future Cardiol 2020; 16:663-674. [PMID: 32524837 DOI: 10.2217/fca-2020-0037] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Aim: To evaluate the relative importance of CYP2C19 genotype-guided treatment attributes to patients. Patients & methods: A discrete choice experiment questionnaire was administered to 63 patients with acute coronary syndrome. Attributes examined in the discrete choice experiment questionnaire were: cost of genetic testing (S$50, S$100, S$200); cost of antiplatelet medication (S$100, S$500, S$1000); heart attack or stroke risk (5 in 100, 15 in 100, 25 in 100); bleeding risk (5 in 100, 15 in 100, 25 in 100); doctor's recommendation (yes, neutral). Mixed logit model was used for analysis. Results & conclusion: All attributes were important in patients' decision-making. Most displayed strong preference for doctor's recommendation and reduced heart attack or stroke risk. Genotyping was chosen by 63.5% of the patients.
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Affiliation(s)
- Juliana Wt Wee
- Department of Pharmacy, National University of Singapore, 18 Science Drive 4, Singapore 117559, Singapore
| | - Wan Yu Png
- Department of Pharmacy, Khoo Teck Puat Hospital, 90 Yishun Central, Singapore 768828, Singapore
| | - Xin Yi Wong
- Department of Pharmacy, National University of Singapore, 18 Science Drive 4, Singapore 117559, Singapore
| | - Yu Heng Kwan
- Program in Health Services and Systems Research, Duke-NUS Medical School, 8 College Road, Singapore 169857, Singapore
| | - Ying Ying Lin
- Department of Pharmacy, Khoo Teck Puat Hospital, 90 Yishun Central, Singapore 768828, Singapore
| | - Doreen S-Y Tan
- Department of Pharmacy, Khoo Teck Puat Hospital, 90 Yishun Central, Singapore 768828, Singapore
| | - Hwee Lin Wee
- Department of Pharmacy, National University of Singapore, 18 Science Drive 4, Singapore 117559, Singapore
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36
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Abstract
To date, many questions about the extent and cause of pharmacokinetic (PK) variability of even the most widely studied and prescribed β1-adrenergic receptor blockers, such as metoprolol and bisoprolol, remain unanswered. Given that there are still no published population pharmacokinetic (PopPK) analyses of bisoprolol in routinely treated patients with acute coronary syndrome (ACS), the aim of this study was to determine its PK variability in 71 Serbian patients with ACS. PopPK analysis was conducted using a nonlinear mixed-effects model (NONMEM), version 7.3.0 (Icon Development Solutions). In each patient, the same formulation of bisoprolol was administered once or twice daily at a total daily dose of 0.625-7.5 mg. We separately assessed the effects of 31 covariates on the PKs of bisoprolol, and our results indicated that only 2 covariates could have possible influence on the variability of the clearance of bisoprolol: the mean daily dose of the drug and smoking habits of patients. These findings suggest that possible autoinduction of drug metabolism by higher total daily doses and induction of cytochrome P450 isoform 3A4 (CYP3A4) by cigarette smoke in liver could be the potential causes of increased total clearance of bisoprolol in patients with ACS.
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37
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Martínez-Magaña JJ, Genis-Mendoza AD, Villatoro Velázquez JA, Camarena B, Martín Del Campo Sanchez R, Fleiz Bautista C, Bustos Gamiño M, Reséndiz E, Aguilar A, Medina-Mora ME, Nicolini H. The Identification of Admixture Patterns Could Refine Pharmacogenetic Counseling: Analysis of a Population-Based Sample in Mexico. Front Pharmacol 2020; 11:324. [PMID: 32390825 PMCID: PMC7188951 DOI: 10.3389/fphar.2020.00324] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Accepted: 03/05/2020] [Indexed: 12/12/2022] Open
Abstract
Pharmacogenetic analysis has generated translational data that could be applied to guide treatments according to individual genetic variations. However, pharmacogenetic counseling in some mestizo (admixed) populations may require tailoring to different patterns of admixture. The identification and clustering of individuals with related admixture patterns in such populations could help to refine the practice of pharmacogenetic counseling. This study identifies related groups in a highly admixed population-based sample from Mexico, and analyzes the differential distribution of actionable pharmacogenetic variants. A subsample of 1728 individuals from the Mexican Genomic Database for Addiction Research (MxGDAR/Encodat) was analyzed. Genotyping was performed with the commercial PsychArray BeadChip, genome-wide ancestry was estimated using EIGENSOFT, and model-based clustering was applied to defined admixture groups. Actionable pharmacogenetic variants were identified with a query to the Pharmacogenomics Knowledge Base (PharmGKB) database, and functional prediction using the Variant Effect Predictor (VEP). Allele frequencies were compared with chi-square tests and differentiation was estimated by FST. Seven admixture groups were identified in Mexico. Some, like Group 1, Group 4, and Group 5, were found exclusively in certain geographic areas. More than 90% of the individuals, in some groups (Group 1, Group 4 and Group 5) were found in the Central-East and Southeast region of the country. MTRR p.I49M, ABCG2 p.Q141K, CHRNA5 p.D398N, SLCO2B1 rs2851069 show a low degree of differentiation between admixture groups. ANKK1 p.G318R and p.H90R, had the lowest allele frequency of Group 1. The reduction in these alleles reduces the risk of toxicity from anticancer and antihypercholesterolemic drugs. Our analysis identified different admixture patterns and described how they could be used to refine the practice of pharmacogenetic counseling for this admixed population.
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Affiliation(s)
- José Jaime Martínez-Magaña
- Laboratorio de Genómica de Enfermedades Psiquiátricas y Neurodegenerativas, Instituto Nacional de Medicina Genómica (INMEGEN), Mexico City, Mexico
| | - Alma Delia Genis-Mendoza
- Laboratorio de Genómica de Enfermedades Psiquiátricas y Neurodegenerativas, Instituto Nacional de Medicina Genómica (INMEGEN), Mexico City, Mexico.,Hospital Psiquiátrico Infantil "Juan N. Navarro," Servicios de Atención Psiquiátrica, Mexico City, Mexico
| | - Jorge Ameth Villatoro Velázquez
- Unidad de Encuestas y Análisis de Datos, Insituto Nacional de Psiquiatría Ramón de la Fuente Muñiz (INPRFM).,Global Studies Seminar, Faculty of Medicine, National Autonomous University of Mexico (UNAM), Mexico City, Mexico
| | - Beatriz Camarena
- Laboratorio de Farmacogenética, Insituto Nacional de Psiquiatría Ramón de la Fuente Muñiz (INPRFM), Mexico City, Mexico
| | - Raul Martín Del Campo Sanchez
- Unidad de Encuestas y Análisis de Datos, Insituto Nacional de Psiquiatría Ramón de la Fuente Muñiz (INPRFM).,Global Studies Seminar, Faculty of Medicine, National Autonomous University of Mexico (UNAM), Mexico City, Mexico
| | - Clara Fleiz Bautista
- Unidad de Encuestas y Análisis de Datos, Insituto Nacional de Psiquiatría Ramón de la Fuente Muñiz (INPRFM).,Global Studies Seminar, Faculty of Medicine, National Autonomous University of Mexico (UNAM), Mexico City, Mexico
| | - Marycarmen Bustos Gamiño
- Unidad de Encuestas y Análisis de Datos, Insituto Nacional de Psiquiatría Ramón de la Fuente Muñiz (INPRFM)
| | - Esbehidy Reséndiz
- Unidad de Encuestas y Análisis de Datos, Insituto Nacional de Psiquiatría Ramón de la Fuente Muñiz (INPRFM)
| | - Alejandro Aguilar
- Laboratorio de Farmacogenética, Insituto Nacional de Psiquiatría Ramón de la Fuente Muñiz (INPRFM), Mexico City, Mexico
| | - María Elena Medina-Mora
- Unidad de Encuestas y Análisis de Datos, Insituto Nacional de Psiquiatría Ramón de la Fuente Muñiz (INPRFM).,Global Studies Seminar, Faculty of Medicine, National Autonomous University of Mexico (UNAM), Mexico City, Mexico
| | - Humberto Nicolini
- Laboratorio de Genómica de Enfermedades Psiquiátricas y Neurodegenerativas, Instituto Nacional de Medicina Genómica (INMEGEN), Mexico City, Mexico
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Fredrikson KM, Fasolino T. Pharmacogenetic Testing: The Ethics of Implementing in Clinical Practice for Chronic Pain Patients. J Pain Palliat Care Pharmacother 2020; 34:69-76. [DOI: 10.1080/15360288.2019.1707929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
- Karin M. Fredrikson
- Karin M. Fredrikson, is with School of Nursing, Healthcare Genetics, College of Behavioral, Social, & Health Sciences, Clemson University, Clemson, South Carolina, USA; Tracy Fasolino, is with School of Nursing, College of Behavioral, Social, & Health Sciences, Clemson University, Clemson, South Carolina, USA
| | - Tracy Fasolino
- Karin M. Fredrikson, is with School of Nursing, Healthcare Genetics, College of Behavioral, Social, & Health Sciences, Clemson University, Clemson, South Carolina, USA; Tracy Fasolino, is with School of Nursing, College of Behavioral, Social, & Health Sciences, Clemson University, Clemson, South Carolina, USA
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Zhou PY, Lim TP, Tang SLS, Liew Y, Chua SGN, Lim LLC, Lee HLW, Tan SX, Lai OF, Tan TT, Wong GC, Kwa LHA. The utility of voriconazole therapeutic drug monitoring in a multi-racial cohort in Southeast Asia. J Glob Antimicrob Resist 2019; 21:427-433. [PMID: 31846723 DOI: 10.1016/j.jgar.2019.12.004] [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] [Received: 08/09/2019] [Revised: 12/04/2019] [Accepted: 12/09/2019] [Indexed: 12/27/2022] Open
Abstract
OBJECTIVES Voriconazole serum concentration, which is affected by several factors, is associated with treatment response and toxicity. There is paucity of data on voriconazole therapeutic drug monitoring (TDM) among Southeast Asians, who exhibit a higher prevalence of CYP2C19-poor metabolisers compared with Caucasians and East Asians. Hence, there are concerns for higher risk of voriconazole accumulation and toxicity. We aim to determine the utility of voriconazole TDM through establishing: (1) proportion of patients achieving therapeutic troughs without dose adjustments; (2) characterisation of patients with sub-therapeutic, therapeutic and supra-therapeutic levels; (3) appropriate dose titrations/dose required for therapeutic troughs; (4) correlation between troughs and adverse events, treatment response/fungal breakthrough. PATIENTS AND METHODS A single-centre retrospective analysis of data from adults (≥21 years old) with ≥1 voriconazole trough measured at Singapore General Hospital from 2015 to 2017 was performed. RESULTS Thirty-two patients (45.7%) among 70 patients achieved therapeutic troughs (defined as 2.0-5.5 mg/L) without dose adjustments. Eleven patients (15.7%) experienced hepatotoxicity (troughs 0.5 to >7.5 mg/L). Neurotoxicity occurred in three patients (4.3%) (troughs ≥6.7 mg/L) and all patients had symptom resolution upon dose reduction. Treatment failure of invasive fungal infection appeared less in patients with therapeutic troughs compared with sub-therapeutic troughs (11.4% vs. 14.2%). Two patients experienced treatment failure despite supra-therapeutic voriconazole troughs. CONCLUSIONS TDM should be implemented due to significant unpredictability in dose exposure. TDM can reduce unnecessary switches to alternatives due to intolerability and rule in the possibility of resistant organisms in the event of treatment failure despite therapeutic troughs, alerting clinicians to switch to alternatives promptly.
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Affiliation(s)
- Peijun Yvonne Zhou
- Department of Pharmacy, Singapore General Hospital, Singapore, Singapore
| | - Tze Peng Lim
- Department of Pharmacy, Singapore General Hospital, Singapore, Singapore
| | - Si Lin Sarah Tang
- Department of Pharmacy, Singapore General Hospital, Singapore, Singapore
| | - Yixin Liew
- Department of Pharmacy, Singapore General Hospital, Singapore, Singapore
| | | | - Li Ling Cheryl Lim
- Department of Pharmacy, Singapore General Hospital, Singapore, Singapore
| | | | - Si Xuan Tan
- Department of Pharmacy, Singapore General Hospital, Singapore, Singapore
| | - Oi Fah Lai
- Department of Clinical Translational Research, Singapore General Hospital, Singapore, Singapore
| | - Thuan Tong Tan
- Department of Infectious Diseases, Singapore General Hospital, Singapore, Singapore
| | - Gee Chuan Wong
- Department of Haematology, Singapore General Hospital, Singapore, Singapore
| | - Lay Hoon Andrea Kwa
- Department of Pharmacy, Singapore General Hospital, Singapore, Singapore; Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore; Singhealth Duke-NUS Medicine Academic Clinical Programme, Singapore, Singapore.
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40
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Tan DSY, Aw JWX, Winther M, Goh LL, Ong HY, Wee E, Liu J, Ho HK. CYP2C19 phenotype in South-East Asian Acute Coronary Syndrome patients and impact on major adverse cardiovascular events. J Clin Pharm Ther 2019; 45:52-58. [PMID: 31670842 DOI: 10.1111/jcpt.13062] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2019] [Revised: 09/17/2019] [Accepted: 09/20/2019] [Indexed: 12/13/2022]
Abstract
WHAT IS KNOWN AND OBJECTIVE Several Caucasian cohort studies have associated at least one loss-of-function CYP2C19 on Clopidogrel (LoF-Clopidogrel) with major adverse cardiovascular events (MACE), and only a couple have used Clinical Pharmacogenetics Implementation Consortium (CPIC® ) phenotype grouping to study the associations. We primarily aimed to study the impact of use of platelet reactivity testing to escalate antiplatelet therapy and secondarily to study the association of CPIC phenotype with MACE outcomes in South-East Asian Acute Coronary Syndrome (ACS) subjects. METHOD A retrospective genotype study was performed on 238 percutaneous coronary intervention subjects, originally planned for escalation of antiplatelets using platelet reactivity testing. RESULTS AND DISCUSSION There was no difference in MACE between the switched and unswitched groups; however, 'all bleeds' and 'clinically significant bleeds' (CSB) were statistically higher in the patients who were switched to prasugrel. The subgroup of patients who remained on clopidogrel (n = 199) were analysed using phenotype categories and MACE. Eleven percent (11.4%) of CYP2C19 poor metabolizers (PM) suffered MACE, compared with 1.3% of extensive metabolizers (EM). LoF-Clopidogrel patients are significantly more likely to experience MACE compared with non-LoF subjects (8.0% vs 5.4%, P: .041). WHAT IS NEW AND CONCLUSION In our multivariate analysis, LoF-Clopidogrel, malay ethnicity, diabetics and use of proton pump inhibitors were independent predictors of MACE. There were numerically more bleeds in LoF subjects who were on prasugrel compared with Clopidogrel (23.5% vs 11%, P = .082). Our data corroborate with current findings on platelet reactivity testing, suggesting that the assay would not be sensitive enough to pick up sufficient 'at-risk' subjects as compared to the use of CYP2C19 genotyping.
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Affiliation(s)
| | | | | | | | - Hean Yee Ong
- Mount Elizabeth Hospital, Singapore City, Singapore
| | - Eric Wee
- Mount Elizabeth Medical Centre, Singapore City, Singapore
| | - Jianjun Liu
- Genome Institute of Singapore, Singapore City, Singapore
| | - Han Kiat Ho
- National University of Singapore, Singapore City, Singapore
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41
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11th International Congress on Psychopharmacology & 7th International Symposium on Child and Adolescent Psychopharmacology. PSYCHIAT CLIN PSYCH 2019. [DOI: 10.1080/24750573.2019.1606883] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
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42
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Zhang F, Finkelstein J. Inconsistency in race and ethnic classification in pharmacogenetics studies and its potential clinical implications. PHARMACOGENOMICS & PERSONALIZED MEDICINE 2019; 12:107-123. [PMID: 31308725 PMCID: PMC6612983 DOI: 10.2147/pgpm.s207449] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/03/2019] [Accepted: 05/30/2019] [Indexed: 12/11/2022]
Abstract
Introduction Racial and ethnic categories are frequently used in pharmacogenetics literature to stratify patients; however, these categories can be inconsistent across different studies. To address the ongoing debate on the applicability of traditional concepts of race and ethnicity in the context of precision medicine, we aimed to review the application of current racial and ethnic categories in pharmacogenetics and its potential impact on clinical care. Methods One hundred and three total pharmacogenetics papers involving the CYP2C9, CYP2C19, and CYP2D6 genes were analyzed for their country of origin, racial, and ethnic categories used, and allele frequency data. Correspondence between the major continental racial categories promulgated by National Institutes of Health (NIH) and those reported by the pharmacogenetics papers was evaluated. Results The racial and ethnic categories used in the papers we analyzed were highly heterogeneous. In total, we found 66 different racial and ethnic categories used which fall under the NIH race category “White”, 47 different racial and ethnic categories for “Asian”, and 62 different categories for “Black”. The number of categories used varied widely based on country of origin: Japan used the highest number of different categories for “White” with 17, Malaysia used the highest number for “Asian” with 24, and the US used the highest number for “Black” with 28. Significant variation in allele frequency between different ethnic subgroups was identified within 3 major continental racial categories. Conclusion Our analysis showed that racial and ethnic classification is highly inconsistent across different papers as well as between different countries. Evidence-based consensus is necessary for optimal use of self-identified race as well as geographical ancestry in pharmacogenetics. Common taxonomy of geographical ancestry which reflects specifics of particular countries and is accepted by the entire scientific community can facilitate reproducible pharmacogenetic research and clinical implementation of its results.
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Affiliation(s)
- Frederick Zhang
- Center for Bioinformatics and Data Analytics, Columbia University Irving Medical Center, New York, NY, USA
| | - Joseph Finkelstein
- Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY, USA
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43
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Chen WC, Bye H, Matejcic M, Amar A, Govender D, Khew YW, Beynon V, Kerr R, Singh E, Prescott NJ, Lewis CM, Babb de Villiers C, Parker MI, Mathew CG. Association of genetic variants in CHEK2 with oesophageal squamous cell carcinoma in the South African Black population. Carcinogenesis 2019; 40:513-520. [PMID: 30753320 PMCID: PMC6556703 DOI: 10.1093/carcin/bgz026] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Revised: 12/18/2018] [Accepted: 02/07/2019] [Indexed: 12/15/2022] Open
Abstract
Oesophageal squamous cell carcinoma (OSCC) has a high incidence in southern Africa and a poor prognosis. Limited information is available on the contribution of genetic variants in susceptibility to OSCC in this region. However, recent genome-wide association studies have identified multiple susceptibility loci in Asian and European populations. In this study, we investigated genetic variants from seven OSCC risk loci identified in non-African populations for association with OSCC in the South African Black population. We performed association studies in a total of 1471 cases and 1791 controls from two study sample groups, which included 591 cases and 852 controls from the Western Cape and 880 cases and 939 controls from the Johannesburg region in the Gauteng province. Thereafter, we performed a meta-analysis for 11 variants which had been genotyped in both studies. A single nucleotide polymorphism in the CHEK2 gene, rs1033667, was significantly associated with OSCC [P = 0.002; odds ratio (OR) = 1.176; 95% confidence interval (CI): 1.06-1.30]. However, single nucleotide polymorphisms in the CASP8/ALS2CR12, TMEM173, PLCE1, ALDH2, ATP1B2/TP53 and RUNX1 loci were not associated with the disease (P > 0.05). The lack of association of six of these loci with OSCC in South African populations may reflect different genetic risk factors in non-African and African populations or differences in the genetic architecture of African genomes. The association at CHEK2, a gene with key roles in cell cycle regulation and DNA repair, in an African population provides further support for the contribution of common genetic variants at this locus to the risk of oesophageal cancer.
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Affiliation(s)
- Wenlong C Chen
- National Cancer Registry, National Health Laboratory Service, Johannesburg, South Africa
- Sydney Brenner Institute for Molecular Bioscience, University of the Witwatersrand, Johannesburg, South Africa
- Division of Human Genetics, School of Pathology, National Health Laboratory Service and University of the Witwatersrand, Johannesburg, South Africa
| | - Hannah Bye
- Department of Medical and Molecular Genetics, Faculty of Life Sciences and Medicine, King’s College London, London, United Kingdom
| | - Marco Matejcic
- Division of Medical Biochemistry and Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Ariella Amar
- Department of Medical and Molecular Genetics, Faculty of Life Sciences and Medicine, King’s College London, London, United Kingdom
| | - Dhiren Govender
- Division of Anatomical Pathology, University of Cape Town, Cape Town, South Africa
| | - Yee Wen Khew
- Department of Medical and Molecular Genetics, Faculty of Life Sciences and Medicine, King’s College London, London, United Kingdom
| | - Victoria Beynon
- Department of Medical and Molecular Genetics, Faculty of Life Sciences and Medicine, King’s College London, London, United Kingdom
| | - Robyn Kerr
- Division of Human Genetics, School of Pathology, National Health Laboratory Service and University of the Witwatersrand, Johannesburg, South Africa
| | - Elvira Singh
- National Cancer Registry, National Health Laboratory Service, Johannesburg, South Africa
- School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Natalie J Prescott
- Department of Medical and Molecular Genetics, Faculty of Life Sciences and Medicine, King’s College London, London, United Kingdom
| | - Cathryn M Lewis
- Department of Medical and Molecular Genetics, Faculty of Life Sciences and Medicine, King’s College London, London, United Kingdom
- Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology & Neuroscience, King’s College London, London, United Kingdom
| | - Chantal Babb de Villiers
- Division of Human Genetics, School of Pathology, National Health Laboratory Service and University of the Witwatersrand, Johannesburg, South Africa
| | - M Iqbal Parker
- Division of Medical Biochemistry and Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Christopher G Mathew
- Sydney Brenner Institute for Molecular Bioscience, University of the Witwatersrand, Johannesburg, South Africa
- Division of Human Genetics, School of Pathology, National Health Laboratory Service and University of the Witwatersrand, Johannesburg, South Africa
- Department of Medical and Molecular Genetics, Faculty of Life Sciences and Medicine, King’s College London, London, United Kingdom
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Dorji PW, Tshering G, Na‐Bangchang K. CYP2C9, CYP2C19, CYP2D6 and CYP3A5 polymorphisms in South‐East and East Asian populations: A systematic review. J Clin Pharm Ther 2019; 44:508-524. [DOI: 10.1111/jcpt.12835] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Revised: 02/15/2019] [Accepted: 03/10/2019] [Indexed: 12/22/2022]
Affiliation(s)
- Palden Wangyel Dorji
- Chulabhorn International College of Medicine, Rangsit Center Thammasat University Klong Luang Pathum Thani Thailand
| | - Gyem Tshering
- Chulabhorn International College of Medicine, Rangsit Center Thammasat University Klong Luang Pathum Thani Thailand
| | - Kesara Na‐Bangchang
- Chulabhorn International College of Medicine, Rangsit Center Thammasat University Klong Luang Pathum Thani Thailand
- Center of Excellence in Pharmacology and Molecular Biology of Malaria and Cholangiocarcinoma, Chulabhorn International College of Medicine, Rangsit Center Thammasat University Klong Luang Pathum Thani Thailand
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45
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Routhieaux M, Keels J, Tillery EE. The use of pharmacogenetic testing in patients with schizophrenia or bipolar disorder: A systematic review. Ment Health Clin 2018; 8:294-302. [PMID: 30397571 PMCID: PMC6213894 DOI: 10.9740/mhc.2018.11.294] [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] [Indexed: 12/20/2022] Open
Abstract
Introduction: Pharmacogenetic testing may assist in identifying an individual's risk of developing a mental illness as well as predict an individual's response to treatment. The objective of this study is to report published outcomes of pharmacogenetic testing in patients with schizophrenia or bipolar disorder. Methods: A systematic review using PubMed and EBSCOhost through April 2017 was performed to identify articles that reported pharmacogenetic testing in adult patients with either bipolar disorder or schizophrenia using the keywords pharmacy, pharmacogenomics, pharmacogenetics, psychiatry, bipolar disorder, schizophrenia, mood stabilizer, and antipsychotic. Results: A total of 18 articles were included in the final literature review. A wide variety of genes amongst adult patients with varying ethnicities were found to be correlated with the development of schizophrenia or bipolar disorder as well as response to antipsychotics and mood stabilizers. Discussion: While current studies show a correlation between genetic variations and medication response or disease predisposition for patients with schizophrenia and bipolar disorder, research is unclear on the type of therapeutic recommendations that should occur based on the results of the pharmacogenetic testing. Hopefully interpreting pharmacogenetic results will one day assist with optimizing medication recommendations for individuals with schizophrenia and bipolar disorder.
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Affiliation(s)
- Melanie Routhieaux
- PGY-1 Pharmacy Practice Resident, William Jennings Bryan Dorn VA Medical Center, Columbia, South Carolina
| | - Jessica Keels
- PGY-1 Pharmacy Practice Resident, William Jennings Bryan Dorn VA Medical Center, Columbia, South Carolina
| | - Erika E Tillery
- (Corresponding author) Associate Professor of Pharmacy Practice, Presbyterian College School of Pharmacy, Clinton, South Carolina; Clinical Psychiatric Pharmacist, Division of Inpatient Services, G. Werber Bryan Psychiatric Hospital, Columbia, South Carolina,
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46
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Storelli F, Samer C, Reny JL, Desmeules J, Daali Y. Complex Drug-Drug-Gene-Disease Interactions Involving Cytochromes P450: Systematic Review of Published Case Reports and Clinical Perspectives. Clin Pharmacokinet 2018; 57:1267-1293. [PMID: 29667038 DOI: 10.1007/s40262-018-0650-9] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Drug pharmacokinetics (PK) is influenced by multiple intrinsic and extrinsic factors, among which concomitant medications are responsible for drug-drug interactions (DDIs) that may have a clinical relevance, resulting in adverse drug reactions or reduced efficacy. The addition of intrinsic factors affecting cytochromes P450 (CYPs) activity and/or expression, such as genetic polymorphisms and diseases, may potentiate the impact and clinical relevance of DDIs. In addition, greater variability in drug levels and exposures has been observed when such intrinsic factors are present in addition to concomitant medications perpetrating DDIs. This variability results in poor predictability of DDIs and potentially dramatic clinical consequences. The present review illustrates the issue of complex DDIs using systematically searched published case reports of DDIs involving genetic polymorphisms, renal impairment, cirrhosis, and/or inflammation. Current knowledge on the impact of each of these factors on drug exposure and DDIs is summarized and future perspectives for the management of such complex DDIs in clinical practice are discussed, including the use of advanced Computerized Physician Order Entry (CPOE) systems, the development of model-based dose optimization strategies, and the education of healthcare professionals with respect to personalized medicine.
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Affiliation(s)
- Flavia Storelli
- Division of Clinical Pharmacology and Toxicology, Geneva University Hospitals, University of Geneva, Geneva, Switzerland
- Geneva-Lausanne School of Pharmacy, University of Geneva, Geneva, Switzerland
| | - Caroline Samer
- Division of Clinical Pharmacology and Toxicology, Geneva University Hospitals, University of Geneva, Geneva, Switzerland
- Faculty of Medicine, University of Geneva, Geneva, Switzerland
- Swiss Center for Applied Human Toxicology, Geneva, Switzerland
| | - Jean-Luc Reny
- Faculty of Medicine, University of Geneva, Geneva, Switzerland
- Department of Internal Medicine, Rehabilitation and Geriatrics, Geneva University Hospitals, University of Geneva, Geneva, Switzerland
| | - Jules Desmeules
- Division of Clinical Pharmacology and Toxicology, Geneva University Hospitals, University of Geneva, Geneva, Switzerland
- Geneva-Lausanne School of Pharmacy, University of Geneva, Geneva, Switzerland
- Faculty of Medicine, University of Geneva, Geneva, Switzerland
- Swiss Center for Applied Human Toxicology, Geneva, Switzerland
| | - Youssef Daali
- Division of Clinical Pharmacology and Toxicology, Geneva University Hospitals, University of Geneva, Geneva, Switzerland.
- Geneva-Lausanne School of Pharmacy, University of Geneva, Geneva, Switzerland.
- Faculty of Medicine, University of Geneva, Geneva, Switzerland.
- Swiss Center for Applied Human Toxicology, Geneva, Switzerland.
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Economic burden of adverse drug reactions and potential for pharmacogenomic testing in Singaporean adults. THE PHARMACOGENOMICS JOURNAL 2018; 19:401-410. [PMID: 30250149 DOI: 10.1038/s41397-018-0053-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Revised: 07/03/2018] [Accepted: 08/10/2018] [Indexed: 01/12/2023]
Abstract
Adverse drug reactions (ADRs) contribute to hospitalization but data on its economic burden is scant. Pre-emptive pharmacogenetic (PGx) testing can potentially reduce ADRs and its associated costs. The objectives of this study were to quantify the economic burden of ADRs and to estimate the breakeven cost of pre-emptive PGx testing in Singapore. We collected itemized costs for 1000 random non-elective hospitalizations of adults admitted to a tertiary-care general hospital in Singapore. The presence of ADRs at admission and their clinical characteristics were reported previously. The economic burden of ADRs was assessed from two perspectives: (1) Total cost and (2) incremental costs. The breakeven cost of PGx testing was estimated by dividing avoidable hospitalization costs for ADRs due to selected drugs by the number of patients taking those drugs. The total cost of 81 admissions caused by ADRs was US$570,404. Costs were significantly higher for bleeding/elevated international normalized ratio (US$9906 vs. US$2251, p = 6.58 × 10-3) compared to other ADRs, and for drugs acting on the blood coagulation system (US$9884 vs. US$2229, p = 4.41 × 10-3) compared to other drug classes. There were higher incremental laboratory costs due to ADRs causing or being present at admission. The estimated breakeven cost of a pre-emptive PGx test for patients taking warfarin, clopidogrel, chemotherapeutic and neuropsychiatric drugs was US$114 per patient. These results suggest that future studies designed to directly measure the clinical and cost impact of a pre-emptive genotyping program will help inform clinical practice and health policy decisions.
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48
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Byeon JY, Kim YH, Lee CM, Kim SH, Chae WK, Jung EH, Choi CI, Jang CG, Lee SY, Bae JW, Lee YJ. CYP2D6 allele frequencies in Korean population, comparison with East Asian, Caucasian and African populations, and the comparison of metabolic activity of CYP2D6 genotypes. Arch Pharm Res 2018; 41:921-930. [PMID: 30191460 DOI: 10.1007/s12272-018-1075-6] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Accepted: 08/30/2018] [Indexed: 01/09/2023]
Abstract
Cytochrome P450 (CYP) 2D6 is present in less than about 2% of all CYP enzymes in the liver, but it is involved in the metabolism of about 25% of currently used drugs. CYP2D6 is the most polymorphic among the CYP enzymes. We determined alleles and genotypes of CYP2D6 in 3417 Koreans, compared the frequencies of CYP2D6 alleles with other populations, and observed the differences in pharmacokinetics of metoprolol, a prototype CYP2D6 substrate, depending on CYP2D6 genotype. A total of 3417 unrelated healthy subjects were recruited for the genotyping of CYP2D6 gene. Among them, 42 subjects with different CYP2D6 genotypes were enrolled in the pharmacokinetic study of metoprolol. The functional allele *1 and *2 were present in frequencies of 34.6 and 11.8%, respectively. In decreased functional alleles, *10 was the most frequent with 46.2% and *41 allele was present in 1.4%. The nonfunctional alleles *5 and *14 were present at 4.5 and 0.5% frequency, respectively. The *X × N allele was present at a frequency of 1.0%. CYP2D6*1/*1, *1/*2 and *2/*2 genotypes with normal enzyme activity were present in 12.1%, 8.6% and 1.4% of the subjects, respectively. CYP2D6*5/*5, *5/*14, and *14/*14 genotypes classified as poor metabolizer were only present in 4, 2, and 1 subjects, respectively. Mutant genotypes with frequencies of more than 1% were CYP2D6*1/*10 (32.0%), *10/*10 (22.3%), *2/*10 (11.7%), *5/*10 (3.7%), *1/*5 (2.5%), and *10/*41 (1.2%). The relative clearance of metoprolol in CYP2D6*1/*10, *1/*5, *10/*10, *5/*10, and *5/*5 genotypes were 69%, 57%, 24%, 14% and 9% of CYP2D6*wt/*wt genotype, respectively. These results will be very useful in establishing a strategy for precision medicine related to the genetic polymorphism of CYP2D6.
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Affiliation(s)
- Ji-Young Byeon
- School of Pharmacy, Sungkyunkwan University, Suwon, 16419, Republic of Korea
| | - Young-Hoon Kim
- School of Pharmacy, Sungkyunkwan University, Suwon, 16419, Republic of Korea
| | - Choong-Min Lee
- School of Pharmacy, Sungkyunkwan University, Suwon, 16419, Republic of Korea
| | - Se-Hyung Kim
- School of Pharmacy, Sungkyunkwan University, Suwon, 16419, Republic of Korea
| | - Won-Ki Chae
- School of Pharmacy, Sungkyunkwan University, Suwon, 16419, Republic of Korea
| | - Eui-Hyun Jung
- School of Pharmacy, Sungkyunkwan University, Suwon, 16419, Republic of Korea
| | - Chang-Ik Choi
- College of Pharmacy, Dongguk University-Seoul, Goyang, 10326, Republic of Korea
| | - Choon-Gon Jang
- School of Pharmacy, Sungkyunkwan University, Suwon, 16419, Republic of Korea
| | - Seok-Yong Lee
- School of Pharmacy, Sungkyunkwan University, Suwon, 16419, Republic of Korea.
| | - Jung-Woo Bae
- College of Pharmacy, Keimyung University, Daegu, 42601, Republic of Korea.
| | - Yun Jeong Lee
- College of Pharmacy, Dankook University, Cheonan, 31116, Republic of Korea.
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49
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Chang WA, Sheu CC, Liu KT, Shen JH, Yen MC, Kuo PL. Identification of mutations in SLC4A1, GP1BA and HFE in a family with venous thrombosis of unknown cause by next-generation sequencing. Exp Ther Med 2018; 16:4172-4180. [PMID: 30344693 DOI: 10.3892/etm.2018.6693] [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] [Received: 02/12/2018] [Accepted: 05/17/2018] [Indexed: 12/28/2022] Open
Abstract
Various risk factors, including high age, female gender, obesity and certain genetic defects have been linked to venous thrombosis. A Taiwanese family with venous thrombosis of unknown cause were enrolled in the present study. In this pedigree, two women without any specific underlying diseases suffered from venous thrombotic events at the same age. No specific risk factors or coagulation abnormalities were identified. The main proband's younger brother also had intestinal arterial thrombosis at 54 years of age. Therefore, it was hypothesized that familial genetic defects may be the cause of venous thrombosis within this family. Blood samples collected from certain members of this pedigree were subjected to whole-exome sequencing, and three genetic variants were identified, including a missense variant of solute carrier family 4 member 1 (SLC4A1) (c.388G>A), a deletion on glycoprotein Ib platelet α subunit (GP1BA) (c.1322_1344del23) and an insertion in the splice site of homeostatic iron regulator (HFE). To date, none of these three genetic variants have been reported to be associated with venous thrombosis, to the best of our knowledge. The present study suggests that these genetic variants of SLC4A1, GP1BA and HFE may be associated with venous thrombosis in an Asian pedigree.
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Affiliation(s)
- Wei-An Chang
- Graduate Institute of Clinical Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan, R.O.C.,Division of Pulmonary and Critical Care Medicine, Kaohsiung Medical University Hospital, Kaohsiung 807, Taiwan, R.O.C
| | - Chau-Chyun Sheu
- Graduate Institute of Clinical Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan, R.O.C.,Division of Pulmonary and Critical Care Medicine, Kaohsiung Medical University Hospital, Kaohsiung 807, Taiwan, R.O.C.,School of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan, R.O.C
| | - Kuan-Ting Liu
- Graduate Institute of Clinical Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan, R.O.C.,School of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan, R.O.C.,Department of Emergency Medicine, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 807, Taiwan, R.O.C
| | - Jheng-Heng Shen
- Graduate Institute of Clinical Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan, R.O.C.,Department of Emergency Medicine, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 807, Taiwan, R.O.C
| | - Meng-Chi Yen
- Graduate Institute of Clinical Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan, R.O.C.,Department of Emergency Medicine, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 807, Taiwan, R.O.C
| | - Po-Lin Kuo
- Graduate Institute of Clinical Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan, R.O.C
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Burbulis IE, Wierman MB, Wolpert M, Haakenson M, Lopes MB, Schiff D, Hicks J, Loe J, Ratan A, McConnell MJ. Improved molecular karyotyping in glioblastoma. Mutat Res 2018; 811:16-26. [PMID: 30055482 DOI: 10.1016/j.mrfmmm.2018.06.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Revised: 06/22/2018] [Accepted: 06/24/2018] [Indexed: 06/08/2023]
Abstract
Uneven replication creates artifacts during whole genome amplification (WGA) that confound molecular karyotype assignment in single cells. Here, we present an improved WGA recipe that increased coverage and detection of copy number variants (CNVs) in single cells. We examined serial resections of glioblastoma (GBM) tumor from the same patient and found low-abundance clones containing CNVs in clinically relevant loci that were not observable using bulk DNA sequencing. We discovered extensive genomic variability in this class of tumor and provide a practical approach for investigating somatic mosaicism.
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Affiliation(s)
- Ian E Burbulis
- Department of Biochemistry and Molecular Genetics, University of Virginia, School of Medicine, Charlottesville, VA, United States; Escuela de Medicina, Universidad San Sebastian, Puerto Montt, Chile
| | - Margaret B Wierman
- Department of Biochemistry and Molecular Genetics, University of Virginia, School of Medicine, Charlottesville, VA, United States
| | - Matt Wolpert
- Department of Biochemistry and Molecular Genetics, University of Virginia, School of Medicine, Charlottesville, VA, United States
| | - Mark Haakenson
- Department of Biochemistry and Molecular Genetics, University of Virginia, School of Medicine, Charlottesville, VA, United States
| | - Maria-Beatriz Lopes
- Department of Pathology, University of Virginia, School of Medicine, Charlottesville, VA, United States
| | - David Schiff
- Department of Neurology, University of Virginia, School of Medicine, Charlottesville, VA, United States
| | - James Hicks
- Michelson Center, University of Southern California, Los Angeles, CA, United States; Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, United States
| | - Justin Loe
- Full Genomes Corp, Inc., Rockville, MD, United States
| | - Aakrosh Ratan
- Department of Biochemistry and Molecular Genetics, University of Virginia, School of Medicine, Charlottesville, VA, United States; Center for Public Health Genomics, University of Virginia, School of Medicine, Charlottesville, VA, United States
| | - Michael J McConnell
- Department of Biochemistry and Molecular Genetics, University of Virginia, School of Medicine, Charlottesville, VA, United States; Department of Neuroscience, University of Virginia, School of Medicine, Charlottesville, VA, United States; Center for Public Health Genomics, University of Virginia, School of Medicine, Charlottesville, VA, United States; Center for Brain Immunology and Glia, University of Virginia, School of Medicine, Charlottesville, VA, United States.
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