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Taylor ZL, Vang J, Lopez-Lopez E, Oosterom N, Mikkelsen T, Ramsey LB. Systematic Review of Pharmacogenetic Factors That Influence High-Dose Methotrexate Pharmacokinetics in Pediatric Malignancies. Cancers (Basel) 2021; 13:cancers13112837. [PMID: 34200242 PMCID: PMC8201112 DOI: 10.3390/cancers13112837] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 05/27/2021] [Accepted: 06/02/2021] [Indexed: 02/07/2023] Open
Abstract
Methotrexate (MTX) is a mainstay therapeutic agent administered at high doses for the treatment of pediatric and adult malignancies, such as acute lymphoblastic leukemia, osteosarcoma, and lymphoma. Despite the vast evidence for clinical efficacy, high-dose MTX displays significant inter-individual pharmacokinetic variability. Delayed MTX clearance can lead to prolonged, elevated exposure, causing increased risks for nephrotoxicity, mucositis, seizures, and neutropenia. Numerous pharmacogenetic studies have investigated the effects of several genes and polymorphisms on MTX clearance in an attempt to better understand the pharmacokinetic variability and improve patient outcomes. To date, several genes and polymorphisms that affect MTX clearance have been identified. However, evidence for select genes have conflicting results or lack the necessary replication and validation needed to confirm their effects on MTX clearance. Therefore, we performed a systematic review to identify and then summarize the pharmacogenetic factors that influence high-dose MTX pharmacokinetics in pediatric malignancies. Using the PRISMA guidelines, we analyzed 58 articles and 24 different genes that were associated with transporter pharmacology or the folate transport pathway. We conclude that there is only one gene that reliably demonstrates an effect on MTX pharmacokinetics: SLCO1B1.
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Affiliation(s)
- Zachary L. Taylor
- Department of Pharmacology and Systems Physiology, University of Cincinnati, Cincinnati, OH 45267, USA;
- Division of Research in Patient Services, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229, USA
- Division of Clinical Pharmacology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Jesper Vang
- Department of Health Technology, Technical University of Denmark, 2800 Lyngby, Denmark;
- Paediatric Oncology Research Laboratory, University Hospital of Copenhagen, Rigshospitalet Blegdamsvej 9, 2100 Copenhagen, Denmark
| | - Elixabet Lopez-Lopez
- Department of Genetics, Physical Anthropology and Animal Physiology, Faculty of Science and Technology, University of the Basque Country, UPV/EHU, 48940 Leioa, Spain;
- Pediatric Oncology Group, BioCruces Bizkaia Health Research Institute, 48903 Barakaldo, Spain
| | - Natanja Oosterom
- Princess Máxima Center for Pediatric Oncology, 3720 Utrecht, The Netherlands;
| | - Torben Mikkelsen
- Department of Pediatric Oncology, Aarhus University Hospital, 8200 Aarhus, Denmark;
| | - Laura B. Ramsey
- Division of Research in Patient Services, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229, USA
- Division of Clinical Pharmacology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229, USA
- Correspondence: ; Tel.: +1-513-803-8963
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Folate pathway genetic polymorphisms modulate methotrexate-induced toxicity in childhood acute lymphoblastic leukemia. Cancer Chemother Pharmacol 2019; 83:755-762. [PMID: 30684021 DOI: 10.1007/s00280-019-03776-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Accepted: 01/13/2019] [Indexed: 01/23/2023]
Abstract
BACKGROUND Acute lymphoblastic leukemia (ALL) is one of the major malignancies affecting children in Jordan. Methotrexate (MTX) is the cornerstone of chemotherapy for ALL, and works by targeting enzymes involved in the folate pathway. We hypothesize that genetic polymorphisms of the folate pathway are associated with MTX toxicity in children with ALL. METHODS A total of 64 children with ALL were included in this study; 31 (48.4%) boys and 33 (51.6%) girls aged 2-16 years. The folate pathway genes were genotyped using polymerase chain reaction followed by sequencing and studying the association between genetic polymorphisms and MTX toxicity. RESULTS The immunophenotype was B-lineage in 55 patients (85.9%) and T-lineage in nine patients (14.1%). All genetic polymorphisms, except for dihydropyrimidine dehydrogenase polymorphisms, were associated with hematological toxicities and did not appear to precipitate any non-hematological adverse events. Patients with ALL carrying dominant alleles of methylene tetrahydrofolate (MTHFR) C677T and dihydrofolate reductase 19 bp deletion were at a higher risk of developing severe leucopenia [OR (95% CI) = 4.5 (1.2-17), p = 0.03; 5.4 (1.6-17.8); p = 0.006] while minor allele carriers of MTHFR A1298C were more likely to develop neutropenia [OR (95% CI) = 6.1 (1.3-29.5); 0.04]. Furthermore, dominant allele carriers of thymidylate synthase 1494 del6 were at a higher risk of developing neutropenia [OR (95% CI) = 6 (1.2-31.1); p = 0.04]. CONCLUSION Genetic polymorphisms of the folate pathway may modulate MTX-induced toxicity in childhood ALL.
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Yao P, He X, Zhang R, Tong R, Xiao H. The influence of MTHFR genetic polymorphisms on adverse reactions after methotrexate in patients with hematological malignancies: a meta-analysis. Hematology 2018; 24:10-19. [PMID: 30024839 DOI: 10.1080/10245332.2018.1500750] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Affiliation(s)
- Pingli Yao
- School of Medicine, University of Electronic Science and Technology, Chengdu, People’s Republic of China
- Department of Pharmacy, Sichuan Academy of Medical Sciences and Sichuan Provincial People’s Hospital, Chengdu, People’s Republic of China
| | - Xia He
- Department of Pharmacy, Sichuan Academy of Medical Sciences and Sichuan Provincial People’s Hospital, Chengdu, People’s Republic of China
- Personalized Drug Therapy Key Laboratory of Sichuan Province, Chengdu, People’s Republic of China
| | - Rong Zhang
- Department of Pediatric, Sichuan Academy of Medical Sciences and Sichuan Provincial People’s Hospital, Chengdu, People’s Republic of China
| | - Rongsheng Tong
- School of Medicine, University of Electronic Science and Technology, Chengdu, People’s Republic of China
- Department of Pharmacy, Sichuan Academy of Medical Sciences and Sichuan Provincial People’s Hospital, Chengdu, People’s Republic of China
- Personalized Drug Therapy Key Laboratory of Sichuan Province, Chengdu, People’s Republic of China
| | - Hongtao Xiao
- School of Medicine, University of Electronic Science and Technology, Chengdu, People’s Republic of China
- Department of Pharmacy, Sichuan Academy of Medical Sciences and Sichuan Provincial People’s Hospital, Chengdu, People’s Republic of China
- Personalized Drug Therapy Key Laboratory of Sichuan Province, Chengdu, People’s Republic of China
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Zou R, He X, Wu Y, Tian X, You Y, Zheng M, Li W, Zou H, Liu H, Zhu X, Zhu C. TS Gene Polymorphisms Correlate with Susceptibility to Acute Lymphocytic Leukemia in Children. Med Sci Monit 2017. [PMID: 28646637 PMCID: PMC5498119 DOI: 10.12659/msm.901494] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Background Acute lymphocytic leukemia (ALL) in children is a clonal disease of bone marrow hematopoietic stem cells. This study aimed to explore the associations between MTHFR or TS genetic polymorphisms and susceptibility to acute lymphocytic leukemia (ALL) in children. Material/Methods This case-control study included 79 ALL patients (case group) and 102 non-ALL patients (control group). Post-PCR genomic DNA sequencing revealed MTHFR C677T and MTHFR A1298C genotypes and TS polymorphisms. The χ2 test was used to compare differences in MTHFR and TS polymorphisms (including genotypic and allelic distributions) between groups. Logistic regression analysis was used to determine genetic polymorphisms and ALL risk associations. Results The results indicated that TS 3R allele frequency was significantly higher in the case group than in the control group (χ2=7.45, P<0.05). The MTHFR C677T and MTHFR A1298C polymorphisms were not associated with ALL risk. Compared to the TS 2R/2R genotype, subjects carrying TS 2R/3R were twice as likely to develop ALL, and the TS 3R/3R+3R/4R genotype carried a 4-fold higher risk of developing ALL (OR=1.96, CI: 1.14–3.36). Conclusions The TS genetic polymorphisms increase the ALL risk. The TS 3R allele was a risk factor for ALL. There were no associations between MTHFR C677T or MTHFR A1298C polymorphisms and ALL susceptibility.
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Affiliation(s)
- Runyin Zou
- Department of Pediatrics, Hunan Province People's Hospital (First Affiliated Hospital of Hunan Normal University), Changsha, Hunan, China (mainland)
| | - Xiangling He
- Department of Pediatrics, Hunan Province People's Hospital (First Affiliated Hospital of Hunan Normal University), Changsha, Hunan, China (mainland)
| | - Yanpeng Wu
- Department of Pediatrics, Guangzhou Red Cross Hospital, Guangzhou, Guangdong, China (mainland)
| | - Xin Tian
- Department of Pediatrics, Hunan Province People's Hospital (First Affiliated Hospital of Hunan Normal University), Changsha, Hunan, China (mainland)
| | - Yalan You
- Department of Pediatrics, Hunan Province People's Hospital (First Affiliated Hospital of Hunan Normal University), Changsha, Hunan, China (mainland)
| | - Mincui Zheng
- Hunan Children's Hospital, Changsha, Hunan, China (mainland)
| | - Wanli Li
- Hunan Children's Hospital, Changsha, Hunan, China (mainland)
| | - Hui Zou
- Department of Pediatrics, Hunan Province People's Hospital (First Affiliated Hospital of Hunan Normal University), Changsha, Hunan, China (mainland)
| | - Hua Liu
- Department of Pediatrics, Hunan Province People's Hospital (First Affiliated Hospital of Hunan Normal University), Changsha, Hunan, China (mainland)
| | - Xiujuan Zhu
- Department of Pediatrics, Hunan Province People's Hospital (First Affiliated Hospital of Hunan Normal University), Changsha, Hunan, China (mainland)
| | - Chengguang Zhu
- Department of Pediatrics, Hunan Province People's Hospital (First Affiliated Hospital of Hunan Normal University), Changsha, Hunan, China (mainland)
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Yazıcıoğlu B, Kaya Z, Güntekin Ergun S, Perçin F, Koçak Ü, Yenicesu İ, Gürsel T. Influence of Folate-Related Gene Polymorphisms on High-Dose Methotrexate-Related Toxicity and Prognosis in Turkish Children with Acute Lymphoblastic Leukemia. Turk J Haematol 2017; 34:143-150. [PMID: 27094381 PMCID: PMC5440866 DOI: 10.4274/tjh.2016.0007] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2016] [Accepted: 03/25/2016] [Indexed: 01/26/2023] Open
Abstract
OBJECTIVE High-dose methotrexate (HD-MTX) is widely used in the consolidation phase of childhood acute lymphoblastic leukemia (ALL), but the roles that polymorphisms in folate-related genes (FRGs) play in HD-MTX toxicity and prognosis in children with ALL are not understood. The aims of this study were to investigate the frequencies of polymorphisms in the genes for thymidylate synthase (TS), methionine synthase reductase (MTRR), and methylene tetrahydrofolate reductase (MTHFR) in Turkish children with ALL and to assess associations between these polymorphisms and HD-MTX-related toxicity and leukemia prognosis in this patient group. MATERIALS AND METHODS FRG polymorphisms were assessed by real-time polymerase chain reaction. Survival status, MTX levels, and toxicity data were retrieved from 106 patients' charts. RESULTS The allele frequencies for the FRG polymorphisms were as follows: TS 2R 41.0%, 3R 57.0%, and 4R 2.0%; MTRR 66A 42.4% and 66G 57.6%; MTHFR 677C 59.3% and 677T 40.7%; and MTHFR 1298A 58.1% and 1298C 41.9%. At the 48th hour of HD-MTX infusion, serum MTX was significantly higher in patients who had TS 2R/3R/4R variants as compared to those with wild-type TS (p<0.05). No significant differences were detected with respect to event-free survival or toxicity between wild-type and other FRG variants. CONCLUSION The frequencies of FRG polymorphisms in Turkish children with ALL are similar to those reported in other Caucasian populations. This is the first published finding of the TS 3R/4R variant in the Turkish population. The results indicate that HD-MTX can be tolerated by leukemic children with some polymorphic variants of FRG; thus, it may prevent future risk of leukemic relapse.
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Affiliation(s)
| | - Zühre Kaya
- Gazi University Faculty of Medicine, Department of Pediatric Hematology, Ankara, Turkey E-mail:
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Umerez M, Gutierrez-Camino Á, Muñoz-Maldonado C, Martin-Guerrero I, Garcia-Orad A. MTHFR polymorphisms in childhood acute lymphoblastic leukemia: influence on methotrexate therapy. PHARMACOGENOMICS & PERSONALIZED MEDICINE 2017; 10:69-78. [PMID: 28392709 PMCID: PMC5376125 DOI: 10.2147/pgpm.s107047] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Methotrexate (MTX) is an important component in the therapy used to treat childhood acute lymphoblastic leukemia (ALL). Methylenetetrahydrofolate reductase (MTHFR) is a key enzyme for MTX pharmacokinetics. Two single-nucleotide polymorphisms in MTHFR gene, C677T and A1298C, affecting MTHFR activity, have been widely studied as potential markers of MTX toxicity and/or outcome in pediatric ALL. In this review, we show that the majority of published reports do not find association or present opposite effect. Therefore, MTHFR C677T and A1298C polymorphisms do not seem to be good markers of MTX-related toxicity and/or outcome in pediatric ALL. The efforts should be focused on other genes, such as transporter genes or microRNA-related genes.
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Affiliation(s)
- Maitane Umerez
- Department of Genetics, Physical Anthropology and Animal Physiology, Faculty of Medicine and Nursery, University of the Basque Country, UPV/EHU, Leioa
| | - Ángela Gutierrez-Camino
- Department of Genetics, Physical Anthropology and Animal Physiology, Faculty of Medicine and Nursery, University of the Basque Country, UPV/EHU, Leioa
| | - Carmen Muñoz-Maldonado
- Department of Genetics, Physical Anthropology and Animal Physiology, Faculty of Medicine and Nursery, University of the Basque Country, UPV/EHU, Leioa
| | - Idoia Martin-Guerrero
- Department of Genetics, Physical Anthropology and Animal Physiology, Faculty of Medicine and Nursery, University of the Basque Country, UPV/EHU, Leioa
| | - Africa Garcia-Orad
- Department of Genetics, Physical Anthropology and Animal Physiology, Faculty of Medicine and Nursery, University of the Basque Country, UPV/EHU, Leioa; BioCruces Health Research Institute, Barakaldo, Spain
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Leonardi DB, Abbate M, Riccheri MC, Nuñez M, Alfonso G, Gueron G, De Siervi A, Vazquez E, Cotignola J. Improving risk stratification of patients with childhood acute lymphoblastic leukemia: Glutathione-S-Transferases polymorphisms are associated with increased risk of relapse. Oncotarget 2017; 8:110-117. [PMID: 27058755 PMCID: PMC5352038 DOI: 10.18632/oncotarget.8606] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2015] [Accepted: 03/10/2016] [Indexed: 12/18/2022] Open
Abstract
The inclusion of genotype at Acute Lymphoblastic Leukemia (ALL) diagnosis as a genetic predictor of disease outcome is under constant study. However, results are inconclusive and seem to be population specific. We analyzed the predictive value of germline polymorphisms for childhood ALL relapse and survival. We retrospectively recruited 140 Argentine patients with de novo ALL. Genotypes were analyzed using PCR-RFLP (GSTP1 c.313A > G, MDR1 c.3435T > C, and MTHFR c.665C > T) and multiplex PCR (GSTT1 null, GSTM1 null). Patients with the GSTP1 c.313GG genotype had an increased risk for relapse in univariate (OR = 2.65, 95% CI = 1.03-6.82, p = 0.04) and multivariate (OR = 3.22, 95% CI = 1.17-8.83, p = 0.02) models. The combined genotype slightly increased risk for relapse in the univariate (OR = 2.82, 95% CI = 1.09-7.32, p = 0.03) and multivariate (OR = 2.98, 95% CI = 1.14-7.79, p = 0.03) models for patients with 2/3-risk-genotypes (GSTT1 null, GSTM1 null, GSTP1 c.313GG). The Recurrence-Free Survival (RFS) was shorter for GSTP1 c.313GG (p = 0.025) and 2/3-risk-genotypes (p = 0.021). GST polymorphisms increased the risk of relapse and RFS of patients with childhood ALL. The inclusion of these genetic markers in ALL treatment protocols might improve risk stratification and reduce the number of relapses and deaths.
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Affiliation(s)
- Daiana B. Leonardi
- Laboratorio de Inflamación y Cáncer, Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales-Universidad de Buenos Aires, IQUIBICEN-CONICET, Intendente Güiraldes 2160 (1428), CABA, Argentina
| | - Mercedes Abbate
- Laboratorio de Inflamación y Cáncer, Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales-Universidad de Buenos Aires, IQUIBICEN-CONICET, Intendente Güiraldes 2160 (1428), CABA, Argentina
| | - María C. Riccheri
- Departamento de Hematología Pediátrica, Hospital Nacional Profesor A. Posadas, Pte. Illia s/n (1684), El Palomar, Buenos Aires, Argentina
| | - Myriam Nuñez
- Departamento de Matemáticas, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Junín 954 (1113), CABA, Argentina
| | - Graciela Alfonso
- Departamento de Hematología, Hospital Nacional Profesor A. Posadas, Pte. Illia s/n (1684), El Palomar, Buenos Aires, Argentina
| | - Geraldine Gueron
- Laboratorio de Inflamación y Cáncer, Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales-Universidad de Buenos Aires, IQUIBICEN-CONICET, Intendente Güiraldes 2160 (1428), CABA, Argentina
| | - Adriana De Siervi
- Current Affiliation: Laboratorio de Oncología Molecular y Nuevos Blancos Terapéuticos, Instituto de Biología y Medicina Experimental (IBYME–CONICET), Vuelta de Obligado 2490 (1428), CABA, Argentina
| | - Elba Vazquez
- Laboratorio de Inflamación y Cáncer, Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales-Universidad de Buenos Aires, IQUIBICEN-CONICET, Intendente Güiraldes 2160 (1428), CABA, Argentina
| | - Javier Cotignola
- Laboratorio de Inflamación y Cáncer, Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales-Universidad de Buenos Aires, IQUIBICEN-CONICET, Intendente Güiraldes 2160 (1428), CABA, Argentina
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Bănescu C, Iancu M, Trifa AP, Macarie I, Dima D, Dobreanu M. The methylenetetrahydrofolate reductase (MTHFR) 677 C>T polymorphism increases the risk of developing chronic myeloid leukemia-a case-control study. Tumour Biol 2014; 36:3101-7. [PMID: 25510667 DOI: 10.1007/s13277-014-2946-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2014] [Accepted: 12/04/2014] [Indexed: 01/10/2023] Open
Abstract
The methylenetetrahydrofolate reductase (MTHFR) 677 C>T and 1298 A>C polymorphisms are associated with variations in folate levels, a phenomenon linked to the development of various malignancies. The aim of this study was to investigate the influence of the 677 C>T and 1298 A>C polymorphisms in the MTHFR gene on the risk of developing chronic myeloid leukemia (CML). Our study included 151 patients with CML and 305 controls. The MTHFR 677 C>T and 1298 A>C polymorphisms were investigated by polymerase chain reaction restriction fragment length polymorphism (PCR-RFLP) and allele-specific PCR techniques. The CT and TT genotypes of the MTHFR 677 C>T polymorphism were associated with an increased risk of developing CML (odds ratio (OR) = 1.556, 95% confidence interval (CI) = 1.017-2.381, p value = 0.041, and OR = 1.897, 95% CI = 1.046-3.44, p value = 0.035, respectively). No association was observed between the prognostic factors (blasts, basophils, additional chromosomal abnormalities, EUTOS score, Sokal and Hasford risk groups) and the MTHFR 677 C>T and 1298 A>C variant genotypes in CML patients. Our study shows that the MTHFR 677 C>T polymorphism is significantly associated with the risk of CML in Romanian patients.
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Affiliation(s)
- Claudia Bănescu
- Department of Medical Genetics, University of Medicine and Pharmacy, Tirgu Mures, Romania
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Polymorphisms of MTHFR Associated with Higher Relapse/Death Ratio and Delayed Weekly MTX Administration in Pediatric Lymphoid Malignancies. LEUKEMIA RESEARCH AND TREATMENT 2013; 2013:238528. [PMID: 24386571 PMCID: PMC3872414 DOI: 10.1155/2013/238528] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/24/2013] [Accepted: 10/10/2013] [Indexed: 11/18/2022]
Abstract
Backgrounds. Outcome of childhood malignancy has been improved mostly due to the advances in diagnostic techniques and treatment strategies. While methotrexate (MTX) related polymorphisms have been under investigation in childhood malignancies, many controversial results have been offered. Objectives. To evaluate associations of polymorphisms related MTX metabolisms and clinical course in childhood lymphoid malignancies. Method. Eighty-two acute lymphoblastic leukemia and 21 non-Hodgkin's lymphoma children were enrolled in this study. Four single nucleotide polymorphisms in 2 genes (MTHFR (rs1801133/c.677C>T/p.Ala222Val and rs1801131/c.1298A>C/p.Glu429Ala) and SLCO1B1 (rs4149056/c.521T>C/p.V174A and rs11045879/c.1865+4846T>C)) were genotyped by Taqman PCR method or direct sequencing. Clinical courses were reviewed retrospectively. Results. No patient who had the AC/CC genotype of rs1801131 (MTHFR) had relapsed or died, in which distribution was statistically different among the AA genotype of rs1801131 (P = 0.004). Polymorphisms of SLCO1B1 (rs11045879 and rs4149056) were not correlated with MTX concentrations, adverse events, or disease outcome. Conclusions. Polymorphisms of MTHFR (rs1801131) could be the plausive candidate for prognostic predictor in childhood lymphoid malignancies.
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Roles of genetic polymorphisms in the folate pathway in childhood acute lymphoblastic leukemia evaluated by Bayesian relevance and effect size analysis. PLoS One 2013; 8:e69843. [PMID: 23940529 PMCID: PMC3734218 DOI: 10.1371/journal.pone.0069843] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2013] [Accepted: 06/12/2013] [Indexed: 12/02/2022] Open
Abstract
In this study we investigated whether polymorphisms in the folate pathway influenced the risk of childhood acute lymphoblastic leukemia (ALL) or the survival rate of the patients. For this we selected and genotyped 67 SNPs in 15 genes in the folate pathway in 543 children with ALL and 529 controls. The results were evaluated by gender adjusted logistic regression and by the Bayesian network based Bayesian multilevel analysis of relevance (BN-BMLA) methods. Bayesian structure based odds ratios for the relevant variables and interactions were also calculated. Altogether 9 SNPs in 8 genes were associated with altered susceptibility to ALL. After correction for multiple testing, two associations remained significant. The genotype distribution of the MTHFD1 rs1076991 differed significantly between the ALL and control population. Analyzing the subtypes of the disease the GG genotype increased only the risk of B-cell ALL (p = 3.52×10−4; OR = 2.00). The GG genotype of the rs3776455 SNP in the MTRR gene was associated with a significantly reduced risk to ALL (p = 1.21×10−3; OR = 0.55), which resulted mainly from the reduced risk to B-cell and hyperdiploid-ALL. The TC genotype of the rs9909104 SNP in the SHMT1 gene was associated with a lower survival rate comparing it to the TT genotype (80.2% vs. 88.8%; p = 0.01). The BN-BMLA confirmed the main findings of the frequentist-based analysis and showed structural interactional maps and the probabilities of the different structural association types of the relevant SNPs especially in the hyperdiploid-ALL, involving additional SNPs in genes like TYMS, DHFR and GGH. We also investigated the statistical interactions and redundancies using structural model properties. These results gave further evidence that polymorphisms in the folate pathway could influence the ALL risk and the effectiveness of the therapy. It was also shown that in gene association studies the BN-BMLA could be a useful supplementary to the traditional frequentist-based statistical method.
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