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Urbančič D, Jukič M, Šmid A, Gobec S, Jazbec J, Mlinarič-Raščan I. Thiopurine S-methyltransferase - An important intersection of drug-drug interactions in thiopurine treatment. Biomed Pharmacother 2025; 184:117893. [PMID: 39923408 DOI: 10.1016/j.biopha.2025.117893] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2024] [Revised: 01/27/2025] [Accepted: 02/03/2025] [Indexed: 02/11/2025] Open
Abstract
Understanding the molecular mechanisms of medicines is crucial for developing novel drugs, for repurposing existing medicines, and for predicting toxicities. Thiopurine S-methyltransferase (TPMT) serves as an exemplary case in personalized medicine, as its activity is influenced by genetic variants, co-factors, substrates, and inhibitors, which lead to diverse outcomes in thiopurine therapy. This comprehensive review explores the role of TPMT in drug-drug interactions by investigating its interactions with co-factors, substrates, and inhibitors. We focus on the principal interactions of TPMT with clinically relevant inhibitors, and add to this information with molecular docking analyses for the substrate and co-factor binding sites of TPMT. Notably, methotrexate and sulfasalazine emerged as the top-ranked compounds with favorable docking scores for the co-factor binding site, while furosemide is presented as the highest ranked inhibitor for the substrate binding site. Furthermore, we highlight the chemical and structural properties governing ligand binding to TPMT. We support the molecular characteristics by using a summary of clinical implications. Examining the molecular interactions between substrates or inhibitors and TPMT not only addresses therapeutic consequences, but also reveals potential novel indications of interacting compounds. These insights are also invaluable for identifying endogenous ligands and enhancing our understanding of TPMT's biological function.
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Affiliation(s)
- Dunja Urbančič
- University of Ljubljana, Faculty of Pharmacy, Aškerčeva cesta 7, Ljubljana 1000, Slovenia.
| | - Marko Jukič
- Faculty of Chemistry and Chemical Engineering, University of Maribor, Smetanova ulica 17, Maribor 2000, Slovenia; Faculty of Mathematics, Natural Sciences and Information Technologies, University of Primorska, Glagoljaška ulica 8, Koper SI-6000, Slovenia.
| | - Alenka Šmid
- University of Ljubljana, Faculty of Pharmacy, Aškerčeva cesta 7, Ljubljana 1000, Slovenia.
| | - Stanislav Gobec
- University of Ljubljana, Faculty of Pharmacy, Aškerčeva cesta 7, Ljubljana 1000, Slovenia.
| | - Janez Jazbec
- Division of Pediatrics, Hematology and Oncology, University Medical Center Ljubljana, Ljubljana SI-1000, Slovenia.
| | - Irena Mlinarič-Raščan
- University of Ljubljana, Faculty of Pharmacy, Aškerčeva cesta 7, Ljubljana 1000, Slovenia.
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2
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Mu H, Ye L, Wang B. Detailed resume of S-methyltransferases: Categories, structures, biological functions and research advancements in related pathophysiology and pharmacotherapy. Biochem Pharmacol 2024; 226:116361. [PMID: 38876259 DOI: 10.1016/j.bcp.2024.116361] [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: 03/05/2024] [Revised: 05/19/2024] [Accepted: 06/10/2024] [Indexed: 06/16/2024]
Abstract
Methylation is a vital chemical reaction in the metabolism of many drugs, neurotransmitters, hormones, and exogenous compounds. Among them, S-methylation plays a significant role in the biotransformation of sulfur-containing compounds, particularly chemicals with sulfhydryl groups. Currently, only three S-methyltransferases have been reported: thiopurine methyltransferase (TPMT), thiol methyltransferase (TMT), and thioether methyltransferase (TEMT). These enzymes are involved in various biological processes such as gene regulation, signal transduction, protein repair, tumor progression, and biosynthesis and degradation reactions in animals, plants, and microorganisms. Furthermore, they play pivotal roles in the metabolic pathways of essential drugs and contribute to the advancement of diseases such as tumors. This paper reviews the research progress on relevant structural features, metabolic mechanisms, inhibitor development, and influencing factors (gene polymorphism, S-adenosylmethionine level, race, sex, age, and disease) of S-methyltransferases. We hope that a better comprehension of S-methyltransferases will help to provide a reference for the development of novel strategies for related disorders and improve long-term efficacy.
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Affiliation(s)
- Hongfei Mu
- Department of Drug Metabolism, Beijing Key Laboratory of Non-Clinical Drug Metabolism and PK/PD Study, State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, PR China.
| | - Lisha Ye
- Department of Drug Metabolism, Beijing Key Laboratory of Non-Clinical Drug Metabolism and PK/PD Study, State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, PR China.
| | - Baolian Wang
- Department of Drug Metabolism, Beijing Key Laboratory of Non-Clinical Drug Metabolism and PK/PD Study, State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, PR China.
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3
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Šmid A, Štajdohar M, Milek M, Urbančič D, Karas Kuželički N, Tamm R, Metspalu A, Mlinarič-Raščan I. Transcriptome analysis reveals involvement of thiopurine S-methyltransferase in oxidation-reduction processes. Eur J Pharm Sci 2024; 192:106616. [PMID: 37865284 DOI: 10.1016/j.ejps.2023.106616] [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: 07/18/2023] [Revised: 10/18/2023] [Accepted: 10/18/2023] [Indexed: 10/23/2023]
Abstract
Thiopurine S-methyltransferase (TPMT) is an important enzyme involved in the deactivation of thiopurines and represents a major determinant of thiopurine-related toxicities. Despite its well-known importance in thiopurine metabolism, the understanding of its endogenous role is lacking. In the present study, we aimed to gain insight into the molecular processes involving TPMT by applying a data fusion approach to analyze whole-genome expression data. The RNA profiling was done on whole blood samples from 1017 adult male and female donors to the Estonian biobank using Illumina HTv3 arrays. Our results suggest that TPMT is closely related to genes involved in oxidoreductive processes. The in vitro experiments on different cell models confirmed that TPMT influences redox capacity of the cell by altering S-adenosylmethionine (SAM) consumption and consequently glutathione (GSH) synthesis. Furthermore, by comparing gene networks of subgroups of individuals, we identified genes, which could have a role in regulating TPMT activity. The biological relevance of identified genes and pathways will have to be further evaluated in molecular studies.
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Affiliation(s)
- Alenka Šmid
- Department of Clinical Biochemistry, Faculty of Pharmacy, University of Ljubljana, Slovenia.
| | | | - Miha Milek
- Department of Clinical Biochemistry, Faculty of Pharmacy, University of Ljubljana, Slovenia; Core Unit Bioinformatics, Berlin Institute of Health at Charite, Germany
| | - Dunja Urbančič
- Department of Clinical Biochemistry, Faculty of Pharmacy, University of Ljubljana, Slovenia
| | - Nataša Karas Kuželički
- Department of Clinical Biochemistry, Faculty of Pharmacy, University of Ljubljana, Slovenia
| | - Riin Tamm
- Estonian Genome Center, Institute of Genomics and Institute of Molecular and Cell Biology, University of Tartu, Estonia; Youth and Talent Policy Department, Estonian Ministry of Education and Research, Estonia
| | - Andres Metspalu
- Estonian Genome Center, Institute of Genomics and Institute of Molecular and Cell Biology, University of Tartu, Estonia
| | - Irena Mlinarič-Raščan
- Department of Clinical Biochemistry, Faculty of Pharmacy, University of Ljubljana, Slovenia.
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4
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Zudeh G, Franca R, Stocco G, Decorti G. Biomarkers for gastrointestinal adverse events related to thiopurine therapy. World J Gastroenterol 2021; 27:6348-6356. [PMID: 34720526 PMCID: PMC8517779 DOI: 10.3748/wjg.v27.i38.6348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 04/29/2021] [Accepted: 09/03/2021] [Indexed: 02/06/2023] Open
Abstract
Thiopurines are immunomodulators used in the treatment of acute lymphoblastic leukemia and inflammatory bowel diseases. Adverse reactions to these agents are one of the main causes of treatment discontinuation or interruption. Myelosuppression is the most frequent adverse effect; however, approximately 5%-20% of patients develop gastrointestinal toxicity. The identification of biomarkers able to prevent and/or monitor these adverse reactions would be useful for clinicians for the proactive management of long-term thiopurine therapy. In this editorial, we discuss evidence supporting the use of PACSIN2, RAC1, and ITPA genes, in addition to TPMT and NUDT15, as possible biomarkers for thiopurine-related gastrointestinal toxicity.
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Affiliation(s)
- Giulia Zudeh
- Department of Life Sciences, University of Trieste, Trieste 34127, Italy
| | - Raffaella Franca
- Department of Medical, Surgical and Health Sciences, University of Trieste, Trieste 34149, Italy
| | - Gabriele Stocco
- Department of Life Sciences, University of Trieste, Trieste 34127, Italy
| | - Giuliana Decorti
- Department of Medical, Surgical and Health Sciences, University of Trieste, Trieste 34149, Italy
- Institute for Maternal and Child Health I.R.C.C.S Burlo Garofolo, Trieste 34137, Italy
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5
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Fu J, Zhang Y, Liu J, Lian X, Tang J, Zhu F. Pharmacometabonomics: data processing and statistical analysis. Brief Bioinform 2021; 22:6236068. [PMID: 33866355 DOI: 10.1093/bib/bbab138] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2021] [Revised: 02/09/2021] [Accepted: 03/23/2021] [Indexed: 12/14/2022] Open
Abstract
Individual variations in drug efficacy, side effects and adverse drug reactions are still challenging that cannot be ignored in drug research and development. The aim of pharmacometabonomics is to better understand the pharmacokinetic properties of drugs and monitor the drug effects on specific metabolic pathways. Here, we systematically reviewed the recent technological advances in pharmacometabonomics for better understanding the pathophysiological mechanisms of diseases as well as the metabolic effects of drugs on bodies. First, the advantages and disadvantages of all mainstream analytical techniques were compared. Second, many data processing strategies including filtering, missing value imputation, quality control-based correction, transformation, normalization together with the methods implemented in each step were discussed. Third, various feature selection and feature extraction algorithms commonly applied in pharmacometabonomics were described. Finally, the databases that facilitate current pharmacometabonomics were collected and discussed. All in all, this review provided guidance for researchers engaged in pharmacometabonomics and metabolomics, and it would promote the wide application of metabolomics in drug research and personalized medicine.
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Affiliation(s)
- Jianbo Fu
- College of Pharmaceutical Sciences in Zhejiang University, China
| | - Ying Zhang
- College of Pharmaceutical Sciences in Zhejiang University, China
| | - Jin Liu
- College of Pharmaceutical Sciences in Zhejiang University, China
| | - Xichen Lian
- College of Pharmaceutical Sciences in Zhejiang University, China
| | - Jing Tang
- Department of Bioinformatics in Chongqing Medical University, China
| | - Feng Zhu
- College of Pharmaceutical Sciences in Zhejiang University, China
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6
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Chansavang A, Maalej S, Narjoz C, Loriot MA, Pallet N. Identification of rare defective allelic variants in cases of thiopurine S-methyltransferase deficient activity. Pharmacogenomics 2020; 21:1217-1226. [PMID: 33118454 DOI: 10.2217/pgs-2020-0124] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Aim: To assess rare TPMT variants in patients carrying a deficient phenotype not predicted by the four more frequent genotypes (*2, *3A, *3B and *3C). Materials & methods: Next-generation sequencing of TPMT in 39 patients with a discordant genotype. Results: None of the variants identified explained the discordances assuming that they are of uncertain significance according to the Clinical Pharmacogenetics Implementation Consortium classification. Two unknown variants were detected and predicted to result in a splicing defect. We show that TPMT*16 and TMPT*21 are defective alleles, and TPMT*8 and TPMT*24 are associated with a normal activity. Conclusion: Whole-exon sequencing for rare TPMT mutations has a low diagnostic yield. A reassessment of the functional impact of rare variants of uncertain significance is a critical issue.
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Affiliation(s)
- Albain Chansavang
- Service de Biochimie, Assistance Publique Hôpitaux de Paris, Hôpital Européen Georges Pompidou, F-75015, Paris, France
| | - Sadok Maalej
- Service de Biochimie, Assistance Publique Hôpitaux de Paris, Hôpital Européen Georges Pompidou, F-75015, Paris, France
| | - Céline Narjoz
- Service de Biochimie, Assistance Publique Hôpitaux de Paris, Hôpital Européen Georges Pompidou, F-75015, Paris, France
| | - Marie-Anne Loriot
- Service de Biochimie, Assistance Publique Hôpitaux de Paris, Hôpital Européen Georges Pompidou, F-75015, Paris, France.,Université de Paris, INSERM U1138, Centre de Recherche des Cordeliers, F-75006, Paris, France
| | - Nicolas Pallet
- Service de Biochimie, Assistance Publique Hôpitaux de Paris, Hôpital Européen Georges Pompidou, F-75015, Paris, France.,Université de Paris, INSERM U1138, Centre de Recherche des Cordeliers, F-75006, Paris, France
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7
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Zimdahl Kahlin A, Helander S, Wennerstrand P, Vikingsson S, Mårtensson LG, Appell ML. Pharmacogenetic studies of thiopurine methyltransferase genotype-phenotype concordance and effect of methotrexate on thiopurine metabolism. Basic Clin Pharmacol Toxicol 2020; 128:52-65. [PMID: 32865889 PMCID: PMC7821157 DOI: 10.1111/bcpt.13483] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Revised: 08/14/2020] [Accepted: 08/21/2020] [Indexed: 12/30/2022]
Abstract
The discovery and implementation of thiopurine methyltransferase (TPMT) pharmacogenetics has been a success story and has reduced the suffering from serious adverse reactions during thiopurine treatment of childhood leukaemia and inflammatory bowel disease. This MiniReview summarizes four studies included in Dr Zimdahl Kahlin's doctoral thesis as well as the current knowledge on this field of research. The genotype‐phenotype concordance of TPMT in a cohort of 12 663 individuals with clinically analysed TPMT status is described. Notwithstanding the high concordance, the benefits of combined genotyping and phenotyping for TPMT status determination are discussed. The results from the large cohort also demonstrate that the factors of gender and age affect TPMT enzyme activity. In addition, characterization of four previously undescribed TPMT alleles (TPMT*41, TPMT*42, TPMT*43 and TPMT*44) shows that a defective TPMT enzyme could be caused by several different mechanisms. Moreover, the folate analogue methotrexate (MTX), used in combination with thiopurines during maintenance therapy of childhood leukaemia, affects the metabolism of thiopurines and interacts with TPMT, not only by binding and inhibiting the enzyme activity but also by regulation of its gene expression.
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Affiliation(s)
- Anna Zimdahl Kahlin
- Division of Drug Research, Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Sara Helander
- Division of Drug Research, Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Patricia Wennerstrand
- Division of Chemistry, Department of Physics, Chemistry, and Biology, Linköping University, Linköping, Sweden
| | - Svante Vikingsson
- Division of Drug Research, Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Lars-Göran Mårtensson
- Division of Chemistry, Department of Physics, Chemistry, and Biology, Linköping University, Linköping, Sweden
| | - Malin Lindqvist Appell
- Division of Drug Research, Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
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8
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Franca R, Stocco G, Favretto D, Giurici N, Del Rizzo I, Locatelli F, Vinti L, Biondi A, Colombini A, Fagioli F, Barisone E, Pelin M, Martellossi S, Ventura A, Decorti G, Rabusin M. PACSIN2 rs2413739 influence on thiopurine pharmacokinetics: validation studies in pediatric patients. THE PHARMACOGENOMICS JOURNAL 2020; 20:415-425. [PMID: 31792371 DOI: 10.1038/s41397-019-0130-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Revised: 11/09/2019] [Accepted: 11/20/2019] [Indexed: 12/11/2022]
Abstract
The aim of the study was to validate the impact of the single-nucleotide polymorphism rs2413739 (T > C) in the PACSIN2 gene on thiopurines pharmacological parameters and clinical response in an Italian cohort of pediatric patients with acute lymphoblastic leukemia (ALL) and inflammatory bowel disease (IBD). In ALL, PACSIN2 rs2413739 T allele was associated with a significant reduction of TPMT activity in erythrocytes (p = 0.0094, linear mixed-effect model, multivariate analysis considering TPMT genotype) and increased severe gastrointestinal toxicity during consolidation therapy (p = 0.049). A similar trend was present also for severe hematological toxicity during maintenance. In IBD, no significant effect of rs2413739 could be found on TPMT activity, however azathioprine effectiveness was reduced in patients carrying the T allele (linear mixed effect, p = 0.0058). In PBMC from healthy donors, a positive correlation between PACSIN2 and TPMT protein concentration could be detected (linear mixed effect, p = 0.045). These results support the role of PACSIN2 polymorphism on TPMT activity and mercaptopurine adverse effects in patients with ALL. Further evidence on PBMC and pediatric patients with IBD supports an association between PACSIN2 variants, TPMT activity, and thiopurines effects, even if more studies are needed since some of these effects may be tissue specific.
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Affiliation(s)
- Raffaella Franca
- Department of Medical, Surgical and Health Sciences, University of Trieste, Trieste, Italy
- Institute for Maternal and Child Health- IRCCS "Burlo Garofolo", Trieste, Italy
| | - Gabriele Stocco
- Department of Life Sciences, University of Trieste, Trieste, Italy
| | - Diego Favretto
- Institute for Maternal and Child Health- IRCCS "Burlo Garofolo", Trieste, Italy
| | - Nagua Giurici
- Institute for Maternal and Child Health- IRCCS "Burlo Garofolo", Trieste, Italy
| | - Irene Del Rizzo
- Institute for Maternal and Child Health- IRCCS "Burlo Garofolo", Trieste, Italy
| | - Franco Locatelli
- Department of Pediatric Hematology and Oncology, IRCCS Bambino Gesù Pediatric Hospital, University of Pavia, Rome, Italy
| | - Luciana Vinti
- Department of Pediatric Hematology and Oncology, IRCCS Bambino Gesù Pediatric Hospital, University of Pavia, Rome, Italy
| | - Andrea Biondi
- Pediatric Clinic, University Milano-Bicocca, Fondazione MBBM/San Gerardo Hospital, Monza, Italy
| | - Antonella Colombini
- Pediatric Clinic, University Milano-Bicocca, Fondazione MBBM/San Gerardo Hospital, Monza, Italy
| | - Franca Fagioli
- Division of Pediatric Oncohematology and Stem Cell Transplant Center, Ospedale Pediatrico Regina Margherita, Turin, Italy
| | - Elena Barisone
- Division of Pediatric Oncohematology and Stem Cell Transplant Center, Ospedale Pediatrico Regina Margherita, Turin, Italy
| | - Marco Pelin
- Department of Life Sciences, University of Trieste, Trieste, Italy
| | - Stefano Martellossi
- Institute for Maternal and Child Health- IRCCS "Burlo Garofolo", Trieste, Italy
- Department of Maternal and Child Health, Ospedale Ca' Foncello, Treviso, Italy
| | - Alessandro Ventura
- Department of Medical, Surgical and Health Sciences, University of Trieste, Trieste, Italy
- Institute for Maternal and Child Health- IRCCS "Burlo Garofolo", Trieste, Italy
| | - Giuliana Decorti
- Department of Medical, Surgical and Health Sciences, University of Trieste, Trieste, Italy.
- Institute for Maternal and Child Health- IRCCS "Burlo Garofolo", Trieste, Italy.
| | - Marco Rabusin
- Institute for Maternal and Child Health- IRCCS "Burlo Garofolo", Trieste, Italy
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9
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Comprehensive study of thiopurine methyltransferase genotype, phenotype, and genotype-phenotype discrepancies in Sweden. Biochem Pharmacol 2019; 164:263-272. [PMID: 31005613 DOI: 10.1016/j.bcp.2019.04.020] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Accepted: 04/17/2019] [Indexed: 12/16/2022]
Abstract
Thiopurines are widely used in the treatment of leukemia and inflammatory bowel diseases. Thiopurine metabolism varies among individuals because of differences in the polymorphic enzyme thiopurine methyltransferase (TPMT, EC 2.1.1.67), and to avoid severe adverse reactions caused by incorrect dosing it is recommended that the patient's TPMT status be determined before the start of thiopurine treatment. This study describes the concordance between genotyping for common TPMT alleles and phenotyping in a Swedish cohort of 12,663 patients sampled before or during thiopurine treatment. The concordance between TPMT genotype and enzyme activity was 94.5%. Compared to the genotype, the first measurement of TPMT enzyme activity was lower than expected for 4.6% of the patients. Sequencing of all coding regions of the TPMT gene in genotype/phenotype discrepant individuals led to the identification of rare and novel TPMT alleles. Fifteen individuals (0.1%) with rare or novel genotypes were identified, and three TPMT alleles (TPMT*42, *43, and *44) are characterized here for the first time. These 15 patients would not have been detected as carrying a deviating TPMT genotype if only genotyping of the most common TPMT variants had been performed. This study highlights the benefit of combining TPMT genotype and phenotype determination in routine testing. More accurate dose recommendations can be made, which might decrease the number of adverse reactions and treatment failures during thiopurine treatment.
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Everett JR. Pharmacometabonomics: The Prediction of Drug Effects Using Metabolic Profiling. Handb Exp Pharmacol 2019; 260:263-299. [PMID: 31823071 DOI: 10.1007/164_2019_316] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Metabonomics, also known as metabolomics, is concerned with the study of metabolite profiles in humans, animals, plants and other systems in order to assess their health or other status and their responses to experimental interventions. Metabonomics is thus widely used in disease diagnosis and in understanding responses to therapies such as drug administration. Pharmacometabonomics, also known as pharmacometabolomics, is a related methodology but with a prognostic as opposed to diagnostic thrust. Pharmacometabonomics aims to predict drug effects including efficacy, safety, metabolism and pharmacokinetics, prior to drug administration, via an analysis of pre-dose metabolite profiles. This article will review the development of pharmacometabonomics as a new field of science that has much promise in helping to deliver more effective personalised medicine, a major goal of twenty-first century healthcare.
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Affiliation(s)
- Jeremy R Everett
- Medway Metabonomics Research Group, University of Greenwich, Kent, UK.
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11
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Urbančič D, Šmid A, Stocco G, Decorti G, Mlinarič-Raščan I, Karas Kuželički N. Novel motif of variable number of tandem repeats in TPMT promoter region and evolutionary association of variable number of tandem repeats with TPMT*3 alleles. Pharmacogenomics 2018; 19:1311-1322. [PMID: 30345902 DOI: 10.2217/pgs-2018-0123] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Accepted: 09/24/2018] [Indexed: 11/21/2022] Open
Abstract
AIM SNPs in the gene for TPMT exemplify one of the most successful translations of pharmacogenomics into clinical practice. This study explains the correlation between common SNPs and variable number of tandem repeats (VNTR) in promoter of the gene. MATERIALS & METHODS We determined VNTR polymorphisms, as well as TPMT*2 and TPMT*3 SNPs and TPMT activity in Slovenian and Italian individuals and lymphoblastoid cell lines. RESULTS We observed a previously unreported VNTR allele, AB7C, in a TPMT*3A heterozygous individual. VNTRs with two (AB2C) and three or more (ABnC, n ≥ 3) B motifs were statistically significant in complete linkage disequilibrium (D' = 1, r2 = 1, p < 0.0001) with the TPMT*3C and TPMT*3A alleles, respectively. CONCLUSION The study provides insights into the stepwise evolution of TPMT*3 alleles from *3C to *3A, with increasing number of B motifs in the VNTR region.
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Affiliation(s)
- Dunja Urbančič
- Department of Clinical Biochemistry, Faculty of Pharmacy, University of Ljubljana, Aškerčeva cesta 7, 1000 Ljubljana, Slovenia
| | - Alenka Šmid
- Department of Clinical Biochemistry, Faculty of Pharmacy, University of Ljubljana, Aškerčeva cesta 7, 1000 Ljubljana, Slovenia
| | - Gabriele Stocco
- Department of Life Sciences, University of Trieste, 34127 Trieste, Italy
| | - Giuliana Decorti
- Laboratorio di Diagnostica Avanzata Traslazionale, Institute for Maternal & Child Health - IRCCS 'Burlo Garofolo', 34127 Trieste, Italy
- Department of Medicine, Surgery & Health Sciences, University of Trieste, 34127 Trieste, Italy
| | - Irena Mlinarič-Raščan
- Department of Clinical Biochemistry, Faculty of Pharmacy, University of Ljubljana, Aškerčeva cesta 7, 1000 Ljubljana, Slovenia
| | - Nataša Karas Kuželički
- Department of Clinical Biochemistry, Faculty of Pharmacy, University of Ljubljana, Aškerčeva cesta 7, 1000 Ljubljana, Slovenia
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12
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Methylation of selenocysteine catalysed by thiopurine S-methyltransferase. Biochim Biophys Acta Gen Subj 2018; 1863:182-190. [PMID: 30308221 DOI: 10.1016/j.bbagen.2018.10.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Revised: 08/25/2018] [Accepted: 10/02/2018] [Indexed: 12/16/2022]
Abstract
BACKGROUND Methylation driven by thiopurine S-methylatransferase (TPMT) is crucial for deactivation of cytostatic and immunosuppressant thiopurines. Despite its remarkable integration into clinical practice, the endogenous function of TPMT is unknown. METHODS To address the role of TPMT in methylation of selenium compounds, we established the research on saturation transfer difference (STD) and 77Se NMR spectroscopy, fluorescence measurements, as well as computational molecular docking simulations. RESULTS Using STD NMR spectroscopy and fluorescence measurements of tryptophan residues in TPMT, we determined the binding of selenocysteine (Sec) to human recombinant TPMT. By comparing binding characteristics of Sec in the absence and in the presence of methyl donor, we confirmed S-adenosylmethionine (SAM)-induced conformational changes in TPMT. Molecular docking analysis positioned Sec into the active site of TPMT with orientation relevant for methylation reaction. Se-methylselenocysteine (MeSec), produced in the enzymatic reaction, was detected by 77Se NMR spectroscopy. A direct interaction between Sec and SAM in the active site of rTPMT and the formation of both products, MeSec and S-adenosylhomocysteine, was demonstrated using NMR spectroscopy. CONCLUSIONS The present study provides evidence on in vitro methylation of Sec by rTPMT in a SAM-dependant manner. GENERAL SIGNIFICANCE Our results suggest novel role of TPMT and demonstrate new insights into enzymatic modifications of the 21st amino acid.
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13
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Lim SZ, Chua EW. Revisiting the Role of Thiopurines in Inflammatory Bowel Disease Through Pharmacogenomics and Use of Novel Methods for Therapeutic Drug Monitoring. Front Pharmacol 2018; 9:1107. [PMID: 30349479 PMCID: PMC6186994 DOI: 10.3389/fphar.2018.01107] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Accepted: 09/10/2018] [Indexed: 12/12/2022] Open
Abstract
Azathioprine and 6-mercaptopurine, often referred to as thiopurine compounds, are commonly used in the management of inflammatory bowel disease. However, patients receiving these drugs are prone to developing adverse drug reactions or therapeutic resistance. Achieving predefined levels of two major thiopurine metabolites, 6-thioguanine nucleotides and 6-methylmercaptopurine, is a long-standing clinical practice in ensuring therapeutic efficacy; however, their correlation with treatment response is sometimes unclear. Various genetic markers have also been used to aid the identification of patients who are thiopurine-sensitive or refractory. The recent discovery of novel Asian-specific DNA variants, namely those in the NUDT15 gene, and their link to thiopurine toxicity, have led clinicians and scientists to revisit the utility of Caucasian biomarkers for Asian individuals with inflammatory bowel disease. In this review, we explore the limitations associated with the current methods used for therapeutic monitoring of thiopurine metabolites and how the recent discovery of ethnicity-specific genetic markers can complement thiopurine metabolites measurement in formulating a strategy for more accurate prediction of thiopurine response. We also discuss the challenges in thiopurine therapy, alongside the current strategies used in patients with reduced thiopurine response. The review is concluded with suggestions for future work aiming at using a more comprehensive approach to optimize the efficacy of thiopurine compounds in inflammatory bowel disease.
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Affiliation(s)
| | - Eng Wee Chua
- Faculty of Pharmacy, Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
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14
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Sobiak J, Skalska-Sadowska J, Chrzanowska M, Resztak M, Kołtan S, Wysocki M, Wachowiak J. Thiopurine methyltransferase activity in children with acute myeloid leukemia. Oncol Lett 2018; 16:4699-4706. [PMID: 30214603 DOI: 10.3892/ol.2018.9191] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2017] [Accepted: 04/16/2018] [Indexed: 12/21/2022] Open
Abstract
Activity of the enzyme thiopurine methyltransferase (TPMT) determines the anti-leukemic effect of thiopurines used in the chemotherapy of acute lymphoblastic leukemia (ALL) and acute myeloblastic leukemia (AML). TPMT status and its effects on treatment outcome have been studied extensively in ALL and autoimmune disorders, but few data is available on TPMT in AML. The present study assessed the genetic polymorphisms and activity of TPMT in children with AML at different treatment stages, and compared the results with those obtained for children with ALL. The study included 33 children with AML (0.7-19.7 years) treated with 6-thioguanine (6-TG) according to the AML-BFM 2004 Protocol. Blood samples were collected at diagnosis, during and following maintenance chemotherapy from 8, 10 and 17 patients with AML (the assay was performed at two time points in 2 patients), respectively. Blood samples from 105 children with ALL were obtained at diagnosis, during the maintenance chemotherapy and following the cessation of the chemotherapy from 16, 55 and 34 children, respectively. The activity of TPMT in red blood cells lysates was measured using an enzymatic reaction based on the conversion of 6-mercaptopurine into 6-methylmercaptopurine, involving S-adenozyl-L-methionine as the methyl group donor. TPMT mutations were determined using a polymerase chain reaction/restriction fragment length polymorphism method. Median TPMT activity at diagnosis, during maintenance chemotherapy and following chemotherapy was 43.1, 47,3 and 41.7 nmol 6-mMP g-1 Hb h-1, respectively. All patients with AML exhibited the homozygous TPMT*1/*1 genotype, with the exception of 1, who was a heterozygote with the TPMT*1/*3C genotype and demonstrated a TPMT activity level at diagnosis of 42.5 nmol 6-mMP g-1 Hb h-1. At each chemotherapy stage, the median TPMT activities in children with AML were significantly increased compared with the median TPMT activities in children with ALL. The preliminary results suggest that the TPMT activity in AML may be increased compared with that in ALL. Comprehensive studies on the association between thiopurine metabolism and treatment outcome in AML are required, with regard to the cytogenetic and molecular factors currently used for AML risk stratification.
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Affiliation(s)
- Joanna Sobiak
- Department of Physical Pharmacy and Pharmacokinetics, Poznan University of Medical Sciences, 60-781 Poznań, Poland
| | - Jolanta Skalska-Sadowska
- Department of Pediatric Oncology, Hematology and Transplantology, Poznan University of Medical Sciences, 60-572 Poznań, Poland
| | - Maria Chrzanowska
- Department of Physical Pharmacy and Pharmacokinetics, Poznan University of Medical Sciences, 60-781 Poznań, Poland
| | - Matylda Resztak
- Department of Physical Pharmacy and Pharmacokinetics, Poznan University of Medical Sciences, 60-781 Poznań, Poland
| | - Sylwia Kołtan
- Department of Pediatrics, Hematology and Oncology, Collegium Medicum, Nicolaus Copernicus University, 85-094 Bydgoszcz, Poland
| | - Mariusz Wysocki
- Department of Pediatrics, Hematology and Oncology, Collegium Medicum, Nicolaus Copernicus University, 85-094 Bydgoszcz, Poland
| | - Jacek Wachowiak
- Department of Pediatric Oncology, Hematology and Transplantology, Poznan University of Medical Sciences, 60-572 Poznań, Poland
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15
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Everett JR. NMR-based pharmacometabonomics: A new paradigm for personalised or precision medicine. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2017; 102-103:1-14. [PMID: 29157489 DOI: 10.1016/j.pnmrs.2017.04.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Revised: 04/23/2017] [Accepted: 04/24/2017] [Indexed: 06/07/2023]
Abstract
Metabolic profiling by NMR spectroscopy or hyphenated mass spectrometry, known as metabonomics or metabolomics, is an important tool for systems-based approaches in biology and medicine. The experiments are typically done in a diagnostic fashion where changes in metabolite profiles are interpreted as a consequence of an intervention or event; be that a change in diet, the administration of a drug, physical exertion or the onset of a disease. By contrast, pharmacometabonomics takes a prognostic approach to metabolic profiling, in order to predict the effects of drug dosing before it occurs. Differences in pre-dose metabolite profiles between groups of subjects are used to predict post-dose differences in response to drug administration. Thus the paradigm is inverted and pharmacometabonomics is the metabolic equivalent of pharmacogenomics. Although the field is still in its infancy, it is expected that pharmacometabonomics, alongside pharmacogenomics, will assist with the delivery of personalised or precision medicine to patients, which is a critical goal of 21st century healthcare.
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Affiliation(s)
- Jeremy R Everett
- Medway Metabonomics Group, University of Greenwich, Chatham Maritime, Kent ME4 4TB, UK.
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16
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One amino acid makes a difference-Characterization of a new TPMT allele and the influence of SAM on TPMT stability. Sci Rep 2017; 7:46428. [PMID: 28462921 PMCID: PMC5411961 DOI: 10.1038/srep46428] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Accepted: 03/16/2017] [Indexed: 12/28/2022] Open
Abstract
Thiopurine induced toxicity is associated with defects in the thiopurine methyltransferase (TPMT) gene. TPMT is a polymorphic enzyme, with most of the single nucleotide polymorphisms (SNPs) causing an amino acid change, altering the enzymatic activity of the TPMT protein. In this study, we characterize a novel patient allele c.719A > C, named TPMT*41, together with the more common variant *3C c.719A > G, resulting in an amino acid shift at tyrosine 240 to serine, p.Y240S and cysteine, p.Y240C respectively. We show that the patient heterozygote for c.719A > C has intermediate enzymatic activity in red blood cells. Furthermore, in vitro studies, using recombinant protein, show that TPMT p.Y240S is less stable than both TPMTwt and TPMT p.Y240C. The addition of SAM increases the stability and, in agreement with Isothermal Titration Calorimetry (ITC) data, higher molar excess of SAM is needed in order to stabilize TPMT p.Y240C and TPMT p.Y240S compared to TPMTwt. Molecular dynamics simulations show that the loss of interactions is most severe for Y240S, which agrees with the thermal stability of the mutations. In conclusion, our study shows that SAM increases the stability of TPMT and that changing only one amino acid can have a dramatic effect on TPMT stability and activity.
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17
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Tamm R, Mägi R, Tremmel R, Winter S, Mihailov E, Smid A, Möricke A, Klein K, Schrappe M, Stanulla M, Houlston R, Weinshilboum R, Mlinarič Raščan I, Metspalu A, Milani L, Schwab M, Schaeffeler E. Polymorphic variation in TPMT is the principal determinant of TPMT phenotype: A meta-analysis of three genome-wide association studies. Clin Pharmacol Ther 2017; 101:684-695. [PMID: 27770449 DOI: 10.1002/cpt.540] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Revised: 09/02/2016] [Accepted: 10/17/2016] [Indexed: 12/20/2022]
Abstract
Thiopurine-related hematotoxicity in pediatric acute lymphoblastic leukemia (ALL) and inflammatory bowel diseases has been linked to genetically defined variability in thiopurine S-methyltransferase (TPMT) activity. While gene testing of TPMT is being clinically implemented, it is unclear if additional genetic variation influences TPMT activity with consequences for thiopurine-related toxicity. To examine this possibility, we performed a genome-wide association study (GWAS) of red blood cell TPMT activity in 844 Estonian individuals and 245 pediatric ALL cases. Additionally, we correlated genome-wide genotypes to human hepatic TPMT activity in 123 samples. Only genetic variants mapping to chromosome 6, including the TPMT gene region, were significantly associated with TPMT activity (P < 5.0 × 10-8 ) in each of the three GWAS and a joint meta-analysis of 1,212 cases (top hit P = 1.2 × 10-72 ). This finding is consistent with TPMT genotype being the primary determinant of TPMT activity, reinforcing the rationale for genetic testing of TPMT alleles in routine clinical practice to individualize mercaptopurine dosage.
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Affiliation(s)
- R Tamm
- Department of Biotechnology, Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia.,Estonian Genome Center, University of Tartu, Tartu, Estonia
| | - R Mägi
- Estonian Genome Center, University of Tartu, Tartu, Estonia
| | - R Tremmel
- Dr Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart, Germany, and University of Tuebingen, Germany
| | - S Winter
- Dr Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart, Germany, and University of Tuebingen, Germany
| | - E Mihailov
- Estonian Genome Center, University of Tartu, Tartu, Estonia
| | - A Smid
- Faculty of Pharmacy, University of Ljubljana, Ljubljana, Slovenia
| | - A Möricke
- Department of Pediatrics, University Hospital Schleswig-Holstein, Kiel, Germany
| | - K Klein
- Dr Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart, Germany, and University of Tuebingen, Germany
| | - M Schrappe
- Department of Pediatrics, University Hospital Schleswig-Holstein, Kiel, Germany
| | - M Stanulla
- Pediatric Hematology and Oncology, Hannover Medical School, Hannover, Germany
| | - R Houlston
- Division of Genetics and Epidemiology, Institute of Cancer Research, Sutton, UK
| | - R Weinshilboum
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, Minnesota, USA
| | | | - A Metspalu
- Department of Biotechnology, Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia.,Estonian Genome Center, University of Tartu, Tartu, Estonia
| | - L Milani
- Estonian Genome Center, University of Tartu, Tartu, Estonia
| | - M Schwab
- Dr Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart, Germany, and University of Tuebingen, Germany.,Department of Clinical Pharmacology, University Hospital Tuebingen, Tuebingen, Germany.,Department of Pharmacy and Biochemistry, University of Tuebingen, Tuebingen, Germany
| | - E Schaeffeler
- Dr Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart, Germany, and University of Tuebingen, Germany
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18
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Everett JR. From Metabonomics to Pharmacometabonomics: The Role of Metabolic Profiling in Personalized Medicine. Front Pharmacol 2016; 7:297. [PMID: 27660611 PMCID: PMC5014868 DOI: 10.3389/fphar.2016.00297] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Accepted: 08/23/2016] [Indexed: 01/08/2023] Open
Abstract
Variable patient responses to drugs are a key issue for medicine and for drug discovery and development. Personalized medicine, that is the selection of medicines for subgroups of patients so as to maximize drug efficacy and minimize toxicity, is a key goal of twenty-first century healthcare. Currently, most personalized medicine paradigms rely on clinical judgment based on the patient's history, and on the analysis of the patients' genome to predict drug effects i.e., pharmacogenomics. However, variability in patient responses to drugs is dependent upon many environmental factors to which human genomics is essentially blind. A new paradigm for predicting drug responses based on individual pre-dose metabolite profiles has emerged in the past decade: pharmacometabonomics, which is defined as “the prediction of the outcome (for example, efficacy or toxicity) of a drug or xenobiotic intervention in an individual based on a mathematical model of pre-intervention metabolite signatures.” The new pharmacometabonomics paradigm is complementary to pharmacogenomics but has the advantage of being sensitive to environmental as well as genomic factors. This review will chart the discovery and development of pharmacometabonomics, and provide examples of its current utility and possible future developments.
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Affiliation(s)
- Jeremy R Everett
- Medway Metabonomics Research Group, University of Greenwich Kent, UK
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19
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Smid A, Karas-Kuzelicki N, Jazbec J, Mlinaric-Rascan I. PACSIN2 polymorphism is associated with thiopurine-induced hematological toxicity in children with acute lymphoblastic leukaemia undergoing maintenance therapy. Sci Rep 2016; 6:30244. [PMID: 27452984 PMCID: PMC4958958 DOI: 10.1038/srep30244] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2016] [Accepted: 07/01/2016] [Indexed: 02/07/2023] Open
Abstract
Adequate maintenance therapy for childhood acute lymphoblastic leukemia (ALL), with 6-mercaptopurine as an essential component, is necessary for retaining durable remission. Interruptions or discontinuations of the therapy due to drug-related toxicities, which can be life threatening, may result in an increased risk of relapse. In this retrospective study including 305 paediatric ALL patients undergoing maintenance therapy, we systematically investigated the individual and combined effects of genetic variants of folate pathway enzymes, as well as of polymorphisms in PACSIN2 and ITPA, on drug-induced toxicities by applying a multi-analytical approach including logistic regression (LR), classification and regression tree (CART) and generalized multifactor dimensionality reduction (GMDR). In addition to the TPMT genotype, confirmed to be a major determinant of drug related toxicities, we identified the PACSIN2 rs2413739TT genotype as being a significant risk factor for 6-MP-induced toxicity in wild-type TPMT patients. A gene-gene interaction between MTRR (rs1801394) and MTHFR (rs1801133) was detected by GMDR and proved to have an independent effect on the risk of stomatitis, as shown by LR analysis. To our knowledge, this is the first study showing PACSIN2 genotype association with hematological toxicity in ALL patients undergoing maintenance therapy.
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Affiliation(s)
- Alenka Smid
- Faculty of Pharmacy, University of Ljubljana, Ljubljana, Slovenia
| | | | - Janez Jazbec
- University Children's Hospital, University Medical Centre Ljubljana, Ljubljana, Slovenia
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