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Vaidhya A, Ghildiyal K, Rajawat D, Nayak SS, Parida S, Panigrahi M. Relevance of pharmacogenetics and pharmacogenomics in veterinary clinical practice: A review. Anim Genet 2024; 55:3-19. [PMID: 37990577 DOI: 10.1111/age.13376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 07/03/2023] [Accepted: 10/24/2023] [Indexed: 11/23/2023]
Abstract
The recent advances in high-throughput next-generation sequencing technologies have heralded the arrival of the Big Data era. As a result, the use of pharmacogenetics in drug discovery and individualized drug therapy has transformed the field of precision medicine. This paradigm shift in drug development programs has effectively reshaped the old drug development practices, which were primarily concerned with the physiological status of patients for drug development. Pharmacogenomics bridges the gap between pharmacodynamics and pharmacokinetics, advancing current diagnostic and treatment strategies and enabling personalized and targeted drug therapy. The primary goals of pharmacogenetic studies are to improve drug efficacy and minimize toxicities, to identify novel drug targets, to estimate drug dosage for personalized medicine, and to incorporate it as a routine diagnostic for disease susceptibility. Although pharmacogenetics has numerous applications in individualized drug therapy and drug development, it is in its infancy in veterinary medicine. The objective of this review is to present an overview of historical landmarks, current developments in various animal species, challenges and future perspectives of genomics in drug development and dosage optimization for individualized medicine in veterinary subjects.
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Affiliation(s)
- Ayushi Vaidhya
- Division of Pharmacology & Toxicology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, UP, India
| | - Kanika Ghildiyal
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly, UP, India
| | - Divya Rajawat
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly, UP, India
| | - Sonali Sonejita Nayak
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly, UP, India
| | - Subhashree Parida
- Division of Pharmacology & Toxicology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, UP, India
| | - Manjit Panigrahi
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly, UP, India
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Díaz-Villamarín X, Fernández-Varón E, Rojas Romero MC, Callejas-Rubio JL, Cabeza-Barrera J, Rodríguez-Nogales A, Gálvez J, Morón R. Azathioprine dose tailoring based on pharmacogenetic information: Insights of clinical implementation. Biomed Pharmacother 2023; 168:115706. [PMID: 37857254 DOI: 10.1016/j.biopha.2023.115706] [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: 07/12/2023] [Revised: 10/05/2023] [Accepted: 10/11/2023] [Indexed: 10/21/2023] Open
Abstract
Azathioprine is commonly used as an immunosuppressive antimetabolite in the treatment of acute lymphoblastic leukemia, autoimmune disorders (such as Crohn's disease and rheumatoid arthritis), and in patients receiving organ transplants. Thiopurine-S-methyltransferase (TPMT) is a cytoplasmic trans-methylase catalyzing the S-methylation of thiopurines. The active metabolites obtained from thiopurines are hydrolyzed into inactive forms by the Nudix hydrolase 15 (NUDT15). The TPMT*2 (defined by rs1800462), *3A (defined by rs1800460 and rs1142345), *3B (defined by rs1800460), *3C (defined by rs1142345), *6 (defined by rs75543815), and NUDT15 rs116855232 genetic variant have been associated, with the highest level of evidence, with the response to azathioprine, and, the approved drug label for azathioprine and main pharmacogenetic dosing guidelines recommend starting with reduced initial doses in TPMT intermediate metabolizer (IM) patients and considering an alternative treatment in TPMT poor metabolizer (PM) patients. This study aims to assess the clinical impact of azathioprine dose tailoring based on TPMT genotyping studying the azathioprine toxicity and efficacy, treatment starts, and dose adjustments during follow-up, comparing TPMT IM/PM and normal metabolizer (NM) patients. It also studied the association of NUDT15 rs116855232 with response to azathioprine in patients receiving a tailored treatment based on TPMT and characterized the TMPT and NUDT15 studied variants in our population. Results show that azathioprine dose reduction in TPMT IM patients (TPMT*1/*2, *1/*3A, or *1/*3C genotypes) is related to lower toxicity events compared to TPMT NM (TPMT *1/*1 genotype), and lower azathioprine dose adjustments during follow-up without showing differences in the efficacy. The results support the hypothesis of existing other genetic variants affecting azathioprine toxicity.
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Affiliation(s)
| | - Emilio Fernández-Varón
- Instituto de Investigación Biosanitaria de Granada (Ibs.Granada), Granada, Spain; Department of Pharmacology, Center for Biomedical Research (CIBM), University of Granada, Granada, Spain
| | | | - José Luis Callejas-Rubio
- Instituto de Investigación Biosanitaria de Granada (Ibs.Granada), Granada, Spain; Internal Medicine Department, Hospital Universitario San Cecilio, Granada, Spain
| | - José Cabeza-Barrera
- Instituto de Investigación Biosanitaria de Granada (Ibs.Granada), Granada, Spain; Hospital Pharmacy Unit. Hospital Universitario San Cecilio, Granada, Spain
| | - Alba Rodríguez-Nogales
- Instituto de Investigación Biosanitaria de Granada (Ibs.Granada), Granada, Spain; Department of Pharmacology, Center for Biomedical Research (CIBM), University of Granada, Granada, Spain
| | - Julio Gálvez
- Instituto de Investigación Biosanitaria de Granada (Ibs.Granada), Granada, Spain; Department of Pharmacology, Center for Biomedical Research (CIBM), University of Granada, Granada, Spain; Centro de Investigaciones Biomédicas en Red - Enfermedades Hepáticas y Digestivas (CIBER-ehd)
| | - Rocío Morón
- Instituto de Investigación Biosanitaria de Granada (Ibs.Granada), Granada, Spain; Hospital Pharmacy Unit. Hospital Universitario San Cecilio, Granada, Spain
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Gallardo-Cóndor J, Naranjo P, Atarihuana S, Coello D, Guevara-Ramírez P, Flores-Espinoza R, Burgos G, López-Cortés A, Cabrera-Andrade A. Population-Specific Distribution of TPMT Deficiency Variants and Ancestry Proportions in Ecuadorian Ethnic Groups: Towards Personalized Medicine. Ther Clin Risk Manag 2023; 19:1005-1018. [PMID: 38050617 PMCID: PMC10693761 DOI: 10.2147/tcrm.s432856] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2023] [Accepted: 11/06/2023] [Indexed: 12/06/2023] Open
Abstract
Purpose Thiopurine S-methyltransferase (TPMT) is an enzyme that metabolizes purine analogs, agents used in the treatment of acute lymphoblastic leukemia. Improper drug metabolism leads to toxicity in chemotherapy patients and reduces treatment effectiveness. TPMT variants associated with reduced enzymatic activity vary across populations. Therefore, studying these variants in heterogeneous populations, such as Ecuadorians, can help identify molecular causes of deficiency for this enzyme. Methods We sequenced the entire TPMT coding region in 550 Ecuadorian individuals from Afro-Ecuadorian, Indigenous, Mestizo, and Montubio ethnicities. Moreover, we conducted an ancestry analysis using 46 informative ancestry markers. Results We identified 8 single nucleotide variants in the coding region of TPMT. The most prevalent alleles were TPMT*3A, TPMT*3B, and TPMT*3C, with frequencies of 0.055, 0.012, and 0.015, respectively. Additionally, we found rare alleles TPMT*4 and TPMT*8 with frequencies of 0.005 and 0.003. Correlating the ancestry proportions with TPMT-deficient genotypes, we observed that the Native American ancestry proportion influenced the distribution of the TPMT*1/TPMT*3A genotype (OR = 5.977, p = 0.002), while the contribution of African ancestral populations was associated with the TPMT*1/TPMT*3C genotype (OR = 9.769, p = 0.003). The rates of TPMT-deficient genotypes observed in Mestizo (f = 0.121) and Indigenous (f = 0.273) groups provide evidence for the influence of Native American ancestry and the prevalence of the TPMT*3A allele. In contrast, although Afro-Ecuadorian groups demonstrate similar deficiency rates (f = 0.160), the genetic factors involved are associated with contributions from African ancestral populations, specifically the prevalent TPMT*3C allele. Conclusion The distribution of TPMT-deficient variants offers valuable insights into the populations under study, underscoring the necessity for genetic screening strategies to prevent thiopurine toxicity events among Latin American minority groups.
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Affiliation(s)
| | - Pablo Naranjo
- Facultad de Ingeniería y Ciencias Aplicadas, Universidad de Las Américas, Quito, Ecuador
| | - Sebastián Atarihuana
- Facultad de Ingeniería y Ciencias Aplicadas, Universidad de Las Américas, Quito, Ecuador
| | - Dayana Coello
- Laboratorios de Investigación, Universidad de Las Américas, Quito, Ecuador
| | - Patricia Guevara-Ramírez
- Centro de Investigación Genética y Genómica, Facultad de Ciencias de la Salud Eugenio Espejo, Universidad UTE, Quito, Ecuador
| | - Rodrigo Flores-Espinoza
- Laboratório de Diagnóstico por DNA (LDD), Universidade do Estado do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Germán Burgos
- One Health Research Group, Facultad de Medicina, Universidad de Las Américas, Quito, Ecuador
- Grupo de Medicina Xenomica, Instituto de Ciencias Forenses, Universidad de Santiago de Compostela, Satiago de Compostela, Spain
| | - Andrés López-Cortés
- Cancer Research Group (CRG), Faculty of Medicine, Universidad de Las Américas, Quito, Ecuador
- Latin American Network for the Implementation and Validation of Clinical Pharmacogenomics Guidelines (RELIVAF-CYTED), Madrid, Spain
| | - Alejandro Cabrera-Andrade
- Escuela de Enfermería, Facultad de Ciencias de la Salud, Universidad de Las Américas, Quito, Ecuador
- Grupo de Bio-Quimioinformática, Universidad de Las Américas, Quito, Ecuador
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Smith LS, Wang X, Shi J, He B, Zhu HJ. Genome-Wide Association Study for the Genetic Determinants of Thiopurine Methyltransferase Protein Expression in Human Livers and Racial Differences. Pharm Res 2023; 40:2525-2531. [PMID: 37430149 DOI: 10.1007/s11095-023-03558-1] [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: 04/30/2023] [Accepted: 06/26/2023] [Indexed: 07/12/2023]
Abstract
INTRODUCTION Polymorphisms in the Thiopurine S-Methyltransferase (TPMT) gene are associated with decreased TPMT activity, but little is known about their impact on TPMT protein expression in the liver. This project is to conduct a genome-wide association study (GWAS) to identify single nucleotide polymorphisms (SNPs) associated with altered TPMT protein expression in human livers and to determine if demographics affect hepatic TPMT protein expression. METHODS Human liver samples (n = 287) were genotyped using a whole genome genotyping panel and quantified for TPMT protein expression using a Data-Independent Acquisition proteomics approach. RESULTS AND DISCUSSION Thirty-one SNPs were found to be associated with differential expression of TPMT protein in the human livers. Subsequent analysis, conditioning on rs1142345, a SNP associated with the TPMT*3A and TPMT*3C alleles, showed no additional independent signals. Mean TPMT expression is significantly higher in wildtype donors compared to those carrying the known TPMT alleles, including TPMT*3A, TPMT*3C, and TPMT*24 (0.107 ± 0.028 vs. 0.052 ± 0.014 pmol/mg total protein, P = 2.2 × 10-16). After removing samples carrying the known TPMT variants, European ancestry donors exhibited significantly higher expression than African ancestry donors (0.109 ± 0.026 vs. 0.090 ± 0.041 pmol/mg total protein, P = 0.020). CONCLUSION The GWAS identified 31 SNPs associated with TPMT protein expression in human livers. Hepatic TPMT protein expression was significantly lower in subjects carrying the TPMT*3A, TPMT*3C, and TPMT*24 alleles compared to non-carriers. European ancestry was associated with significantly higher hepatic TPMT protein expression than African ancestry, independent of known TPMT variants.
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Affiliation(s)
- Logan S Smith
- Department of Clinical Pharmacy, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Xinwen Wang
- Department of Pharmaceutical Sciences, Northeast Ohio Medical University, Rootstown, OH, 44272, USA
| | - Jian Shi
- Bristol Myers Squibb, 3401 Princeton Pike, Lawrence Township, NJ, 08648, USA
| | - Bing He
- Department of Computational Medicine and Bioinformatics, Medical School, University of Michigan, Ann Arbor, MI, USA
| | - Hao-Jie Zhu
- Department of Clinical Pharmacy, University of Michigan, Ann Arbor, MI, 48109, USA.
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Cook KJ, Grusauskas V, Gloe L, Duong BQ, Gresh RC, Kolb EA, Bansal M, Bechtel AS, Nagasubramanian R, Kirwin SM, Blake KV, Seligson ND. Comparison of variants in TPMT and NUDT15 between sequencing and genotyping methods in a multistate pediatric institution. Clin Transl Sci 2023; 16:1352-1358. [PMID: 37415296 PMCID: PMC10432880 DOI: 10.1111/cts.13539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 03/30/2023] [Accepted: 04/23/2023] [Indexed: 07/08/2023] Open
Abstract
The risk of severe adverse events related to thiopurine therapy can be reduced by personalizing dosing based on TPMT and NUDT15 genetic polymorphisms. However, the optimal genetic testing platform has not yet been established. In this study, we report on the TPMT and NUDT15 genotypes and phenotypes generated from 320 patients from a multicenter pediatric healthcare system using both Sanger sequencing and polymerase chain reaction genotyping (hereafter: genotyping) methods to determine the appropriateness of genotyping in our patient population. Sanger sequencing identified variant TPMT alleles including *3A (8, 3.2% of alleles), *3C (4, 1.6%), and *2 (1, 0.4%), and NUDT15 alleles including *2 (5, 3.6%) and *3 (1, 0.7%). For genotyped patients, variants identified in TPMT included *3A (12, 3.1%), *3C (4, 1%), *2 (2, 0.5%), and *8 (1, 0.25%), whereas NUDT15 included *4 (2, 1.9%) and *2 or *3 (1, 1%). Between Sanger sequencing and genotyping, no significant difference in allele, genotype, or phenotype frequency was identified for either TPMT or NUDT15. All patients who were tested using Sanger sequencing would have been accurately phenotyped for either TPMT (124/124), NUDT15 (69/69), or both genes (68/68) if they were assayed using the genotyping method. Considering 193 total TPMT and NUDT15 Sanger Sequencing tests reviewed, all tests would have resulted in an appropriate clinical recommendation if the test had instead been conducted using the comparison genotyping platforms. These results suggest that, in this study population, genotyping would be sufficient to provide accurate phenotype calls and clinical recommendations.
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Affiliation(s)
- Kelsey J. Cook
- Precision MedicineNemours Children's HealthJacksonvilleFloridaUSA
- Department of Pharmacotherapy and Translational ResearchThe University of Florida College of PharmacyJacksonvilleFloridaUSA
| | - Victoria Grusauskas
- Precision MedicineNemours Children's HealthJacksonvilleFloridaUSA
- Department of Pharmacotherapy and Translational ResearchThe University of Florida College of PharmacyJacksonvilleFloridaUSA
| | - Lucy Gloe
- Precision MedicineNemours Children's HealthJacksonvilleFloridaUSA
- Department of Pharmacotherapy and Translational ResearchThe University of Florida College of PharmacyJacksonvilleFloridaUSA
| | | | - Renee C. Gresh
- Department of Pediatric Hematology/OncologyNemours Children's HealthWilmingtonDelawareUSA
| | - E. Anders Kolb
- Department of Pediatric Hematology/OncologyNemours Children's HealthWilmingtonDelawareUSA
| | - Manisha Bansal
- Department of Pediatric Hematology/OncologyNemours Children's HealthJacksonvilleFloridaUSA
| | - Allison S. Bechtel
- Department of Pediatric Hematology/OncologyNemours Children's HealthJacksonvilleFloridaUSA
| | | | - Susan M. Kirwin
- Molecular Diagnostics LaboratoryNemours Children's HealthWilmingtonDelawareUSA
| | - Kathryn V. Blake
- Precision MedicineNemours Children's HealthJacksonvilleFloridaUSA
| | - Nathan D. Seligson
- Precision MedicineNemours Children's HealthJacksonvilleFloridaUSA
- Department of Pharmacotherapy and Translational ResearchThe University of Florida College of PharmacyJacksonvilleFloridaUSA
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Larkin T, Kashif R, Elsayed AH, Greer B, Mangrola K, Raffiee R, Nguyen N, Shastri V, Horn B, Lamba JK. Polygenic Pharmacogenomic Markers as Predictors of Toxicity Phenotypes in the Treatment of Acute Lymphoblastic Leukemia: A Single-Center Study. JCO Precis Oncol 2023; 7:e2200580. [PMID: 36952646 PMCID: PMC10309546 DOI: 10.1200/po.22.00580] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Accepted: 01/31/2023] [Indexed: 03/25/2023] Open
Abstract
PURPOSE Acute lymphoblastic leukemia (ALL) is the most prevalent cause of childhood cancer and requires a long course of therapy consisting of three primary phases with interval intensification blocks. Although these phases are necessary to achieve remission, the primary chemotherapeutic agents have potentially serious toxicities, which may lead to delays or discontinuations of therapy. The purpose of this study was to perform a comprehensive pharmacogenomic evaluation of common antileukemic agents and develop a polygenic toxicity risk score predictive of the most common toxicities observed during ALL treatment. METHODS This cross-sectional study included 75 patients with pediatric ALL treated between 2012 and 2020 at the University of Florida. Toxicity data were collected within 100 days of initiation of therapy using CTCAE v4.0 for toxicity grading. For pharmacogenomic evaluation, single-nucleotide polymorphisms (SNPs) and genes were selected from previous reports or PharmGKB database. 116 unique SNPs were evaluated for incidence of various toxicities. A multivariable multi-SNP modeling for up to 3-SNP combination was performed to develop a polygenic toxicity risk score of prognostic value. RESULTS We identified several SNPs predictive of toxicity phenotypes in univariate analysis. Further multivariable SNP-SNP combination analysis suggest that susceptibility to chemotherapy-induced toxicities is likely multigenic in nature. For 3-SNPscore models, patients with high scores experienced increased risk of GI (P = 2.07E-05, 3 SNPs: TYMS-rs151264360/FPGS-rs1544105/GSTM1-GSTM5-rs3754446), neurologic (P = .0005, 3 SNPs: DCTD-rs6829021/SLC28A3-rs17343066/CTPS1-rs12067645), endocrine (P = 4.77E-08, 3 SNPs: AKR1C3-rs1937840/TYMS-rs2853539/CTH-rs648743), and heme toxicities (P = .053, 3 SNPs: CYP3A5-rs776746/ABCB1-rs4148737/CTPS1-rs12067645). CONCLUSION Our results imply that instead of a single-SNP approach, SNP-SNP combinations in multiple genes in drug pathways increases the robustness of prediction of toxicity. These results further provide promising SNP models that can help establish clinically relevant biomarkers allowing for greater individualization of cancer therapy to maximize efficacy and minimize toxicity for each patient.
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Affiliation(s)
- Trisha Larkin
- Department of Pediatrics, University of Florida College of Medicine, Gainesville, FL
- St Joseph's Children's Hospital/BayCare Medical Group, Tampa, FL
| | - Reema Kashif
- Department of Pediatrics, University of Florida College of Medicine, Gainesville, FL
| | - Abdelrahman H. Elsayed
- Department of Pharmacotherapy and Translational Research, University of Florida College of Pharmacy, Gainesville, FL
| | - Beate Greer
- Pediatrics Division, UF Health Cancer Center, University of Florida, Gainesville, FL
| | - Karna Mangrola
- Department of Pediatrics, University of Florida College of Medicine, Gainesville, FL
| | - Roya Raffiee
- Department of Pharmacotherapy and Translational Research, University of Florida College of Pharmacy, Gainesville, FL
| | - Nam Nguyen
- Department of Pharmacotherapy and Translational Research, University of Florida College of Pharmacy, Gainesville, FL
| | - Vivek Shastri
- Department of Pharmacotherapy and Translational Research, University of Florida College of Pharmacy, Gainesville, FL
| | - Biljana Horn
- Department of Pediatrics, University of Florida College of Medicine, Gainesville, FL
| | - Jatinder K. Lamba
- Department of Pharmacotherapy and Translational Research, University of Florida College of Pharmacy, Gainesville, FL
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Beheshti M, Rabiei N, Taghizadieh M, Eskandari P, Mollazadeh S, Dadgostar E, Hamblin MR, Salmaninejad A, Emadi R, Mohammadi AH, Mirazei H. Correlations between single nucleotide polymorphisms in obsessive-compulsive disorder with the clinical features or response to therapy. J Psychiatr Res 2023; 157:223-238. [PMID: 36508934 DOI: 10.1016/j.jpsychires.2022.11.025] [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: 11/03/2021] [Revised: 11/08/2022] [Accepted: 11/18/2022] [Indexed: 11/25/2022]
Abstract
Obsessive-compulsive disorder (OCD) is a debilitating neuropsychiatric disorder, in which the patient endures intrusive thoughts or is compelled to perform repetitive or ritualized actions. Many cases of OCD are considered to be familial or heritable in nature. It has been shown that a variety of internal and external risk factors are involved in the pathogenesis of OCD. Among the internal factors, genetic modifications play a critical role in the pathophysiological process. Despite many investigations performed to determine the candidate genes, the precise genetic factors involved in the disease remain largely undetermined. The present review summarizes the single nucleotide polymorphisms that have been proposed to be associated with OCD symptoms, early onset disease, neuroimaging results, and response to therapy. This information could help us to draw connections between genetics and OCD symptoms, better characterize OCD in individual patients, understand OCD prognosis, and design more targeted personalized treatment approaches.
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Affiliation(s)
- Masoumeh Beheshti
- Pathophysiology Laboratory, Sina Hospital, Tehran University of Medical Sciences, Tehran, Iran
| | - Nikta Rabiei
- School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Mohammad Taghizadieh
- Department of Pathology, School of Medicine, Center for Women's Health Research Zahra, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Pariya Eskandari
- Department of Biology, School of Basic Sciences, University of Guilan, Rasht, Iran
| | - Samaneh Mollazadeh
- Natural Products and Medicinal Plants Research Center, North Khorasan University of Medical Sciences, Bojnurd, Iran
| | - Ehsan Dadgostar
- Behavioral Sciences Research Center, Isfahan University of Medical Sciences, Isfahan, Iran; Student Research Committee, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Michael R Hamblin
- Laser Research Centre, Faculty of Health Science, University of Johannesburg, Doornfontein, 2028, South Africa
| | - Arash Salmaninejad
- Regenerative Medicine, Organ Procurement and Transplantation Multi Disciplinary Center, Razi Hospital, School of Medicine, Guilan University of Medical Sciences, Rasht, Iran; Department of Medical Genetics, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran.
| | - Raziye Emadi
- School of Medicine, Kashan University of Medical Sciences, Kashan, Iran.
| | - Amir Hossein Mohammadi
- Research Center for Biochemistry and Nutrition in Metabolic Diseases, Institute for Basic Sciences, Kashan University of Medical Sciences, Kashan, Iran.
| | - Hamed Mirazei
- Research Center for Biochemistry and Nutrition in Metabolic Diseases, Institute for Basic Sciences, Kashan University of Medical Sciences, Kashan, Iran.
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A bioinformatics approach to the identification of novel deleterious mutations of human TPMT through validated screening and molecular dynamics. Sci Rep 2022; 12:18872. [PMID: 36344599 PMCID: PMC9640560 DOI: 10.1038/s41598-022-23488-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 11/01/2022] [Indexed: 11/09/2022] Open
Abstract
Polymorphisms of Thiopurine S-methyltransferase (TPMT) are known to be associated with leukemia, inflammatory bowel diseases, and more. The objective of the present study was to identify novel deleterious missense SNPs of TPMT through a comprehensive in silico protocol. The initial SNP screening protocol used to identify deleterious SNPs from the pool of all TPMT SNPs in the dbSNP database yielded an accuracy of 83.33% in identifying extremely dangerous variants. Five novel deleterious missense SNPs (W33G, W78R, V89E, W150G, and L182P) of TPMT were identified through the aforementioned screening protocol. These 5 SNPs were then subjected to conservation analysis, interaction analysis, oncogenic and phenotypic analysis, structural analysis, PTM analysis, and molecular dynamics simulations (MDS) analysis to further assess and analyze their deleterious nature. Oncogenic analysis revealed that all five SNPs are oncogenic. MDS analysis revealed that all SNPs are deleterious due to the alterations they cause in the binding energy of the wild-type protein. Plasticity-induced instability caused by most of the mutations as indicated by the MDS results has been hypothesized to be the reason for this alteration. While in vivo or in vitro protocols are more conclusive, they are often more challenging and expensive. Hence, future research endeavors targeted at TPMT polymorphisms and/or their consequences in relevant disease progressions or treatments, through in vitro or in vivo means can give a higher priority to these SNPs rather than considering the massive pool of all SNPs of TPMT.
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Pratt VM, Cavallari LH, Fulmer ML, Gaedigk A, Hachad H, Ji Y, Kalman LV, Ly RC, Moyer AM, Scott SA, van Schaik RHN, Whirl-Carrillo M, Weck KE. TPMT and NUDT15 Genotyping Recommendations: A Joint Consensus Recommendation of the Association for Molecular Pathology, Clinical Pharmacogenetics Implementation Consortium, College of American Pathologists, Dutch Pharmacogenetics Working Group of the Royal Dutch Pharmacists Association, European Society for Pharmacogenomics and Personalized Therapy, and Pharmacogenomics Knowledgebase. J Mol Diagn 2022; 24:1051-1063. [PMID: 35931343 PMCID: PMC9808500 DOI: 10.1016/j.jmoldx.2022.06.007] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 05/04/2022] [Accepted: 06/14/2022] [Indexed: 02/06/2023] Open
Abstract
The goals of the Association for Molecular Pathology Clinical Practice Committee's Pharmacogenomics (PGx) Working Group are to define the key attributes of pharmacogenetic alleles recommended for clinical testing and a minimum set of variants that should be included in clinical PGx genotyping assays. This article provides recommendations for a minimum panel of variant alleles (Tier 1) and an extended panel of variant alleles (Tier 2) that will aid clinical laboratories when designing assays for PGx testing. The Association for Molecular Pathology PGx Working Group considered the functional impact of the variant alleles, allele frequencies in multiethnic populations, the availability of reference materials, as well as other technical considerations for PGx testing when developing these recommendations. The ultimate goal of this Working Group is to promote standardization of PGx gene/allele testing across clinical laboratories. This article focuses on clinical TPMT and NUDT15 PGx testing, which may be applied to all thiopurine S-methyltransferase (TPMT) and nudix hydrolase 15 (NUDT15)-related medications. These recommendations are not to be interpreted as prescriptive, but to provide a reference guide.
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Affiliation(s)
- Victoria M Pratt
- The Pharmacogenomics (PGx) Working Group of the Clinical Practice Committee, Association for Molecular Pathology (AMP), Rockville, Maryland; Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana.
| | - Larisa H Cavallari
- The Pharmacogenomics (PGx) Working Group of the Clinical Practice Committee, Association for Molecular Pathology (AMP), Rockville, Maryland; Center for Pharmacogenomics and Precision Medicine, Department of Pharmacotherapy and Translational Research, University of Florida, Gainesville, Florida
| | - Makenzie L Fulmer
- The Pharmacogenomics (PGx) Working Group of the Clinical Practice Committee, Association for Molecular Pathology (AMP), Rockville, Maryland; Department of Pathology and ARUP Laboratories, University of Utah School of Medicine, Salt Lake City, Utah
| | - Andrea Gaedigk
- The Pharmacogenomics (PGx) Working Group of the Clinical Practice Committee, Association for Molecular Pathology (AMP), Rockville, Maryland; Division of Clinical Pharmacology, Toxicology and Therapeutic Innovation, Children's Mercy Kansas City, School of Medicine, University of Missouri-Kansas City, Kansas City, Missouri
| | - Houda Hachad
- The Pharmacogenomics (PGx) Working Group of the Clinical Practice Committee, Association for Molecular Pathology (AMP), Rockville, Maryland; Department of Clinical Operations, AccessDx, Houston, Texas
| | - Yuan Ji
- The Pharmacogenomics (PGx) Working Group of the Clinical Practice Committee, Association for Molecular Pathology (AMP), Rockville, Maryland; Department of Pathology and ARUP Laboratories, University of Utah School of Medicine, Salt Lake City, Utah
| | - Lisa V Kalman
- The Pharmacogenomics (PGx) Working Group of the Clinical Practice Committee, Association for Molecular Pathology (AMP), Rockville, Maryland; Division of Laboratory Systems, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Reynold C Ly
- The Pharmacogenomics (PGx) Working Group of the Clinical Practice Committee, Association for Molecular Pathology (AMP), Rockville, Maryland; Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana
| | - Ann M Moyer
- The Pharmacogenomics (PGx) Working Group of the Clinical Practice Committee, Association for Molecular Pathology (AMP), Rockville, Maryland; Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Stuart A Scott
- The Pharmacogenomics (PGx) Working Group of the Clinical Practice Committee, Association for Molecular Pathology (AMP), Rockville, Maryland; Department of Pathology, Stanford University, Stanford, California; Clinical Genomics Laboratory, Stanford Health Care, Palo Alto, California
| | - R H N van Schaik
- The Pharmacogenomics (PGx) Working Group of the Clinical Practice Committee, Association for Molecular Pathology (AMP), Rockville, Maryland; Department of Clinical Chemistry/International Federation of Clinical Chemistry and Laboratory Medicine Expert Center Pharmacogenetics, Erasmus MC University Medical Center, Rotterdam, the Netherlands; European Society of Pharmacogenomics and Personalized Therapy (ESPT), Milan, Italy; Dutch Pharmacogenetics Working Group (DPWG), The Hague, the Netherlands
| | - Michelle Whirl-Carrillo
- The Pharmacogenomics (PGx) Working Group of the Clinical Practice Committee, Association for Molecular Pathology (AMP), Rockville, Maryland; Department of Biomedical Data Science, Stanford University, Stanford, California
| | - Karen E Weck
- The Pharmacogenomics (PGx) Working Group of the Clinical Practice Committee, Association for Molecular Pathology (AMP), Rockville, Maryland; Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, North Carolina; Department of Genetics, University of North Carolina, Chapel Hill, North Carolina
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10
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Pristup J, Schaeffeler E, Arjune S, Hofmann U, Santamaria-Araujo JA, Leuthold P, Friedrich N, Nauck M, Mayr S, Haag M, Muerdter T, Marner FJ, Relling MV, Evans WE, Schwarz G, Schwab M. Molybdenum Cofactor Catabolism Unravels the Physiological Role of the Drug Metabolizing Enzyme Thiopurine S-Methyltransferase. Clin Pharmacol Ther 2022; 112:808-816. [PMID: 35538648 PMCID: PMC9474665 DOI: 10.1002/cpt.2637] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Accepted: 05/04/2022] [Indexed: 12/14/2022]
Abstract
Therapy of molybdenum cofactor (Moco) deficiency has received US Food and Drug Administration (FDA) approval in 2021. Whereas urothione, the urinary excreted catabolite of Moco, is used as diagnostic biomarker for Moco-deficiency, its catabolic pathway remains unknown. Here, we identified the urothione-synthesizing methyltransferase using mouse liver tissue by anion exchange/size exclusion chromatography and peptide mass fingerprinting. We show that the catabolic Moco S-methylating enzyme corresponds to thiopurine S-methyltransferase (TPMT), a highly polymorphic drug-metabolizing enzyme associated with drug-related hematotoxicity but unknown physiological role. Urothione synthesis was investigated in vitro using recombinantly expressed human TPMT protein, liver lysates from Tpmt wild-type and knock-out (Tpmt-/- ) mice as well as human liver cytosol. Urothione levels were quantified by liquid-chromatography tandem mass spectrometry in the kidneys and urine of mice. TPMT-genotype/phenotype and excretion levels of urothione were investigated in human samples and validated in an independent population-based study. As Moco provides a physiological substrate (thiopterin) of TPMT, thiopterin-methylating activity was associated with TPMT activity determined with its drug substrate (6-thioguanin) in mice and humans. Urothione concentration was extremely low in the kidneys and urine of Tpmt-/- mice. Urinary urothione concentration in TPMT-deficient patients depends on common TPMT polymorphisms, with extremely low levels in homozygous variant carriers (TPMT*3A/*3A) but normal levels in compound heterozygous carriers (TPMT*3A/*3C) as validated in the population-based study. Our work newly identified an endogenous substrate for TPMT and shows an unprecedented link between Moco catabolism and drug metabolism. Moreover, the TPMT example indicates that phenotypic consequences of genetic polymorphisms may differ between drug- and endogenous substrates.
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Affiliation(s)
- Julika Pristup
- Institute of Biochemistry, Department of Chemistry, University of Cologne, 50674 Cologne, Germany
| | - Elke Schaeffeler
- Dr. Margarete Fischer-Bosch-Institute of Clinical Pharmacology, 70376 Stuttgart, Germany
- Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tuebingen, 72076 Tuebingen, Germany
| | - Sita Arjune
- Institute of Biochemistry, Department of Chemistry, University of Cologne, 50674 Cologne, Germany
| | - Ute Hofmann
- Dr. Margarete Fischer-Bosch-Institute of Clinical Pharmacology, 70376 Stuttgart, Germany
| | | | - Patrick Leuthold
- Dr. Margarete Fischer-Bosch-Institute of Clinical Pharmacology, 70376 Stuttgart, Germany
| | - Nele Friedrich
- Institute of Clinical Chemistry and Laboratory Medicine, University Medicine Greifswald, 17475 Greifswald, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site Greifswald, University Medicine, 17475 Greifswald, Germany
| | - Matthias Nauck
- Institute of Clinical Chemistry and Laboratory Medicine, University Medicine Greifswald, 17475 Greifswald, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site Greifswald, University Medicine, 17475 Greifswald, Germany
| | - Simon Mayr
- Institute of Biochemistry, Department of Chemistry, University of Cologne, 50674 Cologne, Germany
| | - Mathias Haag
- Dr. Margarete Fischer-Bosch-Institute of Clinical Pharmacology, 70376 Stuttgart, Germany
| | - Thomas Muerdter
- Dr. Margarete Fischer-Bosch-Institute of Clinical Pharmacology, 70376 Stuttgart, Germany
| | - Franz-Josef Marner
- Institute of Biochemistry, Department of Chemistry, University of Cologne, 50674 Cologne, Germany
| | - Mary V Relling
- Hematological Malignancies Program, St. Jude Children's Research Hospital, Memphis, Tennessee 38105-3678, USA
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee 38105-3678, USA
| | - William E Evans
- Hematological Malignancies Program, St. Jude Children's Research Hospital, Memphis, Tennessee 38105-3678, USA
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee 38105-3678, USA
| | - Guenter Schwarz
- Institute of Biochemistry, Department of Chemistry, University of Cologne, 50674 Cologne, Germany
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, 50931 Cologne, Germany
| | - Matthias Schwab
- Dr. Margarete Fischer-Bosch-Institute of Clinical Pharmacology, 70376 Stuttgart, Germany
- Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tuebingen, 72076 Tuebingen, Germany
- Departments of Clinical Pharmacology, Pharmacy and Biochemistry, University Tuebingen, 72076 Tuebingen, Germany
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11
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Moriyama T, Yang W, Smith C, Pui CH, Evans WE, Relling MV, Bhatia S, Yang JJ. Comprehensive characterization of pharmacogenetic variants in TPMT and NUDT15 in children with acute lymphoblastic leukemia. Pharmacogenet Genomics 2022; 32:60-66. [PMID: 34412101 PMCID: PMC8702453 DOI: 10.1097/fpc.0000000000000453] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Thiopurines [e.g. 6-mercaptopurine (6MP)] are essential for the cure of acute lymphoblastic leukemia (ALL) but can cause dose-limiting hematopoietic toxicity. Germline variants in drug-metabolizing enzyme genes TPMT and NUDT15 have been linked to the risk of thiopurine toxicity. However, the full spectrum of genetic polymorphism in these genes and their impact on the pharmacological effects of thiopurines remain unclear. Herein, we comprehensively sequenced the TPMT and NUDT15 genes in 685 children with ALL from the Children's Oncology Group AALL03N1 trial and evaluated their association with 6MP dose intensity. We identified 6 and 5 coding variants in TPMT and NUDT15 respectively, confirming the association at known pharmacogenetic variants. Importantly, we discovered a novel gain-of-function noncoding variants in TPMT associated with increased 6MP tolerance (rs12199316), with independent validation in 380 patients from the St. Jude Total Therapy XV protocol. Located adjacent to a regulatory DNA element, this intergenic variant was strongly associated TPMT transcription, with the variant allele linked to higher expression (P = 2.6 × 10-9). For NUDT15, one noncoding common variant, rs73189762, was identified as potentially related to 6MP intolerance. Collectively, we described pharmacogenetic variants in TPMT and NUDT15 associated with thiopurine sensitivity, providing further insights for implementing pharmacogenetics-based thiopurine individualization.
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Affiliation(s)
- Takaya Moriyama
- Department of Pharmaceutical Sciences, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | - Wenjian Yang
- Department of Pharmaceutical Sciences, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | - Colton Smith
- Department of Pharmaceutical Sciences, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | - Ching-Hon Pui
- Department of Oncology, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | - William E. Evans
- Department of Pharmaceutical Sciences, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | - Mary V. Relling
- Department of Pharmaceutical Sciences, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | - Smita Bhatia
- Institute for Cancer Outcomes and Survivorship and Division of Pediatric Hematology-Oncology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Jun J. Yang
- Department of Pharmaceutical Sciences, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
- Department of Oncology, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
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12
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Geck RC, Boyle G, Amorosi CJ, Fowler DM, Dunham MJ. Measuring Pharmacogene Variant Function at Scale Using Multiplexed Assays. Annu Rev Pharmacol Toxicol 2021; 62:531-550. [PMID: 34516287 DOI: 10.1146/annurev-pharmtox-032221-085807] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
As costs of next-generation sequencing decrease, identification of genetic variants has far outpaced our ability to understand their functional consequences. This lack of understanding is a central challenge to a key promise of pharmacogenomics: using genetic information to guide drug selection and dosing. Recently developed multiplexed assays of variant effect enable experimental measurement of the function of thousands of variants simultaneously. Here, we describe multiplexed assays that have been performed on nearly 25,000 variants in eight key pharmacogenes (ADRB2, CYP2C9, CYP2C19, NUDT15, SLCO1B1, TMPT, VKORC1, and the LDLR promoter), discuss advances in experimental design, and explore key challenges that must be overcome to maximize the utility of multiplexed functional data. Expected final online publication date for the Annual Review of Pharmacology and Toxicology, Volume 62 is January 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Renee C Geck
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA; ,
| | - Gabriel Boyle
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA; ,
| | - Clara J Amorosi
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA; ,
| | - Douglas M Fowler
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA; , .,Department of Bioengineering, University of Washington, Seattle, Washington 98195, USA
| | - Maitreya J Dunham
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA; ,
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13
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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: 0.5] [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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14
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Gebri E, Kiss A, Tóth F, Hortobágyi T. Female sex as an independent prognostic factor in the development of oral mucositis during autologous peripheral stem cell transplantation. Sci Rep 2020; 10:15898. [PMID: 32985512 PMCID: PMC7522228 DOI: 10.1038/s41598-020-72592-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Accepted: 08/28/2020] [Indexed: 11/11/2022] Open
Abstract
Oral mucositis (OM) is a frequent complication of stem cell transplantation-associated toxicity in haematological malignancies, contributing to mortality. Therapy still remains mainly supportive. We assessed risk factors in retrospective analysis of 192 autologous peripheral stem cell transplantation patients with lymphoma and multiple myeloma (MM), respectively. Futhermore, we examined the hormone levels both in serum and saliva during transplantation in 7 postmenopausal female patients with lymphoma compared to healthy controls using electrochemiluminescence immunoassay (ECLIA). Multivariable analysis revealed neutrophil engraftment (p < 0.001; p = 0.021) and female sex (p = 0.023; p = 0.038) as independent predictive factors in the combined patient group and in the lymphoma group, and neutrophil engraftment (p = 0.008) in the MM group. Of the 85 female participants 19 were pre- and 66 postmenopausal. Fifteen of the pre-, and 49 of the postmenopausal women developed ulcerative mucositis (p = 0.769), more often with lymphoma than MM (p = 0.009). Serum estrogen decreased significantly both in postmenopausal controls and transplantated patients compared to premenopausals, with no difference in saliva. Serum progesterone level was significantly (p = 0.026) elevated at day + 7 of transplantation, while salivary progesterone increased at day + 7 and + 14. Our results indicate a predominantly negative effect of female sex hormones on oral immunity with role in the aetiopathogenesis of OM.
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Affiliation(s)
- Enikő Gebri
- Department of Dentoalveolar Surgery and Dental Outpatient Care, Faculty of Dentistry, University of Debrecen, Debrecen, Hungary
| | - Attila Kiss
- Department of Haematopoietic Transplantation Centre, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Ferenc Tóth
- Department of Biomaterials and Prosthetic Dentistry, Faculty of Dentistry, University of Debrecen, Debrecen, Hungary
| | - Tibor Hortobágyi
- MTA-DE Cerebrovascular and Neurodegenerative Research Group, Department of Neurology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary.
- Faculty of Medicine, Institute of Pathology, University of Szeged, Állomás utca 2, Szeged, 6725, Hungary.
- Department of Old Age Psychiatry, Institute of Psychiatry Psychology and Neuroscience, King's College London, London, UK.
- Centre for Age-Related Medicine, SESAM, Stavanger University Hospital, Stavanger, Norway.
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15
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Zhou Y, Dagli Hernandez C, Lauschke VM. Population-scale predictions of DPD and TPMT phenotypes using a quantitative pharmacogene-specific ensemble classifier. Br J Cancer 2020; 123:1782-1789. [PMID: 32973300 PMCID: PMC7722893 DOI: 10.1038/s41416-020-01084-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 08/26/2020] [Accepted: 09/02/2020] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Inter-individual differences in dihydropyrimidine dehydrogenase (DPYD encoding DPD) and thiopurine S-methyltransferase (TPMT) activity are important predictors for fluoropyrimidine and thiopurine toxicity. While several variants in these genes are known to decrease enzyme activities, many additional genetic variations with unclear functional consequences have been identified, complicating informed clinical decision-making in the respective carriers. METHODS We used a novel pharmacogenetically trained ensemble classifier to analyse DPYD and TPMT genetic variability based on sequencing data from 138,842 individuals across eight populations. RESULTS The algorithm accurately predicted in vivo consequences of DPYD and TPMT variants (accuracy 91.4% compared to 95.3% in vitro). Further analysis showed high genetic complexity of DPD deficiency, advocating for sequencing-based DPYD profiling, whereas genotyping of four variants in TPMT was sufficient to explain >95% of phenotypic TPMT variability. Lastly, we provided population-scale profiles of ethnogeographic variability in DPD and TPMT phenotypes, and revealed striking interethnic differences in frequency and genetic constitution of DPD and TPMT deficiency. CONCLUSION These results provide the most comprehensive data set of DPYD and TPMT variability published to date with important implications for population-adjusted genetic profiling strategies of fluoropyrimidine and thiopurine risk factors and precision public health.
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Affiliation(s)
- Yitian Zhou
- Department of Physiology and Pharmacology, Karolinska Institutet, 17177, Stockholm, Sweden
| | - Carolina Dagli Hernandez
- Department of Physiology and Pharmacology, Karolinska Institutet, 17177, Stockholm, Sweden.,Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of Sao Paulo, 05508-000, Sao Paulo, Brazil
| | - Volker M Lauschke
- Department of Physiology and Pharmacology, Karolinska Institutet, 17177, Stockholm, Sweden.
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16
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Pharmacogenetic determinants of thiopurines in an Indian cohort. Pharmacol Rep 2020; 73:278-287. [PMID: 32935219 DOI: 10.1007/s43440-020-00158-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2020] [Revised: 08/25/2020] [Accepted: 09/04/2020] [Indexed: 12/14/2022]
Abstract
BACKGROUND Several genetic variants of thiopurine metabolic pathway are associated with 6-thiopurine-mediated leucopenia. A population-based evaluation of these variants lays the foundation for Pharmacogenetic-guided thiopurine therapy. METHODS A total of 2000 subjects were screened for the pharmacogenetic determinants using the infinium global screening array (GSA). The functional relevance of these variants was deduced using SNAP2, SIFT, Provean, Mutalyzer, Mutation Taster, Phyre2, SwissDock, AGGRESCAN, and CUPSAT. RESULTS The minor allele frequencies of NUDT15*3, NUDT15*5, TPMT*3C, TPMT*3B variant alleles were 6.78%, 0.11%, 1.98% and 0.69%, respectively. TPMT*3A genotype was observed in 0.35% subjects. No gender-based differences were observed in the incidence of these variants. Data from studies of the Indian population showed that 92.86% subjects heterozygous for NUDT15*3 and 60% subjects heterozygous for TPMT*3C exhibit thiopurine-mediated hematological toxicity. NUDT15 variants have no impact on the binding of 'dGTP' to the NUDT protein. NUDT15*3 variant increases aggregation 'hot spot' region and induces unfavourable torsion in the protein. NUDT15*5 destabilizes the protein and impairs Mg/Mn binding. TPMT*3A, TPMT*3B and TPMT*3C variants lower binding affinity to 6-mercaptopurine compared to the wild protein. TPMT*3C variant destabilizes the TPMT protein in the thermal experiment. Compared to the data of European and African/African American populations, NUDT15*3 frequency is higher and TPMT*3C frequency is lower in our population. CONCLUSIONS TPMT variants were less frequent in Indian population, while NUDT15*3 is more frequent compared to European and African/African American populations. NUDT15*3 increases aggregation 'hot spot' and induces unfavourable torsion in the protein. NUDT15*5 and TPMT*3C destabilize the respective proteins. TPMT*3A, TPMT*3B and TPMT*3C are associated with a lower binding affinity towards 6-mercaptopurine.
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17
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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: 1.8] [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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18
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Marin JJG, Serrano MA, Monte MJ, Sanchez-Martin A, Temprano AG, Briz O, Romero MR. Role of Genetic Variations in the Hepatic Handling of Drugs. Int J Mol Sci 2020; 21:E2884. [PMID: 32326111 PMCID: PMC7215464 DOI: 10.3390/ijms21082884] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 04/09/2020] [Accepted: 04/17/2020] [Indexed: 12/18/2022] Open
Abstract
The liver plays a pivotal role in drug handling due to its contribution to the processes of detoxification (phases 0 to 3). In addition, the liver is also an essential organ for the mechanism of action of many families of drugs, such as cholesterol-lowering, antidiabetic, antiviral, anticoagulant, and anticancer agents. Accordingly, the presence of genetic variants affecting a high number of genes expressed in hepatocytes has a critical clinical impact. The present review is not an exhaustive list but a general overview of the most relevant variants of genes involved in detoxification phases. The available information highlights the importance of defining the genomic profile responsible for the hepatic handling of drugs in many ways, such as (i) impaired uptake, (ii) enhanced export, (iii) altered metabolism due to decreased activation of prodrugs or enhanced inactivation of active compounds, and (iv) altered molecular targets located in the liver due to genetic changes or activation/downregulation of alternative/compensatory pathways. In conclusion, the advance in this field of modern pharmacology, which allows one to predict the outcome of the treatments and to develop more effective and selective agents able to overcome the lack of effect associated with the existence of some genetic variants, is required to step forward toward a more personalized medicine.
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Affiliation(s)
- Jose J. G. Marin
- HEVEFARM Group, Center for the Study of Liver and Gastrointestinal Diseases (CIBERehd), Carlos III National Institute of Health, University of Salamanca, IBSAL, 37007 Salamanca, Spain; (M.A.S.); (M.J.M.); (A.S.-M.); (A.G.T.); (O.B.); (M.R.R.)
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19
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20
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Savojardo C, Babbi G, Bovo S, Capriotti E, Martelli PL, Casadio R. Are machine learning based methods suited to address complex biological problems? Lessons from CAGI-5 challenges. Hum Mutat 2019; 40:1455-1462. [PMID: 31066146 DOI: 10.1002/humu.23784] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Revised: 04/02/2019] [Accepted: 05/04/2019] [Indexed: 11/06/2022]
Abstract
In silico approaches are routinely adopted to predict the effects of genetic variants and their relation to diseases. The critical assessment of genome interpretation (CAGI) has established a common framework for the assessment of available predictors of variant effects on specific problems and our group has been an active participant of CAGI since its first edition. In this paper, we summarize our experience and lessons learned from the last edition of the experiment (CAGI-5). In particular, we analyze prediction performances of our tools on five CAGI-5 selected challenges grouped into three different categories: prediction of variant effects on protein stability, prediction of variant pathogenicity, and prediction of complex functional effects. For each challenge, we analyze in detail the performance of our tools, highlighting their potentialities and drawbacks. The aim is to better define the application boundaries of each tool.
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Affiliation(s)
- Castrense Savojardo
- Biocomputing Group, Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Giulia Babbi
- Biocomputing Group, Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Samuele Bovo
- Biocomputing Group, Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Emidio Capriotti
- Biocomputing Group, Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Pier Luigi Martelli
- Biocomputing Group, Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Rita Casadio
- Biocomputing Group, Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy.,Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies (IBIOM), Italian National Research Council (CNR), Bari, Italy
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21
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Rucci F, Cigoli MS, Marini V, Fucile C, Mattioli F, Robbiano L, Cavallari U, Scaglione F, Perno CF, Penco S, Marocchi A. Combined evaluation of genotype and phenotype of thiopurine S-methyltransferase (TPMT) in the clinical management of patients in chronic therapy with azathioprine. Drug Metab Pers Ther 2019; 34:dmpt-2018-0037. [PMID: 30840585 DOI: 10.1515/dmpt-2018-0037] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Accepted: 01/29/2019] [Indexed: 06/09/2023]
Abstract
Background The thiopurine S-methyltransferase (TPMT)/azathioprine (AZA) gene-drug pair is one of the most well-known pharmacogenetic markers. Despite this, few studies investigated the implementation of TPMT testing and the combined evaluation of genotype and phenotype in multidisciplinary clinical settings where patients are undergoing chronic therapy with AZA. Methods A total of 356 AZA-treated patients for chronic autoimmune diseases were enrolled. DNA was isolated from whole blood and the samples were analyzed for the c.460G>A and c.719A>G variants by the restriction fragment length polymorphism (RFLP) technique and sequenced for the c.238G>C variant. The TPMT enzyme activity was determined in erythrocytes by a high-performance liquid chromatography (HPLC) assay. Results All the patients enrolled were genotyped while the TPMT enzyme activity was assessed in 41 patients. Clinical information was available on 181 patients. We found no significant difference in the odds of having adverse drug reactions (ADRs) in wild-type patients and variant allele carriers, but the latter had an extra risk of experiencing hematologically adverse events. The enzyme activity was significantly associated to genotype. Conclusions TPMT variant allele carriers have an extra risk of experiencing hematologically adverse events compared to wild-type patients. Interestingly, only two out of 30 (6.6%) patients had discordant results between genotype, phenotype and onset of ADRs.
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Affiliation(s)
- Francesco Rucci
- Department of Laboratory Medicine, Medical Genetics, ASST Niguarda Hospital, Piazza Ospedale Maggiore, 3-20162 - Milan, Italy, Tel. +39 0264442803
- University of Milan, Department of Oncology and Onco-Hematology, Postgraduate School of Clinical Pharmacology and Toxicology, Milan, Italy
| | - Maria Sole Cigoli
- Department of Laboratory Medicine, Medical Genetics, ASST Niguarda Hospital, Milan, Italy
| | - Valeria Marini
- Department of Internal Medicine, University of Genova, Genova, Italy
| | - Carmen Fucile
- Department of Internal Medicine, University of Genova, Genova, Italy
| | | | - Luigi Robbiano
- Department of Internal Medicine, University of Genova, Genova, Italy
| | - Ugo Cavallari
- Department of Laboratory Medicine, Medical Genetics, ASST Niguarda Hospital, Milan, Italy
| | - Francesco Scaglione
- University of Milan, Department of Oncology and Onco-Hematology, Postgraduate School of Clinical Pharmacology and Toxicology, Milan, Italy
| | - Carlo F Perno
- Department of Laboratory Medicine, ASST Niguarda Hospital, Milan, Italy
| | - Silvana Penco
- Department of Laboratory Medicine, Medical Genetics, ASST Niguarda Hospital, Milan, Italy
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22
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Pashazadeh P, Marjani A, Asadi J, Khoshnia M. Thiopurine Methyltransferase Genetic Polymorphisms and Activity and Metabolic Products of Azathioprine in Patients with Inflammatory Bowel Disease. Endocr Metab Immune Disord Drug Targets 2018; 19:541-547. [PMID: 30451123 DOI: 10.2174/1871530318666181119153522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Revised: 10/01/2018] [Accepted: 10/04/2018] [Indexed: 12/07/2022]
Abstract
BACKGROUND Thiopurine S-methyltransferase (TPMT) is a cytoplasmic enzyme that catalyzes thiopurine drugs such as 6-mercaptopurine, 6-thioguanine, and azathioprine. There is a correlation between thiopurine drug metabolism, response, and toxicity and genetic polymorphism of TPMT. The aim of this study is to assess TPMT genetic polymorphisms activity and metabolic products of AZA in patients with IBD. METHODS Blood samples were obtained from 50 IBD unrelated patients from a private laboratory. We used polymerase chain reaction-restriction length polymorphism (PCR-RFLP) and allele-specific PCRbased assays to determine the TPMT gene for the different variants. A high-performance liquid chromatography system (HPLC) was carried out to determine the whole blood 6-TGN concentration. Determination of serum TMPT activity was done by ELISA kit. RESULTS In IBD patients, 46/50 (92%) subjects were homozygous for the wild-type allele (TPMT*1/*1). Mutant TPMT*1/*2 and TPMT*1/*3C alleles were found in 4/46 (8%) and 3/47 (6%) of IBD patients, respectively. TPMT*1/*3B variant was not detected in any of the IBD patients. TPMT enzyme activity was higher in wild-type than that mutant variants TPMT*1/*2 and TPMT*1/*3C, suggesting that there are statistically significant differences between 6-TG levels and polymorphisms of TMPT enzyme. 6-TG levels significantly increased in IBD patients mutant variants TPMT*1/*2 and TPMT*1/*3C. CONCLUSIONS Our results showed that TPMT polymorphisms are associated with 6-TGN levels in patients using AZA. This study suggests that AZA dosage may be determined according to the high or low prevalence of a TPMT genotype. Moreover, the results present the determination of metabolite for assessing possible safe effective dosage of the drug.
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Affiliation(s)
- Paria Pashazadeh
- Metabolic Disorders Research Center, Department of Biochemistry and Biophysics, Gorgan Faulty of Medicine, Golestan University of Medical Sciences, Gorgan, Golestan Province, Iran
| | - Abdoljalal Marjani
- Metabolic Disorders Research Center, Department of Biochemistry and Biophysics, Gorgan Faulty of Medicine, Golestan University of Medical Sciences, Gorgan, Golestan Province, Iran
| | - Jahanbakhash Asadi
- Metabolic Disorders Research Center, Department of Biochemistry and Biophysics, Gorgan Faulty of Medicine, Golestan University of Medical Sciences, Gorgan, Golestan Province, Iran
| | - Masoud Khoshnia
- Golestan Research Center of Gasteroenterolgy and Hepatology, Golestan University of Medical Sciences, Gorgan, Golestan Province, Iran
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24
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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: 6.2] [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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25
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Hiratsuka M, Hirasawa N, Oshima Y, Kodama S, Miyata T, Dan T, Takatoku H, Kuribayashi H, Nakamura R, Saito Y. Points-to-consider documents: Scientific information on the evaluation of genetic polymorphisms during non-clinical studies and phase I clinical trials in the Japanese population. Drug Metab Pharmacokinet 2018; 33:141-149. [PMID: 29703433 DOI: 10.1016/j.dmpk.2018.01.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Revised: 12/05/2017] [Accepted: 01/15/2018] [Indexed: 01/11/2023]
Abstract
Pharmacotherapy shows striking individual differences in pharmacokinetics and pharmacodynamics, involving drug efficacy and adverse reactions. Recent genetic research has revealed that genetic polymorphisms are important intrinsic factors for these inter-individual differences. This pharmacogenomic information could help develop safer and more effective precision pharmacotherapies and thus, regulatory guidance/guidelines were developed in this area, especially in the EU and US. The Project for the Promotion of Progressive Medicine, Medical Devices, and Regenerative Medicine by the Ministry of Health, Labour and Welfare, performed by Tohoku University, reported scientific information on the evaluation of genetic polymorphisms, mainly on drug metabolizing enzymes and transporters, during non-clinical studies and phase I clinical trials in Japanese subjects/patients. We anticipate that this paper will be helpful in drug development for the regulatory usage of pharmacogenomic information, most notably pharmacokinetics.
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Affiliation(s)
- Masahiro Hiratsuka
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Japan.
| | - Noriyasu Hirasawa
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Japan
| | - Yoshiteru Oshima
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Japan
| | - Susumu Kodama
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Japan; National Institute of Health Sciences (NIHS), Tokyo, Japan; Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama, Japan
| | - Toshio Miyata
- Graduate School of Medicine, Tohoku University, Sendai, Japan
| | - Takashi Dan
- Graduate School of Medicine, Tohoku University, Sendai, Japan
| | | | | | - Ryosuke Nakamura
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Japan; National Institute of Health Sciences (NIHS), Tokyo, Japan
| | - Yoshiro Saito
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Japan; National Institute of Health Sciences (NIHS), Tokyo, Japan
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26
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Clinical Practice Recommendations for the Management and Prevention of Cisplatin-Induced Hearing Loss Using Pharmacogenetic Markers. Ther Drug Monit 2017; 38:423-31. [PMID: 26960170 DOI: 10.1097/ftd.0000000000000298] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Currently no pharmacogenomics-based criteria exist to guide clinicians in identifying individuals who are at risk of hearing loss from cisplatin-based chemotherapy. This review summarizes findings from pharmacogenomic studies that report genetic polymorphisms associated with cisplatin-induced hearing loss and aims to (1) provide up-to-date information on new developments in the field, (2) provide recommendations for the use of pharmacogenetic testing in the prevention, assessment, and management of cisplatin-induced hearing loss in children and adults, and (3) identify knowledge gaps to direct and prioritize future research. These practice recommendations for pharmacogenetic testing in the context of cisplatin-induced hearing loss reflect a review and evaluation of recent literature, and are designed to assist clinicians in providing optimal clinical care for patients receiving cisplatin-based chemotherapy.
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27
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Lee M, Seo J, Bang D, Kim DY. Thiopurine S-Methyltransferase Polymorphisms in Korean Dermatologic Patients. Ann Dermatol 2017; 29:529-535. [PMID: 28966507 PMCID: PMC5597644 DOI: 10.5021/ad.2017.29.5.529] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Revised: 09/29/2016] [Accepted: 10/14/2016] [Indexed: 11/08/2022] Open
Abstract
Background Thiopurine S-methyltransferase (TPMT) is an important enzyme in the metabolism of thiopurines including azathioprine (AZA), 6-mercaptopurine, and 6-thioguanine. TPMT genotyping is widely used for screening of AZA-related toxicity during routine clinical practice in Korea. However, the data of TPMT genotypes and its AZA-related toxicity have not been studied in the field of dermatology. Objective The aim of this study was to evaluate the genetic basis of TPMT polymorphism in Korean dermatologic patients and subsequently to investigate the relationship between mutant TPMT and adverse responses to AZA treatment. Methods This study was retrospective, single-center study. One hundred forty-nine Korean dermatologic patients who underwent TPMT screening test were included. Each patient's medical records, the result of TPMT screening test, dose and treatment period of AZA, and side effects, were reviewed. Laboratory tests were assessed at each visit in order to monitor adverse drug reactions. Leukopenia grading was used in accordance with the common terminology criteria for adverse events (CTCAE) ver. 4.03. Results Behçet's disease was the leading disorder among the patients. The frequency of TPMT mutation was 4.0% (6/149) among the participants in this study. Four of the six patients with genetic alterations were treated with a low-dose AZA regimen, but no AZA-related adverse events were observed. Conclusion Our results suggest that 1) TPMT polymorphisms in Korean dermatologic patients are similar to those previously reported in Asian patients with the most common mutant allele being TPMT*3C and 2) AZA can be used in the patients with these polymorphisms under a careful dosing regimen.
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Affiliation(s)
- Minseok Lee
- Department of Dermatology, Severance Hospital, Cutaneous Biology Research Institute, Yonsei University College of Medicine, Seoul, Korea
| | - Jimyung Seo
- Department of Dermatology, Severance Hospital, Cutaneous Biology Research Institute, Yonsei University College of Medicine, Seoul, Korea
| | - Dongsik Bang
- Department of Dermatology, Catholic Kwandong University International St. Mary's Hospital, Incheon, Korea
| | - Do Young Kim
- Department of Dermatology, Severance Hospital, Cutaneous Biology Research Institute, Yonsei University College of Medicine, Seoul, Korea
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28
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Wennerstrand P, Blissing A, Mårtensson LG. In Vitro Protein Stability of Two Naturally Occurring Thiopurine S-Methyltransferase Variants: Biophysical Characterization of TPMT*6 and TPMT*8. ACS OMEGA 2017; 2:4991-4999. [PMID: 30023734 PMCID: PMC6044926 DOI: 10.1021/acsomega.7b00801] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Accepted: 07/18/2017] [Indexed: 06/02/2023]
Abstract
Thiopurine S-methyltransferase (TPMT) is a polymorphic enzyme involved in the metabolism and inactivation of thiopurine substances administered as immunosuppressants in the treatment of malignancies and autoimmune diseases. In this study, the naturally occurring variants, TPMT*6 (Y180F) and TPMT*8 (R215H), have been biophysically characterized. Despite being classified as low and intermediate in vivo enzyme activity variants, respectively, our results demonstrate a discrepancy because both TPMT*6 and TPMT*8 were found to exhibit normal functionality in vitro. While TPMT*8 exhibited biophysical properties almost indistinguishable from those of TPMTwt, the TPMT*6 variant was found to be destabilized. Furthermore, the contributions of the cofactor S-adenosylmethionine (SAM) to the thermodynamic stability of TPMT were investigated, but only a modest stabilizing effect was observed. Also presented herein is a new method for studies of the biophysical characteristics of TPMT and its variants using the extrinsic fluorescent probe 8-anilinonaphthalene-1-sulfonic acid (ANS). ANS was found to bind strongly to all investigated TPMT variants with a Kd of approximately 0.2 μM and a 1:1 binding ratio as determined by isothermal titration calorimetry (ITC). Circular dichroism and fluorescence measurements showed that ANS binds exclusively to the native state of TPMT, and binding to the active site was confirmed by molecular modeling and simulated docking as well as ITC measurements. The strong binding of the probe to native TPMT and the conformity of the obtained results demonstrate the advantages of using ANS binding characteristics in studies of this protein and its variants.
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29
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Li X, Mei S, Gong X, Zhou H, Yang L, Zhou A, Liu Y, Li X, Zhao Z, Zhang X. Relationship between Azathioprine metabolites and therapeutic efficacy in Chinese patients with neuromyelitis optica spectrum disorders. BMC Neurol 2017; 17:130. [PMID: 28679367 PMCID: PMC5498874 DOI: 10.1186/s12883-017-0903-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2017] [Accepted: 06/22/2017] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND Neuromyelitis optica spectrum disorders (NMOSD) are demyelinating autoimmune diseases in the central nervous system (CNS) that are characterized by a high relapse rate and the presence of anti-aquaporin 4 antibodies (AQP4-IgG) in the serum. Azathioprine (AZA) is a first-line immunomodulatory drug that is widely used for the treatment of patients with NMOSD. However, the efficacy and safety of AZA vary in different individuals. METHOD Thirty-two patients with NMOSD who regularly took AZA were enrolled in the study at Beijing Tiantan Hospital, Capital Medical University. The efficacy of AZA was evaluated using the expanded disability status scale (EDSS) and the annual relapse rate (ARR). The erythrocyte concentrations of AZA metabolites were detected using an LC-MS/MS method. RESULTS The erythrocyte concentrations of 6-thioguanine nucleotides (6-TGNs) and 6-methylmercaptopurine nucleotides (6-MMPNs) were 202.03 ± 63.35 pmol/8*108 RBC and 1618.90 ± 1607.06 pmol/8*108 RBC, respectively. After the patients had received AZA therapy for more than one year, the EDSS score decreased from 5.21 ± 0.24 to 2.57 ± 0.33 (p < 0.0001), and the ARR decreased from 1.41 ± 0.23 to 0.36 ± 0.09 (p < 0.0001). The 6-TGN and 6-MMPN levels were significantly different between the non-relapsed and relapsed groups (p < 0.0001, p = 0.006, respectively). A higher ARR was significantly correlated with higher erythrocyte concentrations of 6-TGNs (p < 0.0001) and 6-MMPNs (p = 0.004). CONCLUSION AZA can reduce the EDSS score and ARR in NMOSD patients. Additionally, the efficacy of AZA is significantly related to the erythrocyte concentrations of 6-TGNs and 6-MMPNs. Within the safe upper limits, a higher concentration of 6-TGNs is associated with better efficacy of AZA. TRIAL REGISTRATION NUMBER ISRCTN16551495 , retrospectively registered on May 22, 2017.
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Affiliation(s)
- Xindi Li
- Neuroinfection and Neuroimmunology Center, Department of Neurology, Beijing Tiantan Hospital, Capital Medical University, 6 TiantanXili, Dongcheng District, Beijing, 100050, People's Republic of China.,China National Clinical Research Center for Neurological Diseases, Beijing Tiantan Hospital, Capital Medical University, 6 TiantanXili, Dongcheng District, Beijing, 100050, People's Republic of China
| | - Shenghui Mei
- Department of Pharmacy, Beijing Tiantan Hospital, Capital Medical University, 6 TiantanXili, Dongcheng District, Beijing, 100050, People's Republic of China
| | - Xiaoqing Gong
- Neuroinfection and Neuroimmunology Center, Department of Neurology, Beijing Tiantan Hospital, Capital Medical University, 6 TiantanXili, Dongcheng District, Beijing, 100050, People's Republic of China.,China National Clinical Research Center for Neurological Diseases, Beijing Tiantan Hospital, Capital Medical University, 6 TiantanXili, Dongcheng District, Beijing, 100050, People's Republic of China
| | - Heng Zhou
- Neuroinfection and Neuroimmunology Center, Department of Neurology, Beijing Tiantan Hospital, Capital Medical University, 6 TiantanXili, Dongcheng District, Beijing, 100050, People's Republic of China.,China National Clinical Research Center for Neurological Diseases, Beijing Tiantan Hospital, Capital Medical University, 6 TiantanXili, Dongcheng District, Beijing, 100050, People's Republic of China
| | - Li Yang
- Department of Pharmacy, Beijing Tiantan Hospital, Capital Medical University, 6 TiantanXili, Dongcheng District, Beijing, 100050, People's Republic of China
| | - Anna Zhou
- Neuroinfection and Neuroimmunology Center, Department of Neurology, Beijing Tiantan Hospital, Capital Medical University, 6 TiantanXili, Dongcheng District, Beijing, 100050, People's Republic of China.,China National Clinical Research Center for Neurological Diseases, Beijing Tiantan Hospital, Capital Medical University, 6 TiantanXili, Dongcheng District, Beijing, 100050, People's Republic of China
| | - Yonghong Liu
- Neuroinfection and Neuroimmunology Center, Department of Neurology, Beijing Tiantan Hospital, Capital Medical University, 6 TiantanXili, Dongcheng District, Beijing, 100050, People's Republic of China.,China National Clinical Research Center for Neurological Diseases, Beijing Tiantan Hospital, Capital Medical University, 6 TiantanXili, Dongcheng District, Beijing, 100050, People's Republic of China
| | - Xingang Li
- Department of Pharmacy, Beijing Tiantan Hospital, Capital Medical University, 6 TiantanXili, Dongcheng District, Beijing, 100050, People's Republic of China
| | - Zhigang Zhao
- Department of Pharmacy, Beijing Tiantan Hospital, Capital Medical University, 6 TiantanXili, Dongcheng District, Beijing, 100050, People's Republic of China.
| | - Xinghu Zhang
- Neuroinfection and Neuroimmunology Center, Department of Neurology, Beijing Tiantan Hospital, Capital Medical University, 6 TiantanXili, Dongcheng District, Beijing, 100050, People's Republic of China. .,China National Clinical Research Center for Neurological Diseases, Beijing Tiantan Hospital, Capital Medical University, 6 TiantanXili, Dongcheng District, Beijing, 100050, People's Republic of China.
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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: 16] [Impact Index Per Article: 2.3] [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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31
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Bhavsar AP, Gunaretnam EP, Li Y, Hasbullah JS, Carleton BC, Ross CJD. Pharmacogenetic variants in TPMT alter cellular responses to cisplatin in inner ear cell lines. PLoS One 2017; 12:e0175711. [PMID: 28406961 PMCID: PMC5391095 DOI: 10.1371/journal.pone.0175711] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Accepted: 03/30/2017] [Indexed: 11/19/2022] Open
Abstract
Cisplatin is a highly-effective and widely-used chemotherapeutic agent that causes ototoxicity in many patients. Pharmacogenomic studies of key genes controlling drug biotransformation identified variants in thiopurine methyltransferase (TPMT) as predictors of cisplatin-induced ototoxicity, although the mechanistic basis of this interaction has not been reported. Expression constructs of TPMT*3A, *3B and *3C variants were generated and monitored in cultured cells. Cellular TPMT*3A levels were detected at >20-fold lower amounts than the wild type confirming the unstable nature of this variant. The expression of wild type TPMT (TPMT*1) in two murine ear cell lines, HEI-OC1 and UB/OC-1, significantly mitigated their susceptibility to cisplatin toxicity. Cisplatin treatment induced Tlr4 gene expression in HEI-OC1 cells and this response was blunted by the expression of wild type TPMT but not TPMT*3A. In line with the significant mitigation of TPMT*1-expressing cells to cisplatin cytotoxicity, these findings demonstrate a drug-gene interaction between increased TPMT activity and decreased susceptibility to cisplatin-induced toxicity of inner ear cells.
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Affiliation(s)
- Amit P. Bhavsar
- Faculty of Pharmaceutical Sciences, The University of British Columbia, Vancouver, British Columbia, Canada
- BC Children’s Hospital Research Institute, Vancouver, British Columbia, Canada
| | - Erandika P. Gunaretnam
- Faculty of Pharmaceutical Sciences, The University of British Columbia, Vancouver, British Columbia, Canada
- BC Children’s Hospital Research Institute, Vancouver, British Columbia, Canada
- Division of Translational Therapeutics, Department of Pediatrics, Faculty of Medicine, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Yuling Li
- BC Children’s Hospital Research Institute, Vancouver, British Columbia, Canada
- Division of Translational Therapeutics, Department of Pediatrics, Faculty of Medicine, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Jafar S. Hasbullah
- BC Children’s Hospital Research Institute, Vancouver, British Columbia, Canada
- Department of Medical Genetics, Faculty of Medicine, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Bruce C. Carleton
- BC Children’s Hospital Research Institute, Vancouver, British Columbia, Canada
- Division of Translational Therapeutics, Department of Pediatrics, Faculty of Medicine, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Colin J. D. Ross
- Faculty of Pharmaceutical Sciences, The University of British Columbia, Vancouver, British Columbia, Canada
- BC Children’s Hospital Research Institute, Vancouver, British Columbia, Canada
- * E-mail:
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32
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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: 4.4] [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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Kim MG, Ko M, Kim IW, Oh JM. Meta-analysis of the impact of thioprine S-methyltransferase polymorphisms on the tolerable 6-mercaptopurine dose considering initial dose and ethnic difference. Onco Targets Ther 2016; 9:7133-7139. [PMID: 27920553 PMCID: PMC5125793 DOI: 10.2147/ott.s110800] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
A meta-analysis was conducted to decide whether to reduce an initial 6-mercaptopurine (6-MP) dose in TPMT heterozygote in the case of an initial 6-MP dose of <75 mg/m2/d and to compare the tolerable 6-MP dose among different ethnic groups. The study was undertaken according to Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines. The differences in mean values of the tolerable 6-MP dose were calculated by using Comprehensive Meta-Analysis version 3. The results of the meta-analysis indicated that the tolerable 6-MP dose was significantly lower in the TPMT heterozygote group (difference in mean values =11.729, 95% confidence interval =7.617-15.842, P<0.001) even when the initial 6-MP dose was <75 mg/m2/d. The TPMT*3C allele-dominant ethnic group (Asian) needed less reduction in mean 6-MP dose in comparison to the TPMT*3A allele-dominant ethnic group (Caucasian, Mediterranean, South American) (difference in mean values =8.884 vs 15.324). In conclusion, the initial 6-MP dose needs to be reduced in TPMT heterozygote when compared to the wild-type, and ethnic difference might influence the tolerable 6-MP dose in TPMT heterozygotes.
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Affiliation(s)
- Myeong Gyu Kim
- College of Pharmacy and Research Institute of Pharmaceutical Sciences, Seoul National University, Seoul, Korea
| | - Minoh Ko
- College of Pharmacy and Research Institute of Pharmaceutical Sciences, Seoul National University, Seoul, Korea
| | - In-Wha Kim
- College of Pharmacy and Research Institute of Pharmaceutical Sciences, Seoul National University, Seoul, Korea
| | - Jung Mi Oh
- College of Pharmacy and Research Institute of Pharmaceutical Sciences, Seoul National University, Seoul, Korea
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Mlakar V, Huezo-Diaz Curtis P, Satyanarayana Uppugunduri CR, Krajinovic M, Ansari M. Pharmacogenomics in Pediatric Oncology: Review of Gene-Drug Associations for Clinical Use. Int J Mol Sci 2016; 17:ijms17091502. [PMID: 27618021 PMCID: PMC5037779 DOI: 10.3390/ijms17091502] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Revised: 08/02/2016] [Accepted: 08/15/2016] [Indexed: 02/07/2023] Open
Abstract
During the 3rd congress of the European Society of Pharmacogenomics and Personalised Therapy (ESPT) in Budapest in 2015, a preliminary meeting was held aimed at establishing a pediatric individualized treatment in oncology and hematology committees. The main purpose was to facilitate the transfer and harmonization of pharmacogenetic testing from research into clinics, to bring together basic and translational research and to educate health professionals throughout Europe. The objective of this review was to provide the attendees of the meeting as well as the larger scientific community an insight into the compiled evidence regarding current pharmacogenomics knowledge in pediatric oncology. This preliminary evaluation will help steer the committee’s work and should give the reader an idea at which stage researchers and clinicians are, in terms of personalizing medicine for children with cancer. From the evidence presented here, future recommendations to achieve this goal will also be suggested.
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Affiliation(s)
- Vid Mlakar
- Cansearch Research Laboratory, Geneva University Medical School, Avenue de la Roseraie 64, 1205 Geneva, Switzerland.
| | - Patricia Huezo-Diaz Curtis
- Cansearch Research Laboratory, Geneva University Medical School, Avenue de la Roseraie 64, 1205 Geneva, Switzerland.
| | | | - Maja Krajinovic
- Charles-Bruneau Cancer Center, Centre hospitalier universitaire Sainte-Justine, 4515 Rue de Rouen, Montreal, QC H1V 1H1, Canada.
- Department of Pediatrics, University of Montreal, 2900 Boulevard Edouard-Montpetit, Montreal, QC H3T 1J4, Canada.
- Department of Pharmacology, Faculty of Medicine, University of Montreal, 2900 Boulevard Edouard-Montpetit, Montreal, QC H3T 1J4, Canada.
| | - Marc Ansari
- Cansearch Research Laboratory, Geneva University Medical School, Avenue de la Roseraie 64, 1205 Geneva, Switzerland.
- Pediatric Department, Onco-Hematology Unit, Geneva University Hospital, Rue Willy-Donzé 6, 1205 Geneva, Switzerland.
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Lawrence J, Cameron D, Argyle D. Species differences in tumour responses to cancer chemotherapy. Philos Trans R Soc Lond B Biol Sci 2016; 370:rstb.2014.0233. [PMID: 26056373 DOI: 10.1098/rstb.2014.0233] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Despite advances in chemotherapy, radiotherapy and targeted drug development, cancer remains a disease of high morbidity and mortality. The treatment of human cancer patients with chemotherapy has become commonplace and accepted over the past 100 years. In recent years, and with a similar incidence of cancer to people, the use of cancer chemotherapy drugs in veterinary patients such as the dog has also become accepted clinical practice. The poor predictability of tumour responses to cancer chemotherapy drugs in rodent models means that the standard drug development pathway is costly, both in terms of money and time, leading to many drugs failing in Phase I and II clinical trials. This has led to the suggestion that naturally occurring cancers in pet dogs may offer an alternative model system to inform rational drug development in human oncology. In this review, we will explore the species variation in tumour responses to conventional chemotherapy and highlight our understanding of the differences in pharmacodynamics, pharmacokinetics and pharmacogenomics between humans and dogs. Finally, we explore the potential hurdles that need to be overcome to gain the greatest value from comparative oncology studies.
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Affiliation(s)
- Jessica Lawrence
- Royal (Dick) School of Veterinary Studies and Roslin Institute, University of Edinburgh, Easter Bush EH25 9RG, UK
| | - David Cameron
- University of Edinburgh Cancer Research Centre, Western General Hospital, Edinburgh EH4 2LF, UK
| | - David Argyle
- Royal (Dick) School of Veterinary Studies and Roslin Institute, University of Edinburgh, Easter Bush EH25 9RG, UK
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Serpe L, Canaparo R, Scordo MG, Spina E. Pharmacogenetics of drug-metabolizing enzymes in Italian populations. Drug Metab Pers Ther 2016; 30:107-20. [PMID: 25527811 DOI: 10.1515/dmdi-2014-0028] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2014] [Accepted: 11/21/2014] [Indexed: 11/15/2022]
Abstract
Drug-metabolizing enzymes play a major role in the biotransformation and subsequent elimination of most drugs and xenobiotics from the body. Both phase I and phase II enzymes are highly polymorphic. Inter-individual differences in genes coding for drug-metabolizing enzymes are important for understanding variability in drug response and for individualization of drug prescription. The prevalence of genetic polymorphisms in drug metabolism varies widely with ethnicity, and marked differences in the distribution of allelic variants of genes encoding drug-metabolizing enzymes have been documented in populations of different racial origin. This review aimed to summarize the available studies on genetic polymorphisms associated with drug metabolism conducted in Italian populations and to compare the frequency of the various metabolizer phenotypes and most common variant alleles (and resulting genotypes) with corresponding values from other populations. Notably, published data are not extensive, and most studies were performed on relatively low numbers of individuals. In general, the frequency of polymorphisms in the cytochrome P450 (CYP) genes as well as in the investigated phase II enzymes in the Italian population was similar to values reported for other Caucasian populations. However, the prevalence of CYP2D6 gene duplication among Italians was found to be very high, confirming the higher frequency of CYP2D6 ultrarapid metabolizers in the Mediterranean area compared to Northern Europe. It is worth noting that a geographic gradient in the flavin-containing monooxygenase 3 polymorphism distribution was also seen, the Italian population showing higher similarity to other Mediterranean populations than to North Europeans.
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Fazel-Najafabadi E, Vahdat Ahar E, Fattahpour S, Sedghi M. Structural and functional impact of missense mutations in TPMT: An integrated computational approach. Comput Biol Chem 2015; 59 Pt A:48-55. [PMID: 26410243 DOI: 10.1016/j.compbiolchem.2015.09.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2015] [Revised: 08/17/2015] [Accepted: 09/06/2015] [Indexed: 11/26/2022]
Abstract
BACKGROUND Thiopurine S-methyltransferase (TPMT) detoxifies thiopurine drugs which are used for treatment of various diseases including inflammatory bowel disease (IBD), and hematological malignancies. Individual variation in TPMT activity results from mutations in TPMT gene. In this study, the effects of all the known missense mutations in TPMT enzyme were studied at the sequence and structural level METHODS A broad set of bioinformatic tools was used to assess all the known missense mutations affecting enzyme activity. The effects of these mutations on protein stability, aggregation propensity, and residue interaction network were analyzed. RESULTS Our results indicate that the missense mutations have diverse effects on TPMT structure and function. Stability and aggregation propensities are affected by various mutations. Several mutations also affect residues in ligand binding site. CONCLUSIONS In vitro study of missense mutation is laborious and time-consuming. However, computational methods can be used to obtain information about effects of missense mutations on protein structure. In this study, the effects of most of the mutations on enzyme activity could be explained by computational methods. Thus, the present approach can be used for understanding the protein structure-function relationships.
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Affiliation(s)
- Esmat Fazel-Najafabadi
- Medical Genetics Laboratory, Alzahra University Hospital, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Elham Vahdat Ahar
- Institute of Biochemistry and Biophysics, University of Tehran, Iran
| | - Shirin Fattahpour
- Medical Genetics Laboratory, Alzahra University Hospital, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Maryam Sedghi
- Medical Genetics Laboratory, Alzahra University Hospital, Isfahan University of Medical Sciences, Isfahan, Iran; Pediatric Inherited Diseases Research Center, Research Institute for Primordial Prevention of Non-communicable disease, Isfahan University of Medical Sciences, Isfahan, Iran.
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TPMT Polymorphism: When Shield Becomes Weakness. Interdiscip Sci 2015; 8:150-155. [PMID: 26297310 DOI: 10.1007/s12539-015-0111-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2014] [Revised: 11/17/2014] [Accepted: 12/25/2014] [Indexed: 01/14/2023]
Abstract
Thiopurine methyltransferase (TPMT) is a cytoplasmic transmethylase present in both prokaryotes and eukaryotes. In humans, it shows its presence in almost all of the tissues, predominantly in liver and kidney. TPMT is one of the important metabolic enzymes of phase II metabolic pathway and catalyzes methylation of thiopurine drugs such as azathioprine, 6-thioguanine and 6-mercaptopurine, which are used to treat patients with neoplasia and autoimmune disease as well as transplant recipients. In this sense, TPMT acts as shield against toxic effect of these drugs. Pharmacogenomic studies revealed that genetic polymorphism in TPMT is responsible for variable and, in some cases, adverse drug reaction. Those human groups who carry variants of TPMT (i.e., [Formula: see text], [Formula: see text], [Formula: see text]) are at high risk, because they are unable to metabolize thiopurine drugs thus becoming a weakness of patients against these drugs. Keeping in the mind the importance of TPMT, this review discusses the existence and distribution of various TPMT variants throughout different ethnic groups and risk of adverse drug reactions to them, and how they can avoid this risk of side effects. The review also highlighted factors responsible for variable reactions of TPMT, how this TPMT polymorphism can be considered in drug designing process to avoid toxic effects, designing precautions against them and more importantly designing personalized medicine.
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Roberts RL, Barclay ML. Update on thiopurine pharmacogenetics in inflammatory bowel disease. Pharmacogenomics 2015; 16:891-903. [PMID: 26067482 DOI: 10.2217/pgs.15.29] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Azathioprine and 6-mercaptopurine remain pivotal therapies for the maintenance of disease remission in patients with Crohn's disease and ulcerative colitis. While thiopurine S-methyltransferase deficiency was the first pharmacogenetic phenomenon to be recognized to influence thiopurine toxicity and reliably predict leukopenia, it does not predict other adverse effects, nor does it explain most cases of thiopurine resistance. In recent years, a number of other genetic polymorphisms have received increasing attention in the literature. In particular, SNPs in NUDT15 and in the class II HLA locus have been shown to predict thiopurine-related leukopenia and pancreatitis. The aim of this review is to provide a concise update of genetic variability which may influence patient response to azathioprine and 6-mercaptopurine.
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Affiliation(s)
- Rebecca L Roberts
- Department of Surgical Sciences, Dunedin School of Medicine, PO Box 56, Dunedin, New Zealand
| | - Murray L Barclay
- Department of Medicine, University of Otago Christchurch, PO Box 4345, Christchurch, New Zealand.,Department of Gastroenterology, Christchurch Hospital, Private Bag 4710, Christchurch, New Zealand
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Shu WY, Li JL, Wang XD, Huang M. Pharmacogenomics and personalized medicine: a review focused on their application in the Chinese population. Acta Pharmacol Sin 2015; 36:535-43. [PMID: 25891088 DOI: 10.1038/aps.2015.10] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2014] [Accepted: 01/21/2015] [Indexed: 12/22/2022] Open
Abstract
The field of pharmacogenomics was initiated in the 1950s and began to thrive after the completion of the human genome project 10 years ago. Thus far, more than 100 drug labels and clinical guidelines referring to pharmacogenomic biomarkers have been published, and several key pharmacogenomic markers for either drug safety or efficacy have been identified and subsequently adopted in clinical practice as pre-treatment genetic tests. However, a tremendous variation of genetic backgrounds exists between different ethnic groups. The application of pharmacogenomics in the Chinese population is still a long way off, since the published guidelines issued by the organizations such as US Food and Drug Administration require further confirmation in the Chinese population. This review highlights important pharmacogenomic discoveries in the Chinese population and compares the Chinese population with other nations regarding the pharmacogenomics of five most commonly used drugs, ie, tacrolimus, cyclosporine A, warfarin, cyclophosphamide and azathioprine.
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Single nucleotide polymorphism and its dynamics for pharmacogenomics. Interdiscip Sci 2014; 6:85-92. [PMID: 25172446 DOI: 10.1007/s12539-013-0007-x] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2013] [Revised: 06/04/2013] [Accepted: 12/17/2014] [Indexed: 12/18/2022]
Abstract
Pharmacogenomics is the study of how the genetic makeup determines the response to a therapeutic intervention. It has the capability to revolutionize the practice of medicine by personalized approach for treatment through the use of novel diagnostic tools. Pharmacogenomic based approaches reduce the trial-and-error approach and restrict the exposure of patients to those drugs which are not effective or are toxic for them. Single Nucleotide Polymorphisms (SNPs) hold the key in defining the risk of an individual's susceptibility to various illnesses and response to drugs. There is an ongoing process of identifying the common, biologically relevant SNPs, in particular those that are associated with the risk of disease and adverse drug reaction. The identification and characterization of these SNPs are necessary before their use as genetic tools. Most of the ongoing SNP related studies are biased deliberately towards coding regions and the data generated from them are therefore unlikely to reflect genome wide distribution of SNPs. To avoid this biasing towards the coding regions SNP, SNP consortium protocol was designed. Though, projects like the HapMap increase credibility and use of SNPs, still there are some concern like the required sample (patient) sizes, the number of SNPs required for mapping, number of association studies, the cost of SNP genotyping, and the interpretation and explanation of results are some of the challenges that surround this field.
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New genetic biomarkers predicting azathioprine blood concentrations in combination therapy with 5-aminosalicylic acid. PLoS One 2014; 9:e95080. [PMID: 24762746 PMCID: PMC3999094 DOI: 10.1371/journal.pone.0095080] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2013] [Accepted: 03/23/2014] [Indexed: 01/29/2023] Open
Abstract
BACKGROUND AND AIMS Azathioprine (AZA) is widely used for the treatment of inflammatory bowel disease (IBD) patients. AZA is catabolized by thiopurine S-methyltransferase (TPMT), which exhibits genetic polymorphisms. It has also been reported that 5-aminosalicylic acid (5-ASA) inhibits TPMT activity, and that increased 6-thioguanine nucleotide (6-TGN, a metabolite of AZA) blood concentrations result in an increased number of ADRs. In this study, single nucleotide polymorphisms (SNPs) related to differential gene expression affecting AZA drug metabolism in combination therapy with 5-ASA were examined. METHODS To identify genetic biomarkers for the prediction of 6-TGN blood concentration, ExpressGenotyping analysis was used. ExpressGenotyping analysis is able to detect critical pharmacogenetic SNPs by analyzing drug-induced expression allelic imbalance (EAI) of premature RNA in HapMap lymphocytes. We collected blood samples on 38 patients with inflammatory bowel disease treated with AZA and corroboration of the obtained SNPs was attempted in clinical samples. RESULTS A large number of SNPs with AZA/5-ASA-induced EAI within the investigated HapMap lymphocytes was identified by ExpressGenotyping analysis. The respective SNPs were analyzed in IBD patients' blood samples. Among these SNPs, several that have not yet been described to be induced by AZA/5-ASA were found. SNPs within SLC38A9 showed a particular correlation with patients' 6-TGN blood concentrations. CONCLUSIONS Based on these results, ExpressGenotyping analysis and genotyping of patients appears to be a useful way to identify inter-individual differences in drug responses and ADRs to AZA/5-ASA. This study provides helpful information on genetic biomarkers for optimized AZA/5-ASA treatment of IBD patients.
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Lennard L, Cartwright CS, Wade R, Richards SM, Vora A. Thiopurine methyltransferase genotype-phenotype discordance and thiopurine active metabolite formation in childhood acute lymphoblastic leukaemia. Br J Clin Pharmacol 2014; 76:125-36. [PMID: 23252716 DOI: 10.1111/bcp.12066] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2012] [Accepted: 12/09/2012] [Indexed: 12/14/2022] Open
Abstract
AIMS In children with acute lymphoblastic leukaemia (ALL) bone marrow activity can influence red blood cell (RBC) kinetics, the surrogate tissue for thiopurine methyltransferase (TPMT) measurements. The aim of this study was to investigate TPMT phenotype-genotype concordance in ALL, and the influence of TPMT on thiopurine metabolite formation. METHODS We measured TPMT (activity, as units ml(-1) packed RBCs and genotype) at diagnosis (n = 1150) and TPMT and thioguanine nucleotide (TGN) and methylmercaptopurine nucleotide (MeMPN) metabolites (pmol/8 × 10(8) RBCs) during chemotherapy (n = 1131) in children randomized to thioguanine or mercaptopurine on the United Kingdom trial ALL97. RESULTS Median TPMT activity at diagnosis (8.5 units) was significantly lower than during chemotherapy (13.8 units, median difference 5.1 units, 95% confidence interval (CI) 4.8, 5.4, P < 0.0001). At diagnosis genotype-phenotype was discordant. During chemotherapy the overall concordance was 92%, but this fell to 55% in the intermediate activity cohort (45% had wild-type genotypes). For both thiopurines TGN concentrations differed by TPMT status. For mercaptopurine, median TGNs were higher in TPMT heterozygous genotype (754 pmol) than wild-type (360 pmol) patients (median difference 406 pmol, 95% CI 332, 478, P < 0.0001), whilst median MeMPNs, products of the TPMT reaction, were higher in wild-type (10 650 pmol) than heterozygous patients (3868 pmol) (P < 0.0001). In TPMT intermediate activity patients with a wild-type genotype, TGN (median 366 pmol) and MeMPN (median 8590 pmol) concentrations were similar to those in wild-type, high activity patients. CONCLUSIONS In childhood ALL, TPMT activity should not be used to predict heterozygosity particularly in blood samples obtained at disease diagnosis. Genotype is a better predictor of TGN accumulation during chemotherapy.
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Affiliation(s)
- Lynne Lennard
- Clinical Pharmacology Unit, Department of Human Metabolism, University of Sheffield, Sheffield, UK.
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Abstract
The drug-metabolizing enzyme thiopurine methyltransferase (TPMT) has become one of the best examples of pharmacogenomics to be translated into routine clinical practice. TPMT metabolizes the thiopurines 6-mercaptopurine, 6-thioguanine, and azathioprine, drugs that are widely used for treatment of acute leukemias, inflammatory bowel diseases, and other disorders of immune regulation. Since the discovery of genetic polymorphisms in the TPMT gene, many sequence variants that cause a decreased enzyme activity have been identified and characterized. Increasingly, to optimize dose, pretreatment determination of TPMT status before commencing thiopurine therapy is now routine in many countries. Novel TPMT sequence variants are currently numbered sequentially using PubMed as a source of information; however, this has caused some problems as exemplified by two instances in which authors' articles appeared on PubMed at the same time, resulting in the same allele numbers given to different polymorphisms. Hence, there is an urgent need to establish an order and consensus to the numbering of known and novel TPMT sequence variants. To address this problem, a TPMT nomenclature committee was formed in 2010, to define the nomenclature and numbering of novel variants for the TPMT gene. A website (http://www.imh.liu.se/tpmtalleles) serves as a platform for this work. Researchers are encouraged to submit novel TPMT alleles to the committee for designation and reservation of unique allele numbers. The committee has decided to renumber two alleles: nucleotide position 106 (G>A) from TPMT*24 to TPMT*30 and position 611 (T>C, rs79901429) from TPMT*28 to TPMT*31. Nomenclature for all other known alleles remains unchanged.
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Fareed M, Afzal M. Single nucleotide polymorphism in genome-wide association of human population: A tool for broad spectrum service. EGYPTIAN JOURNAL OF MEDICAL HUMAN GENETICS 2013. [DOI: 10.1016/j.ejmhg.2012.08.001] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
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Benkov K, Lu Y, Patel A, Rahhal R, Russell G, Teitelbaum J. Role of thiopurine metabolite testing and thiopurine methyltransferase determination in pediatric IBD. J Pediatr Gastroenterol Nutr 2013; 56:333-40. [PMID: 23287804 DOI: 10.1097/mpg.0b013e3182844705] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Thiopurines have been used in inflammatory bowel disease (IBD) for >30 years, and measurements of both thiopurine methyltransferase (TPMT) and thiopurine (TP) metabolites, 6-thioguanine nucleotides (6-TGN) and 6-methylmercaptopurine (6-MMP), have been readily available. The North American Society for Pediatric Gastroenterology, Hepatology, and Nutrition (NASPGHAN) Committee on Inflammatory Bowel Disease thought it appropriate to review the present indications for use of TPMT and TP metabolite testing. Substantial evidence demonstrates that TP therapy is useful for both Crohn disease and ulcerative colitis. Review of the existing data yielded the following recommendations. TPMT testing is recommended before initiation of TPs to identify individuals who are homozygote recessive or have extremely low TPMT activity, with the latter having more reliability than the former. Individuals who are homozygous recessive or have extremely low TPMT activity should avoid the use of TPs because of concerns for significant leukopenia. TMPT testing does not predict all cases of leukopenia and has no value to predict hypersensitivity adverse effects such as pancreatitis. Any potential value to reduce the risk of malignancy has not been studied. All individuals taking TPs should have routine monitoring with complete blood cell count and white blood cell count differential to evaluate for leukopenia regardless of TPMT testing results. Metabolite testing can be used to determine adherence with TP therapy. Metabolite testing can be used to guide dose increases or modifications in patients with active disease. Consideration would include either increasing the dose, changing therapy or for those with elevated transaminases or an elevated 6-MMP, using adjunctive allopurinol to help raise 6-thioguanine metabolites and suppress formation of 6-MMP. Routine and repetitive metabolite testing has little or no role in patients who are doing well and taking an acceptable dose of a TP.
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Affiliation(s)
- Keith Benkov
- Mount Sinai School of Medicine, New York, NY 10029, USA.
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Skrzypczak-Zielinska M, Borun P, Milanowska K, Jakubowska-Burek L, Zakerska O, Dobrowolska-Zachwieja A, Plawski A, Froster UG, Szalata M, Slomski R. High-resolution melting analysis of the TPMT gene: a study in the Polish population. Genet Test Mol Biomarkers 2012; 17:153-9. [PMID: 23252704 DOI: 10.1089/gtmb.2012.0192] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The thiopurine S-methyltransferase (TPMT) gene encoding thiopurine methyltransferase is a crucial enzyme in metabolism of thiopurine drugs: azathioprine and 6-mercoptopurine, which are used in the treatment of leukemia or inflammatory bowel diseases. Genetic polymorphism of the TPMT gene correlates with activity of this enzyme, individual reaction, and dosing of thiopurines. Thirty-one variants of the TPMT gene with low enzymatic activity have been described with three major alleles: TPMT*2 (c.238G>C), *3A (c.460 G>A, c.719A>G), and *3C (c.719A>G), accounting for 80% to 95% of inherited TPMT deficiency in different populations in the world. The aim of the study was to establish a rapid and highly sensitive method of analysis for the complete coding sequence of the TPMT gene and to determine the spectrum and prevalence of the TPMT gene sequence variations in the Polish population. Recently, high-resolution melting analysis (HRMA) has become a highly sensitive, automated, and economical technique for mutation screening or genotyping. We applied HRMA for the first time to TPMT gene scanning. In total, we analyzed 548 alleles of the Polish population. We found 11 different sequence variations, where two are novel changes: c.200T>C (p.P67S, TPMT*30) and c.595G>A (p.V199I, TPMT*31). Detection of these new rare alleles TPMT*30 and *31 in the Polish population suggests the need to analyze the whole TPMT gene and maybe also the extension of routinely used tests containing three major alleles, TPMT*2, *3A, and *3C. Identification of sequence variants using HRMA is highly sensitive and less time consuming compared to standard sequencing. We conclude that HRMA can be easy integrated into genetic testing of the TPMT gene in patients treated with thiopurines.
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Ouerhani S, Cherif N, Bahri I, Safra I, Menif S, Abbes S. Genetic polymorphisms of NQO1, CYP1A1 and TPMT and susceptibility to acute lymphoblastic leukemia in a Tunisian population. Mol Biol Rep 2012; 40:1307-14. [PMID: 23065291 DOI: 10.1007/s11033-012-2174-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2012] [Accepted: 10/08/2012] [Indexed: 12/01/2022]
Abstract
Acute lymphoblastic leukemia (ALL) is the major pediatric cancer in developed countries. The etiology of ALL remains poorly understood, with few established environmental risk factors. These risks were influenced by co-inheritance of multiple low-risk genetic polymorphisms such as variants within cytochrome P450A1 (CYP1A1), NADPH: quinone oxidoreductase (NQO1) and Thiopurine methyltransferase (TPMT) genes. In this work, we conduct a case-control study to assess the impact of CYP1A1*2A (CYP1A1 T6235C); NQO1*2 (NQO1 C609T); TPMT*2 (TPMT G238C) and TPMT A719G polymorphisms on the risk of developing ALL. The frequencies of TPMT*2, TPMT A719G, NQO1*2 and CYP1A1*2 variants were examined in 100 patients with ALL and 106 healthy controls by allele specific PCR and/or PCR-RFLP methods using blood samples. We have found that NQO1 609CT genotype was overrepresented in patients and was associated with an aggravating effect compared to the reference group with NQO1 609CC genotype (p = 0.028, OR = 1.41; CI 95 %: 1.04-1.93). However, TPMT*2, TPMT 719*G and CYP1A1*2 variants did not appear to influence ALL susceptibility (p > 0.05). Moreover we have not found a significant correlation between the studied variants and Bcr-Abl transcript. In conclusion we retain that leukemogenesis of ALL is associated with carcinogens metabolism and consequently related to environmental exposures.
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Affiliation(s)
- Slah Ouerhani
- Laboratory of Molecular and Cellular Haematology, Pasteur Institute of Tunis, University of Tunis El Manar, Tunis, Tunisia.
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49
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Wennerstrand P, Dametto P, Hennig J, Klingstedt T, Skoglund K, Lindqvist Appell M, Mårtensson LG. Structural Characteristics Determine the Cause of the Low Enzyme Activity of Two Thiopurine S-Methyltransferase Allelic Variants: A Biophysical Characterization of TPMT*2 and TPMT*5. Biochemistry 2012; 51:5912-20. [DOI: 10.1021/bi300377d] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Patricia Wennerstrand
- Department of Physics, Chemistry,
and Biology, Linköping University, SE-581 83 Linköping, Sweden
| | - Paolo Dametto
- Department of Physics, Chemistry,
and Biology, Linköping University, SE-581 83 Linköping, Sweden
| | - Janosch Hennig
- Division of Molecular Biotechnology, Department of Physics, Chemistry,
and Biology, Linköping University, SE-581 83 Linköping, Sweden
| | - Therése Klingstedt
- Department of Physics, Chemistry,
and Biology, Linköping University, SE-581 83 Linköping, Sweden
| | - Karin Skoglund
- Division of Drug Research/Clinical Pharmacology, Department of Medical
and Health Sciences, Faculty of Health Sciences, Linköping University, SE-581 83 Linköping, Sweden
| | - Malin Lindqvist Appell
- Division of Drug Research/Clinical Pharmacology, Department of Medical
and Health Sciences, Faculty of Health Sciences, Linköping University, SE-581 83 Linköping, Sweden
| | - Lars-Göran Mårtensson
- Department of Physics, Chemistry,
and Biology, Linköping University, SE-581 83 Linköping, Sweden
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50
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Gastal GR, Moreira S, Noble CF, Ferreira LE, França PHCD, Pinho M. Toxicity of azathioprine: why and when? analysis of the prevalence of polymorphism in Joinville, SC, Brazil. ARQUIVOS DE GASTROENTEROLOGIA 2012; 49:130-4. [DOI: 10.1590/s0004-28032012000200007] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2011] [Accepted: 11/30/2011] [Indexed: 11/22/2022]
Abstract
CONTEXT: The use of thiopurine drugs such as azathioprine and 6-mercaptopurine has become quite common in the treatment of inflammatory bowel disease, transplantation and acute leukemias. Despite their effectiveness, these drugs are capable of causing drug-induced toxicity with the risk of death by myelosuppression. It is now known that these complications occur because of genetic polymorphisms of the thiopurinemethyltransferase (TPMT) enzyme, responsible for its metabolism. OBJECTIVE: To assess the prevalence of thiopurine methyltransferase polymorphisms in the population of Joinville, SC, Brazil. METHODS: We analyzed the frequency of four main allelic variants of the TPMT gene in 199 blood donors from Joinville, from February to April 2010. RESULTS: The normal allele ("wild-type") was found in 93.9% of subjects studied. TPMT variants were detected in 12 subjects (6.03%). CONCLUSIONS: From this study, it was estimated at 6% the risk of toxicity by the administration of azathioprine and 6-mercaptopurine to patients in Joinville.
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