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Yang C, Zhang G, Shu C, Lv L, Liu Z, Tian Y, Tan Q, Wang Z, Hu S, Yang L, Sun N. Exploring CYP2D6 polymorphisms and angiotensin receptor blocker response in the Bai hypertensive population. Pharmacogenet Genomics 2024; 34:199-208. [PMID: 38848263 PMCID: PMC11221794 DOI: 10.1097/fpc.0000000000000537] [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: 01/25/2024] [Accepted: 04/30/2024] [Indexed: 06/09/2024]
Abstract
OBJECTIVE The CYP2D6 enzyme is crucial for the metabolism and disposition of a variety of drugs. This study was conducted to examine the relationship between CYP2D6 gene polymorphisms and the response to angiotensin receptor blocker (ARB)-based treatment in patients of Chinese Bai ethnicity with hypertension. METHODS Seventy-two hypertensive adults from the Chinese Bai ethnic group, exhibiting systolic blood pressure (SBP) ≥ 140 mmHg or diastolic blood pressure (DBP) ≥ 90 mmHg, were recruited. Targeted regional sequencing was utilized to genotype single nucleotide polymorphisms in the CYP2D6 gene, aiming to assess their frequency and to evaluate their influence on the therapeutic efficacy of ARB medications. RESULTS Our research identified nine significant CYP2D6 polymorphisms associated with the efficacy of ARB treatment in the Bai hypertensive cohort. Specifically, patients possessing certain mutant genotype at rs111564371 exhibited substantially greater reductions in SBP and DBP, with P -values of 0.021 and 0.016, respectively, compared to those carrying the wild genotype. Additionally, these mutant genotype at rs111564371 and rs112568578 were linked to approximately 20% higher overall efficacy rates and a 10% increased achievement rate relative to the wild genotype. CONCLUSION Our research with the Bai hypertensive group shows that certain CYP2D6 polymorphisms significantly influence ARB treatment outcomes. Mutations at rs111564371 led to better blood pressure control ( P -values: 0.021 for SBP, 0.016 for DBP), improving ARB efficacy by appromixately 20% and increasing treatment goal achievement by 10% over the wild-type genotype. STATEMENTS Our investigation into CYP2D6 polymorphisms within the Bai hypertensive cohort marks a substantial advancement towards personalized healthcare, underscoring the pivotal influence of genetic constitution on the effectiveness of ARB therapy.
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Affiliation(s)
| | | | - Chang Shu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences
| | - Linxi Lv
- Dali First People’s Hospital, Yunnan
| | | | - Yan Tian
- Beijing E-Seq Medical Technology Co. Ltd
| | - Qi Tan
- Beijing HuaGengYuan Pharmacogenomics Research Institute Co., Ltd
| | - Zhaobin Wang
- Beijing HuaGengYuan Pharmacogenomics Research Institute Co., Ltd
| | - Songnian Hu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences
- University of Chinese Academy of Sciences
| | - Libo Yang
- Dali First People’s Hospital, Yunnan
| | - Ningling Sun
- Department of Hypertension, People’s Hospital, Peking University, Beijing, China
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Duarte JD, Thomas CD, Lee CR, Huddart R, Agundez JAG, Baye JF, Gaedigk A, Klein TE, Lanfear DE, Monte AA, Nagy M, Schwab M, Stein CM, Uppugunduri CRS, van Schaik RHN, Donnelly RS, Caudle KE, Luzum JA. Clinical Pharmacogenetics Implementation Consortium Guideline (CPIC) for CYP2D6, ADRB1, ADRB2, ADRA2C, GRK4, and GRK5 Genotypes and Beta-Blocker Therapy. Clin Pharmacol Ther 2024. [PMID: 38951961 DOI: 10.1002/cpt.3351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Accepted: 05/30/2024] [Indexed: 07/03/2024]
Abstract
Beta-blockers are widely used medications for a variety of indications, including heart failure, myocardial infarction, cardiac arrhythmias, and hypertension. Genetic variability in pharmacokinetic (e.g., CYP2D6) and pharmacodynamic (e.g., ADRB1, ADRB2, ADRA2C, GRK4, GRK5) genes have been studied in relation to beta-blocker exposure and response. We searched and summarized the strength of the evidence linking beta-blocker exposure and response with the six genes listed above. The level of evidence was high for associations between CYP2D6 genetic variation and both metoprolol exposure and heart rate response. Evidence indicates that CYP2D6 poor metabolizers experience clinically significant greater exposure and lower heart rate in response to metoprolol compared with those who are not poor metabolizers. Therefore, we provide therapeutic recommendations regarding genetically predicted CYP2D6 metabolizer status and metoprolol therapy. However, there was insufficient evidence to make therapeutic recommendations for CYP2D6 and other beta-blockers or for any beta-blocker and the other five genes evaluated (updates at www.cpicpgx.org).
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Affiliation(s)
- Julio D Duarte
- Department of Pharmacotherapy and Translational Research, University of Florida College of Pharmacy, Gainesville, Florida, USA
- Center for Pharmacogenomics and Precision Medicine, University of Florida, Gainesville, Florida, USA
| | - Cameron D Thomas
- Department of Pharmacotherapy and Translational Research, University of Florida College of Pharmacy, Gainesville, Florida, USA
- Center for Pharmacogenomics and Precision Medicine, University of Florida, Gainesville, Florida, USA
| | - Craig R Lee
- Division of Pharmacotherapy and Experimental Therapeutics, University of North Carolina Eshelman School of Pharmacy, Chapel Hill, North Carolina, USA
| | - Rachel Huddart
- Department of Biomedical Data Science, Stanford University, Stanford, California, USA
| | - Jose A G Agundez
- Institute of Molecular Pathology Biomarkers, University of Extremadura, Cáceres, Spain
| | - Jordan F Baye
- Department of Pharmacy Practice, South Dakota State University College of Pharmacy & Allied Health Professions, Brookings, South Dakota, USA
- Sanford Imagenetics, Sioux Falls, South Dakota, USA
| | - Andrea Gaedigk
- Division of Clinical Pharmacology, Toxicology & Therapeutic Innovation, Children's Mercy Research Institute and School of Medicine, University of Missouri-Kansas City, Kansas City, Missouri, USA
| | - Teri E Klein
- Department of Biomedical Data Science, Stanford University, Stanford, California, USA
| | - David E Lanfear
- Center for Individualized and Genomic Medicine Research (CIGMA), Henry Ford Hospital, Detroit, Michigan, USA
- Heart and Vascular Institute, Henry Ford Health, Detroit, Michigan, USA
| | - Andrew A Monte
- Department of Emergency Medicine, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Mohamed Nagy
- Department of Pharmaceutical Services, Children's Cancer Hospital Egypt 57357, Cairo, Egypt
- Personalized Medication Management Unit, Children's Cancer Hospital Egypt 57357, Cairo, Egypt
| | - Matthias Schwab
- Dr. Margarete Fischer-Bosch-Institute of Clinical Pharmacology, Stuttgart, Germany
- Department of Clinical Pharmacology, University Hospital Tuebingen, Tuebingen, Germany
- Department of Biochemistry and Pharmacy, University Tuebingen, Tuebingen, Germany
| | - C Michael Stein
- Division of Clinical Pharmacology, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
- Department of Pharmacology, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Chakradhara Rao S Uppugunduri
- Division of Pediatric Oncology and Hematology, Department of Women, Child and Adolescent, University Geneva Hospitals, Geneva, Switzerland
- Department of Pediatrics, Gynecology and Obstetrics, Cansearch Research Platform for Pediatric Oncology and Hematology, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Ron H N van Schaik
- Department of Clinical Chemistry, Erasmus MC University Medical Center, Rotterdam, The Netherlands
| | - Roseann S Donnelly
- Department of Pharmacy Practice, Massachusetts College of Pharmacy and Health Sciences, Boston, Massachusetts, USA
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Kelly E Caudle
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Jasmine A Luzum
- Center for Individualized and Genomic Medicine Research (CIGMA), Henry Ford Hospital, Detroit, Michigan, USA
- Department of Clinical Pharmacy, University of Michigan College of Pharmacy, Ann Arbor, Michigan, USA
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3
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Wang Z, Gao Y, Ji X, Wu T, Pu L, Qiu W. Effects of CYP2D6 *10 and *41 Variants in Healthy Chinese Men on the Pharmacokinetics of Dapoxetine. J Clin Pharmacol 2024; 64:601-608. [PMID: 38059315 DOI: 10.1002/jcph.2391] [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: 09/28/2023] [Accepted: 12/04/2023] [Indexed: 12/08/2023]
Abstract
Dapoxetine is a selective serotonin reuptake inhibitor (SSRI) used to treat premature ejaculation (PE), and is mainly metabolized by CYP2D6, CYP3A4, and flavin-containing monooxygenase 1. The purpose of the study was to evaluate the effect of CYP2D6 polymorphism on the pharmacokinetics of dapoxetine in healthy Chinese men. Thirty-nine subjects who received a single oral dose of 30 mg dapoxetine hydrochloride were classified based on their CYP2D6 genotype: *1/*1 (n = 9), *1/*41 (n = 1), *1/*10 (n = 12), *10/*41 (n = 3), or *10/*10 (n = 14). The difference in pharmacokinetic parameters between different genotype groups was analyzed and then scored according to the activity score system. Compared with the wild-type subjects of CYP2D6 *1/*1, the peak plasma concentration (Cmax) and the area under the plasma drug concentration-time curve (AUCinf) of dapoxetine in the *10/*10 and *10/*41 groups were notably increased (P ≤ .05). Significant differences in Cmax, AUC, volume of distribution/bioavailability (V/F) and clearance/bioavailability (CL/F) were observed among dapoxetine activity score groups (P ≤ .05). The AUCinf was increased significantly (154% and 89.73%, P ≤ .05) and the Cmax was increased significantly (73.45% and 42.67%, P ≤ .05) in CYP2D6 *10/*41 subjects, compared with CYP2D6 *1/*1 and *1/*10 subjects. The results obtained indicated that CYP2D6 *10 and *41 polymorphisms have significant effects on the pharmacokinetic properties of dapoxetine.
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Affiliation(s)
- Zhipeng Wang
- School of Pharmacy Lanzhou University, Lanzhou, Gansu, China
| | - Yuan Gao
- School of Pharmacy Lanzhou University, Lanzhou, Gansu, China
| | - Xingfang Ji
- School of Pharmacy Lanzhou University, Lanzhou, Gansu, China
| | - Tong Wu
- School of Pharmacy Lanzhou University, Lanzhou, Gansu, China
| | - Libin Pu
- School of Pharmacy Lanzhou University, Lanzhou, Gansu, China
| | - Wen Qiu
- National Drug Clinical Trial Institution, Lanzhou University Second Hospital, Lanzhou, Gansu, China
- Pharmacy Department, Lanzhou University Second Hospital, Lanzhou, Gansu, China
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Shen C, Yang H, Shao W, Zheng L, Zhang W, Xie H, Jiang X, Wang L. Physiologically Based Pharmacokinetic Modeling to Unravel the Drug-gene Interactions of Venlafaxine: Based on Activity Score-dependent Metabolism by CYP2D6 and CYP2C19 Polymorphisms. Pharm Res 2024; 41:731-749. [PMID: 38443631 DOI: 10.1007/s11095-024-03680-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2023] [Accepted: 02/19/2024] [Indexed: 03/07/2024]
Abstract
BACKGROUND Venlafaxine (VEN) is a commonly utilized medication for alleviating depression and anxiety disorders. The presence of genetic polymorphisms gives rise to considerable variations in plasma concentrations across different phenotypes. This divergence in phenotypic responses leads to notable differences in both the efficacy and tolerance of the drug. PURPOSE A physiologically based pharmacokinetic (PBPK) model for VEN and its metabolite O-desmethylvenlafaxine (ODV) to predict the impact of CYP2D6 and CYP2C19 gene polymorphisms on VEN pharmacokinetics (PK). METHODS The parent-metabolite PBPK models for VEN and ODV were developed using PK-Sim® and MoBi®. Leveraging prior research, derived and implemented CYP2D6 and CYP2C19 activity score (AS)-dependent metabolism to simulate exposure in the drug-gene interactions (DGIs) scenarios. The model's performance was evaluated by comparing predicted and observed values of plasma concentration-time (PCT) curves and PK parameters values. RESULTS In the base models, 91.1%, 94.8%, and 94.6% of the predicted plasma concentrations for VEN, ODV, and VEN + ODV, respectively, fell within a twofold error range of the corresponding observed concentrations. For DGI scenarios, these values were 81.4% and 85% for VEN and ODV, respectively. Comparing CYP2D6 AS = 2 (normal metabolizers, NM) populations to AS = 0 (poor metabolizers, PM), 0.25, 0.5, 0.75, 1.0 (intermediate metabolizers, IM), 1.25, 1.5 (NM), and 3.0 (ultrarapid metabolizers, UM) populations in CYP2C19 AS = 2.0 group, the predicted DGI AUC0-96 h ratios for VEN were 3.65, 3.09, 2.60, 2.18, 1.84, 1.56, 1.34, 0.61, and for ODV, they were 0.17, 0.35, 0.51, 0.64, 0.75, 0.83, 0.90, 1.11, and the results were similar in other CYP2C19 groups. It should be noted that PK differences in CYP2C19 phenotypes were not similar across different CYP2D6 groups. CONCLUSIONS In clinical practice, the impact of genotyping on the in vivo disposition process of VEN should be considered to ensure the safety and efficacy of treatment.
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Affiliation(s)
- Chaozhuang Shen
- Department of Clinical Pharmacy and Pharmacy Administration, School of Pharmacy, Sichuan University, Chengdu, 610064, West China, China
| | - Hongyi Yang
- Department of Clinical Pharmacy and Pharmacy Administration, School of Pharmacy, Sichuan University, Chengdu, 610064, West China, China
| | - Wenxin Shao
- Anhui Provincial Center for Drug Clinical Evaluation, Yijishan Hospital of Wannan Medical College, Wuhu, 241001, Anhui, China
| | - Liang Zheng
- Department of Clinical Pharmacology, The Second Affiliated Hospital of Anhui Medical University, Hefei, 230601, Anhui, China
| | - Wei Zhang
- Department of Clinical Pharmacology, The Second Affiliated Hospital of Anhui Medical University, Hefei, 230601, Anhui, China
| | - Haitang Xie
- Anhui Provincial Center for Drug Clinical Evaluation, Yijishan Hospital of Wannan Medical College, Wuhu, 241001, Anhui, China
| | - Xuehua Jiang
- Department of Clinical Pharmacy and Pharmacy Administration, School of Pharmacy, Sichuan University, Chengdu, 610064, West China, China
| | - Ling Wang
- Department of Clinical Pharmacy and Pharmacy Administration, School of Pharmacy, Sichuan University, Chengdu, 610064, West China, China.
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Walton M, Wagner JB. Pediatric Beta Blocker Therapy: A Comprehensive Review of Development and Genetic Variation to Guide Precision-Based Therapy in Children, Adolescents, and Young Adults. Genes (Basel) 2024; 15:379. [PMID: 38540438 PMCID: PMC10969836 DOI: 10.3390/genes15030379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Revised: 03/08/2024] [Accepted: 03/15/2024] [Indexed: 06/14/2024] Open
Abstract
Beta adrenergic receptor antagonists, known as beta blockers, are one of the most prescribed medications in both pediatric and adult cardiology. Unfortunately, most of these agents utilized in the pediatric clinical setting are prescribed off-label. Despite regulatory efforts aimed at increasing pediatric drug labeling, a majority of pediatric cardiovascular drug agents continue to lack pediatric-specific data to inform precision dosing for children, adolescents, and young adults. Adding to this complexity is the contribution of development (ontogeny) and genetic variation towards the variability in drug disposition and response. In the absence of current prospective trials, the purpose of this comprehensive review is to illustrate the current knowledge gaps regarding the key drivers of variability in beta blocker drug disposition and response and the opportunities for investigations that will lead to changes in pediatric drug labeling.
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Affiliation(s)
- Mollie Walton
- Ward Family Heart Center, Kansas City, MO 64108, USA
| | - Jonathan B. Wagner
- Ward Family Heart Center, Kansas City, MO 64108, USA
- Division of Clinical Pharmacology, Toxicology and Therapeutic Innovation, Children’s Mercy, 2401 Gillham Road, Kansas City, MO 64108, USA
- Department of Pediatrics, University of Missouri-Kansas City School of Medicine, Kansas City, MO 64108, USA
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Shilbayeh SAR, Adeen IS, Alhazmi AS, Aljurayb H, Altokhais RS, Alhowaish N, Aldilaijan KE, Kamal M, Alnakhli AM. The polymorphisms of candidate pharmacokinetic and pharmacodynamic genes and their pharmacogenetic impacts on the effectiveness of risperidone maintenance therapy among Saudi children with autism. Eur J Clin Pharmacol 2024:10.1007/s00228-024-03658-w. [PMID: 38421437 DOI: 10.1007/s00228-024-03658-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 02/22/2024] [Indexed: 03/02/2024]
Abstract
BACKGROUND Antipsychotics, including risperidone (RIS), are frequently indicated for various autism spectrum disorder (ASD) manifestations; however, "actionable" PGx testing in psychiatry regarding antipsychotic dosing and selection has limited applications in routine clinical practice because of the lack of standard guidelines, mostly due to the inconsistency and scarcity of genetic variant data. The current study is aimed at examining the association of RIS effectiveness, according to ABC-CV and CGI indexes, with relevant pharmacokinetics (PK) and pharmacodynamics (PD) genes. METHODS Eighty-nine ASD children who received a consistent RIS-based regimen for at least 8 weeks were included. The Axiom PharmacoFocus Array technique was employed to generate accurate star allele-predicted phenotypes of 3 PK genes (CYP3A4, CYP3A5, and CYP2D6). Genotype calls for 5 candidate PD receptor genes (DRD1, DRD2, DRD3, HTR2C, and HTR2A) were obtained and reported as wild type, heterozygous, or homozygous for 11 variants. RESULTS Based on the ABC total score, 42 (47.2%) children were classified as responders, while 47 (52.8%) were classified as nonresponders. Multivariate logistic regression analyses, adjusted for nongenetic factors, suggested nonsignificant impacts of the star allele-predicted phenotypes of all 3 PK genes on improvement in ASD symptoms or CGI scores. However, significant positive or negative associations of certain PD variants involved in dopaminergic and serotonergic pathways were observed with specific ASD core and noncore symptom subdomains. Our significant polymorphism findings, mainly those in DRD2 (rs1800497, rs1799978, and rs2734841), HTR2C (rs3813929), and HTR2A (rs6311), were largely consistent with earlier findings (predictors of RIS effectiveness in adult schizophrenia patients), confirming their validity for identifying ASD children with a greater likelihood of core symptom improvement compared to noncarriers/wild types. Other novel findings of this study, such as significant improvements in DRD3 rs167771 carriers, particularly in ABC total and lethargy/social withdrawal scores, and DRD1 rs1875964 homozygotes and DRD2 rs1079598 wild types in stereotypic behavior, warrant further verification in biochemical and clinical studies to confirm their feasibility for inclusion in a PGx panel. CONCLUSION In conclusion, we provide evidence of potential genetic markers involved in clinical response variability to RIS therapy in ASD children. However, replication in prospective samples with greater ethnic diversity and sample sizes is necessary.
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Affiliation(s)
- Sireen Abdul Rahim Shilbayeh
- Department of Pharmacy Practice, College of Pharmacy, Princess Nourah bint Abdulrahman University, Riyadh, Saudi Arabia.
| | - Iman Sharaf Adeen
- Department of Pediatric Behavior and Development and Adolescent Medicine, King Fahad Medical City, Riyadh, Saudi Arabia
| | - Ayman Shawqi Alhazmi
- Department of Pediatric Behavior and Development and Adolescent Medicine, King Saud Medical City, Riyadh, Saudi Arabia
| | - Haya Aljurayb
- Molecular Pathology Laboratory, Pathology and Clinical Laboratory Medicine Administration, King Fahad Medical City, Riyadh, Saudi Arabia
| | - Rana Saad Altokhais
- Department of Pediatric Behavior and Development and Adolescent Medicine, King Fahad Medical City, Riyadh, Saudi Arabia
| | - Nourah Alhowaish
- Department of Prevention and Research, King Abdullah International Medical Research Center (KAIMRC), King Abdulaziz Medical City, Ministry of National Guard - Health Affairs, Riyadh, Saudi Arabia
| | - Khawlah Essa Aldilaijan
- Health Sciences Research Center, King Abdullah Bin Abdulaziz University Hospital, Princess Nourah bint Abdulrahman University, Riyadh, Saudi Arabia
| | - Mostafa Kamal
- Department of Life Science Application Support, Gulf Scientific Corporation, Riyadh, Saudi Arabia
| | - Anwar Mansour Alnakhli
- Department of Pharmaceutical Sciences, College of Pharmacy, Princess Nourah bint Abdulrahman University, Riyadh, Saudi Arabia
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Stern S, Hyland PL, Pacanowski M, Schuck RN. Leveraging in Vitro Models for Clinically Relevant Rare CYP2D6 Variants in Pharmacogenomics. Drug Metab Dispos 2024; 52:159-170. [PMID: 38167410 PMCID: PMC10877705 DOI: 10.1124/dmd.123.001512] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 11/09/2023] [Accepted: 12/19/2023] [Indexed: 01/05/2024] Open
Abstract
Cytochrome P450 2D6 (CYP2D6) is responsible for the metabolism of up to 20% of small-molecule drugs and therefore, may impact the safety and efficacy of medicines in broad therapeutic areas. CYP2D6 is highly polymorphic, and the frequency of variants can differ across racial and ethnic populations, significantly affecting enzymatic function and drug metabolism. However, rare variants of CYP2D6 present a unique challenge for academia, industry, and regulatory agencies alike due to the lack of feasibility of characterizing their clinical relevance in clinical trials, particularly in variants that exhibit population-specific frequencies in racial and ethnic groups that are poorly represented in clinical trials. Despite significant advancement in pharmacogenomics, the substrate specificity and related clinical relevance of these CYP2D6 rare variants remain largely unclear, and further efforts are warranted to characterize the burden of these variants on adverse drug reactions and drug efficacy. Thus, cell-based in vitro systems can be used to inform substrate-specific effects and the overall relevance of a rare variant. Liver microsomes, cell-based expression systems, ex vivo primary samples, and purified variant protein have all been used with various substrates to potentially predict the clinical impact of new substrates. In this review, we identify rare variants of CYP2D6 that demonstrate differences across races in prevalence and thus are often unassessed in clinical trials. Accordingly, we examine current pharmacogenomic in vitro models used to analyze the functional impact of these rare variants in a substrate-specific manner. SIGNIFICANCE STATEMENT: Variants of CYP2D6 play a clinically relevant role in drug metabolism, leading to potential safety and efficacy concerns. Although the influence of prevalent variants is often well characterized, rare variants are traditionally not included in clinical trials. This review captures the clinical relevance of rare variants in CYP2D6 by highlighting in vitro models that analyze their impact on the metabolism of CYP2D6 substrates.
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Affiliation(s)
- Sydney Stern
- Center for Drug Evaluation and Research, Office of Translational Science, Office of Clinical Pharmacology, US Food and Drug Administration, Silver Spring, Maryland
| | - Paula L Hyland
- Center for Drug Evaluation and Research, Office of Translational Science, Office of Clinical Pharmacology, US Food and Drug Administration, Silver Spring, Maryland
| | - Michael Pacanowski
- Center for Drug Evaluation and Research, Office of Translational Science, Office of Clinical Pharmacology, US Food and Drug Administration, Silver Spring, Maryland
| | - Robert N Schuck
- Center for Drug Evaluation and Research, Office of Translational Science, Office of Clinical Pharmacology, US Food and Drug Administration, Silver Spring, Maryland
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Biswas M, Vanwong N, Sukasem C. Pharmacogenomics and non-genetic factors affecting drug response in autism spectrum disorder in Thai and other populations: current evidence and future implications. Front Pharmacol 2024; 14:1285967. [PMID: 38375208 PMCID: PMC10875059 DOI: 10.3389/fphar.2023.1285967] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Accepted: 12/26/2023] [Indexed: 02/21/2024] Open
Abstract
Autism spectrum disorder (ASD) may affect family and social life profoundly. Although there is no selective pharmacotherapy for ASD, the Food and Drug Administration (FDA) has recommended risperidone/aripiprazole to treat the associated symptoms of ASD, such as agitation/irritability. Strong associations of some pharmacokinetic/pharmacodynamic gene variants, e.g., CYP2D6 and DRD2, with risperidone-induced hyperprolactinemia have been found in children with ASD, but such strong genetic associations have not been found directly for aripiprazole in ASD. In addition to pharmacogenomic (PGx) factors, drug-drug interactions (DDIs) and possibly cumulative effects of DDIs and PGx may affect the safety or effectiveness of risperidone/aripiprazole, which should be assessed in future clinical studies in children with ASD. Reimbursement, knowledge, and education of healthcare professionals are the key obstacles preventing the successful implementation of ASD pharmacogenomics into routine clinical practice. The preparation of national and international PGx-based dosing guidelines for risperidone/aripiprazole based on robust evidence may advance precision medicine for ASD.
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Affiliation(s)
- Mohitosh Biswas
- Department of Pharmacy, University of Rajshahi, Rajshahi, Bangladesh
- Division of Pharmacogenomics and Personalized Medicine, Department of Pathology, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
- Laboratory for Pharmacogenomics, Ramathibodi Hospital, Somdech Phra Debaratana Medical Center SDMC, Bangkok, Thailand
| | - Natchaya Vanwong
- Department of Clinical Chemistry, Faculty of Allied Health Sciences, Chulalongkorn University, Bangkok, Thailand
- Cardiovascular Precision Medicine Research Group, Special Task Force of Activating Research (STAR), Chulalongkorn University, Bangkok, Thailand
| | - Chonlaphat Sukasem
- Division of Pharmacogenomics and Personalized Medicine, Department of Pathology, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
- Laboratory for Pharmacogenomics, Ramathibodi Hospital, Somdech Phra Debaratana Medical Center SDMC, Bangkok, Thailand
- Pharmacogenomics and Precision Medicine Clinic, Bumrungrad Genomic Medicine Institute (BGMI), Bumrungrad International Hospital, Bangkok, Thailand
- Faculty of Pharmaceutical Sciences, Burapha University, Mueang, Thailand
- Department of Pharmacology and Therapeutics, MRC Centre for Drug Safety Science, Institute of Systems, Molecular, and Integrative Biology, University of Liverpool, Liverpool, United Kingdom
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9
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Kiiski JI, Neuvonen M, Kurkela M, Hirvensalo P, Hämäläinen K, Tarkiainen EK, Sistonen J, Korhonen M, Khan S, Orpana A, Filppula AM, Lehtonen M, Niemi M. Solanidine is a sensitive and specific dietary biomarker for CYP2D6 activity. Hum Genomics 2024; 18:11. [PMID: 38303026 PMCID: PMC10835938 DOI: 10.1186/s40246-024-00579-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Accepted: 01/24/2024] [Indexed: 02/03/2024] Open
Abstract
BACKGROUND Individual assessment of CYP enzyme activities can be challenging. Recently, the potato alkaloid solanidine was suggested as a biomarker for CYP2D6 activity. Here, we aimed to characterize the sensitivity and specificity of solanidine as a CYP2D6 biomarker among Finnish volunteers with known CYP2D6 genotypes. RESULTS Using non-targeted metabolomics analysis, we identified 9152 metabolite features in the fasting plasma samples of 356 healthy volunteers. Machine learning models suggested strong association between CYP2D6 genotype-based phenotype classes with a metabolite feature identified as solanidine. Plasma solanidine concentration was 1887% higher in genetically poor CYP2D6 metabolizers (gPM) (n = 9; 95% confidence interval 755%, 4515%; P = 1.88 × 10-11), 74% higher in intermediate CYP2D6 metabolizers (gIM) (n = 89; 27%, 138%; P = 6.40 × 10-4), and 35% lower in ultrarapid CYP2D6 metabolizers (gUM) (n = 20; 64%, - 17%; P = 0.151) than in genetically normal CYP2D6 metabolizers (gNM; n = 196). The solanidine metabolites m/z 444 and 430 to solanidine concentration ratios showed even stronger associations with CYP2D6 phenotypes. Furthermore, the areas under the receiver operating characteristic and precision-recall curves for these metabolic ratios showed equal or better performances for identifying the gPM, gIM, and gUM phenotype groups than the other metabolites, their ratios to solanidine, or solanidine alone. In vitro studies with human recombinant CYP enzymes showed that solanidine was metabolized mainly by CYP2D6, with a minor contribution from CYP3A4/5. In human liver microsomes, the CYP2D6 inhibitor paroxetine nearly completely (95%) inhibited the metabolism of solanidine. In a genome-wide association study, several variants near the CYP2D6 gene associated with plasma solanidine metabolite ratios. CONCLUSIONS These results are in line with earlier studies and further indicate that solanidine and its metabolites are sensitive and specific biomarkers for measuring CYP2D6 activity. Since potato consumption is common worldwide, this biomarker could be useful for evaluating CYP2D6-mediated drug-drug interactions and to improve prediction of CYP2D6 activity in addition to genotyping.
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Affiliation(s)
- Johanna I Kiiski
- Individualized Drug Therapy Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Department of Clinical Pharmacology, University of Helsinki, Helsinki, Finland
| | - Mikko Neuvonen
- Individualized Drug Therapy Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Department of Clinical Pharmacology, University of Helsinki, Helsinki, Finland
| | - Mika Kurkela
- Individualized Drug Therapy Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Department of Clinical Pharmacology, University of Helsinki, Helsinki, Finland
| | - Päivi Hirvensalo
- Individualized Drug Therapy Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Department of Clinical Pharmacology, University of Helsinki, Helsinki, Finland
| | - Kreetta Hämäläinen
- Individualized Drug Therapy Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Department of Clinical Pharmacology, University of Helsinki, Helsinki, Finland
| | - E Katriina Tarkiainen
- Individualized Drug Therapy Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Department of Clinical Pharmacology, University of Helsinki, Helsinki, Finland
- Department of Clinical Pharmacology, HUS Diagnostic Center, Helsinki University Hospital, Helsinki, Finland
| | - Johanna Sistonen
- Individualized Drug Therapy Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Department of Clinical Pharmacology, University of Helsinki, Helsinki, Finland
- Genetics Laboratory, HUS Diagnostic Center, Helsinki University Hospital, Helsinki, Finland
| | - Mari Korhonen
- Genetics Laboratory, HUS Diagnostic Center, Helsinki University Hospital, Helsinki, Finland
| | - Sofia Khan
- Individualized Drug Therapy Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Department of Clinical Pharmacology, University of Helsinki, Helsinki, Finland
- Genetics Laboratory, HUS Diagnostic Center, Helsinki University Hospital, Helsinki, Finland
| | - Arto Orpana
- Genetics Laboratory, HUS Diagnostic Center, Helsinki University Hospital, Helsinki, Finland
| | - Anne M Filppula
- Individualized Drug Therapy Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Department of Clinical Pharmacology, University of Helsinki, Helsinki, Finland
- Pharmaceutical Sciences Laboratory, Åbo Akademi University, Turku, Finland
| | - Marko Lehtonen
- School of Pharmacy, University of Eastern Finland, Kuopio, Finland
| | - Mikko Niemi
- Individualized Drug Therapy Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland.
- Department of Clinical Pharmacology, University of Helsinki, Helsinki, Finland.
- Department of Clinical Pharmacology, HUS Diagnostic Center, Helsinki University Hospital, Helsinki, Finland.
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10
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Varma R, Staab JP, Matey ET, Wright JA, Deb B, Lazaridis KN, Szarka LA, Bailey KR, Bharucha AE. Most patients with disorders of gut-brain interaction receive pharmacotherapy with major or moderate drug-gene interactions. Neurogastroenterol Motil 2024; 36:e14722. [PMID: 38072827 DOI: 10.1111/nmo.14722] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 10/25/2023] [Accepted: 11/28/2023] [Indexed: 01/25/2024]
Abstract
BACKGROUND How variations predicted by pharmacogenomic testing to alter drug metabolism and therapeutic response affect outcomes for patients with disorders of gut- brain interaction is unclear. AIMS To assess the prevalence of pharmacogenomics-predicted drug-gene interactions and symptom outcomes for patients with disorders of gut-brain interaction. METHODS Patients who were treated in our clinical practice for functional dyspepsia/bowel disorder underwent pharmacogenomic testing. The change in symptoms from baseline to 6 months was compared for patients with variations in CYP2D6 and CYP2C19, which metabolize neuromodulators, and SLC6A4, which encodes the sodium- dependent serotonin transporter. RESULTS At baseline, 79 of 94 participants (84%) had at least one predicted major drug- gene interaction, and all 94 (100%) had at least one predicted moderate interaction. For the 44 participants who completed a survey of their symptoms at 6 months, the mean (SD) irritable bowel syndrome-symptom severity score decreased from 284 (71) at baseline to 231 (95) at 6 months (p < 0.001). Among patients taking selective serotonin reuptake inhibitors, the decrease in symptom severity (p = 0.03) and pain (p = 0.002) scores from baseline to 6 months was greater for patients with a homozygous SLC6A4 long/long genotype (n = 30) (ie, increased serotonin transporter activity) than for patients with homozygous short/short or heterozygous long/short genotypes (n = 64). Symptom outcomes were not affected by CYP2D6 or CYP2C19 variations. CONCLUSIONS The homozygous SLC6A4 long/long genotype confers better symptom resolution for patients with disorders of gut-brain interaction who take selective serotonin reuptake inhibitors than do the homozygous short/short or heterozygous long/short genotypes.
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Affiliation(s)
- Revati Varma
- Research Fellow in the Division of Gastroenterology and Hepatology, Mayo Clinic School of Graduate Medical Education, Mayo Clinic College of Medicine and Science, Rochester, Minnesota, USA
| | - Jeffrey P Staab
- Department of Psychiatry and Psychology, Mayo Clinic, Rochester, Minnesota, USA
| | - Eric T Matey
- Department of Pharmacy, Mayo Clinic, Rochester, Minnesota, USA
| | | | - Brototo Deb
- Research Fellow in the Division of Gastroenterology and Hepatology, Mayo Clinic School of Graduate Medical Education, Mayo Clinic College of Medicine and Science, Rochester, Minnesota, USA
| | | | - Lawrence A Szarka
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota, USA
| | - Kent R Bailey
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, Minnesota, USA
| | - Adil E Bharucha
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota, USA
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11
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Smith D, He B, Shi J, Zhu HJ, Wang X. Novel Independent Trans- and Cis-Genetic Variants Associated with CYP2D6 Expression and Activity in Human Livers. Drug Metab Dispos 2024; 52:143-152. [PMID: 38050015 PMCID: PMC10801631 DOI: 10.1124/dmd.123.001548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 11/01/2023] [Accepted: 11/21/2023] [Indexed: 12/06/2023] Open
Abstract
Cytochrome P450 2D6 (CYP2D6) is a critical hepatic drug-metabolizing enzyme in humans, responsible for metabolizing approximately 20%-25% of commonly used medications such as codeine, desipramine, fluvoxamine, paroxetine, and tamoxifen. The CYP2D6 gene is highly polymorphic, resulting in substantial interindividual variability in its catalytic function and the pharmacokinetics and therapeutic outcomes of its substrate drugs. Although many functional CYP2D6 variants have been discovered and validated, a significant portion of the variability in the expression and activity of CYP2D6 remains unexplained. In this study, we performed a genome-wide association study (GWAS) to identify novel variants associated with CYP2D6 protein expression in individual human livers, followed by a conditional analysis to control for the effect of functional CYP2D6 star alleles. We also examined their impact on hepatic CYP2D6 activity. Genotyping on a genome-wide scale was achieved using the Illumina Multi-Ethnic Genotyping Array (MEGA). A data-independent acquisition (DIA)-based proteomics method was used to quantify CYP2D6 protein concentrations. CYP2D6 activity was determined by measuring the dextromethorphan O-demethylation in individual human liver s9 fractions. The GWAS identified 44 single nuclear polymorphisms (SNPs) that are significantly associated with CYP2D6 protein expressions with a P value threshold of 5.0 × 10-7 After the conditional analysis, five SNPs, including the cis-variants rs1807493 and rs1062753 and the trans-variants rs4073010, rs729559, and rs80274432, emerged as independent variants significantly correlated with hepatic CYP2D6 protein expressions. Notably, four of these SNPs, except for rs80274432, also exhibited a significant association with CYP2D6 activities in human livers, suggesting their potential as novel and independent cis- and trans-variants regulating CYP2D6. SIGNIFICANT STATEMENT: Using individual human livers, we identified four novel cis- and trans-pQTLs/aQTLs (protein quantitative trait loci/activity quantitative trait loci) of Cytochrome P450 2D6 (CYP2D6) that are independent from known functional CYP2D6 star alleles. This study connects the CYP2D6 gene expression and activity, enhancing our understanding of the genetic variants associated with CYP2D6 protein expression and activity, potentially advancing our insight into the interindividual variability in CYP2D6 substrate medication response.
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Affiliation(s)
- Dylan Smith
- Department of Pharmaceutical Sciences, Northeast Ohio Medical University, Rootstown, Ohio (D.S., X.W.); Department of Clinical Pharmacy, University of Michigan, Ann Arbor, Michigan (H.-J.Z.); Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, Michigan (B.H.); and Bristol Myers Squibb, Lawrence Township, New Jersey (J.S.)
| | - Bing He
- Department of Pharmaceutical Sciences, Northeast Ohio Medical University, Rootstown, Ohio (D.S., X.W.); Department of Clinical Pharmacy, University of Michigan, Ann Arbor, Michigan (H.-J.Z.); Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, Michigan (B.H.); and Bristol Myers Squibb, Lawrence Township, New Jersey (J.S.)
| | - Jian Shi
- Department of Pharmaceutical Sciences, Northeast Ohio Medical University, Rootstown, Ohio (D.S., X.W.); Department of Clinical Pharmacy, University of Michigan, Ann Arbor, Michigan (H.-J.Z.); Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, Michigan (B.H.); and Bristol Myers Squibb, Lawrence Township, New Jersey (J.S.)
| | - Hao-Jie Zhu
- Department of Pharmaceutical Sciences, Northeast Ohio Medical University, Rootstown, Ohio (D.S., X.W.); Department of Clinical Pharmacy, University of Michigan, Ann Arbor, Michigan (H.-J.Z.); Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, Michigan (B.H.); and Bristol Myers Squibb, Lawrence Township, New Jersey (J.S.)
| | - Xinwen Wang
- Department of Pharmaceutical Sciences, Northeast Ohio Medical University, Rootstown, Ohio (D.S., X.W.); Department of Clinical Pharmacy, University of Michigan, Ann Arbor, Michigan (H.-J.Z.); Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, Michigan (B.H.); and Bristol Myers Squibb, Lawrence Township, New Jersey (J.S.)
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12
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Krejčí V, Murínová I, Slanař O, Šíma M. Evidence for Therapeutic Drug Monitoring of Atypical Antipsychotics. Prague Med Rep 2024; 125:101-129. [PMID: 38761044 DOI: 10.14712/23362936.2024.10] [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: 05/20/2024] Open
Abstract
Second-generation antipsychotics (SGAs), also known as atypical antipsychotics, are a newer class of antipsychotic drugs used to treat schizophrenia, bipolar disorder, and related psychiatric conditions. The plasma concentration of antipsychotic drugs is a valid measure of the drug at its primary target structure in the brain, and therefore determines the efficacy and safety of these drugs. However, despite the well-known high variability in pharmacokinetics of these substances, psychiatric medication is usually administered in uniform dosage schedules. Therapeutic drug monitoring (TDM), as the specific method that can help personalised medicine in dose adjustment according to the characteristics of the individual patient, minimizing the risk of toxicity, monitoring adherence, and increasing cost-effectiveness in the treatment, thus seems to be an elegant tool to solve this problem. Non-response to therapeutic doses, uncertain adherence to medication, suboptimal tolerability, or pharmacokinetic drug-drug interactions are typical indications for TDM of SGAs. This review aims to summarize an overview of the current knowledge and evidence of the possibilities to tailor the dosage of selected SGAs using TDM, including the necessary pharmacokinetic parameters for personalised pharmacotherapy.
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Affiliation(s)
- Veronika Krejčí
- Department of Clinical Pharmacy, Military University Hospital Prague, Prague, Czech Republic.
- Institute of Pharmacology, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, Czech Republic.
| | - Irena Murínová
- Department of Applied Pharmacy, Faculty of Pharmacy, Masaryk University, Brno, Czech Republic
- Department of Clinical Pharmacy, Military University Hospital Prague, Prague, Czech Republic
| | - Ondřej Slanař
- Institute of Pharmacology, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, Czech Republic
| | - Martin Šíma
- Institute of Pharmacology, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, Czech Republic
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13
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Shilbayeh SAR, Adeen IS, Alhazmi AS, Ibrahim SF, Al Enazi FAR, Ghanem EH, Binduraihem AM. The Frequency of CYP2D6 and CYP3A4/5 Genotypes and The Impact of Their Allele Translation and Phenoconversion-Predicted Enzyme Activity on Risperidone Pharmacokinetics in Saudi Children with Autism. Biochem Genet 2023:10.1007/s10528-023-10580-w. [PMID: 38041757 DOI: 10.1007/s10528-023-10580-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 10/28/2023] [Indexed: 12/03/2023]
Abstract
Data on the role of CYP2D6 and CYP3A4/5 polymorphisms in relation to risperidone (RIS) pharmacokinetics (PK) in children are relatively limited and inconsistent. This is partially attributable to the limited coverage of CYP2D6 and CYP3A4/5 metabolizer phenotypes, particularly those of poor and ultrarapid metabolizers (PMs and UMs), which has led to calls for studies of populations with a non-European background that may carry variants that are less frequent in Europeans. Children ≤ 18 years old with at least 8 weeks of a RIS-based regimen were recruited from three autism centers in Riyadh, Saudi Arabia. The primary outcomes measured were plasma concentrations of RIS and 9-hydroxyrisperidone (9-OH-RIS) and their dose-adjusted (C/D) ratios as a function of phenotypes and activity score (AS). For accurate DNA genotyping, targeted pharmacogenomic testing with the Axiom PharmacoFocus Array was performed via examination of a broad collection of probesets targeting CYP2D6 and CYP3A4/5 variants. The frequency of genotypes/phenotypes and the impact of their allele translation and phenoconversion-predicted enzyme activity were examined. The final cohort included 83 individuals. The most common CYP2D6 phenotype in our population was normal metabolizers (NMs, 66.3%). Inconsistent with some previous studies, the three phenotypes of intermediate metabolizers (IMs), NMs, and UMs were significantly different in terms of RIS concentration, the RIS/9-OH-RIS ratio, the RIS C/D ratio and the 9-OH-RIS C/D ratio. According to AS analyses, there were statistically significant differences in the RIS concentration (P = 0.013), RIS/9-OH-RIS ratio (P < 0.001) and RIS C/D ratio (P = 0.030) when patients were categorized into AS ≤ 1 vs. AS > 1. None of the CYP3A4/5 star allele translated phenotypes revealed a significant influence on any of the RIS PK parameters. Notably, neither CYP2D6 nor CYP3A4/5 phenotyping demonstrated a significant impact on the total active moiety, suggesting that other gene variants could modulate RIS PK. The study confirmed the previously reported partial impact of the CYP2D6 gene on RIS PK. However, future studies using contemporary genotyping techniques targeting a wide range of variants in other candidate genes must be conducted to further examine their interactive effects on RIS PK and the clinical response.
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Affiliation(s)
- Sireen Abdul Rahim Shilbayeh
- Department of Pharmacy Practice, College of Pharmacy, Princess Nourah bint Abdulrahman University (PNU), P.O. Box 84428, 11671, Riyadh, Saudi Arabia.
| | - Iman Sharaf Adeen
- Department of Pediatric Behavior and Development and Adolescent Medicine, King Fahad Medical City, Riyadh, Saudi Arabia
| | - Ayman Shawqi Alhazmi
- Department of Pediatric Behavior and Development and Adolescent Medicine, King Saud Medical City, Riyadh, Saudi Arabia
| | - Samah Fathy Ibrahim
- College of Medicine, Princess Nourah bint Abdulrahman University, Riyadh, Saudi Arabia
| | - Fawwaz Abdul Razaq Al Enazi
- Department of Pediatric Behavior and Development and Adolescent Medicine, King Fahad Medical City, Riyadh, Saudi Arabia
| | - Ezzeldeen Hasan Ghanem
- Pharmaceutical Analysis Section, King Abdullah International Medical Research Center (KAIMRC), King Abdulaziz Medical City, Ministry of National Guard - Health Affairs, Riyadh, Saudi Arabia
| | - Adel Mohammed Binduraihem
- Health Sciences Research Center, King Abdullah Bin Abdulaziz University Hospital, Princess Nourah bint Abdulrahman University, Riyadh, Saudi Arabia
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14
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Mosley SA, Cicali E, Del Cueto A, Portman DG, Donovan KA, Gong Y, Langaee T, Gopalan P, Schmit J, Starr JS, Silver N, Chang YD, Rajasekhara S, Smith JE, Soares HP, Clare-Salzler M, Starostik P, George TJ, McLeod HL, Fillingim RB, Hicks JK, Cavallari LH. CYP2D6-guided opioid therapy for adults with cancer pain: A randomized implementation clinical trial. Pharmacotherapy 2023; 43:1286-1296. [PMID: 37698371 PMCID: PMC10840965 DOI: 10.1002/phar.2875] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 07/31/2023] [Accepted: 08/02/2023] [Indexed: 09/13/2023]
Abstract
INTRODUCTION The CYP2D6 enzyme metabolizes opioids commonly prescribed for cancer-related pain, and CYP2D6 polymorphisms may contribute to variability in opioid response. We evaluated the feasibility of implementing CYP2D6-guided opioid prescribing for patients with cancer and reported pilot outcome data. METHODS Adult patients from two cancer centers were prospectively enrolled into a hybrid implementation-effectiveness clinical trial and randomized to CYP2D6-genotype-guided opioid selection, with clinical recommendations, or usual care. Implementation metrics, including provider response, medication changes consistent with recommendations, and patient-reported pain and symptom scores at baseline and up to 8 weeks, were assessed. RESULTS Most (87/114, 76%) patients approached for the study agreed to participate. Of 85 patients randomized, 71% were prescribed oxycodone at baseline. The median (range) time to receive CYP2D6 test results was 10 (3-37) days; 24% of patients had physicians acknowledge genotype results in a clinic note. Among patients with CYP2D6-genotype-guided recommendations to change therapy (n = 11), 18% had a change congruent with recommendations. Among patients who completed baseline and follow-up questionnaires (n = 48), there was no difference in change in mean composite pain score (-1.01 ± 2.1 vs. -0.41 ± 2.5; p = 0.19) or symptom severity at last follow-up (3.96 ± 2.18 vs. 3.47 ± 1.78; p = 0.63) between the usual care arm (n = 26) and genotype-guided arm (n = 22), respectively. CONCLUSION Our study revealed high acceptance of pharmacogenetic testing as part of a clinical trial among patients with cancer pain. However, provider response to genotype-guided recommendations was low, impacting assessment of pain-related outcomes. Addressing barriers to utility of pharmacogenetics results and clinical recommendations will be critical for implementation success.
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Affiliation(s)
- Scott A Mosley
- Department of Pharmacotherapy and Translational Research and Center for Pharmacogenomics and Precision Medicine, University of Florida, Gainesville, Florida, USA
- Department of Clinical Pharmacy, University of Southern California, Los Angeles, California, USA
| | - Emily Cicali
- Department of Pharmacotherapy and Translational Research and Center for Pharmacogenomics and Precision Medicine, University of Florida, Gainesville, Florida, USA
| | - Alex Del Cueto
- Department of Individualized Cancer Management, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, USA
| | - Diane G Portman
- Department of Supportive Care Medicine, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, USA
| | - Kristine A Donovan
- Department of Supportive Care Medicine, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, USA
| | - Yan Gong
- Department of Pharmacotherapy and Translational Research and Center for Pharmacogenomics and Precision Medicine, University of Florida, Gainesville, Florida, USA
| | - Taimour Langaee
- Department of Pharmacotherapy and Translational Research and Center for Pharmacogenomics and Precision Medicine, University of Florida, Gainesville, Florida, USA
| | - Priya Gopalan
- Division of Hematology and Oncology, Department of Medicine, College of Medicine, University of Florida, Gainesville, Florida, USA
| | - Jessica Schmit
- Division of Hematology and Oncology, Department of Medicine, College of Medicine, University of Florida, Gainesville, Florida, USA
| | - Jason S Starr
- Division of Hematology/Oncology, Mayo Clinic, Jacksonville, Florida, USA
| | - Natalie Silver
- Department of Otolaryngology, College of Medicine, University of Florida, Gainesville, Florida, USA
| | - Young D Chang
- Department of Supportive Care Medicine, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, USA
| | - Sahana Rajasekhara
- Department of Supportive Care Medicine, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, USA
| | - Joshua E Smith
- Department of Supportive Care Medicine, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, USA
| | - Heloisa P Soares
- Department of Gastrointestinal Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, USA
| | - Michael Clare-Salzler
- Department of Pathology, Immunology & Laboratory Medicine, College of Medicine, University of Florida, Gainesville, Florida, USA
| | - Petr Starostik
- Department of Pathology, Immunology & Laboratory Medicine, College of Medicine, University of Florida, Gainesville, Florida, USA
| | - Thomas J George
- Division of Hematology and Oncology, Department of Medicine, College of Medicine, University of Florida, Gainesville, Florida, USA
| | | | - Roger B Fillingim
- Department of Community Dentistry and Behavioral Science, College of Dentistry, Gainesville, Florida, USA
- Clinical and Translational Science Institute, University of Florida, Gainesville, Florida, USA
| | - J Kevin Hicks
- Department of Individualized Cancer Management, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, USA
| | - Larisa H Cavallari
- Department of Pharmacotherapy and Translational Research and Center for Pharmacogenomics and Precision Medicine, University of Florida, Gainesville, Florida, USA
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15
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Kim EK, Shrime MG. Cost of open access publishing in otolaryngology-head and neck surgery. World J Otorhinolaryngol Head Neck Surg 2023; 9:352-356. [PMID: 38059140 PMCID: PMC10696265 DOI: 10.1002/wjo2.78] [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: 05/25/2022] [Accepted: 07/20/2022] [Indexed: 11/12/2022] Open
Abstract
Objective Open access (OA) publishing makes research more accessible but is associated with steep article processing charges (APCs). The study objective was to characterize the APCs of OA publishing in otolaryngology-head and neck surgery (OHNS) journals. Methods We conducted a cross-sectional analysis of published policies of 110 OHNS journals collated from three databases. The primary outcomes were the publishing model, APC for original research, and APC waiver policy. Results We identified 110 OHNS journals (57 fully OA, 47 hybrid, 2 subscription-only, 4 unknown model). After excluding 12 journals (2 subscription-only, 4 unknown model, 5 OA with unspecified APCs, and 1 OA that accepts publications only from society members), we analyzed 98 journals, 23 of which did not charge APCs. Among 75 journals with nonzero APCs, the mean and median APCs were $2452 and $2900 (interquartile range: $1082-3520). Twenty-five journals (33.3%) offered APC subsidies for authors in low- and middle-income countries (LMICs) and/or on a case-by-case basis. Eighty-five and 25 journals were based in high-income countries (HICs) and LMICs, respectively. The mean APC was higher among HIC journals than LMIC journals ($2606 vs. $958, p < 0.001). Conclusion APCs range from tens to thousands of dollars with limited waivers for authors in LMICs.
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Affiliation(s)
- Eric K. Kim
- Program in Global Surgery and Social ChangeHarvard Medical SchoolBostonMassachusettsUSA
- School of MedicineUniversity of California, San FranciscoSan FranciscoCaliforniaUSA
| | - Mark G. Shrime
- Program in Global Surgery and Social ChangeHarvard Medical SchoolBostonMassachusettsUSA
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16
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Turner AJ, Nofziger C, Ramey BE, Ly RC, Bousman CA, Agúndez JAG, Sangkuhl K, Whirl-Carrillo M, Vanoni S, Dunnenberger HM, Ruano G, Kennedy MA, Phillips MS, Hachad H, Klein TE, Moyer AM, Gaedigk A. PharmVar Tutorial on CYP2D6 Structural Variation Testing and Recommendations on Reporting. Clin Pharmacol Ther 2023; 114:1220-1237. [PMID: 37669183 PMCID: PMC10840842 DOI: 10.1002/cpt.3044] [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: 06/16/2023] [Accepted: 08/23/2023] [Indexed: 09/07/2023]
Abstract
The Pharmacogene Variation Consortium (PharmVar) provides nomenclature for the highly polymorphic human CYP2D6 gene locus and a comprehensive summary of structural variation. CYP2D6 contributes to the metabolism of numerous drugs and, thus, genetic variation in its gene impacts drug efficacy and safety. To accurately predict a patient's CYP2D6 phenotype, testing must include structural variants including gene deletions, duplications, hybrid genes, and combinations thereof. This tutorial offers a comprehensive overview of CYP2D6 structural variation, terms, and definitions, a review of methods suitable for their detection and characterization, and practical examples to address the lack of standards to describe CYP2D6 structural variants or any other pharmacogene. This PharmVar tutorial offers practical guidance on how to detect the many, often complex, structural variants, as well as recommends terms and definitions for clinical and research reporting. Uniform reporting is not only essential for electronic health record-keeping but also for accurate translation of a patient's genotype into phenotype which is typically utilized to guide drug therapy.
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Affiliation(s)
- Amy J Turner
- Department of Pediatrics, Children’s Research Institute, The Medical College of Wisconsin, Milwaukee, Wisconsin, USA
- RPRD Diagnostics LLC, Wauwatosa, Wisconsin, USA
| | | | | | - Reynold C Ly
- Department of Medical and Molecular Genetics, Division of Diagnostic Genomics, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Chad A Bousman
- Department of Medical Genetics, University of Calgary, Calgary, Alberta, Canada
| | - José AG Agúndez
- University of Extremadura, Cáceres, Spain
- Institute of Molecular Pathology Biomarkers, Cáceres, Spain
| | - Katrin Sangkuhl
- Department of Biomedical Data Science, Stanford University, Stanford, California, USA
| | | | | | - Henry M Dunnenberger
- Mark R. Neaman Center for Personalized Medicine, NorthShore University Health System, Evanston, Illinois, USA
| | - Gualberto Ruano
- Institute of Living, Hartford Hospital (Hartford CT) and Department of Psychiatry, University of Connecticut School of Medicine (Farmington CT), USA
| | - Martin A Kennedy
- Department of Pathology and Biomedical Science, University of Otago, Christchurch, New Zealand
| | | | - Houda Hachad
- Houda Hachad, Department of Clinical Operations, AccessDx Laboratories, Houston, Texas, USA
| | - Teri E Klein
- Departments of Biomedical Data Science and Medicine (BMIR), Stanford University, Stanford, California, USA
| | - Ann M Moyer
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Andrea Gaedigk
- Children’s Mercy Research Institute (CMRI), Kansas City, Missouri, USA
- School of Medicine, University of Missouri-Kansas City, Kansas City, Missouri, USA
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17
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Fekete F, Menus Á, Tóth K, Kiss ÁF, Minus A, Sirok D, Belič A, Póti Á, Csukly G, Monostory K. CYP1A2 expression rather than genotype is associated with olanzapine concentration in psychiatric patients. Sci Rep 2023; 13:18507. [PMID: 37898643 PMCID: PMC10613299 DOI: 10.1038/s41598-023-45752-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 10/23/2023] [Indexed: 10/30/2023] Open
Abstract
Olanzapine is a commonly prescribed atypical antipsychotic agent for treatment of patients with schizophrenia and bipolar disorders. Previous in vitro studies using human liver microsomes identified CYP1A2 and CYP2D6 enzymes being responsible for CYP-mediated metabolism of olanzapine. The present work focused on the impact of CYP1A2 and CYP2D6 genetic polymorphisms as well as of CYP1A2 metabolizing capacity influenced by non-genetic factors (sex, age, smoking) on olanzapine blood concentration in patients with psychiatric disorders (N = 139). CYP2D6 genotype-based phenotype appeared to have negligible contribution to olanzapine metabolism, whereas a dominant role of CYP1A2 in olanzapine exposure was confirmed. However, CYP1A2 expression rather than CYP1A2 genetic variability was demonstrated to be associated with olanzapine concentration in patients. Significant contribution of - 163C > A (rs762551), the most common SNP (single nucleotide polymorphism) in CYP1A2 gene, to enhanced inducibility was confirmed by an increase in CYP1A2 mRNA expression in smokers carrying - 163A, and smoking was found to have appreciable impact on olanzapine concentration normalized by the dose/bodyweight. Furthermore, patients' olanzapine exposure was in strong association with CYP1A2 expression; therefore, assaying CYP1A2 mRNA level in leukocytes can be an appropriate tool for the estimation of patients' olanzapine metabolizing capacity and may be relevant in optimizing olanzapine dosage.
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Affiliation(s)
- Ferenc Fekete
- Institute of Enzymology, HUN-REN Research Centre for Natural Sciences, Magyar tudósok 2, Budapest, 1117, Hungary
- Doctoral School of Biology and Institute of Biology, Eötvös Loránd University, Pázmány Péter Sétány 1/A, Budapest, 1117, Hungary
| | - Ádám Menus
- Department of Psychiatry and Psychotherapy, Semmelweis University, Balassa 6, Budapest, 1082, Hungary
| | - Katalin Tóth
- Institute of Enzymology, HUN-REN Research Centre for Natural Sciences, Magyar tudósok 2, Budapest, 1117, Hungary
| | - Ádám Ferenc Kiss
- Institute of Enzymology, HUN-REN Research Centre for Natural Sciences, Magyar tudósok 2, Budapest, 1117, Hungary
| | - Annamária Minus
- Institute of Enzymology, HUN-REN Research Centre for Natural Sciences, Magyar tudósok 2, Budapest, 1117, Hungary
| | - Dávid Sirok
- Institute of Enzymology, HUN-REN Research Centre for Natural Sciences, Magyar tudósok 2, Budapest, 1117, Hungary
- Toxi-Coop Toxicological Research Center, Magyar jakobinusok 4/B, Budapest, 1122, Hungary
| | - Aleš Belič
- Lek Pharmaceuticals d.d., Kolodvorska 27, 1234, Menges, Slovenia
| | - Ádám Póti
- Institute of Enzymology, HUN-REN Research Centre for Natural Sciences, Magyar tudósok 2, Budapest, 1117, Hungary
| | - Gábor Csukly
- Department of Psychiatry and Psychotherapy, Semmelweis University, Balassa 6, Budapest, 1082, Hungary
| | - Katalin Monostory
- Institute of Enzymology, HUN-REN Research Centre for Natural Sciences, Magyar tudósok 2, Budapest, 1117, Hungary.
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18
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Gelineau-Morel R, Smyser C, Leeder JS. Identifying Effective Treatments for Dystonia in Patients With Cerebral Palsy: A Precision Therapeutics Approach. Neurology 2023; 101:752-759. [PMID: 37463749 PMCID: PMC10624496 DOI: 10.1212/wnl.0000000000207593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Accepted: 05/12/2023] [Indexed: 07/20/2023] Open
Abstract
Recent focus on improving the recognition of dystonia in cerebral palsy (DCP) has highlighted the need for more effective treatments. Evidence supports improved functional outcomes with early interventions for patients with cerebral palsy, but it is not known which interventions are most effective for DCP. Current pharmacologic recommendations for DCP are based largely on anecdotal evidence, with medications demonstrating minimal to moderate improvements in dystonia and variable efficacy between patients. Patients, families, and clinicians have identified the need for new and improved treatments in DCP, naming this as the top research theme in a recent Neurology® publication. Precision therapeutics focuses on providing early effective interventions that are individualized to every patient and can guide research priorities to improve treatments for DCP. This commentary outlines current obstacles to improving treatment of DCP and addresses how precision therapeutics can address each of these obstacles through 4 key components: (1) identification of predictive biomarkers to select patients likely to develop DCP in the future and for whom early intervention may be appropriate to delay or prevent full manifestation of dystonia, (2) stratification of patients with DCP into subgroups according to shared features (clinical, functional, biochemical, etc) to provide a targeted intervention based on those shared features, (3) administration of an individualized dose of an effective intervention to ensure adequate concentrations of the therapeutic entity at the site of action, and (4) monitoring of objective biomarkers of response to intervention. With implementation of each of these components of precision therapeutics, new and more effective treatments for every person with DCP can be realized.
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Affiliation(s)
- Rose Gelineau-Morel
- From the Division of Neurology (R.G.-M.), Children's Mercy Kansas City; School of Medicine (R.G.-M., J.S.L.), University of Missouri-Kansas City; Department of Pediatrics (R.G.-M., J.S.L.), University of Kansas Medical Center, Kansas City; Department of Pediatrics (C.S.), Department of Neurology (C.S.), and Mallinckrodt Institute of Radiology (C.S.), Washington University in St. Louis; and Division of Clinical Pharmacology, Toxicology & Therapeutic Innovation (J.S.L.), Children's Mercy Kansas City, MO.
| | - Christopher Smyser
- From the Division of Neurology (R.G.-M.), Children's Mercy Kansas City; School of Medicine (R.G.-M., J.S.L.), University of Missouri-Kansas City; Department of Pediatrics (R.G.-M., J.S.L.), University of Kansas Medical Center, Kansas City; Department of Pediatrics (C.S.), Department of Neurology (C.S.), and Mallinckrodt Institute of Radiology (C.S.), Washington University in St. Louis; and Division of Clinical Pharmacology, Toxicology & Therapeutic Innovation (J.S.L.), Children's Mercy Kansas City, MO
| | - J Steven Leeder
- From the Division of Neurology (R.G.-M.), Children's Mercy Kansas City; School of Medicine (R.G.-M., J.S.L.), University of Missouri-Kansas City; Department of Pediatrics (R.G.-M., J.S.L.), University of Kansas Medical Center, Kansas City; Department of Pediatrics (C.S.), Department of Neurology (C.S.), and Mallinckrodt Institute of Radiology (C.S.), Washington University in St. Louis; and Division of Clinical Pharmacology, Toxicology & Therapeutic Innovation (J.S.L.), Children's Mercy Kansas City, MO
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19
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Mbavha BT, Thelingwani RS, Chikwambi Z, Nyakabau AM, Masimirembwa C. Pharmacogenetics and pharmacokinetics of tamoxifen in a Zimbabwean breast cancer cohort. Br J Clin Pharmacol 2023; 89:3209-3216. [PMID: 37337448 PMCID: PMC10529681 DOI: 10.1111/bcp.15827] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 06/06/2023] [Accepted: 06/07/2023] [Indexed: 06/21/2023] Open
Abstract
Tamoxifen is the most used hormonal therapy for oestrogen receptor-positive breast cancer. CYP2D6 is the main enzyme in the metabolic pathway of tamoxifen to endoxifen. Variations in endoxifen plasma concentrations are associated with CYP2D6 polymorphisms. This study aimed to determine the association between the CYP2D6 polymorphisms and endoxifen plasma concentrations in a cohort of Zimbabwean breast cancer patients (n = 40). TaqMan genotyping and copy number assays were done to determine CYP2D6 genotypes. Tamoxifen and metabolites were quantitated using LC-MS/MS. The population had high frequencies of the CYP2D6 reduced function alleles, *17 (15%) and *29 (18%). The median endoxifen concentration was 4.78 ng/mL, and in 55% of the patients, mostly intermediate metabolizers were below the endoxifen therapeutic threshold of 5.97 ng/mL. The CYP2D6 phenotypes and activity scores were significantly associated with endoxifen plasma concentrations (P = 0.0151) and with endoxifen to N-desmethyl-tamoxifen ratios (P = 0.0006).
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Affiliation(s)
- Bianza Tinotenda Mbavha
- Department of Genomic Medicine, African Institute of Biomedical Science and Technology (AiBST), 911 Boronia Township, Beatrice, Zimbabwe
- Department of Biotechnology, Chinhoyi University of Technology, Private Bag 7724, Chinhoyi, Zimbabwe
| | - Roslyn Stella Thelingwani
- Department of Genomic Medicine, African Institute of Biomedical Science and Technology (AiBST), 911 Boronia Township, Beatrice, Zimbabwe
| | - Zedias Chikwambi
- Department of Genomic Medicine, African Institute of Biomedical Science and Technology (AiBST), 911 Boronia Township, Beatrice, Zimbabwe
- Department of Biotechnology, Chinhoyi University of Technology, Private Bag 7724, Chinhoyi, Zimbabwe
| | - Anna Mary Nyakabau
- Parirenyatwa Hospital Radiotherapy and Oncology Center, Harare, Zimbabwe
| | - Collen Masimirembwa
- Department of Genomic Medicine, African Institute of Biomedical Science and Technology (AiBST), 911 Boronia Township, Beatrice, Zimbabwe
- Sydney Brenner Institute for Molecular Bioscience (SBIMB), University of the Witwatersrand, Johannesburg 2000, South Africa
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20
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Tremmel R, Zhou Y, Schwab M, Lauschke VM. Structural variation of the coding and non-coding human pharmacogenome. NPJ Genom Med 2023; 8:24. [PMID: 37684227 PMCID: PMC10491600 DOI: 10.1038/s41525-023-00371-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Accepted: 08/29/2023] [Indexed: 09/10/2023] Open
Abstract
Genetic variants in drug targets and genes encoding factors involved in drug absorption, distribution, metabolism and excretion (ADME) can have pronounced impacts on drug pharmacokinetics, response, and toxicity. While the landscape of genetic variability at the level of single nucleotide variants (SNVs) has been extensively studied in these pharmacogenetic loci, their structural variation is only poorly understood. Thus, we systematically analyzed the genetic structural variability across 908 pharmacogenes (344 ADME genes and 564 drug targets) based on publicly available whole genome sequencing data from 10,847 unrelated individuals. Overall, we extracted 14,984 distinct structural variants (SVs) ranging in size from 50 bp to 106 Mb. Each individual harbored on average 10.3 and 1.5 SVs with putative functional effects that affected the coding regions of ADME genes and drug targets, respectively. In addition, by cross-referencing pharmacogenomic SVs with experimentally determined binding data of 224 transcription factors across 130 cell types, we identified 1276 non-coding SVs that overlapped with gene regulatory elements. Based on these data, we estimate that non-coding structural variants account for 22% of the genetically encoded pharmacogenomic variability. Combined, these analyses provide the first comprehensive map of structural variability across pharmacogenes, derive estimates for the functional impact of non-coding SVs and incentivize the incorporation of structural genomic data into personalized drug response predictions.
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Affiliation(s)
- Roman Tremmel
- Dr Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart, Germany
- University Tübingen, Tübingen, Germany
| | - Yitian Zhou
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden
| | - Matthias Schwab
- Dr Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart, Germany
- University Tübingen, Tübingen, Germany
- Departments of Clinical Pharmacology and Pharmacy and Biochemistry, University Tübingen, Tübingen, Germany
| | - Volker M Lauschke
- Dr Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart, Germany.
- University Tübingen, Tübingen, Germany.
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden.
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21
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Kemp S, Orsini JJ, Ebberink MS, Engelen M, Lund TC. VUS: Variant of uncertain significance or very unclear situation? Mol Genet Metab 2023; 140:107678. [PMID: 37574344 DOI: 10.1016/j.ymgme.2023.107678] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 08/01/2023] [Accepted: 08/02/2023] [Indexed: 08/15/2023]
Abstract
The advancements in population screening, including newborn screening, enables the identification of disease-causing variants and timely initiation of treatment. However, screening may also identify mild variants, non-disease variants, and variants of uncertain significance (VUS). The identification of a VUS poses a challenge in terms of diagnostic uncertainty and confusion. X-linked adrenoleukodystrophy (ALD) serves as an illustrative example of this complex issue. ALD is a monogenic neurometabolic disease with a complex clinical presentation and a lack of predictive tests for clinical severity. Despite the success of ALD newborn screening, a significant proportion (62%) of missense variants identified through newborn screening exhibit uncertainty regarding their pathogenicity. Resolving this issue requires ongoing efforts to accurately classify variants and refine screening protocols. While it is undisputable that ALD newborn screening greatly benefits boys with the disease, the identification of VUS underscores the need for continuous research and collaboration in improving screening practices.
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Affiliation(s)
- Stephan Kemp
- Laboratory Genetic Metabolic Diseases, Department of Clinical Chemistry, Amsterdam UMC location University of Amsterdam, Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam, the Netherlands.
| | - Joseph J Orsini
- Newborn Screening Program, Wadsworth Center, New York State Department of Health, Albany, NY, USA
| | - Merel S Ebberink
- Laboratory Genetic Metabolic Diseases, Department of Clinical Chemistry, Amsterdam UMC location University of Amsterdam, Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam, the Netherlands
| | - Marc Engelen
- Department of Pediatric Neurology, Amsterdam UMC location University of Amsterdam, Amsterdam Leukodystrophy Center, Emma Children's Hospital, Amsterdam Neuroscience, Amsterdam, the Netherlands
| | - Troy C Lund
- Department of Pediatrics, Blood and Marrow Transplant Program, University of Minnesota Medical School, Minneapolis, MN, USA
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22
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Ding Y, Liu A, Wang Y, Zhao S, Huang S, Zhu H, Ma L, Han L, Shu S, Zheng L, Chen X. Genetic polymorphisms are associated with individual susceptibility to dexmedetomidine. Front Genet 2023; 14:1187415. [PMID: 37693312 PMCID: PMC10483403 DOI: 10.3389/fgene.2023.1187415] [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: 03/17/2023] [Accepted: 08/09/2023] [Indexed: 09/12/2023] Open
Abstract
Introduction: Dexmedetomidine (DXM) is widely used as an adjuvant to anesthesia or a sedative medicine, and differences in individual sensitivity to the drug exist. This study aimed to investigate the effect of genetic polymorphisms on these differences. Methods: A total of 112 patients undergoing hand surgery were recruited. DXM 0.5 μg/kg was administered within 10 min and then continuously injected (0.4 μg/kg/h). Narcotrend index, effective dose and onset time of sedation, MAP, and HR were measured. Forty-five single nucleotide polymorphisms (SNPs) were selected for genotype. Results: We observed individual differences in the sedation and hemodynamics induced by DXM. ABCG2 rs2231142, CYP2D6 rs16947, WBP2NL rs5758550, KATP rs141294036, KCNMB1 rs11739136, KCNMA1 rs16934182, ABCC9 rs11046209, ADRA2A rs1800544, and ADRB2 rs1042713 were shown to cause statistically significant (p < 0.05) influence on the individual variation of DXM on sedation and hemodynamics. Moreover, the multiple linear regression analysis indicated sex, BMI, and ADRA2A rs1800544 are statistically related to the effective dose of DXM sedation. Discussion: The evidence suggests that the nine SNPs involved in transport proteins, metabolic enzymes, and target proteins of DXM could explain the individual variability in the sedative and hemodynamic effects of DXM. Therefore, with SNP genotyping, these results could guide personalized medication and promote clinical and surgical management.
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Affiliation(s)
- Yuanyuan Ding
- Department of Anesthesiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Aiqing Liu
- Department of Anesthesiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yafeng Wang
- Department of Anesthesiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Shuai Zhao
- Department of Anesthesiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Shiqian Huang
- Department of Anesthesiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Hongyu Zhu
- Department of Anesthesiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Lulin Ma
- Department of Anesthesiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Linlin Han
- Department of Anesthesiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Shaofang Shu
- Department of Anesthesiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Lidong Zheng
- Department of Anesthesiology, Lu’an Hospital Affiliated to Anhui Medical University, Lu’an, China
| | - Xiangdong Chen
- Department of Anesthesiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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23
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Skryabin VY, Zastrozhin MS, Parkhomenko AA, Pankratenko EP, Pozdnyakov SA, Denisenko NP, Akmalova KA, Bryun EA, Sychev DA. Investigating the Use of Pharmacogenetic and Pharmacometabolomic Markers to Predict Haloperidol Efficacy and Safety Rates. Hosp Pharm 2023; 58:363-367. [PMID: 37360210 PMCID: PMC10288459 DOI: 10.1177/00185787231155842] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/20/2023]
Abstract
Background: Haloperidol is commonly prescribed to patients with alcohol-induced psychotic disorder (AIPD). Notably however, individuals differ extensively with regards to therapeutic response and adverse drug reactions (ADRs). Previous studies have shown that haloperidol biotransformation is mainly metabolized by CYP2D6. Objective: The objective of our study was to investigate the use of pharmacogenetic (CYP2D6*4 genetic polymorphism) and pharmacometabolomic biomarkers to predict haloperidol efficacy and safety rates. Material and Methods: The study enrolled 150 patients with AIPD. Therapy included haloperidol in a daily dose of 5 to 10 mg/day by injections for 5 days. Efficacy and safety of treatment were evaluated using the validated psychometric scales PANSS, UKU, and SAS. Results: No association of the urinary 6-НО-ТНВС/pinoline ratio values which could be evidence of the CYP2D6 activity level with both the efficacy and safety rates of haloperidol was demonstrated. However, a statistically significant association between haloperidol safety profile and CYP2D6*4 genetic polymorphism was demonstrated (P < .001). Conclusion: To predict haloperidol efficacy and safety rates, utilization of pharmacogenetic testing that defines CYP2D6*4 genetic polymorphism is found preferable over the use of the pharmacometabolomic marker in a clinical setting.
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Affiliation(s)
- Valentin Yurievich Skryabin
- Moscow Research and Practical Centre on Addictions of the Moscow, Department of Healthcare, Moscow, Russia
- Russian Medical Academy of Continuous Professional Education of the Ministry of Health of the Russian Federation, Moscow, Russia
| | - Mikhail Sergeevich Zastrozhin
- Moscow Research and Practical Centre on Addictions of the Moscow, Department of Healthcare, Moscow, Russia
- Russian Medical Academy of Continuous Professional Education of the Ministry of Health of the Russian Federation, Moscow, Russia
- University of California, San Francisco, San Francisco, CA, USA
| | | | | | | | - Natalia Pavlovna Denisenko
- Russian Medical Academy of Continuous Professional Education of the Ministry of Health of the Russian Federation, Moscow, Russia
| | - Kristina Anatolyevna Akmalova
- Russian Medical Academy of Continuous Professional Education of the Ministry of Health of the Russian Federation, Moscow, Russia
| | - Evgeny Alekseevich Bryun
- Moscow Research and Practical Centre on Addictions of the Moscow, Department of Healthcare, Moscow, Russia
- Russian Medical Academy of Continuous Professional Education of the Ministry of Health of the Russian Federation, Moscow, Russia
| | - Dmitry Alekseevich Sychev
- Russian Medical Academy of Continuous Professional Education of the Ministry of Health of the Russian Federation, Moscow, Russia
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24
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Alsultan A, Alalwan AA, Alshehri B, Jeraisy MA, Alghamdi J, Alqahtani S, Albassam AA. Interethnic differences in drug response: projected impact of genetic variations in the Saudi population. Pharmacogenomics 2023; 24:685-696. [PMID: 37610881 DOI: 10.2217/pgs-2023-0105] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/25/2023] Open
Abstract
Ethnicity is known to have an impact on drug responses. This is particularly important for drugs that have a narrow therapeutic window, nonlinearity in pharmacokinetics and are metabolized by enzymes that demonstrate genetic polymorphisms. However, most clinical trials are conducted among Caucasians, which might limit the usefulness of the findings of such studies for other ethnicities. The representation of participants from Saudi Arabia in global clinical trials is low. Therefore, there is a paucity of evidence to assess the impact of ethnic variability in the Saudi population on drug response. In this article, the authors assess the projected impact of genetic polymorphisms in drug-metabolizing enzymes and drug targets on drug response in the Saudi population.
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Affiliation(s)
- Abdullah Alsultan
- Department of Clinical Pharmacy, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Abdullah A Alalwan
- Department of Clinical Pharmacy, College of Pharmacy, Prince Sattam bin Abdulaziz University, Al-Kharj, Saudi Arabia
| | - Bashayer Alshehri
- Pharmaceutical Care Department, King Abdulaziz Medical City, Riyadh, Saudi Arabia
| | - Majed Al Jeraisy
- Pharmaceutical Care Department, King Abdulaziz Medical City, Riyadh, Saudi Arabia
- College of Pharmacy, King Saud bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
- King Abdullah International Medical Research Center, Riyadh, Saudi Arabia
| | - Jahad Alghamdi
- Saudi Food and Drug Authority, Drug Sector, Riyadh, Saudi Arabia
| | - Saeed Alqahtani
- Department of Clinical Pharmacy, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Ahmed A Albassam
- Department of Clinical Pharmacy, College of Pharmacy, Prince Sattam bin Abdulaziz University, Al-Kharj, Saudi Arabia
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25
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Collins JM, Lester H, Shabnaz S, Wang D. A frequent CYP2D6 variant promotes skipping of exon 3 and reduces CYP2D6 protein expression in human liver samples. Front Pharmacol 2023; 14:1186540. [PMID: 37576811 PMCID: PMC10412816 DOI: 10.3389/fphar.2023.1186540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 07/17/2023] [Indexed: 08/15/2023] Open
Abstract
CYP2D6 is one of the most polymorphic drug-metabolizing enzymes in the liver. While genetic CYP2D6 variants serve as clinical biomarkers to predict CYP2D6 activity, large inter-person variability in CYP2D6 expression remains unaccounted for. Previous results suggest that there is variable expression of a CYP2D6 splice isoform with an in-frame deletion of exon 3 (CYP2D6ΔE3) encoding a protein lacking numerous active site residues. Here, using fragment analysis and RT-qPCR, we revealed that rs1058164 G (MAF = 27%-43%) is associated with increased formation of CYP2D6∆E3 in human liver samples (1.4-2.5-fold) and transfected cells. Furthermore, western blots showed that rs1058164 G was associated with a 50% decrease in full-length hepatic CYP2D6 protein expression. In addition, by studying a larger liver cohort, we confirmed our previous results that rs16947 (CYP2D6*2) reduces full-length CYP2D6 mRNA by increasing the production of an unstable splice isoform lacking exon 6 (CYP2D6ΔE6) and that the impact of CYP2D6ΔE6 is offset in carriers of the downstream enhancer variant rs5758550. The three frequent SNPs (rs1058164, rs16947, and rs5758550) form various 3-SNP-haplotypes, each with distinct CYP2D6 expression characteristics. Using an expression score (ES) system, we tested the impact of the 3-SNP-haplotype on improving the standard model to predict hepatic CYP2D6 protein expression based on genotype. A model that incorporates the 3-SNP-haplotype provided the best fit for CYP2D6 expression and also accounted for more variability in CYP2D6 protein levels (59%) than a model based on the accepted standard (36%) or one that only adds rs16947 and rs5758550 (42%). Clinical studies are needed to determine whether including the 3-SNP-haplotype alongside current standard CYP2D6 models improves the predictive value of CYP2D6 panels.
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Affiliation(s)
| | | | | | - Danxin Wang
- Department of Pharmacotherapy and Translational Research, Center for Pharmacogenomics, College of Pharmacy, University of Florida, Gainesville, FL, United States
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26
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Fink FM, Bognar M, Hengl P, Paulmichl M, Nofziger C. Case report: metoclopramide induced acute dystonic reaction in adolescent CYP2D6 poor metabolizers. Front Pharmacol 2023; 14:1201566. [PMID: 37497103 PMCID: PMC10366597 DOI: 10.3389/fphar.2023.1201566] [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: 04/06/2023] [Accepted: 06/20/2023] [Indexed: 07/28/2023] Open
Abstract
Metoclopramide is indicated for the management of gastroesophageal reflux, gastric stasis, nausea, and vomiting. Metoclopramide-induced acute dystonic reactions (MIADRs), along with repetitive involuntary protrusion of the tongue, are well-known phenomena in children and young adults that may appear after the first dose. The drug is primarily metabolized via oxidation by the cytochrome P450 enzyme CYP2D6 and to a lesser extent by CYP3A4 and CYP1A2. A recommendation to decrease metoclopramide dosing in patients with severely limited to no CYP2D6 activity (i.e., poor metabolizers, PMs) is included in the drug label. It is important to note, however, that a requirement or recommendation for pre-emptive testing for CYP2D6 metabolizer status is not included in the drug label. We present two cases of acute dystonia in two non-consanguineous male adolescents: one following metoclopramide and cimetidine administration in a 14-year-old to treat gastroesophageal reflux, and another following metoclopramide and pantoprazole administration in a 17-year-old with acute gastroenteritis. A retrospective pharmacogenetic analysis revealed both patients as CYP2D6 PMs.
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Affiliation(s)
- Franz-Martin Fink
- Department of Pediatrics, Regional Hospital, St Johann in Tirol, Austria
| | - Marta Bognar
- Department of Pediatrics, Regional Hospital, St Johann in Tirol, Austria
| | - Petra Hengl
- Department of Pediatrics, Regional Hospital, St Johann in Tirol, Austria
| | - Markus Paulmichl
- Department for Personalized Medicine, Privatklinik Maria Hilf, Klagenfurt, Austria
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27
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Bousman CA, Stevenson JM, Ramsey LB, Sangkuhl K, Kevin Hicks J, Strawn JR, Singh AB, Ruaño G, Mueller DJ, Tsermpini EE, Brown JT, Bell GC, Steven Leeder J, Gaedigk A, Scott SA, Klein TE, Caudle KE, Bishop JR. Clinical Pharmacogenetics Implementation Consortium (CPIC) Guideline for CYP2D6, CYP2C19, CYP2B6, SLC6A4, and HTR2A Genotypes and Serotonin Reuptake Inhibitor Antidepressants. Clin Pharmacol Ther 2023; 114:51-68. [PMID: 37032427 PMCID: PMC10564324 DOI: 10.1002/cpt.2903] [Citation(s) in RCA: 62] [Impact Index Per Article: 62.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Accepted: 03/29/2023] [Indexed: 04/11/2023]
Abstract
Serotonin reuptake inhibitor antidepressants, including selective serotonin reuptake inhibitors (SSRIs; i.e., citalopram, escitalopram, fluoxetine, fluvoxamine, paroxetine, and sertraline), serotonin and norepinephrine reuptake inhibitors (i.e., desvenlafaxine, duloxetine, levomilnacipran, milnacipran, and venlafaxine), and serotonin modulators with SSRI-like properties (i.e., vilazodone and vortioxetine) are primary pharmacologic treatments for major depressive and anxiety disorders. Genetic variation in CYP2D6, CYP2C19, and CYP2B6 influences the metabolism of many of these antidepressants, which may potentially affect dosing, efficacy, and tolerability. In addition, the pharmacodynamic genes SLC6A4 (serotonin transporter) and HTR2A (serotonin-2A receptor) have been examined in relation to efficacy and side effect profiles of these drugs. This guideline updates and expands the 2015 Clinical Pharmacogenetics Implementation Consortium (CPIC) guideline for CYP2D6 and CYP2C19 genotypes and SSRI dosing and summarizes the impact of CYP2D6, CYP2C19, CYP2B6, SLC6A4, and HTR2A genotypes on antidepressant dosing, efficacy, and tolerability. We provide recommendations for using CYP2D6, CYP2C19, and CYP2B6 genotype results to help inform prescribing these antidepressants and describe the existing data for SLC6A4 and HTR2A, which do not support their clinical use in antidepressant prescribing.
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Affiliation(s)
- Chad A. Bousman
- Departments of Medical Genetics, Psychiatry, Physiology & Pharmacology, and Community Health Sciences, University of Calgary, Alberta, Canada
- Alberta Children’s Hospital Research Institute, University of Calgary, Alberta, Canada
- Mathison Centre for Mental Health Research and Education, Hotchkiss Brain Institute, University of Calgary, Alberta, Canada
| | - James M. Stevenson
- Departments of Medicine and Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Laura B. Ramsey
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
- Divisions of Clinical Pharmacology and Research in Patient Services, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA
| | - Katrin Sangkuhl
- Department of Biomedical Data Science, Stanford University, Stanford, CA, USA
| | - J. Kevin Hicks
- Department of Individualized Cancer Management, Moffitt Cancer Center, Tampa, FL, USA
| | - Jeffrey R. Strawn
- Department of Psychiatry & Behavioral Neuroscience, University of Cincinnati, Cincinnati, OH, USA
- Divisions of Child & Adolescent Psychiatry and Clinical Pharmacology Cincinnati, Children’s Hospital Medical Center, Cincinnati, OH, USA
| | - Ajeet B. Singh
- School of Medicine, IMPACT Institute, Deakin University, Australia
| | - Gualberto Ruaño
- Institute of Living at Hartford Hospital, Hartford, CT, USA
- Department of Psychiatry, University of Connecticut School of Medicine, Farmington, Connecticut, USA
| | - Daniel J. Mueller
- Pharmacogenetics Research Clinic, Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Ontario, Canada
- Department of Psychiatry, University of Toronto, Ontario, Canada
| | - Evangelia Eirini Tsermpini
- Pharmacogenetics Laboratory, Institute of Biochemistry and Molecular Genetics, Faculty of Medicine, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Jacob T. Brown
- Department of Pharmacy Practice & Pharmaceutical Sciences, University of Minnesota College of Pharmacy, Duluth, MN, USA
| | | | - J. Steven Leeder
- Division of Clinical Pharmacology, Toxicology & Therapeutic Innovation, Children’s Mercy Research Institute (CMRI), Kansas City, MO, USA
- School of Medicine, University of Missouri-Kansas City, Kansas City, MO, USA
| | - Andrea Gaedigk
- Division of Clinical Pharmacology, Toxicology & Therapeutic Innovation, Children’s Mercy Research Institute (CMRI), Kansas City, MO, USA
- School of Medicine, University of Missouri-Kansas City, Kansas City, MO, USA
| | - Stuart A. Scott
- Department of Pathology, Stanford University, Palo Alto, CA, USA
- Stanford Medicine Clinical Genomics Program, Stanford Medicine, Stanford, CA, USA
| | - Teri E. Klein
- Department of Biomedical Data Science, Stanford University, Stanford, CA, USA
| | - Kelly E. Caudle
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Jeffrey R. Bishop
- Department of Experimental and Clinical Pharmacology, University of Minnesota College of Pharmacy, Minneapolis, MN, USA
- Department of Psychiatry and Behavioral Sciences, University of Minnesota Medical School, Minneapolis, MN, USA
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Macêdo MM, Almeida ACG, Silva GS, Oliveira AC, Mwangi VI, Shuan AC, Barbosa LRA, Rodrigues-Soares F, Melo GC. Association of CYP2C19, CYP2D6 and CYP3A4 Genetic Variants on Primaquine Hemolysis in G6PD-Deficient Patients. Pathogens 2023; 12:895. [PMID: 37513742 PMCID: PMC10384057 DOI: 10.3390/pathogens12070895] [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: 05/06/2023] [Revised: 06/23/2023] [Accepted: 06/27/2023] [Indexed: 07/30/2023] Open
Abstract
In the Amazon, the treatment for Plasmodium vivax is chloroquine plus primaquine. However, this regimen is limited due to the risk of acute hemolytic anemia in glucose-6-phosphate dehydrogenase deficiency. Primaquine is a prodrug that requires conversion by the CYP2D6 enzyme to be effective against malaria. A series of cases were performed at an infectious diseases reference hospital in the Western Brazilian Amazon. The STANDARD G6PD (SD Biosensor®) assay was used to infer G6PD status and real-time PCR to genotype G6PD, CYP2C19, CYP2D6 and CYP3A4. Eighteen patients were included, of which 55.6% had African A- variant (G202A/A376G), 11.1% African A+ variant (A376G), 5.6% Mediterranean variant (C563T) and 27.8% were wild type. CYP2C19, CYP2D6 and CYP3A4 genotyping showed no statistically significant differences in the frequency of star alleles between the groups G6PD deficient and G6PD normal. Elevated levels of liver and kidney markers in the G6PDd patients were observed in gNM, gRM and gUM of CYP2C19 and CYP2D6 (p < 0.05). Furthermore, in this study there was no influence of CYPs on hemolysis. These findings reinforce the importance of studies on the mapping of G6PD deficiency and genetic variations of CYP2C19, CYP2D6 and CYP3A4. This mapping will allow us to validate the prevalence of CYPs and determine their influence on hemolysis in patients with malaria, helping to decide on the treatment regimen.
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Affiliation(s)
- Marielle M Macêdo
- Programa de Pós-graduação em Ciências Aplicadas à Hematologia, Universidade do Estado do Amazonas, Manaus 69040-000, AM, Brazil
| | - Anne C G Almeida
- Fundação de Medicina Tropical Dr. Heitor Vieira Dourado, Manaus 69040-000, AM, Brazil
- Programa de Pós-graduação em Medicina Tropical, Universidade do Estado do Amazonas, Manaus 69040-000, AM, Brazil
| | - Gabrielly S Silva
- Fundação de Medicina Tropical Dr. Heitor Vieira Dourado, Manaus 69040-000, AM, Brazil
- Programa de Pós-graduação em Medicina Tropical, Universidade do Estado do Amazonas, Manaus 69040-000, AM, Brazil
| | - Amanda C Oliveira
- Fundação de Medicina Tropical Dr. Heitor Vieira Dourado, Manaus 69040-000, AM, Brazil
- Programa de Pós-graduação em Medicina Tropical, Universidade do Estado do Amazonas, Manaus 69040-000, AM, Brazil
| | - Victor I Mwangi
- Fundação de Medicina Tropical Dr. Heitor Vieira Dourado, Manaus 69040-000, AM, Brazil
- Programa de Pós-graduação em Medicina Tropical, Universidade do Estado do Amazonas, Manaus 69040-000, AM, Brazil
| | - Ana C Shuan
- Programa de Pós-graduação em Ciências Aplicadas à Hematologia, Universidade do Estado do Amazonas, Manaus 69040-000, AM, Brazil
- Fundação de Medicina Tropical Dr. Heitor Vieira Dourado, Manaus 69040-000, AM, Brazil
| | - Laila R A Barbosa
- Fundação de Medicina Tropical Dr. Heitor Vieira Dourado, Manaus 69040-000, AM, Brazil
- Programa de Pós-graduação em Medicina Tropical, Universidade do Estado do Amazonas, Manaus 69040-000, AM, Brazil
| | - Fernanda Rodrigues-Soares
- Departamento de Patologia, Genética e Evolução, Instituto de Ciências Biológicas e Naturais, Universidade Federal do Triângulo Mineiro, Uberaba 35025-250, MG, Brazil
| | - Gisely C Melo
- Fundação de Medicina Tropical Dr. Heitor Vieira Dourado, Manaus 69040-000, AM, Brazil
- Programa de Pós-graduação em Medicina Tropical, Universidade do Estado do Amazonas, Manaus 69040-000, AM, Brazil
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Palmen R, Sandritter T, Malloy-Walton L, Follansbee C, Wagner JB. Case report: Use of therapeutic drug monitoring and pharmacogenetic testing as opportunities to individualize care in a case of flecainide toxicity after fetal supraventricular tachycardia. Front Pediatr 2023; 11:1168619. [PMID: 37449265 PMCID: PMC10337585 DOI: 10.3389/fped.2023.1168619] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 06/12/2023] [Indexed: 07/18/2023] Open
Abstract
Flecainide is a class IC antiarrhythmic utilized in prophylaxis of refractory paroxysmal supraventricular tachycardias in pediatric populations. Despite being a highly effective agent, its narrow therapeutic index increases the risk of toxicity and proarrhythmic events, including wide-complex tachycardia. In the absence of direct plasma sampling in the fetus to quantitate flecainide systemic concentrations, clinicians typically make drug dosing decisions from maternal plasma concentrations and QRS duration on maternal ECGs. There remains a paucity of standard guidelines and data to inform the timing and frequency of the aforementioned test in pregnancy and timing of flecainide discontinuation prior to childbirth. Flecainide primarily undergoes metabolism via cytochrome P450 (CYP). Given the variance of CYP-mediated metabolism at the level of the individual patient, pharmacogenomics can be considered in patients who present with flecainide toxicity to determine the maternal vs. fetal factors as an etiology for the event. Finally, pharmacogenetic testing can be utilized as an adjunct to guide flecainide dosing decisions, but must be done with caution in neonates <2 weeks of age. This case report highlights utilization of pharmacogenomic testing and therapeutic drug monitoring as adjuncts to guide therapy for a newborn with refractory supraventricular tachycardia, who experienced flecainide toxicity immediately post-partum and was trialed unsuccessfully on multiple alternative antiarrhythmics without rhythm control.
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Affiliation(s)
- Ronald Palmen
- Children’s Mercy, Kansas City, MO, United States
- Department of Pediatrics, University of Missouri-Kansas City School of Medicine, Kansas City, MO, United States
- University of Missouri-Kansas City School of Medicine, Kansas City, MO, United States
| | - Tracy Sandritter
- Children’s Mercy, Kansas City, MO, United States
- University of Missouri-Kansas City School of Pharmacy, Kansas City, MO, United States
| | - Lindsey Malloy-Walton
- Children’s Mercy, Kansas City, MO, United States
- Department of Pediatrics, University of Missouri-Kansas City School of Medicine, Kansas City, MO, United States
- Ward Family Heart Center, Kansas City, MO, United States
| | - Christopher Follansbee
- Children’s Mercy, Kansas City, MO, United States
- Department of Pediatrics, University of Missouri-Kansas City School of Medicine, Kansas City, MO, United States
- Ward Family Heart Center, Kansas City, MO, United States
| | - Jonathan B. Wagner
- Children’s Mercy, Kansas City, MO, United States
- Department of Pediatrics, University of Missouri-Kansas City School of Medicine, Kansas City, MO, United States
- University of Missouri-Kansas City School of Medicine, Kansas City, MO, United States
- Ward Family Heart Center, Kansas City, MO, United States
- Division of Clinical Pharmacology, Toxicology and Therapeutic Innovation, Kansas City, MO, United States
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Ramsey LB, Prows CA, Chidambaran V, Sadhasivam S, Quinn CT, Teusink-Cross A, Tang Girdwood S, Dawson DB, Vinks AA, Glauser TA. Implementation of CYP2D6-guided opioid therapy at Cincinnati Children's Hospital Medical Center. Am J Health Syst Pharm 2023; 80:852-859. [PMID: 36715063 PMCID: PMC11004919 DOI: 10.1093/ajhp/zxad025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2023] [Indexed: 01/31/2023] Open
Abstract
PURPOSE We describe the implementation of CYP2D6-focused pharmacogenetic testing to guide opioid prescribing in a quaternary care, nonprofit pediatric academic medical center. SUMMARY Children are often prescribed oral opioids after surgeries, for cancer pain, and occasionally for chronic pain. In 2004, Cincinnati Children's Hospital Medical Center implemented pharmacogenetic testing for CYP2D6 metabolism phenotype to inform codeine prescribing. The test and reports were updated to align with changes over time in the testing platform, the interpretation of genotype to phenotype, the electronic health record, and Food and Drug Administration (FDA) guidance. The use of the test increased when a research project required testing and decreased as prescribing of oxycodone increased due to FDA warnings about codeine. Education about the opioid-focused pharmacogenetic test was provided to prescribers (eg, the pain and sickle cell teams) as well as patients and families. Education and electronic health record capability increased provider compliance with genotype-guided postsurgical prescribing of oxycodone, although there was a perceived lack of utility for oxycodone prescribing. CONCLUSION The implementation of pharmacogenetic testing to inform opioid prescribing for children has evolved with accumulating evidence and guidelines, requiring changes in reporting of results and recommendations.
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Affiliation(s)
- Laura B Ramsey
- Department of Pediatrics, Division of Clinical Pharmacology and Division of Research in Patient Services, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH
- College of Medicine, University of Cincinnati, Cincinnati, OH, USA
| | - Cynthia A Prows
- Division of Human Genetics and Division of Patient Services, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA
| | - Vidya Chidambaran
- Department of Anesthesiology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH
- College of Medicine, University of Cincinnati, Cincinnati, OH, USA
| | - Senthilkumar Sadhasivam
- Department of Anesthesiology and Perioperative Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Charles T Quinn
- Department of Pediatrics and Division of Hematology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH
- College of Medicine, University of Cincinnati, Cincinnati, OH, USA
| | - Ashley Teusink-Cross
- Division of Pharmacy, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA
| | - Sonya Tang Girdwood
- Department of Pediatrics, Division of Clinical Pharmacology; and Division of Hospital Medicine, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH
- College of Medicine, University of Cincinnati, Cincinnati, OH, USA
| | - D Brian Dawson
- Department of Pediatrics and Division of Human Genetics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA
| | - Alexander A Vinks
- Department of Pediatrics, Division of Clinical Pharmacology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH
- College of Medicine, University of Cincinnati, Cincinnati, OH, USA
| | - Tracy A Glauser
- Department of Pediatrics, Division of Neurology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH
- College of Medicine, University of Cincinnati, Cincinnati, OH, USA
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Turner AJ, Derezinski AD, Gaedigk A, Berres ME, Gregornik DB, Brown K, Broeckel U, Scharer G. Characterization of complex structural variation in the CYP2D6-CYP2D7-CYP2D8 gene loci using single-molecule long-read sequencing. Front Pharmacol 2023; 14:1195778. [PMID: 37426826 PMCID: PMC10324673 DOI: 10.3389/fphar.2023.1195778] [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: 03/28/2023] [Accepted: 05/30/2023] [Indexed: 07/11/2023] Open
Abstract
Complex regions in the human genome such as repeat motifs, pseudogenes and structural (SVs) and copy number variations (CNVs) present ongoing challenges to accurate genetic analysis, particularly for short-read Next-Generation-Sequencing (NGS) technologies. One such region is the highly polymorphic CYP2D loci, containing CYP2D6, a clinically relevant pharmacogene contributing to the metabolism of >20% of common drugs, and two highly similar pseudogenes, CYP2D7 and CYP2D8. Multiple complex SVs, including CYP2D6/CYP2D7-derived hybrid genes are known to occur in different configurations and frequencies across populations and are difficult to detect and characterize accurately. This can lead to incorrect enzyme activity assignment and impact drug dosing recommendations, often disproportionally affecting underrepresented populations. To improve CYP2D6 genotyping accuracy, we developed a PCR-free CRISPR-Cas9 based enrichment method for targeted long-read sequencing that fully characterizes the entire CYP2D6-CYP2D7-CYP2D8 loci. Clinically relevant sample types, including blood, saliva, and liver tissue were sequenced, generating high coverage sets of continuous single molecule reads spanning the entire targeted region of up to 52 kb, regardless of SV present (n = 9). This allowed for fully phased dissection of the entire loci structure, including breakpoints, to accurately resolve complex CYP2D6 diplotypes with a single assay. Additionally, we identified three novel CYP2D6 suballeles, and fully characterized 17 CYP2D7 and 18 CYP2D8 unique haplotypes. This method for CYP2D6 genotyping has the potential to significantly improve accurate clinical phenotyping to inform drug therapy and can be adapted to overcome testing limitations of other clinically challenging genomic regions.
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Affiliation(s)
| | | | - Andrea Gaedigk
- Children’s Mercy Research Institute, Kansas City, MO, United States
| | - Mark E. Berres
- Biotechnology Center, University of Wisconsin Madison, Madison, WI, United States
| | | | - Keith Brown
- Jumpcode Genomics, San Diego, CA, United States
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Qu K, Zhou Q, Zhu H, Zhou Z, Shen Y, Tian L, Su X. The Association Between Clozapine Plasma Concentration, CYP2D6 (*10, *2) Polymorphisms and Risk of Adverse Reactions. PSYCHIAT CLIN PSYCH 2023; 33:76-83. [PMID: 38765922 PMCID: PMC11082567 DOI: 10.5152/pcp.2023.22392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Accepted: 04/27/2023] [Indexed: 05/22/2024] Open
Abstract
Background The aim of this article was to study the relationships between the risk of adverse reactions, plasma concentration, and cytochrome P450 2D6 rs1065852 (*10) and rs16947 (*2) polymorphisms for clozapine. Methods The steady-state clozapine plasma concentration of 100 Chinese inpatients with schizophrenia was determined using 2-dimensional liquid chromatography. The polymorphisms of cytochrome P450 2D6 (*10 and *2) were determined using fluorescent in situ hybridization protocols. Results The decreased percentages of white blood cells and neutrophils and the elevated percentages of creatine kinase, alanine aminotransferase, and aspartate transferase in patients treated with clozapine for 6 months were linearly associated with clozapine plasma concentration. Compared with the corresponding groups, the clozapine plasma concentrations of individuals with the *10TT genotype and individuals with the *2CC genotype were the highest (P < .05). The decreased percentages of white blood cells and neutrophils and elevated percentages of creatine kinase, alanine aminotransferase, and aspartate transferase for patients with the *10TT genotype were significantly higher than those for patients with the *10CC and *10CT genotypes (P < .05). The decreased percentages of white blood cells and neutrophils and increased percentages of creatine kinase, alanine aminotransferase, and aspartate transferase for patients with the *2CC genotype were significantly higher than those of the other groups (P < .05). The therapeutic reference range of clozapine for Chinese patients with schizophrenia was defined as 102.5-483.1 ng/mL. Conclusion This study demonstrated that the determination of cytochrome P450 2D6 polymorphisms and therapeutic drug monitoring of clozapine might be beneficial for identifying patients with a higher risk of adverse reactions.
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Affiliation(s)
- Kankan Qu
- The Affiliated Mental Health Center of Jiangnan University, Wuxi Central Rehabilitation Hospital, Wuxi, Jiangsu, China
| | - Qin Zhou
- The Affiliated Mental Health Center of Jiangnan University, Wuxi Central Rehabilitation Hospital, Wuxi, Jiangsu, China
| | - Haohao Zhu
- The Affiliated Mental Health Center of Jiangnan University, Wuxi Central Rehabilitation Hospital, Wuxi, Jiangsu, China
| | - Zhenhe Zhou
- The Affiliated Mental Health Center of Jiangnan University, Wuxi Central Rehabilitation Hospital, Wuxi, Jiangsu, China
| | - Yuan Shen
- The Affiliated Mental Health Center of Jiangnan University, Wuxi Central Rehabilitation Hospital, Wuxi, Jiangsu, China
| | - Lin Tian
- The Affiliated Mental Health Center of Jiangnan University, Wuxi Central Rehabilitation Hospital, Wuxi, Jiangsu, China
| | - Xujiang Su
- The Affiliated Mental Health Center of Jiangnan University, Wuxi Central Rehabilitation Hospital, Wuxi, Jiangsu, China
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Trilla-Fuertes L, Gámez-Pozo A, Nogué M, Busquier I, Arias F, López-Campos F, Fernández-Montes A, Ruiz A, Velázquez C, Martín-Bravo C, Pérez-Ruiz E, Asensio E, Hernández-Yagüe X, Rodrigues A, Ghanem I, López-Vacas R, Hafez A, Arias P, Dapía I, Solís M, Dittmann A, Ramos R, Llorens C, Maurel J, Campos-Barros Á, Fresno Vara JÁ, Feliu J. Utility of CYP2D6 copy number variants as prognostic biomarker in localized anal squamous cell carcinoma. Cancer 2023. [PMID: 37096763 DOI: 10.1002/cncr.34797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 03/01/2023] [Accepted: 03/03/2023] [Indexed: 04/26/2023]
Abstract
BACKGROUND Anal squamous cell carcinoma (ASCC) is an infrequent tumor whose treatment has not changed since the 1970s. The aim of this study is the identification of biomarkers allowing personalized treatments and improvement of therapeutic outcomes. METHODS Forty-six paraffin tumor samples from ASCC patients were analyzed by whole-exome sequencing. Copy number variants (CNVs) were identified and their relation to disease-free survival (DFS) was studied and validated in an independent retrospective cohort of 101 ASCC patients from the Multidisciplinary Spanish Digestive Cancer Group (GEMCAD). GEMCAD cohort proteomics allowed assessing the biological features of these tumors. RESULTS On the discovery cohort, the median age was 61 years old, 50% were males, stages I/II/III: 3 (7%)/16 (35%)/27 (58%), respectively, median DFS was 33 months, and overall survival was 45 months. Twenty-nine genes whose duplication was related to DFS were identified. The most representative was duplications of the CYP2D locus, including CYP2D6, CYP2D7P, and CYP2D8P genes. Patients with CYP2D6 CNV had worse DFS at 5 years than those with two CYP2D6 copies (21% vs. 84%; p < .0002, hazard ratio [HR], 5.8; 95% confidence interval [CI], 2.7-24.9). In the GEMCAD validation cohort, patients with CYP2D6 CNV also had worse DFS at 5 years (56% vs. 87%; p = .02, HR = 3.6; 95% CI, 1.1-5.7). Mitochondria and mitochondrial cell-cycle proteins were overexpressed in patients with CYP2D6 CNV. CONCLUSIONS Tumor CYP2D6 CNV identified patients with a significantly worse DFS at 5 years among localized ASCC patients treated with 5-fluorouracil, mitomycin C, and radiotherapy. Proteomics pointed out mitochondria and mitochondrial cell-cycle genes as possible therapeutic targets for these high-risk patients. PLAIN LANGUAGE SUMMARY Anal squamous cell carcinoma is an infrequent tumor whose treatment has not been changed since the 1970s. However, disease-free survival in late staged tumors is between 40% and 70%. The presence of an alteration in the number of copies of CYP2D6 gene is a biomarker of worse disease-free survival. The analysis of the proteins in these high-risk patients pointed out mitochondria and mitochondrial cell-cycle genes as possible therapeutic targets. Therefore, the determination of the number of copies of CYP2D6 allows the identification of anal squamous carcinoma patients with a high-risk of relapse that could be redirected to a clinical trial. Additionally, this study may be useful to suggest new treatment strategies to increase current therapy efficacy.
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Affiliation(s)
| | - Angelo Gámez-Pozo
- Molecular Oncology Lab, Hospital Universitario La Paz-IdiPAZ, Madrid, Spain
- Biomedica Molecular Medicine SL, Madrid, Spain
| | - Miguel Nogué
- Spanish Multidisciplinary Group of Digestive Cancer, Barcelona, Spain
- Medical Oncology Service, Hospital de Granollers, Barcelona, Spain
| | - Isabel Busquier
- Spanish Multidisciplinary Group of Digestive Cancer, Barcelona, Spain
- Medical Oncology Service, Hospital Provincial de Castellón, Castellón, Spain
| | - Fernando Arias
- Spanish Multidisciplinary Group of Digestive Cancer, Barcelona, Spain
- Radiotherapy Oncology Service, Complejo Hospitalario de Navarra, Navarra, Spain
| | - Fernando López-Campos
- Spanish Multidisciplinary Group of Digestive Cancer, Barcelona, Spain
- Radiotherapy Oncology Service, Hospital Ramón y Cajal, Madrid, Spain
| | - Ana Fernández-Montes
- Spanish Multidisciplinary Group of Digestive Cancer, Barcelona, Spain
- Medical Oncology Service, Complejo Hospitalario Universitario de Ourense, Ourense, Spain
| | - Ana Ruiz
- Spanish Multidisciplinary Group of Digestive Cancer, Barcelona, Spain
- Medical Oncology Service, Hospital Universitario Puerta de Hierro Majadahonda, IDIPHISA, Madrid, Spain
| | - Concepción Velázquez
- Spanish Multidisciplinary Group of Digestive Cancer, Barcelona, Spain
- Medical Oncology Service, Hospital Miguel Servet, Zaragoza, Spain
| | | | - Elisabeth Pérez-Ruiz
- Unidad de Gestión Clínica Intercentros de Oncología Médica, Hospitales Universitarios Regional y Virgen de la Victoria, Instituto de Investigación Biomédica de Málaga, Hospitales Universitarios Regional y Virgen de la Victoria, Málaga, Spain
| | - Elena Asensio
- Spanish Multidisciplinary Group of Digestive Cancer, Barcelona, Spain
- Medical Oncology Service, Hospital General Universitario de Elche, Elche, Spain
| | - Xavier Hernández-Yagüe
- Spanish Multidisciplinary Group of Digestive Cancer, Barcelona, Spain
- Medical Oncology Service, Instituto Catalán de Oncología-Girona, Girona, Spain
| | - Aline Rodrigues
- Spanish Multidisciplinary Group of Digestive Cancer, Barcelona, Spain
- Medical Oncology Service, Hospital Universitario de Salamanca, Salamanca, Spain
| | - Ismael Ghanem
- Spanish Multidisciplinary Group of Digestive Cancer, Barcelona, Spain
- Medical Oncology Service, Hospital Universitario La Paz, Madrid, Spain
| | - Rocío López-Vacas
- Molecular Oncology Lab, Hospital Universitario La Paz-IdiPAZ, Madrid, Spain
| | - Ahmed Hafez
- Biotechvana SL, Parque Científico de Madrid, Madrid, Spain
| | - Pedro Arias
- Pharmacogenetics Lab, Institute of Medical and Molecular Genetics-INGEMM, La Paz University Hospital-IdiPAZ, Autonomous University of Madrid, Madrid, Spain
| | - Irene Dapía
- Pharmacogenetics Lab, Institute of Medical and Molecular Genetics-INGEMM, La Paz University Hospital-IdiPAZ, Autonomous University of Madrid, Madrid, Spain
| | - Mario Solís
- Bioinformatics Unit, Institute of Medical and Molecular Genetics-INGEMM, La Paz University Hospital-IdiPAZ, Madrid, Spain
| | - Antje Dittmann
- Functional Genomics Center Zurich, University of Zurich/ETH Zurich, Zurich, Switzerland
| | - Ricardo Ramos
- Genomics Unit, Parque Científico de Madrid, Madrid, Spain
| | - Carlos Llorens
- Biotechvana SL, Parque Científico de Madrid, Madrid, Spain
| | - Joan Maurel
- Spanish Multidisciplinary Group of Digestive Cancer, Barcelona, Spain
- Medical Oncology Department, Hospital Clínic of Barcelona, Translational Genomics and Targeted Therapeutics in Solid Tumors Group, IDIBAPS, University of Barcelona, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas, Madrid, Spain
| | - Ángel Campos-Barros
- Institute of Medical and Molecular Genetics, IdiPAZ, Hospital Universitario La Paz/CIBERER Unit 753, ISCIII, Madrid, Spain
| | - Juan Ángel Fresno Vara
- Molecular Oncology Lab, Hospital Universitario La Paz-IdiPAZ, Madrid, Spain
- Biomedica Molecular Medicine SL, Madrid, Spain
- Biomedical Research Networking Center on Oncology-CIBERONC, ISCIII, Madrid, Spain
| | - Jaime Feliu
- Spanish Multidisciplinary Group of Digestive Cancer, Barcelona, Spain
- Medical Oncology Service, Hospital Universitario La Paz, Madrid, Spain
- Biomedical Research Networking Center on Oncology-CIBERONC, ISCIII, Madrid, Spain
- Cátedra UAM-Amgen, Universidad Autónoma de Madrid, Madrid, Spain
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Langlois AWR, El-Boraie A, Pouget JG, Cox LS, Ahluwalia JS, Fukunaga K, Mushiroda T, Knight J, Chenoweth MJ, Tyndale RF. Genotyping, characterization, and imputation of known and novel CYP2A6 structural variants using SNP array data. J Hum Genet 2023:10.1038/s10038-023-01148-y. [PMID: 37059825 DOI: 10.1038/s10038-023-01148-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 03/23/2023] [Accepted: 03/30/2023] [Indexed: 04/16/2023]
Abstract
CYP2A6 metabolically inactivates nicotine. Faster CYP2A6 activity is associated with heavier smoking and higher lung cancer risk. The CYP2A6 gene is polymorphic, including functional structural variants (SV) such as gene deletions (CYP2A6*4), duplications (CYP2A6*1 × 2), and hybrids with the CYP2A7 pseudogene (CYP2A6*12, CYP2A6*34). SVs are challenging to genotype due to their complex genetic architecture. Our aims were to develop a reliable protocol for SV genotyping, functionally phenotype known and novel SVs, and investigate the feasibility of CYP2A6 SV imputation from SNP array data in two ancestry populations. European- (EUR; n = 935) and African- (AFR; n = 964) ancestry individuals from smoking cessation trials were genotyped for SNPs using an Illumina array and for CYP2A6 SVs using Taqman copy number (CN) assays. SV-specific PCR amplification and Sanger sequencing was used to characterize a novel SV. Individuals with SVs were phenotyped using the nicotine metabolite ratio, a biomarker of CYP2A6 activity. SV diplotype and SNP array data were integrated and phased to generate ancestry-specific SV reference panels. Leave-one-out cross-validation was used to investigate the feasibility of CYP2A6 SV imputation. A minimal protocol requiring three Taqman CN assays for CYP2A6 SV genotyping was developed and known SV associations with activity were replicated. The first domain swap CYP2A6-CYP2A7 hybrid SV, CYP2A6*53, was identified, sequenced, and associated with lower CYP2A6 activity. In both EURs and AFRs, most SV alleles were identified using imputation (>70% and >60%, respectively); importantly, false positive rates were <1%. These results confirm that CYP2A6 SV imputation can identify most SV alleles, including a novel SV.
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Affiliation(s)
- Alec W R Langlois
- Department of Pharmacology and Toxicology, University of Toronto, 1 King's College Circle, Toronto, ON, M5S 1A8, Canada
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, 100 Stokes Street, Toronto, ON, M6J 1H4, Canada
| | - Ahmed El-Boraie
- Department of Pharmacology and Toxicology, University of Toronto, 1 King's College Circle, Toronto, ON, M5S 1A8, Canada
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, 100 Stokes Street, Toronto, ON, M6J 1H4, Canada
| | - Jennie G Pouget
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, 100 Stokes Street, Toronto, ON, M6J 1H4, Canada
- Department of Psychiatry, University of Toronto, 250 College Street, Toronto, ON, M5T 1R8, Canada
| | - Lisa Sanderson Cox
- Department of Population Health, University of Kansas School of Medicine, Kansas City, KS, 66160, USA
| | - Jasjit S Ahluwalia
- Departments of Behavioral and Social Sciences and Medicine, Brown University School of Public Health, Providence, RI, 02912, USA
| | - Koya Fukunaga
- Center for Integrative Medical Sciences, RIKEN, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
| | - Taisei Mushiroda
- Center for Integrative Medical Sciences, RIKEN, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
| | - Jo Knight
- Data Science Institute and Medical School, Lancaster University, Lancaster, UK
| | - Meghan J Chenoweth
- Department of Pharmacology and Toxicology, University of Toronto, 1 King's College Circle, Toronto, ON, M5S 1A8, Canada
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, 100 Stokes Street, Toronto, ON, M6J 1H4, Canada
- Department of Psychiatry, University of Toronto, 250 College Street, Toronto, ON, M5T 1R8, Canada
| | - Rachel F Tyndale
- Department of Pharmacology and Toxicology, University of Toronto, 1 King's College Circle, Toronto, ON, M5S 1A8, Canada.
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, 100 Stokes Street, Toronto, ON, M6J 1H4, Canada.
- Department of Psychiatry, University of Toronto, 250 College Street, Toronto, ON, M5T 1R8, Canada.
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Asif M, Saquib M, Rahman Khan A, Aqil F, salem Almalki A, Ali Alasmary F, Singh J, Nasibullah M. Synthesis of Functionalized 2′,5‐Oxo‐spiro[furan‐2,3′‐indoline]‐3‐carboxylate Derivatives as Antiproliferative Agents: ADMET Studies, and Molecular Docking against P2Y12 Inhibitors. ChemistrySelect 2023. [DOI: 10.1002/slct.202204536] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/16/2023]
Affiliation(s)
- Mohd Asif
- Department of Chemistry Integral University Lucknow 226026, U.P. India
| | - Mohammad Saquib
- Department of Chemistry University of Allahabad Prayagraj (Allahabad) 211002 India
| | - Abdul Rahman Khan
- Department of Chemistry Integral University Lucknow 226026, U.P. India
| | - Farrukh Aqil
- UofL Health-Brown Cancer Center and Department of Medicine University of Louisville Louisville KY40202 USA
| | - Amani salem Almalki
- Chemistry Department College of Science King Saud University Riyadh 11451 Saudi Arabia
| | - Fatmah Ali Alasmary
- Chemistry Department College of Science King Saud University Riyadh 11451 Saudi Arabia
| | - Jaya Singh
- Department of Chemistry LRPG College Sahibabad Ghaziabad 201005 India
| | - Malik Nasibullah
- Department of Chemistry Integral University Lucknow 226026, U.P. India
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Twesigomwe D, Drögemöller BI, Wright GE, Adebamowo C, Agongo G, Boua PR, Matshaba M, Paximadis M, Ramsay M, Simo G, Simuunza MC, Tiemessen CT, Lombard Z, Hazelhurst S. Characterization of CYP2D6 Pharmacogenetic Variation in Sub-Saharan African Populations. Clin Pharmacol Ther 2023; 113:643-659. [PMID: 36111505 PMCID: PMC9957841 DOI: 10.1002/cpt.2749] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2022] [Accepted: 09/11/2022] [Indexed: 11/07/2022]
Abstract
Cytochrome P450 2D6 (CYP2D6) is a key enzyme in drug response owing to its involvement in the metabolism of ~ 25% of clinically prescribed medications. The encoding CYP2D6 gene is highly polymorphic, and many pharmacogenetics studies have been performed worldwide to investigate the distribution of CYP2D6 star alleles (haplotypes); however, African populations have been relatively understudied to date. In this study, the distributions of CYP2D6 star alleles and predicted drug metabolizer phenotypes-derived from activity scores-were examined across multiple sub-Saharan African populations based on bioinformatics analysis of 961 high-depth whole genome sequences. This was followed by characterization of novel star alleles and suballeles in a subset of the participants via targeted high-fidelity Single-Molecule Real-Time resequencing (Pacific Biosciences). This study revealed varying frequencies of known CYP2D6 alleles and predicted phenotypes across different African ethnolinguistic groups. Twenty-seven novel CYP2D6 star alleles were predicted computationally and two of them were further validated. This study highlights the importance of studying variation in key pharmacogenes such as CYP2D6 in the African context to better understand population-specific allele frequencies. This will aid in the development of better genotyping panels and star allele detection approaches with a view toward supporting effective implementation of precision medicine strategies in Africa and across the African diaspora.
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Affiliation(s)
- David Twesigomwe
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health SciencesUniversity of the WitwatersrandJohannesburgSouth Africa
- Division of Human Genetics, National Health Laboratory Service, and School of Pathology, Faculty of Health SciencesUniversity of the WitwatersrandJohannesburgSouth Africa
| | - Britt I. Drögemöller
- Department of Biochemistry and Medical Genetics, Rady Faculty of Health SciencesUniversity of ManitobaWinnipegManitobaCanada
| | - Galen E.B. Wright
- Neuroscience Research Program, Kleysen Institute for Advanced Medicine, Winnipeg Health Sciences Centre and Max Rady College of MedicineUniversity of ManitobaWinnipegManitobaCanada
- Department of Pharmacology and Therapeutics, Rady Faculty of Health SciencesUniversity of ManitobaWinnipegManitobaCanada
| | - Clement Adebamowo
- Institute for Human VirologyAbujaNigeria
- Division of Cancer Epidemiology, Department of Epidemiology and Public Health, and the Marlene and Stewart Greenebaum Comprehensive Cancer CentreUniversity of Maryland School of MedicineBaltimoreMarylandUSA
| | - Godfred Agongo
- Navrongo Health Research CentreGhana Health ServiceNavrongoGhana
- C.K. Tedam University of Technology and Applied SciencesNavrongoGhana
| | - Palwendé R. Boua
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health SciencesUniversity of the WitwatersrandJohannesburgSouth Africa
- Clinical Research Unit of NanoroInstitut de Recherche en Sciences de la SantéNanoroBurkina Faso
| | - Mogomotsi Matshaba
- Botswana‐Baylor Children's Clinical Centre of ExcellenceGaboroneBotswana
- RetrovirologyDepartment of Pediatrics, Baylor College of MedicineHoustonTexasUSA
| | - Maria Paximadis
- Centre for HIV and STIs, National Institute for Communicable Diseases, National Health Laboratory Services and Faculty of Health SciencesUniversity of the WitwatersrandJohannesburgSouth Africa
- School of Molecular and Cell BiologyUniversity of the WitwatersrandJohannesburgSouth Africa
| | - Michèle Ramsay
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health SciencesUniversity of the WitwatersrandJohannesburgSouth Africa
- Division of Human Genetics, National Health Laboratory Service, and School of Pathology, Faculty of Health SciencesUniversity of the WitwatersrandJohannesburgSouth Africa
| | - Gustave Simo
- Molecular Parasitology and Entomology Unit, Department of Biochemistry, Faculty of ScienceUniversity of DschangDschangCameroon
| | - Martin C. Simuunza
- Department of Disease Control, School of Veterinary MedicineUniversity of ZambiaLusakaZambia
| | - Caroline T. Tiemessen
- Centre for HIV and STIs, National Institute for Communicable Diseases, National Health Laboratory Services and Faculty of Health SciencesUniversity of the WitwatersrandJohannesburgSouth Africa
| | - Zané Lombard
- Division of Human Genetics, National Health Laboratory Service, and School of Pathology, Faculty of Health SciencesUniversity of the WitwatersrandJohannesburgSouth Africa
| | - Scott Hazelhurst
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health SciencesUniversity of the WitwatersrandJohannesburgSouth Africa
- School of Electrical and Information EngineeringUniversity of the WitwatersrandJohannesburgSouth Africa
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Abstract
Inter-individual variability in drug response, be it efficacy or safety, is common and likely to become an increasing problem globally given the growing elderly population requiring treatment. Reasons for this inter-individual variability include genomic factors, an area of study called pharmacogenomics. With genotyping technologies now widely available and decreasing in cost, implementing pharmacogenomics into clinical practice - widely regarded as one of the initial steps in mainstreaming genomic medicine - is currently a focus in many countries worldwide. However, major challenges of implementation lie at the point of delivery into health-care systems, including the modification of current clinical pathways coupled with a massive knowledge gap in pharmacogenomics in the health-care workforce. Pharmacogenomics can also be used in a broader sense for drug discovery and development, with increasing evidence suggesting that genomically defined targets have an increased success rate during clinical development.
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Liu Y, Lin Z, Chen Q, Chen Q, Sang L, Wang Y, Shi L, Guo L, Yu Y. PAnno: A pharmacogenomics annotation tool for clinical genomic testing. Front Pharmacol 2023; 14:1008330. [PMID: 36778023 PMCID: PMC9909284 DOI: 10.3389/fphar.2023.1008330] [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: 07/31/2022] [Accepted: 01/16/2023] [Indexed: 01/27/2023] Open
Abstract
Introduction: Next-generation sequencing (NGS) technologies have been widely used in clinical genomic testing for drug response phenotypes. However, the inherent limitations of short reads make accurate inference of diplotypes still challenging, which may reduce the effectiveness of genotype-guided drug therapy. Methods: An automated Pharmacogenomics Annotation tool (PAnno) was implemented, which reports prescribing recommendations and phenotypes by parsing the germline variant call format (VCF) file from NGS and the population to which the individual belongs. Results: A ranking model dedicated to inferring diplotypes, developed based on the allele (haplotype) definition and population allele frequency, was introduced in PAnno. The predictive performance was validated in comparison with four similar tools using the consensus diplotype data of the Genetic Testing Reference Materials Coordination Program (GeT-RM) as ground truth. An annotation method was proposed to summarize prescribing recommendations and classify drugs into avoid use, use with caution, and routine use, following the recommendations of the Clinical Pharmacogenetics Implementation Consortium (CPIC), etc. It further predicts phenotypes of specific drugs in terms of toxicity, dosage, efficacy, and metabolism by integrating the high-confidence clinical annotations in the Pharmacogenomics Knowledgebase (PharmGKB). PAnno is available at https://github.com/PreMedKB/PAnno. Discussion: PAnno provides an end-to-end clinical pharmacogenomics decision support solution by resolving, annotating, and reporting germline variants.
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Affiliation(s)
- Yaqing Liu
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, School of Life Sciences and Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Zipeng Lin
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, School of Life Sciences and Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Qingwang Chen
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, School of Life Sciences and Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Qiaochu Chen
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, School of Life Sciences and Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Leqing Sang
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, School of Life Sciences and Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Yunjin Wang
- Department of Breast Surgery, Precision Cancer Medicine Center, Key Laboratory of Breast Cancer in Shanghai, Fudan University Shanghai Cancer Center, Shanghai, China,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Leming Shi
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, School of Life Sciences and Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Li Guo
- State Key Laboratory of Multiphase Complex Systems, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, China,School of Chemical Engineering, University of Chinese Academy of Sciences, Beijing, China,*Correspondence: Li Guo, ; Ying Yu,
| | - Ying Yu
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, School of Life Sciences and Shanghai Cancer Center, Fudan University, Shanghai, China,*Correspondence: Li Guo, ; Ying Yu,
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Guo L, Zhang W, Meng W, Zhao W, Hao J, Hu X, Jin T. Very important pharmacogenes polymorphism landscape and potential clinical relevance in the Chinese Mongolian. Gene 2023; 850:146960. [DOI: 10.1016/j.gene.2022.146960] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 09/29/2022] [Accepted: 10/04/2022] [Indexed: 11/05/2022]
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Zhou Y, Lauschke VM. Challenges Related to the Use of Next-Generation Sequencing for the Optimization of Drug Therapy. Handb Exp Pharmacol 2023; 280:237-260. [PMID: 35792943 DOI: 10.1007/164_2022_596] [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: 06/15/2023]
Abstract
Over the last decade, next-generation sequencing (NGS) methods have become increasingly used in various areas of human genomics. In routine clinical care, their use is already implemented in oncology to profile the mutational landscape of a tumor, as well as in rare disease diagnostics. However, its utilization in pharmacogenomics is largely lacking behind. Recent population-scale genome data has revealed that human pharmacogenes carry a plethora of rare genetic variations that are not interrogated by conventional array-based profiling methods and it is estimated that these variants could explain around 30% of the genetically encoded functional pharmacogenetic variability.To interpret the impact of such variants on drug response a multitude of computational tools have been developed, but, while there have been major advancements, it remains to be shown whether their accuracy is sufficient to improve personalized pharmacogenetic recommendations in robust trials. In addition, conventional short-read sequencing methods face difficulties in the interrogation of complex pharmacogenes and high NGS test costs require stringent evaluations of cost-effectiveness to decide about reimbursement by national healthcare programs. Here, we illustrate current challenges and discuss future directions toward the clinical implementation of NGS to inform genotype-guided decision-making.
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Affiliation(s)
- Yitian Zhou
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden
| | - Volker M Lauschke
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden.
- Dr Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart, Germany.
- University of Tuebingen, Tuebingen, Germany.
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Skryabin V, Zastrozhin M, Parkhomenko A, Lauschke VM, Smirnov V, Petukhov A, Pankratenko E, Pozdnyakov S, Koporov S, Denisenko N, Akmalova K, Bryun E, Sychev D. Genetic testing is superior over endogenous pharmacometabolomic markers to predict safety of haloperidol in patients with alcohol-induced psychotic disorder. Curr Drug Metab 2022; 23:CDM-EPUB-128492. [PMID: 36579390 DOI: 10.2174/1389200224666221228112643] [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: 08/12/2022] [Revised: 11/23/2022] [Accepted: 12/07/2022] [Indexed: 12/30/2022]
Abstract
BACKGROUND Previous studies have shown that haloperidol biotransformation is mainly metabolized by CYP2D6. The CYP2D6 gene is highly polymorphic, contributing to inter-individual differences in enzymatic activity, and may impact haloperidol biotransformation rates, resulting in variable drug efficacy and safety profiles. OBJECTIVE The study aimed to investigate the correlation of the CYPD6 activity with haloperidol's efficacy and safety rates in patients with alcohol-induced psychotic disorders. METHOD One hundred male patients received 5-10 mg/day haloperidol by injections for 5 days. The efficacy and safety assessments were performed using PANSS, UKU, and SAS-validated psychometric scales. RESULTS No relationship between haloperidol efficacy or safety and the experimental endogenous pharmacometabolomic marker for CYP2D6 activity, urinary 6-НО-ТНВС/pinoline ratio was identified. In contrast, we found a statistically significant association between haloperidol adverse events and the most common CYP2D6 loss-of-function allele CYP2D6*4 (p<0.001). CONCLUSION Evaluation of the single polymorphism rs3892097 that defines CYP2D6*4 can predict the safety profile of haloperidol in patients with AIPD, whereas metabolic evaluation using an endogenous marker was not a suitable predictor. Furthermore, our results suggest haloperidol dose reductions could be considered in AIPD patients with at least one inactive CYP2D6 allele.
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Affiliation(s)
- Valentin Skryabin
- Moscow Research and Practical Centre on Addictions of the Moscow Department of Healthcare, 37/1 Lyublinskaya street, Moscow, Russia, 109390
- Russian Medical Academy of Continuous Professional Education of the Ministry of Health of the Russian Federation, 2/1 Barrikadnaya street, Moscow, Russian Federation, 123995
| | - Mikhail Zastrozhin
- Moscow Research and Practical Centre on Addictions of the Moscow Department of Healthcare, 37/1 Lyublinskaya street, Moscow, Russia, 109390
- Russian Medical Academy of Continuous Professional Education of the Ministry of Health of the Russian Federation, 2/1 Barrikadnaya street, Moscow, Russian Federation, 123995
- University of California, San Francisco, 1701 Divisadero St, San Francisco, CA 94115, USA
| | - Alexandra Parkhomenko
- Russian Medical Academy of Continuous Professional Education of the Ministry of Health of the Russian Federation, 2/1 Barrikadnaya street, Moscow, Russian Federation, 123995
| | - Volker M Lauschke
- Karolinska Institutet, Department of Physiology and Pharmacology, Solnavägen 1, 171 77 Solna, Sweden
- Dr Margarete Fischer-Bosch Institute of Clinical Pharmacology, Auerbachstraße 112, 70376 Stuttgart, Germany
- University of Tuebingen, Geschwister-Scholl-Platz, 72074 Tuebingen, Germany
| | - Valery Smirnov
- I.M. Sechenov First Moscow State Medical University (Sechenov University), 8с2 Trubetskaya street, Moscow, Russian Federation, 119991
- NRC Institute of Immunology FMBA of Russia, 24 Kashirskoe shosse, Moscow, Russian Federation, 115478
| | - Aleksey Petukhov
- Moscow Research and Practical Centre on Addictions of the Moscow Department of Healthcare, 37/1 Lyublinskaya street, Moscow, Russia, 109390
- I.M. Sechenov First Moscow State Medical University (Sechenov University), 8с2 Trubetskaya street, Moscow, Russian Federation, 119991
| | - Elena Pankratenko
- Moscow Research and Practical Centre on Addictions of the Moscow Department of Healthcare, 37/1 Lyublinskaya street, Moscow, Russia, 109390
| | - Sergei Pozdnyakov
- Moscow Research and Practical Centre on Addictions of the Moscow Department of Healthcare, 37/1 Lyublinskaya street, Moscow, Russia, 109390
| | - Sergei Koporov
- Moscow Research and Practical Centre on Addictions of the Moscow Department of Healthcare, 37/1 Lyublinskaya street, Moscow, Russia, 109390
| | - Natalia Denisenko
- Russian Medical Academy of Continuous Professional Education of the Ministry of Health of the Russian Federation, 2/1 Barrikadnaya street, Moscow, Russian Federation, 123995
| | - Kristina Akmalova
- Russian Medical Academy of Continuous Professional Education of the Ministry of Health of the Russian Federation, 2/1 Barrikadnaya street, Moscow, Russian Federation, 123995
| | - Evgeny Bryun
- Moscow Research and Practical Centre on Addictions of the Moscow Department of Healthcare, 37/1 Lyublinskaya street, Moscow, Russia, 109390
- Russian Medical Academy of Continuous Professional Education of the Ministry of Health of the Russian Federation, 2/1 Barrikadnaya street, Moscow, Russian Federation, 123995
| | - Dmitry Sychev
- Russian Medical Academy of Continuous Professional Education of the Ministry of Health of the Russian Federation, 2/1 Barrikadnaya street, Moscow, Russian Federation, 123995
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Mouterde M, Daali Y, Rollason V, Čížková M, Mulugeta A, Al Balushi KA, Fakis G, Constantinidis TC, Al-Thihli K, Černá M, Makonnen E, Boukouvala S, Al-Yahyaee S, Yimer G, Černý V, Desmeules J, Poloni ES. Joint Analysis of Phenotypic and Genomic Diversity Sheds Light on the Evolution of Xenobiotic Metabolism in Humans. Genome Biol Evol 2022; 14:6852765. [PMID: 36445690 PMCID: PMC9750130 DOI: 10.1093/gbe/evac167] [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: 02/21/2022] [Revised: 11/03/2022] [Accepted: 11/22/2022] [Indexed: 11/30/2022] Open
Abstract
Variation in genes involved in the absorption, distribution, metabolism, and excretion of drugs (ADME) can influence individual response to a therapeutic treatment. The study of ADME genetic diversity in human populations has led to evolutionary hypotheses of adaptation to distinct chemical environments. Population differentiation in measured drug metabolism phenotypes is, however, scarcely documented, often indirectly estimated via genotype-predicted phenotypes. We administered seven probe compounds devised to target six cytochrome P450 enzymes and the P-glycoprotein (P-gp) activity to assess phenotypic variation in four populations along a latitudinal transect spanning over Africa, the Middle East, and Europe (349 healthy Ethiopian, Omani, Greek, and Czech volunteers). We demonstrate significant population differentiation for all phenotypes except the one measuring CYP2D6 activity. Genome-wide association studies (GWAS) evidenced that the variability of phenotypes measuring CYP2B6, CYP2C9, CYP2C19, and CYP2D6 activity was associated with genetic variants linked to the corresponding encoding genes, and additional genes for the latter three. Instead, GWAS did not indicate any association between genetic diversity and the phenotypes measuring CYP1A2, CYP3A4, and P-gp activity. Genome scans of selection highlighted multiple candidate regions, a few of which included ADME genes, but none overlapped with the GWAS candidates. Our results suggest that different mechanisms have been shaping the evolution of these phenotypes, including phenotypic plasticity, and possibly some form of balancing selection. We discuss how these contrasting results highlight the diverse evolutionary trajectories of ADME genes and proteins, consistent with the wide spectrum of both endogenous and exogenous molecules that are their substrates.
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Affiliation(s)
| | - Youssef Daali
- Division of Clinical Pharmacology and Toxicology, Geneva University Hospitals and University of Geneva, Geneva, Switzerland
| | - Victoria Rollason
- Division of Clinical Pharmacology and Toxicology, Geneva University Hospitals and University of Geneva, Geneva, Switzerland
| | - Martina Čížková
- Institute of Archaeology of the Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Anwar Mulugeta
- Department of Pharmacology and Clinical Pharmacy, College of Health Sciences, Addis Ababa University, Addis Ababa, Ethiopia
| | - Khalid A Al Balushi
- College of Pharmacy, National University of Science and Technology, Muscat, Sultanate of Oman
| | - Giannoulis Fakis
- Department of Molecular Biology and Genetics, Democritus University of Thrace, Alexandroupolis, Greece
| | | | - Khalid Al-Thihli
- Department of Genetics, Sultan Qaboos University Hospital, Muscat, Sultanate of Oman
| | - Marie Černá
- Department of Medical Genetics, Third Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Eyasu Makonnen
- Department of Pharmacology and Clinical Pharmacy, College of Health Sciences, Addis Ababa University, Addis Ababa, Ethiopia,Center for Innovative Drug Development and Therapeutic Trials for Africa, College of Health Sciences, Addis Ababa University, Addis Ababa, Ethiopia
| | - Sotiria Boukouvala
- Department of Molecular Biology and Genetics, Democritus University of Thrace, Alexandroupolis, Greece
| | - Said Al-Yahyaee
- Department of Genetics, College of Medicine and Health Sciences, Sultan Qaboos University, Muscat, Sultanate of Oman
| | - Getnet Yimer
- Center for Global Genomics & Health Equity, Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Viktor Černý
- Department of Anthropology and Human Genetics, Faculty of Science, Charles University, Prague, Czech Republic
| | - Jules Desmeules
- Division of Clinical Pharmacology and Toxicology, Geneva University Hospitals and University of Geneva, Geneva, Switzerland
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Chaichana J, Khamenkhetkarn M, Sastraruji T, Monum T, O’Brien TE, Amornlertwatana Y, Jaikang C. Categorization of Cytochrome P4502D6 Activity Score by Urinary Amphetamine/Methamphetamine Ratios. Metabolites 2022; 12:metabo12121174. [PMID: 36557212 PMCID: PMC9788588 DOI: 10.3390/metabo12121174] [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: 09/30/2022] [Revised: 11/14/2022] [Accepted: 11/23/2022] [Indexed: 11/26/2022] Open
Abstract
Methamphetamine (MA) level in urine has been used for judgment in MA consumption. Metabolism and intoxication of MA are correlated with the activity of cytochrome P450 2D6 (CYP2D6). The activity score (AS) is a potential tool for predicting exposure and personalized dose of drugs metabolized by CYP2D6. Prediction of the CYP2D6 activity score might be described as MA intoxication. The objective of this study was to categorize the CYP2D6 activity score using the urinary amphetamine (AM)/MA ratio. Urine samples (n = 23,258) were collected. The levels of MA and AM were determined by a gas chromatography-nitrogen-phosphorus detector. The log AS was calculated by an AM/MA ratio and classified into four groups following the percentile position: lower than the 2.5th, the 2.5th-the 50th, the 50th-97.5th, and greater than the 97.5th percentile, respectively. The AS value for males presented was less than 0.024, 0.024-0.141, 0.141-0.836, and greater than 0.836. Meanwhile, the AS values were revealed to be lower than 0.023, 0.023-0.148, 0.148-0.850, and higher than 0.850 for females. The AS value of CYP2D6 can be applied to describe the toxicity of MA in forensic crime scenes and relapse behavior.
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Affiliation(s)
- Jatuporn Chaichana
- Toxicology Section, Regional Medical Science Center 1 Chiang Mai 191 Tumbon Don Keaw, Ampher Mae Rim, Chiang Mai 50180, Thailand
| | - Manee Khamenkhetkarn
- Toxicology Section, Regional Medical Science Center 1 Chiang Mai 191 Tumbon Don Keaw, Ampher Mae Rim, Chiang Mai 50180, Thailand
- Correspondence: (M.K.); (C.J.); Tel.:+66-53112188 (M.K.); +66-53935432 (C.J.)
| | | | - Tawachai Monum
- Department of Forensic Medicine, Faculty of Medicine, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Timothy E. O’Brien
- Department of Mathematics and Statistics, Loyola University Chicago, 1032 W.Sheridan Road, Chicago, IL 60660-1537, USA
| | - Yutti Amornlertwatana
- Department of Forensic Medicine, Faculty of Medicine, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Churdsak Jaikang
- Department of Forensic Medicine, Faculty of Medicine, Chiang Mai University, Chiang Mai 50200, Thailand
- Correspondence: (M.K.); (C.J.); Tel.:+66-53112188 (M.K.); +66-53935432 (C.J.)
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Medwid S, Kim RB. Implementation of pharmacogenomics: Where are we now? Br J Clin Pharmacol 2022. [PMID: 36366858 DOI: 10.1111/bcp.15591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 11/01/2022] [Accepted: 11/07/2022] [Indexed: 11/13/2022] Open
Abstract
Pharmacogenomics (PGx), examining the effect of genetic variation on interpatient variation in drug disposition and response, has been widely studied for several decades. However, as cost, as well as turnaround time associated with PGx testing, has significantly improved, the use of PGx in the clinical setting has been gaining momentum. Nevertheless, challenges have emerged in the broader clinical implementation of PGx. In this review, we will outline current models of PGx delivery and methodologies of evaluation, and discuss clinically relevant PGx tests and associated medications. Additionally, we will describe our approach for the broad implementation of pre-emptive DPYD genotyping in patients taking fluoropyrimidines in Ontario, Canada, as an example of clinically actionable PGx testing with sufficient clinical evidence of patient benefit that can become a new standard of patient care. We will highlight challenges associated with PGx testing, including a lack of diversity in PGx studies as well as general limitations that impact the broad adoption of PGx testing. Lastly, we examine the future of PGx, discussing new clinical targets, methodologies and analysis approaches.
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Affiliation(s)
- Samantha Medwid
- Department of Medicine, University of Western Ontario, London, Ontario, Canada
- Lawson Health Research Institute, London, Ontario, Canada
- London Health Sciences Centre, London, Ontario, Canada
| | - Richard B Kim
- Department of Medicine, University of Western Ontario, London, Ontario, Canada
- Lawson Health Research Institute, London, Ontario, Canada
- London Health Sciences Centre, London, Ontario, Canada
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Scott ER, Yang Y, Botton MR, Seki Y, Hoshitsuki K, Harting J, Baybayan P, Cody N, Nicoletti P, Moriyama T, Chakraborty S, Yang JJ, Edelmann L, Schadt EE, Korlach J, Scott SA. Long-read HiFi sequencing of NUDT15: Phased full-gene haplotyping and pharmacogenomic allele discovery. Hum Mutat 2022; 43:1557-1566. [PMID: 36057977 PMCID: PMC9875722 DOI: 10.1002/humu.24457] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 08/22/2022] [Accepted: 08/29/2022] [Indexed: 01/27/2023]
Abstract
To determine the phase of NUDT15 sequence variants for more comprehensive star (*) allele diplotyping, we developed a novel long-read single-molecule real-time HiFi amplicon sequencing method. A 10.5 kb NUDT15 amplicon assay was validated using reference material positive controls and additional samples for specimen type and blinded accuracy assessment. Triplicate NUDT15 HiFi sequencing of two reference material samples had nonreference genotype concordances of >99.9%, indicating that the assay is robust. Notably, short-read genome sequencing of a subset of samples was unable to determine the phase of star (*) allele-defining NUDT15 variants, resulting in ambiguous diplotype results. In contrast, long-read HiFi sequencing phased all variants across the NUDT15 amplicons, including a *2/*9 diplotype that previously was characterized as *1/*2 in the 1000 Genomes Project v3 data set. Assay throughput was also tested using 8.5 kb amplicons from 100 Ashkenazi Jewish individuals, which identified a novel NUDT15 *1 suballele (c.-121G>A) and a rare likely deleterious coding variant (p.Pro129Arg). Both novel alleles were Sanger confirmed and assigned as *1.007 and *20, respectively, by the PharmVar Consortium. Taken together, NUDT15 HiFi amplicon sequencing is an innovative method for phased full-gene characterization and novel allele discovery, which could improve NUDT15 pharmacogenomic testing and subsequent phenotype prediction.
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Affiliation(s)
- Erick R Scott
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Yao Yang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Mariana R Botton
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Sema4, Stamford, Connecticut, USA
| | - Yoshinori Seki
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Keito Hoshitsuki
- School of Pharmacy, University of Pittsburgh, Pennsylvania, Pittsburgh, USA
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - John Harting
- Pacific Biosciences, Menlo Park, California, USA
| | | | - Neal Cody
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Sema4, Stamford, Connecticut, USA
| | - Paola Nicoletti
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Sema4, Stamford, Connecticut, USA
| | - Takaya Moriyama
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | | | - Jun J Yang
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Lisa Edelmann
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Sema4, Stamford, Connecticut, USA
| | - Eric E Schadt
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Sema4, Stamford, Connecticut, USA
| | | | - Stuart A Scott
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Sema4, Stamford, Connecticut, USA
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Parkhomenko AA, Zastrozhin MS, Pozdnyakov SA, Noskov VV, Zaytsev IA, Ivanchenko VA, Denisenko NP, Akmalova KA, Skryabin VY, Bryun EA, Sychev DA. Association of CYP2D6*4 Polymorphism with the Steady-State Concentration of Haloperidol in Patients with Alcohol-Induced Psychotic Disorders. PSYCHOPHARMACOLOGY BULLETIN 2022; 52:52-60. [PMID: 36339274 PMCID: PMC9611797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Background CYP2D6 subfamily isoenzymes play an important role in the biotransformation of haloperidol, and their activity may influence the efficacy and safety of haloperidol. The use of haloperidol is often associated with the occurrence of adverse drug reactions (ADRs), such as dyskinesia, acute dystonia, and orthostatic hypotension. Previous studies have demonstrated the relationship between the CYP2D6*4 genetic polymorphism and CYP2D6 activity, as well as haloperidol efficacy and safety rates. Purpose To evaluate the association of CYP2D6*4 genetic polymorphism with the steady-state concentration of haloperidol in patients with acute alcohol-induced psychotic disorders (AIPDs). Material and methods The study involved 100 male patients with AIPD (average age 41.4 ± 14.4 years) who received haloperidol by injections in a dose of 5-10 mg/day. The efficacy profile was assessed using a validated psychometric PANSS scale (Positive and Negative Syndrome Scale). Therapy safety was assessed using the internationally validated UKU (Side-Effect Rating Scale) and SAS (Simpson-Angus Scale for Extrapyramidal Symptoms) scales. Genotyping was performed with the real-time polymerase chain reaction. Results We revealed the statistically significant results in terms of therapy safety evaluation (dynamics of the UKU scores: (GG) 8.00 [7.00; 10.00], (GA) 15.0 [9.25; 18.0], p < 0.001; dynamics of the SAS scores: (GG) 11.0 [9.0; 14.0], (GA) 14.50 [12.0; 18.0], p < 0.001. Pharmacokinetic study showed a statistically significant difference across the groups with different genotypes: (GG) 3.13 [2.32; 3.95], (GA) 3.89 [2.92; 5.26], p = 0.010. Conclusion It can be concluded that patients with the GA genotype have a higher risk of ADRs compared to patients who carry the GG genotype. It was shown that CYP2D6*4 genetic polymorphism has a statistically significant effect on the steady-state concentration of haloperidol.
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Affiliation(s)
- A A Parkhomenko
- Parkhomenko, postgraduate student of addiction psychiatry department
| | - M S Zastrozhin
- Zastrozhin, MD, PhD, associate professor of addiction psychiatry department, head of laboratory of genetics and fundamental studies, Russian Medical Academy of Continuous Professional Education of the Ministry of Health of the Russian Federation, Moscow, Russian Federation; Moscow Research and Practical Centre on Addictions of the Moscow Department of Healthcare, Moscow, Russia; University of California, San Francisco, San Francisco, CA, USA
| | - S A Pozdnyakov
- Pozdnyakov, researcher of the laboratory of genetics and fundamental studies
| | - V V Noskov
- Noskov, laboratory assistants, Moscow Research and Practical Centre on Addictions of the Moscow Department of Healthcare, Moscow, Russia
| | - I A Zaytsev
- Zaytsev, laboratory assistants, Moscow Research and Practical Centre on Addictions of the Moscow Department of Healthcare, Moscow, Russia
| | - V A Ivanchenko
- Ivanchenko, laboratory assistants, Moscow Research and Practical Centre on Addictions of the Moscow Department of Healthcare, Moscow, Russia
| | - N P Denisenko
- Denisenko, PhD in Medicine, Head of the Department of Personalized Medicine
| | - K A Akmalova
- Akmalova, Researcher in the Department of Molecular Medicine
| | - VYu Skryabin
- Skryabin, MD, PhD, associate professor of addiction psychiatry department, head of clinical department
| | - E A Bryun
- Bryun, MD, PhD, professor, head of addiction psychiatry department, president, Russian Medical Academy of Continuous Professional Education of the Ministry of Health of the Russian Federation, Moscow, Russian Federation; Moscow Research and Practical Centre on Addictions of the Moscow Department of Healthcare, Moscow, Russia
| | - D A Sychev
- Sychev, corresponding member of the Academy of Sciences of Russia, MD, PhD, professor, rector, head of clinical pharmacology and therapy department, Russian Medical Academy of Continuous Professional Education of the Ministry of Health of the Russian Federation, Moscow, Russian Federation
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Alshabeeb MA, Alyabsi M, Aziz MA, Abohelaika S. Pharmacogenes that demonstrate high association evidence according to CPIC, DPWG, and PharmGKB. Front Med (Lausanne) 2022; 9:1001876. [PMID: 36388934 PMCID: PMC9640910 DOI: 10.3389/fmed.2022.1001876] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2022] [Accepted: 09/22/2022] [Indexed: 12/20/2023] Open
Abstract
BACKGROUND Different levels of evidence related to the variable responses of individuals to drug treatment have been reported in various pharmacogenomic (PGx) databases. Identification of gene-drug pairs with strong association evidence can be helpful in prioritizing the implementation of PGx guidelines and focusing on a gene panel. This study aimed to determine the pharmacogenes with the highest evidence-based association and to indicate their involvement in drug-gene interactions. METHODOLOGY The publicly available datasets CPIC, DPWG, and PharmGKB were selected to determine the pharmacogenes with the highest drug outcome associations. The upper two levels of evidence rated by the three scoring methods were specified (levels A-B in CPIC, 3-4 in DPWG, or 1-2 levels in PharmGKB). The identified pharmacogenes were further ranked in this study based on the number of medications they interacted with. RESULTS Fifty pharmacogenes, with high to moderately high evidence of associations with drug response alterations, with potential influence on the therapeutic and/or toxicity outcomes of 152 drugs were identified. CYP2D6, CYP2C9, CYP2C19, G6PD, HLA-B, SLCO1B1, CACNA1S, RYR1, MT-RNR1, and IFNL4 are the top 10 pharmacogenes, where each is predicted to impact patients' responses to ≥5 drugs. CONCLUSION This study identified the most important pharmacogenes based on the highest-ranked association evidence and their frequency of involvement in affecting multiple drugs. The obtained data is useful for customizing a gene panel for PGx testing. Identifying the strength of scientific evidence supporting drug-gene interactions aids drug prescribers in making the best clinical decision.
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Affiliation(s)
- Mohammad A. Alshabeeb
- Population Health Research Section, King Abdullah International Medical Research Center, Riyadh, Saudi Arabia
- King Saud Bin Abdulaziz University for Health Sciences, Ministry of National Guard Health Affairs (MNGHA), Riyadh, Saudi Arabia
| | - Mesnad Alyabsi
- Population Health Research Section, King Abdullah International Medical Research Center, Riyadh, Saudi Arabia
- King Saud Bin Abdulaziz University for Health Sciences, Ministry of National Guard Health Affairs (MNGHA), Riyadh, Saudi Arabia
| | - Mohammad A. Aziz
- Interdisciplinary Nanotechnology Centre, Aligarh Muslim University, Aligarh, India
| | - Salah Abohelaika
- Department of Pharmacy, Qatif Central Hospital, Qatif, Saudi Arabia
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Tilleman L, Rubben K, Van Criekinge W, Deforce D, Van Nieuwerburgh F. Haplotyping pharmacogenes using TLA combined with Illumina or Nanopore sequencing. Sci Rep 2022; 12:17734. [PMID: 36273027 PMCID: PMC9587992 DOI: 10.1038/s41598-022-22499-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 10/16/2022] [Indexed: 01/18/2023] Open
Abstract
The currently used pharmacogenetic genotyping assays offer limited haplotype information, which can potentially cause specific functional effects to be missed. This study tested if Targeted Locus Amplification (TLA), when using non-patient-specific primers combined with Illumina or Nanopore sequencing, can offer an advantage in terms of accurate phasing. The TLA method selectively amplifies and sequences entire genes based on crosslinking DNA in close physical proximity. This way, DNA fragments that were initially further apart in the genome are ligated into one molecule, making it possible to sequence distant variants within one short read. In this study, four pharmacogenes, CYP2D6, CYP2C19, CYP1A2 and BRCA1, were sequenced after enrichment using different primer pairs. Only 24% or 38% of the nucleotides mapped on target when using Illumina or Nanopore sequencing, respectively. With an average depth of more than 1000X for the regions of interest, none of the genes were entirely covered with either sequencing method. For three of the four genes, less than half of the variants were phased correctly compared to the reference. The Nanopore dataset with the optimized primer pair for CYP2D6 resulted in the correct haplotype, showing that this method can be used for reliable genotyping and phasing of pharmacogenes but does require patient-specific primer design and optimization to be effective.
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Affiliation(s)
- Laurentijn Tilleman
- Laboratory of Pharmaceutical Biotechnology, Ghent University, Ottergemsesteenweg 460, 9000, Ghent, Belgium
| | - Kaat Rubben
- Laboratory of Pharmaceutical Biotechnology, Ghent University, Ottergemsesteenweg 460, 9000, Ghent, Belgium
| | - Wim Van Criekinge
- Laboratory of Bioinformatics and Computational Genomics, Ghent University, Coupure Links 653, 9000, Ghent, Belgium
| | - Dieter Deforce
- Laboratory of Pharmaceutical Biotechnology, Ghent University, Ottergemsesteenweg 460, 9000, Ghent, Belgium
| | - Filip Van Nieuwerburgh
- Laboratory of Pharmaceutical Biotechnology, Ghent University, Ottergemsesteenweg 460, 9000, Ghent, Belgium.
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Hitchman LM, Faatoese A, Merriman TR, Miller AL, Liau Y, Graham OEE, Kee PS, Pearson JF, Fakahau T, Cameron VA, Kennedy MA, Maggo SDS. Allelic diversity of the pharmacogene CYP2D6 in New Zealand Māori and Pacific peoples. Front Genet 2022; 13:1016416. [DOI: 10.3389/fgene.2022.1016416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Accepted: 09/26/2022] [Indexed: 11/13/2022] Open
Abstract
The enzyme cytochrome P450 2D6 (CYP2D6) metabolises approximately 25% of commonly prescribed drugs, including analgesics, anti-hypertensives, and anti-depressants, among many others. Genetic variation in drug metabolising genes can alter how an individual responds to prescribed drugs, including predisposing to adverse drug reactions. The majority of research on the CYP2D6 gene has been carried out in European and East Asian populations, with many Indigenous and minority populations, such as those from Oceania, greatly underrepresented. However, genetic variation is often population specific and analysis of diverse ethnic groups can reveal differences in alleles that may be of clinical significance. For this reason, we set out to examine the range and frequency of CYP2D6 variants in a sample of 202 Māori and Pacific people living in Aotearoa (New Zealand). We carried out long PCR to isolate the CYP2D6 region before performing nanopore sequencing to identify all variants and alleles in these samples. We identified twelve variants which have previously not been reported in the PharmVar CYP2D6 database, three of which were exonic missense variations. Six of these occurred in single samples and one was found in 19 samples (9.4% of the cohort). The remaining five variants were identified in two samples each. Identified variants formed twelve new CYP2D6 suballeles and four new star alleles, now recorded in the PharmVar database. One striking finding was that CYP2D6*71, an allele of uncertain functional status which has been rarely observed in previous studies, occurs at a relatively high frequency (8.9%) within this cohort. These data will help to ensure that CYP2D6 genetic analysis for pharmacogenetic purposes can be carried out accurately and effectively in this population group.
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An Investigation of O-Demethyl Tramadol/Tramadol Ratio for Cytochrome P450 2D6 Phenotyping: The CYTRAM Study. Pharmaceutics 2022; 14:pharmaceutics14102177. [PMID: 36297612 PMCID: PMC9611900 DOI: 10.3390/pharmaceutics14102177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 09/28/2022] [Accepted: 10/07/2022] [Indexed: 12/03/2022] Open
Abstract
Cytochrome P450 2D6 (CYP2D6) gene polymorphisms influence the exposure to tramadol (T) and its pharmacologically active metabolite, O-demethyl tramadol (O-dT). Tramadol has been considered as a candidate probe drug for CYP2D6 phenotyping. The objective of the CYTRAM study was to investigate the value of plasma O-dT/T ratio for CYP2D6 phenotyping. European adult patients who received IV tramadol after surgery were included. CYP2D6 genotyping was performed and subjects were classified as extensive (EM), intermediate (IM), poor (PM), or ultra-rapid (UM) CYP2D6 metabolizers. Plasma concentrations of tramadol and O-dT were determined at 24 h and 48 h. The relationship between O-dT/T ratio and CYP2D6 phenotype was examined in both a learning and a validation group. Genotype data were obtained in 301 patients, including 23 PM (8%), 117 IM (39%), 154 EM (51%), and 7 UM (2%). Tramadol trough concentrations at 24 h were available in 297 patients. Mean value of O-dT/T ratio was significantly lower in PM than in non-PM individuals (0.061 ± 0.031 versus 0.178 ± 0.09, p < 0.01). However, large overlap was observed in the distributions of O-dT/T ratio between groups. Statistical models based on O-dT/T ratio failed to identify CYP2D6 phenotype with acceptable sensitivity and specificity. Those results suggest that tramadol is not an adequate probe drug for CYP2D6 phenotyping.
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