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Šmid A, Štajdohar M, Milek M, Urbančič D, Karas Kuželički N, Tamm R, Metspalu A, Mlinarič-Raščan I. Transcriptome analysis reveals involvement of thiopurine S-methyltransferase in oxidation-reduction processes. Eur J Pharm Sci 2024; 192:106616. [PMID: 37865284 DOI: 10.1016/j.ejps.2023.106616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 10/18/2023] [Accepted: 10/18/2023] [Indexed: 10/23/2023]
Abstract
Thiopurine S-methyltransferase (TPMT) is an important enzyme involved in the deactivation of thiopurines and represents a major determinant of thiopurine-related toxicities. Despite its well-known importance in thiopurine metabolism, the understanding of its endogenous role is lacking. In the present study, we aimed to gain insight into the molecular processes involving TPMT by applying a data fusion approach to analyze whole-genome expression data. The RNA profiling was done on whole blood samples from 1017 adult male and female donors to the Estonian biobank using Illumina HTv3 arrays. Our results suggest that TPMT is closely related to genes involved in oxidoreductive processes. The in vitro experiments on different cell models confirmed that TPMT influences redox capacity of the cell by altering S-adenosylmethionine (SAM) consumption and consequently glutathione (GSH) synthesis. Furthermore, by comparing gene networks of subgroups of individuals, we identified genes, which could have a role in regulating TPMT activity. The biological relevance of identified genes and pathways will have to be further evaluated in molecular studies.
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Affiliation(s)
- Alenka Šmid
- Department of Clinical Biochemistry, Faculty of Pharmacy, University of Ljubljana, Slovenia.
| | | | - Miha Milek
- Department of Clinical Biochemistry, Faculty of Pharmacy, University of Ljubljana, Slovenia; Core Unit Bioinformatics, Berlin Institute of Health at Charite, Germany
| | - Dunja Urbančič
- Department of Clinical Biochemistry, Faculty of Pharmacy, University of Ljubljana, Slovenia
| | - Nataša Karas Kuželički
- Department of Clinical Biochemistry, Faculty of Pharmacy, University of Ljubljana, Slovenia
| | - Riin Tamm
- Estonian Genome Center, Institute of Genomics and Institute of Molecular and Cell Biology, University of Tartu, Estonia; Youth and Talent Policy Department, Estonian Ministry of Education and Research, Estonia
| | - Andres Metspalu
- Estonian Genome Center, Institute of Genomics and Institute of Molecular and Cell Biology, University of Tartu, Estonia
| | - Irena Mlinarič-Raščan
- Department of Clinical Biochemistry, Faculty of Pharmacy, University of Ljubljana, Slovenia.
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Selvestrel D, Stocco G, Aloi M, Arrigo S, Cardile S, Cecchin E, Congia M, Curci D, Gatti S, Graziano F, Langefeld CD, Lucafò M, Martelossi S, Martinelli M, Pagarin S, Scarallo L, Stacul EF, Strisciuglio C, Thompson S, Zuin G, Decorti G, Bramuzzo M. DNA methylation of the TPMT gene and azathioprine pharmacokinetics in children with very early onset inflammatory bowel disease. Biomed Pharmacother 2023; 157:113901. [PMID: 36462311 DOI: 10.1016/j.biopha.2022.113901] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 10/12/2022] [Accepted: 10/17/2022] [Indexed: 12/05/2022] Open
Abstract
BACKGROUND Thiopurine methyltransferase (TPMT) is a crucial enzyme for azathioprine biotransformation and its activity is higher in very early onset inflammatory bowel disease (VEO-IBD) patients than in adolescents with IBD (aIBD). AIMS The aims of this pharmacoepigenetic study were to evaluate differences in peripheral blood DNA methylation of the TPMT gene and in azathioprine pharmacokinetics in patients with VEO-IBD compared to aIBD. METHODS The association of age with whole genome DNA methylation profile was evaluated in a pilot group of patients and confirmed by a meta-analysis on 3 cohorts of patients available on the public functional genomics data repository. Effects of candidate CpG sites in the TPMT gene were validated in a larger cohort using pyrosequencing. TPMT activity and azathioprine metabolites (TGN) were measured in patients' erythrocytes by HPLC and associated with patients' age group and TPMT DNA methylation. RESULTS Whole genome DNA methylation pilot analysis, combined with the meta-analysis revealed cg22736354, located on TPMT downstream neighboring region, as the only statistically significant CpG whose methylation increases with age, resulting lower in VEO-IBD patients compared to aIBD (median 9.6% vs 12%, p = 0.029). Pyrosequencing confirmed lower cg22736354 methylation in VEO-IBD patients (median 4.0% vs 6.0%, p = 4.6 ×10-5). No differences in TPMT promoter methylation were found. Reduced cg22736354 methylation was associated with lower TGN concentrations (rho = 0.31, p = 0.01) in patients with VEO-IBD and aIBD. CONCLUSION Methylation of cg22736354 in TPMT gene neighborhood is lower in patients with VEO-IBD and is associated with reduced azathioprine inactivation and increased TGN concentrations.
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Affiliation(s)
| | - Gabriele Stocco
- Institute for Maternal and Child Health, IRCCS "Burlo Garofolo", Trieste, Italy; Department of Medical, Surgical and Health Sciences, University of Trieste, Trieste, Italy
| | - Marina Aloi
- Women's and Children's Health Department, Pediatric Gastroenterology and Hepatology Unit, Sapienza University of Rome, Rome, Italy
| | - Serena Arrigo
- Pediatric Gastroenterology and Endoscopy Unit, Institute 'Giannina Gaslini', Genoa, Italy
| | - Sabrina Cardile
- Hepatology and Gastroenterology Unit, Bambino Gesù Hospital, Rome, Italy
| | - Erika Cecchin
- Experimental and Clinical Pharmacology, Centro di Riferimento Oncologico di Aviano (CRO) IRCCS, Aviano, Italy
| | - Mauro Congia
- Pediatric Clinic and Rare Diseases, Microcitemic Pediatric Hospital Antonio Cao, Azienda Ospedaliera Brotzu, Cagliari, Italy
| | - Debora Curci
- Institute for Maternal and Child Health, IRCCS "Burlo Garofolo", Trieste, Italy
| | - Simona Gatti
- Department of Pediatrics, Università Politecnica delle Marche, Ancona, Italy
| | | | - Carl D Langefeld
- Department of Biostatistics and Data Science, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Marianna Lucafò
- Department of Medical, Surgical and Health Sciences, University of Trieste, Trieste, Italy
| | | | - Massimo Martinelli
- Department of Translational Medical Science, Section of Pediatrics, University of Naples "Federico II", Naples, Italy
| | - Sofia Pagarin
- Department of Medical, Surgical and Health Sciences, University of Trieste, Trieste, Italy
| | - Luca Scarallo
- University of Florence-Meyer Hospital, Florence, Italy
| | | | - Caterina Strisciuglio
- Departement of Woman, Child and General and Specialistic Surgery, University of Campania "Luigi Vanvitelli", Naples, Italy
| | - Susan Thompson
- Cincinnati Children's Hospital Medical Center, University of Cincinnati, Cincinnati, OH, USA
| | - Giovanna Zuin
- Department of Pediatrics, University of Milano-Bicocca, Foundation MBBM/San Gerardo Hospital, Monza, Italy
| | - Giuliana Decorti
- Institute for Maternal and Child Health, IRCCS "Burlo Garofolo", Trieste, Italy; Department of Medical, Surgical and Health Sciences, University of Trieste, Trieste, Italy.
| | - Matteo Bramuzzo
- Gastroenterology, Digestive Endoscopy and Nutrition Unit, Institute for Maternal and Child Health - IRCCS "Burlo Garofolo", Trieste, Italy
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Franca R, Braidotti S, Stocco G, Decorti G. Understanding thiopurine methyltransferase polymorphisms for the targeted treatment of hematologic malignancies. Expert Opin Drug Metab Toxicol 2021; 17:1187-1198. [PMID: 34452592 DOI: 10.1080/17425255.2021.1974398] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
INTRODUCTION Thiopurine methyltransferase (TPMT) catalyzes the S-methylation of thiopurines (mercaptopurine (MP) and tioguanine (TG)), chemotherapeutic agents used in the treatment of acute lymphoblastic leukemia (ALL). Polymorphisms in TPMT gene encode diminished activity enzyme, enhancing accumulation of active metabolites, and partially explaining the inter-individual differences in patients' clinical response. AREAS COVERED This review gives an overview on TPMT gene and function, and discusses the pharmacogenomic implications of TPMT variants in the prevention of severe thiopurine-induced hematological toxicities and the less known implication on TG-induced sinusoidal obstruction syndrome. Additional genetic and non-genetic factors impairing TPMT activity are considered. Literature search was done in PubMed for English articles published since1990, and on PharmGKB. EXPERT OPINION To titrate thiopurines safely and effectively, achieve the right degree of lymphotoxic effect and avoid excessive myelosuppression, the optimal management will combine a preemptive TPMT genotyping to establish a safe initial dose with a close phenotypic monitoring of TPMT activity and/or of active metabolites during long-term treatment. Compared to current ALL protocols, replacement of TG by MP during reinduction phase in TPMT heterozygotes and novel individualized TG regimens in maintenance for TPMT wild-type subjects could be investigated to improve outcomes while avoiding risk of severe hepatotoxicity.
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Affiliation(s)
- R Franca
- Department of Medical, Surgical and Health Sciences, University of Trieste, Trieste, Italy
| | - S Braidotti
- Department of Medical, Surgical and Health Sciences, University of Trieste, Trieste, Italy
| | - G Stocco
- Department of Life Sciences, University of Trieste, Trieste, Italy
| | - G Decorti
- Department of Medical, Surgical and Health Sciences, University of Trieste, Trieste, Italy.,Institute for Maternal & Child Health (I.r.c.c.s) Burlo Garofolo, Trieste, Italy
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Han N, Oh JM, Kim IW. Combination of Genome-Wide Polymorphisms and Copy Number Variations of Pharmacogenes in Koreans. J Pers Med 2021; 11:33. [PMID: 33430289 PMCID: PMC7825650 DOI: 10.3390/jpm11010033] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 12/16/2020] [Accepted: 01/04/2021] [Indexed: 12/12/2022] Open
Abstract
For predicting phenotypes and executing precision medicine, combination analysis of single nucleotide variants (SNVs) genotyping with copy number variations (CNVs) is required. The aim of this study was to discover SNVs or common copy CNVs and examine the combined frequencies of SNVs and CNVs in pharmacogenes using the Korean genome and epidemiology study (KoGES), a consortium project. The genotypes (N = 72,299) and CNV data (N = 1000) were provided by the Korean National Institute of Health, Korea Centers for Disease Control and Prevention. The allele frequencies of SNVs, CNVs, and combined SNVs with CNVs were calculated and haplotype analysis was performed. CYP2D6 rs1065852 (c.100C>T, p.P34S) was the most common variant allele (48.23%). A total of 8454 haplotype blocks in 18 pharmacogenes were estimated. DMD ranked the highest in frequency for gene gain (64.52%), while TPMT ranked the highest in frequency for gene loss (51.80%). Copy number gain of CYP4F2 was observed in 22 subjects; 13 of those subjects were carriers with CYP4F2*3 gain. In the case of TPMT, approximately one-half of the participants (N = 308) had loss of the TPMT*1*1 diplotype. The frequencies of SNVs and CNVs in pharmacogenes were determined using the Korean cohort-based genome-wide association study.
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Affiliation(s)
| | | | - In-Wha Kim
- College of Pharmacy and Research Institute of Pharmaceutical Sciences, Seoul National University, Seoul 08826, Korea; (N.H.); (J.M.O.)
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Burgueño-Rodríguez G, Méndez Y, Olano N, Dabezies A, Bertoni B, Souto J, Castillo L, da Luz J, Soler AM. Ancestry and TPMT-VNTR Polymorphism: Relationship with Hematological Toxicity in Uruguayan Patients with Acute Lymphoblastic Leukemia. Front Pharmacol 2020; 11:594262. [PMID: 33424606 PMCID: PMC7789872 DOI: 10.3389/fphar.2020.594262] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Accepted: 09/24/2020] [Indexed: 12/14/2022] Open
Abstract
6-Mercaptopurine (6-MP) is a thiopurine drug widely used in childhood acute lymphoblastic leukemia (ALL) therapy. Genes such as TPMT and NUDT15 have an outstanding role in 6-MP metabolism. Mutations in both genes explain a significant portion of hematological toxicities suffered by ALL Uruguayan pediatric patients. A variable number tandem repeat in the TPMT promoter (TPMT-VNTR) has been associated with TPMT expression. This VNTR has a conservative architecture (AnBmC). To explore new causes of hematological toxicities related to ALL therapy, we genotyped the TPMT-VNTR of 130 Uruguayan pediatric patients. Additionally, individual genetic ancestry was estimated by 45 ancestry-informative markers (AIMs). Hematological toxicity was measured as the number of leukopenia events and 6-MP dose along the maintenance phase. As previously reported, we found TPMT*2 and TPMT*3C alleles were associated to TPMT-VNTR A2BC and AB2C, respectively. However, contrasting with other reports, TPMT*3A allele was found in a heterogeneous genetic background in linkage equilibrium. Patients carrying more than 5 A repeats present a significant higher number of leukopenia events among patients without TPMT and/or NUDT15 variants. Native American ancestry and the number of A repeats were significantly correlated with the number of leukopenia events. However, the correlation between Native American ancestry and the number of leukopenia events was lost when the number of A repeats was considered as covariate. This suggests that TPMT-VNTR alleles are more relevant than Native American ancestry in the hematological toxicity. Our results emphasize that TPMT-VNTR may be used as a pharmacogenetic biomarker to predict 6-MP-related hematological toxicity in ALL childhood therapy.
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Affiliation(s)
- Gabriela Burgueño-Rodríguez
- Laboratorio de Genética Molecular Humana, Centro Universitario Regional (CENUR) Litoral Norte-Sede Salto, Universidad de la República (UdelaR), Salto, Uruguay
| | - Yessika Méndez
- Servicio Hemato Oncológico Pediátrico (SHOP), Centro Hospitalario Pereira Rossell (CHPR), Montevideo, Uruguay
| | - Natalia Olano
- Servicio Hemato Oncológico Pediátrico (SHOP), Centro Hospitalario Pereira Rossell (CHPR), Montevideo, Uruguay
| | - Agustín Dabezies
- Servicio Hemato Oncológico Pediátrico (SHOP), Centro Hospitalario Pereira Rossell (CHPR), Montevideo, Uruguay
| | - Bernardo Bertoni
- Departamento de Genética, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - Jorge Souto
- Departamento de Genética, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - Luis Castillo
- Servicio Hemato Oncológico Pediátrico (SHOP), Centro Hospitalario Pereira Rossell (CHPR), Montevideo, Uruguay
| | - Julio da Luz
- Laboratorio de Genética Molecular Humana, Centro Universitario Regional (CENUR) Litoral Norte-Sede Salto, Universidad de la República (UdelaR), Salto, Uruguay
| | - Ana María Soler
- Laboratorio de Genética Molecular Humana, Centro Universitario Regional (CENUR) Litoral Norte-Sede Salto, Universidad de la República (UdelaR), Salto, Uruguay
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Comprehensive study of thiopurine methyltransferase genotype, phenotype, and genotype-phenotype discrepancies in Sweden. Biochem Pharmacol 2019; 164:263-272. [PMID: 31005613 DOI: 10.1016/j.bcp.2019.04.020] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Accepted: 04/17/2019] [Indexed: 12/16/2022]
Abstract
Thiopurines are widely used in the treatment of leukemia and inflammatory bowel diseases. Thiopurine metabolism varies among individuals because of differences in the polymorphic enzyme thiopurine methyltransferase (TPMT, EC 2.1.1.67), and to avoid severe adverse reactions caused by incorrect dosing it is recommended that the patient's TPMT status be determined before the start of thiopurine treatment. This study describes the concordance between genotyping for common TPMT alleles and phenotyping in a Swedish cohort of 12,663 patients sampled before or during thiopurine treatment. The concordance between TPMT genotype and enzyme activity was 94.5%. Compared to the genotype, the first measurement of TPMT enzyme activity was lower than expected for 4.6% of the patients. Sequencing of all coding regions of the TPMT gene in genotype/phenotype discrepant individuals led to the identification of rare and novel TPMT alleles. Fifteen individuals (0.1%) with rare or novel genotypes were identified, and three TPMT alleles (TPMT*42, *43, and *44) are characterized here for the first time. These 15 patients would not have been detected as carrying a deviating TPMT genotype if only genotyping of the most common TPMT variants had been performed. This study highlights the benefit of combining TPMT genotype and phenotype determination in routine testing. More accurate dose recommendations can be made, which might decrease the number of adverse reactions and treatment failures during thiopurine treatment.
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