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Svyatova G, Boranbayeva R, Berezina G, Manzhuova L, Murtazaliyeva A. Genes of Predisposition to Childhood Beta-Cell Acute Lymphoblastic Leukemia in the Kazakh Population. Asian Pac J Cancer Prev 2023; 24:2653-2666. [PMID: 37642051 PMCID: PMC10685230 DOI: 10.31557/apjcp.2023.24.8.2653] [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: 02/22/2023] [Accepted: 08/09/2023] [Indexed: 08/31/2023] Open
Abstract
BACKGROUND Today, acute lymphoblastic leukemia is one of the most common malignant diseases of the hematopoietic system. The genetic predisposition to ALL is not fully explored in various ethnic populations. OBJECTIVE The study aimed to conduct a comparative analysis of the population frequencies of alleles and genotypes of polymorphic gene variants: immune regulation GATA3 (rs3824662); transcription and differentiation of B cells: ARID5B (rs7089424, rs10740055), IKZF1 (rs4132601); differentiation of hematopoietic cells: PIP4K2A (rs7088318); apoptosis: CEBPE (rs2239633), tumor suppressors: CDKN2A (rs3731249), TP53 (rs1042522); carcinogen metabolism: CBR3 (rs1056892), CYP1A1 (rs104894, rs4646903), according to genome-wide association studies analyses associated with the risk of developing pediatric beta-cell acute lymphoblastic leukemia (B-cell ALL), in an ethnically homogeneous population of Kazakhs with studied populations. METHODS The genomic database consists of 1800 conditionally healthy persons of Kazakh nationality, genotyped using OmniChip 2.5-8 Illumina chips at the deCODE genetics as part of the InterPregGen 7 project of the European Union (EU) framework program under Grant Agreement No. 282540. RESULTS High population frequencies of single nucleotide polymorphism (SNP) minor alleles identified for immune regulation genes - GATA3 rs3824662 - 42.5%; transcription and differentiation of B-cells genes - ARID5B rs7089424 - 33.1% and rs10740055 - 48.5%, which suggests their significant genetic contribution to the risk of development and prognosis of the effectiveness of B-cell ALL therapy in the Kazakh population. The significantly lower population frequency of the minor allele G rs1056892 CBR3 gene - 38.6% in the Kazakhs suggests its significant protective effect in reducing the risk of childhood B-cell ALL and the smaller number of cardiac complications after anthracycline therapy. CONCLUSION The obtained results will serve as a basis for developing effective methods for predicting the risk of development, early diagnosis, and effectiveness of treatment of B-cell ALL in children.
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Affiliation(s)
- Gulnara Svyatova
- Republican Medical Genetic Consultation, Scientific Center of Obstetrics, Gynecology and Perinatology, 050020, 125 Dostyk Ave., Almaty, Kazakhstan.
| | - Riza Boranbayeva
- Scientific Center of Pediatrics and Pediatric Surgery, 050060, 146 Al-Farabi Ave., Almaty, Kazakhstan.
| | - Galina Berezina
- Republican Medical Genetic Consultation, Scientific Center of Obstetrics, Gynecology and Perinatology, 050020, 125 Dostyk Ave., Almaty, Kazakhstan.
| | - Lyazat Manzhuova
- Scientific Center of Pediatrics and Pediatric Surgery, 050060, 146 Al-Farabi Ave., Almaty, Kazakhstan.
| | - Alexandra Murtazaliyeva
- Republican Medical Genetic Consultation, Scientific Center of Obstetrics, Gynecology and Perinatology, 050020, 125 Dostyk Ave., Almaty, Kazakhstan.
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2
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Sattarzadeh Bardsiri M, Zehtab S, Karami N, Farsinejad A, Ehsan M, Fatemi A. Association of IKZF1 and CDKN2A gene polymorphisms with childhood acute lymphoblastic leukemia: a high-resolution melting analysis. BMC Med Genomics 2022; 15:171. [PMID: 35932035 PMCID: PMC9354342 DOI: 10.1186/s12920-022-01325-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 07/30/2022] [Indexed: 11/10/2022] Open
Abstract
Background Acute lymphoblastic leukemia is the most prevailing pediatric hematologic malignancy, and various factors such as environmental exposures and genetic variation affect ALL susceptibility and patients outcome. According to genome-wide association studies, several single nucleotide polymorphisms (SNPs) in IKZF1 (rs4132601) and CDKN2A (rs3731249 and rs3731217) genes are associated with ALL susceptibility. Hereupon, this study aimed to discover the association between these SNPs and the risk of childhood ALL among a sample of the Iranian population.
Methods A total of fifty children with ALL were included in this case–control study, along with an additional fifty healthy children, matched for age and gender. High-resolution melting (HRM) analysis was employed to genotyping rs4132601, rs3731249, and rs3731217.
Results In the patient group, the CT genotype and T allele frequency of rs3731249 were significantly greater than controls (p = 0.01 and p = 0.005, respectively). Moreover, the positive association of CT and dominant model (CT + TT) genotypes and T allele at rs3731249 with the risk of ALL was confirmed (OR = 9.56, OR = 10.76 and OR = 11.00, respectively). There was no significant relation between rs4132601 (IKZF1), rs3731217 (CDKN2A), and childhood ALL. Conclusion The present study indicates that CT genotype and T allele at rs3731249 (CDKN2A) can significantly increase the risk of ALL among children.
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Affiliation(s)
- Mahla Sattarzadeh Bardsiri
- Cell Therapy and Regenerative Medicine Comprehensive Center, Kerman University of Medical Sciences, Kerman, Iran.,Department of Hematology and Medical Laboratory Sciences, Faculty of Allied Medicine, Kerman University of Medical Sciences, Kerman, Iran
| | - Shahrzad Zehtab
- Department of Hematology and Medical Laboratory Sciences, Faculty of Allied Medicine, Kerman University of Medical Sciences, Kerman, Iran
| | - Najibe Karami
- Department of Hematology and Medical Laboratory Sciences, Faculty of Allied Medicine, Kerman University of Medical Sciences, Kerman, Iran
| | - Alireza Farsinejad
- Cell Therapy and Regenerative Medicine Comprehensive Center, Kerman University of Medical Sciences, Kerman, Iran.,Department of Hematology and Medical Laboratory Sciences, Faculty of Allied Medicine, Kerman University of Medical Sciences, Kerman, Iran
| | - Mohsen Ehsan
- Department of Hematology and Medical Laboratory Sciences, Faculty of Allied Medicine, Kerman University of Medical Sciences, Kerman, Iran.,Department of Hematology and Blood Banking, Faculty of Allied Medicine, Iran University of Medical Science, Tehran, Iran
| | - Ahmad Fatemi
- Department of Hematology and Medical Laboratory Sciences, Faculty of Allied Medicine, Kerman University of Medical Sciences, Kerman, Iran. .,Cellular and Molecular Research Center, Gerash University of Medical Sciences, Gerash, Iran.
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3
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Liu J, Weiling G, Xueqin L, Liang X, Linhong W, Zhongwen C. The CEBPE rs2239633 genetic polymorphism on susceptibility to childhood acute lymphoblastic leukemia: an updated meta-analysis. Environ Health Prev Med 2021; 26:2. [PMID: 33397280 PMCID: PMC7784308 DOI: 10.1186/s12199-020-00920-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 11/25/2020] [Indexed: 11/28/2022] Open
Abstract
Objectives We performed an updated meta-analysis to clarify the relationship between the CEBPE rs2239633 polymorphism and the childhood acute lymphoblastic leukemia (CALL) susceptibility. Methods All the case-control studies were updated on October 5, 2020, through Web of Science, PubMed, Cochrane Library, Embase, and China National Knowledge Infrastructure (CNKI) electronic database. The heterogeneity in the study was tested by the Q test and I2, and then the random ratio or fixed effect was utilized to merge the odds ratios (OR) and 95% confidence interval (CI). We also performed sensitivity analysis to estimate the impact of individual studies on aggregate estimates. Publication bias was investigated by using funnel plot and Egger’s regression test. All statistical analyses were performed using Stata 12.0. Results A total of 20 case-control studies were selected, including 7014 patients and 16,428 controls. There was no association of CEBPE rs2239633 polymorphism with CALL (CC vs CT + TT: OR = 1.08, 95% CI = 0.94–1.26; CC + CT vs TT: OR = 1.10, 95% CI = 0.94–1.30; C vs T: OR = 1.02, 95% CI = 0.92–1.13). In the subgroup analysis by ethnicity, there is no significant association of this polymorphism and CALL risks among Asian and Caucasian populations in the three genetic models (CC vs CT + TT, CC + CT vs TT, and C vs T). Conclusion This meta-analysis found no significant association between the CEBPE rs2239633 polymorphism and susceptibility to CALL.
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Affiliation(s)
- Jin Liu
- Department of Control and Prevention of Chronic Non-communicable Diseases, Jiaxing Center for Disease Control and Prevention, Jiaxing, Zhejiang, 314050, China
| | - Gu Weiling
- Office, Jiaxing Center for Disease Control and Prevention, No.486 Wenqiao Road, Jiaxing, Zhejiang, 314050, China
| | - Li Xueqin
- Department of Control and Prevention of Chronic Non-communicable Diseases, Jiaxing Center for Disease Control and Prevention, Jiaxing, Zhejiang, 314050, China
| | - Xie Liang
- Department of Control and Prevention of Chronic Non-communicable Diseases, Jiaxing Center for Disease Control and Prevention, Jiaxing, Zhejiang, 314050, China
| | - Wang Linhong
- Department of Control and Prevention of Chronic Non-communicable Diseases, Jiaxing Center for Disease Control and Prevention, Jiaxing, Zhejiang, 314050, China
| | - Chen Zhongwen
- Office, Jiaxing Center for Disease Control and Prevention, No.486 Wenqiao Road, Jiaxing, Zhejiang, 314050, China.
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Wang P, Deng Y, Yan X, Zhu J, Yin Y, Shu Y, Bai D, Zhang S, Xu H, Lu X. The Role of ARID5B in Acute Lymphoblastic Leukemia and Beyond. Front Genet 2020; 11:598. [PMID: 32595701 PMCID: PMC7303299 DOI: 10.3389/fgene.2020.00598] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2020] [Accepted: 05/18/2020] [Indexed: 02/05/2023] Open
Abstract
Acute lymphoblastic leukemia (ALL) is the most common malignancy in children with distinct characteristics among different subtypes. Although the etiology of ALL has not been fully unveiled, initiation of ALL has been demonstrated to partly depend on genetic factors. As indicated by several genome wide association studies (GWASs) and candidate gene analyses, ARID5B, a member of AT-rich interactive domain (ARID) protein family, is associated with the occurrence and prognosis of ALL. However, the mechanisms by which ARID5B genotype impact on the susceptibility and treatment outcome remain vague. In this review, we outline developments in the understanding of ARID5B in the susceptibility of ALL and its therapeutic perspectives, and summarize the underlying mechanisms based on the limited functional studies, hoping to illustrate the possible mechanisms of ARID5B impact and highlight the potential treatment regimens.
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Affiliation(s)
- Peiqi Wang
- Department of Pediatric Hematology/Oncology, West China Second University Hospital, Sichuan University, Chengdu, China.,State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Yun Deng
- State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, China
| | - Xinyu Yan
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Jianhui Zhu
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Yuanyuan Yin
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Yang Shu
- State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, China
| | - Ding Bai
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Shouyue Zhang
- State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, China
| | - Heng Xu
- State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, China.,Department of Laboratory Medicine/Research Center of Clinical Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, China.,Precision Medicine Center, State Key Laboratory of Biotherapy and Precision Medicine, Key Laboratory of Sichuan Province, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, China
| | - Xiaoxi Lu
- Department of Pediatric Hematology/Oncology, West China Second University Hospital, Sichuan University, Chengdu, China
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5
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Csoma Z, Gál Z, Gézsi A, Herjavecz I, Szalai C. Prevalence and characterization of severe asthma in Hungary. Sci Rep 2020; 10:9274. [PMID: 32518278 PMCID: PMC7283249 DOI: 10.1038/s41598-020-66445-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Accepted: 05/13/2020] [Indexed: 12/02/2022] Open
Abstract
Background: Severe asthma (SA) database was established in Hungary to estimate the prevalence of SA and to define and analyze clinical phenotypes of the patients. Methods: SA questionnaires were sent out to 143 public pulmonary dispensaries specialized for diagnosing and caring pulmonary patients. Data of 520 SA patients were evaluated. Results: The prevalence of SA within the asthmatic population in Hungary was 0.89%. The mean age of patients were 56.4 ± 13.4 years, SA were more frequent in females (64%), the prevalence of allergy was 56.6%, 72.1% of patients had persistent airflow limitation (FEV1 < 80%), 37.9% severe airway obstruction (FEV1 ≤ 60%), 33.6% required systemic corticosteroid maintenance therapy, 21.5% had salicylate intolerance and 43.2% rhinosinusitis. A Bayesian dependency network was calculated which revealed several interdependencies between the characteristics. E.g. there was a strong association between salicylate intolerance and rhinosinusitis, more patients received regular systemic corticosteroid treatment who had salicylate intolerance and the proportion of salicylate intolerance was significantly higher in females. Conclusion: The prevalence of SA was determined in Hungary which was lower than in other studies. Using a Bayesian-based network analysis several interdependencies were revealed between patient characteristics.
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Affiliation(s)
- Zsuzsanna Csoma
- National Korányi Institute of Pulmonology, Budapest, Hungary
| | - Zsófia Gál
- Department of Genetics, Cell- and Immunobiology, Semmelweis University, Budapest, Hungary
| | - András Gézsi
- Department of Genetics, Cell- and Immunobiology, Semmelweis University, Budapest, Hungary.,Department of Measurement and Information Systems, Budapest University of Technology and Economics, Budapest, Hungary
| | - Irén Herjavecz
- National Korányi Institute of Pulmonology, Budapest, Hungary
| | - Csaba Szalai
- Department of Genetics, Cell- and Immunobiology, Semmelweis University, Budapest, Hungary. .,Heim Pál Pediatric Hospital, Budapest, Hungary.
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Lyu M, Jiao L, Zhou J, Li H, Meng Z, Xie W, Ren J, Bian Q, Ying B. Do genetic polymorphisms of B-cell CLL/lymphoma 2 confer susceptibility to anti-tuberculous therapy-associated drug-induced liver injury? Int J Infect Dis 2020; 91:223-231. [PMID: 31838216 DOI: 10.1016/j.ijid.2019.12.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Revised: 11/29/2019] [Accepted: 12/01/2019] [Indexed: 02/05/2023] Open
Abstract
OBJECTIVES The aim of this study was to identify the relationship between B-cell CLL/lymphoma 2 (BCL2) polymorphisms and susceptibility to anti-tuberculous therapy-associated drug-induced liver injury (ATT-DILI). METHODS A total of 746 tuberculosis (TB) patients were enrolled in this study. Twenty-one selected single nucleotide polymorphisms in BCL2 were analyzed by custom-by-design 2×48-Plex SNPscan kit. The allele and genotype frequencies between patients with and without ATT-DILI were compared using three different genetic models. RESULTS A total of 727/746 participants were successfully genotyped, and 112 of them were diagnosed with ATT-DILI. The A allele of rs8085707, G allele of rs76986960, and A allele of rs949037 conferred an increased risk of ATT-DILI, with estimated odd ratios (ORs) of 2.181 (95% confidence interval (CI) 1.345-3.536, p=0.001), 1.983 (95% CI 1.060-3.709, p=0.029), and 1.390 (95% CI 1.032-1.873, p=0.03), respectively. Bonferroni correction indicated that the A allele of rs8085707 was a risk factor for ATT-DILI (Bonferroni correction: p=0.026). The additive model suggested that patients with the AA genotype of rs8085707 had a significantly higher risk of ATT-DILI compared with those with the GG genotype (Bonferroni correction: p=0.036). The influence of BCL2 polymorphisms on clinical characteristics (clinical symptoms, disease subtypes, and laboratory indicators) was also identified. CONCLUSIONS This study is novel in suggesting an association between BCL2 polymorphisms and the risk of ATT-DILI.
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Affiliation(s)
- Mengyuan Lyu
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan, China; West China School of Medicine, Sichuan University, Chengdu, Sichuan, China
| | - Lin Jiao
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan, China; West China School of Medicine, Sichuan University, Chengdu, Sichuan, China
| | - Jian Zhou
- West China School of Medicine, Sichuan University, Chengdu, Sichuan, China
| | - Haijun Li
- Clinical Laboratory, Guangyuan Central Hospital, Guangyuan, Sichuan, China
| | - Zirui Meng
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan, China; West China School of Medicine, Sichuan University, Chengdu, Sichuan, China
| | - Wanhong Xie
- Clinical Laboratory, Wangcang Country People's Hospital, Guangyuan, Sichuan, China
| | - Jing Ren
- Clinical Laboratory, Guangyuan Central Hospital, Guangyuan, Sichuan, China
| | - Qin Bian
- Clinical Laboratory, Guangyuan Central Hospital, Guangyuan, Sichuan, China
| | - Binwu Ying
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan, China; West China School of Medicine, Sichuan University, Chengdu, Sichuan, China.
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7
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Mahjoub S, Chayeb V, Zitouni H, Ghali RM, Regaieg H, Almawi WY, Mahjoub T. IKZF1 genetic variants rs4132601 and rs11978267 and acute lymphoblastic leukemia risk in Tunisian children: a case-control study. BMC MEDICAL GENETICS 2019; 20:159. [PMID: 31604453 PMCID: PMC6788013 DOI: 10.1186/s12881-019-0900-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Accepted: 09/30/2019] [Indexed: 12/21/2022]
Abstract
BACKGROUND Associations between IKZF1 gene variants and Acute Lymphoblastic Leukemia (ALL) was recently reported. We examined whether the common IKZF1 polymorphisms rs4132601 T/G and rs111978267 A/G are associated with ALL among a Tunisian pediatric cohort. METHODS This case-control study involved 170 patients with ALL and 150 control subjects. SNP genotyping was performed by TaqMan® SNP Genotyping Assay. RESULTS The minor allele G of IKZF1 gene polymorphism rs4132601 T/G was significantly higher in ALL cases than in control subjects (P = 0.029), with 1.54-fold increased risk of ALL. The association of rs4132601 with ALL was seen under co-dominant (P = 0.009), recessive (P = 0.006), and additive (P = 0.027) genetic models, of which the co-dominant (P = 0.027) and recessive (P = 0.027) association remained significant after adjusting for covariates, and False Discovery Rate correction. In contrast, no association was noted for rs111978267 variant. Two-locus (rs4132601-rs11978267) IKZF1 haplotype analysis demonstrated association of GA (P = 0.053), with increased ALL risk [OR (95% CI) = 1.58 (1.00-2.51)], which remained significant after controlling for key covariates [aP = 0.046; aOR (95% CI) = 1.61 (1.01-2.57)]. CONCLUSION We demonstrated the association of IKZF1 polymorphism rs4132601 T/G with increased risk of ALL among Tunisian pediatric cohort, with altered phenotypic changes among ALL patients.
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Affiliation(s)
- Sana Mahjoub
- Laboratory of Human Genome and Multifactorial Diseases (LR12ES07), Faculty of Pharmacy of Monastir, University of Monastir, Monastir, Tunisia
| | - Vera Chayeb
- Laboratory of Human Genome and Multifactorial Diseases (LR12ES07), Faculty of Pharmacy of Monastir, University of Monastir, Monastir, Tunisia
| | - Hedia Zitouni
- Laboratory of Human Genome and Multifactorial Diseases (LR12ES07), Faculty of Pharmacy of Monastir, University of Monastir, Monastir, Tunisia
| | - Rabeb M Ghali
- Laboratory of Human Genome and Multifactorial Diseases (LR12ES07), Faculty of Pharmacy of Monastir, University of Monastir, Monastir, Tunisia
| | - Haifa Regaieg
- Hematology Department ; Faculty of Medicine Ibn Jazzar, University of Sousse, Sousse, Tunisia
| | - Wassim Y Almawi
- Faculty of Sciences, El-Manar University, Tunis, Tunisia.,School of Medicine, Nazarbayev University, Nur-Sultan, Astana, Kazakhstan
| | - Touhami Mahjoub
- Laboratory of Human Genome and Multifactorial Diseases (LR12ES07), Faculty of Pharmacy of Monastir, University of Monastir, Monastir, Tunisia.
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8
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ARID5B gene polymorphisms and the risk of childhood acute lymphoblastic leukemia: a meta-analysis. Int J Hematol 2019; 110:272-284. [PMID: 31111395 DOI: 10.1007/s12185-019-02658-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Revised: 05/08/2019] [Accepted: 05/08/2019] [Indexed: 12/11/2022]
Abstract
Genome-wide association studies have implicated several single-nucleotide polymorphisms (SNPs) in the AT-rich interactive domain 5B (ARID5B) gene in children with ALL; however, whether ARID5B variants (rs10821936, rs10994982, rs7089424) are associated with childhood ALL remains controversial. We performed this study to obtain more conclusive results. Eligible studies were searched in PubMed, Web of Science, and EMBASE. Odds ratios and 95% confidence intervals were calculated. A total of 26 studies were included. Analyses stratified by ethnicity revealed that three polymorphisms are significantly associated with the odds of childhood ALL in Caucasians, and rs10994982 and rs7089424 with the odds of childhood ALL in Asian populations. Furthermore, subtype analyses provided strong evidence that the three polymorphisms are highly associated with the risk of B-cell ALL. Our findings indicate that the ARID5B variants (rs10821936, rs10994982, rs7089424) are significantly associated with the risk of childhood ALL.
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9
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Williams LA, Yang JJ, Hirsch BA, Marcotte EL, Spector LG. Is There Etiologic Heterogeneity between Subtypes of Childhood Acute Lymphoblastic Leukemia? A Review of Variation in Risk by Subtype. Cancer Epidemiol Biomarkers Prev 2019; 28:846-856. [PMID: 30770347 PMCID: PMC6500468 DOI: 10.1158/1055-9965.epi-18-0801] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Revised: 09/19/2018] [Accepted: 02/05/2019] [Indexed: 02/07/2023] Open
Abstract
Although substantial advances in the identification of cytogenomic subtypes of childhood acute lymphoblastic leukemia (ALL) have been made in recent decades, epidemiologic research characterizing the etiologic heterogeneity of ALL by subtype has not kept pace. The purpose of this review is to summarize the current literature concerning subtype-specific epidemiologic risk factor associations with ALL subtype defined by immunophenotype (e.g., B-cell vs. T-cell) and cytogenomics (including gross chromosomal events characterized by recurring numerical and structural abnormalities, along with cryptic balanced rearrangements, and focal gene deletions). In case-control analyses investigating nongenetic risk factors, home paint exposure is associated with hyperdiploid, MLL-rearranged, and ETV6-RUNX1 subtypes, yet there are few differences in risk factor associations between T- and B-ALL. Although the association between maternal smoking and ALL overall has been null, maternal smoking is associated with an increasing number of gene deletions among cases. GWAS-identified variants in ARID5B have been the most extensively studied and are strongly associated with hyperdiploid B-ALL. GATA3 single nucleotide variant rs3824662 shows a strong association with Ph-like ALL (OR = 3.14). However, there have been relatively few population-based studies of adequate sample size to uncover risk factors that may define etiologic heterogeneity between and within the currently defined cytogenomic ALL subtypes.
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Affiliation(s)
- Lindsay A Williams
- Division of Epidemiology & Clinical Research, Department of Pediatrics, University of Minnesota, Minneapolis, Minnesota
| | - Jun J Yang
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Betsy A Hirsch
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, Minnesota
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota
| | - Erin L Marcotte
- Division of Epidemiology & Clinical Research, Department of Pediatrics, University of Minnesota, Minneapolis, Minnesota
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota
| | - Logan G Spector
- Division of Epidemiology & Clinical Research, Department of Pediatrics, University of Minnesota, Minneapolis, Minnesota.
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota
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10
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Shi Y, Zhang Z, Qu X, Zhu X, Zhao L, Wei R, Guo Q, Sun L, Yin X, Zhang Y, Li X. Roles of STAT3 in leukemia (Review). Int J Oncol 2018; 53:7-20. [PMID: 29749432 DOI: 10.3892/ijo.2018.4386] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Accepted: 04/24/2018] [Indexed: 11/06/2022] Open
Abstract
Leukemia is a type of hematopoietic malignancy, and the incidence rate in the United States and European Union increases by an average of 0.6 to 0.7% annually. The incidence rate in China is approximately 5.17/100,000 individuals, and the mortality rate is 3.94/100,000 individuals. Leukemia is the most common tumor affecting children and adults under 35 years of age, and is one of the major diseases leading to the death of adolescents. Signal transducer and activator of transcription 3 (STAT3) is a vital regulatory factor of signal transduction and transcriptional activation, and once activated, the phosphorylated form of STAT3 (p-STAT3) is transferred into the nucleus to regulate the transcription of target genes, and plays important roles in cell proliferation, differentiation, apoptosis and other physiological processes. An increasing number of studies have confirmed that the abnormal activation of STAT3 is involved in the development of tumors. In this review, the roles of STAT3 in the pathogenesis, diagnosis, treatment and prognosis of leukemia are discussed in the aspects of cell proliferation, differentiation and apoptosis, with the aim to further clarify the roles of STAT3 in leukemia, and shed light into possible novel targets and strategies for clinical diagnosis and treatment.
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Affiliation(s)
- Yin Shi
- School of Medicine and Life Sciences, University of Jinan-Shandong Academy of Medical Sciences, Jinan, Shandong 250062, P.R. China
| | - Zhen Zhang
- Laboratory for Molecular Immunology, Institute of Basic Medicine, Shandong Academy of Medical Sciences, Jinan, Shandong 250062, P.R. China
| | - Xintao Qu
- Department of Bone and Joint Surgery Jinan Central Hospital Affiliated to Shandong University, Jinan, Shandong 250013, P.R. China
| | - Xiaoxiao Zhu
- Laboratory for Molecular Immunology, Institute of Basic Medicine, Shandong Academy of Medical Sciences, Jinan, Shandong 250062, P.R. China
| | - Lin Zhao
- Laboratory for Molecular Immunology, Institute of Basic Medicine, Shandong Academy of Medical Sciences, Jinan, Shandong 250062, P.R. China
| | - Ran Wei
- Laboratory for Molecular Immunology, Institute of Basic Medicine, Shandong Academy of Medical Sciences, Jinan, Shandong 250062, P.R. China
| | - Qiang Guo
- Laboratory for Molecular Immunology, Institute of Basic Medicine, Shandong Academy of Medical Sciences, Jinan, Shandong 250062, P.R. China
| | - Linlin Sun
- School of Medicine and Life Sciences, University of Jinan-Shandong Academy of Medical Sciences, Jinan, Shandong 250062, P.R. China
| | - Xunqiang Yin
- School of Medicine and Life Sciences, University of Jinan-Shandong Academy of Medical Sciences, Jinan, Shandong 250062, P.R. China
| | - Yunhong Zhang
- School of Medicine and Life Sciences, University of Jinan-Shandong Academy of Medical Sciences, Jinan, Shandong 250062, P.R. China
| | - Xia Li
- Laboratory for Molecular Immunology, Institute of Basic Medicine, Shandong Academy of Medical Sciences, Jinan, Shandong 250062, P.R. China
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11
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Pharmacogenetic analysis of high-dose methotrexate treatment in children with osteosarcoma. Oncotarget 2018; 8:9388-9398. [PMID: 27566582 PMCID: PMC5354739 DOI: 10.18632/oncotarget.11543] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2016] [Accepted: 08/09/2016] [Indexed: 01/08/2023] Open
Abstract
Inter-individual differences in toxic symptoms and pharmacokinetics of high-dose methotrexate (MTX) treatment may be caused by genetic variants in the MTX pathway. Correlations between polymorphisms and pharmacokinetic parameters and the occurrence of hepato- and myelotoxicity were studied. Single nucleotide polymorphisms (SNPs) of the ABCB1, ABCC1, ABCC2, ABCC3, ABCC10, ABCG2, GGH, SLC19A1 and NR1I2 genes were analyzed in 59 patients with osteosarcoma. Univariate association analysis and Bayesian network-based Bayesian univariate and multilevel analysis of relevance (BN-BMLA) were applied. Rare alleles of 10 SNPs of ABCB1, ABCC2, ABCC3, ABCG2 and NR1I2 genes showed a correlation with the pharmacokinetic values and univariate association analysis. The risk of toxicity was associated with five SNPs in the ABCC2 and NR1I2 genes. Pharmacokinetic parameters were associated with four SNPs of the ABCB1, ABCC3, NR1I2, and GGH genes, and toxicity was shown to be associated with ABCC1 rs246219 and ABCC2 rs717620 using the univariate and BN-BMLA method. BN-BMLA analysis detected relevant effects on the AUC0-48 in the following SNPs: ABCB1 rs928256, ABCC3 rs4793665, and GGH rs3758149. In both univariate and multivariate analyses the SNPs ABCB1 rs928256, ABCC3 rs4793665, GGH rs3758149, and NR1I2 rs3814058 SNPs were relevant. These SNPs should be considered in future dose individualization during treatment.
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12
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Roman ÁC, Carvajal-Gonzalez JM, Merino JM, Mulero-Navarro S, Fernández-Salguero PM. The aryl hydrocarbon receptor in the crossroad of signalling networks with therapeutic value. Pharmacol Ther 2017; 185:50-63. [PMID: 29258844 DOI: 10.1016/j.pharmthera.2017.12.003] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The aryl hydrocarbon receptor (AhR) is well-known for its major contributions to the cellular responses against environmental toxins and carcinogens. Notably, AhR has also emerged as a key transcription factor controlling many physiological processes including cell proliferation and apoptosis, differentiation, adhesion and migration, pluripotency and stemness. These novel functions have broadened our understanding of the signalling pathways and molecular intermediates interacting with AhR under both homeostatic and pathological conditions. Recent discoveries link AhR with the function of essential organs such as liver, skin and gonads, and with complex organismal structures including the immune and cardiovascular systems. The identification of potential endogenous ligands able to regulate AhR activity, opens the possibility of designing ad hoc molecules with pharmacological and/or therapeutic value to treat human diseases in which AhR may have a causal role. Integration of experimental data from in vitro and in vivo studies with "omic" analyses of human patients affected with cancer, immune diseases, inflammation or neurological disorders will likely contribute to validate the clinical relevance of AhR and the possible benefits of modulating its activity by pharmacologically-driven strategies. In this review, we will highlight signalling pathways involved in human diseases that could be targetable by AhR modulators and discuss the feasibility of using such molecules in therapy. The pros and cons of AhR-aimed approaches will be also mentioned.
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Affiliation(s)
- Ángel C Roman
- Champalimaud Neuroscience Programme, Champalimoud Center for the Unknown, Lisbon, Portugal
| | - José M Carvajal-Gonzalez
- Departamento de Bioquímica y Biología Molecular y Genética, Facultad de Ciencias, Universidad de Extremadura, 06071 Badajoz, Spain
| | - Jaime M Merino
- Departamento de Bioquímica y Biología Molecular y Genética, Facultad de Ciencias, Universidad de Extremadura, 06071 Badajoz, Spain
| | - Sonia Mulero-Navarro
- Departamento de Bioquímica y Biología Molecular y Genética, Facultad de Ciencias, Universidad de Extremadura, 06071 Badajoz, Spain.
| | - Pedro M Fernández-Salguero
- Departamento de Bioquímica y Biología Molecular y Genética, Facultad de Ciencias, Universidad de Extremadura, 06071 Badajoz, Spain.
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13
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Genetic susceptibility in childhood acute lymphoblastic leukemia. Med Oncol 2017; 34:179. [PMID: 28905228 DOI: 10.1007/s12032-017-1038-7] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Accepted: 09/05/2017] [Indexed: 12/27/2022]
Abstract
Acute lymphoblastic leukemia (ALL) is the most common childhood malignancy and a leading cause of death due to disease in children. The genetic basis of ALL susceptibility has been supported by its association with certain congenital disorders and, more recently, by several genome-wide association studies (GWAS). These GWAS identified common variants in ARID5B, IKZF1, CEBPE, CDKN2A, PIP4K2A, LHPP and ELK3 influencing ALL risk. However, the risk variants of these SNPs were not validated in all populations, suggesting that some of the loci could be population specific. On the other hand, the currently identified risk SNPs in these genes only account for 19% of the additive heritable risk. This estimation indicates that additional susceptibility variants could be discovered. In this review, we will provide an overview of the most important findings carried out in genetic susceptibility of childhood ALL in all GWAS and subsequent studies and we will also point to future directions that could be explored in the near future.
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14
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Al-Absi B, Razif MFM, Noor SM, Saif-Ali R, Aqlan M, Salem SD, Ahmed RH, Muniandy S. Contributions of IKZF1, DDC, CDKN2A, CEBPE, and LMO1 Gene Polymorphisms to Acute Lymphoblastic Leukemia in a Yemeni Population. Genet Test Mol Biomarkers 2017; 21:592-599. [PMID: 28768142 DOI: 10.1089/gtmb.2017.0084] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
BACKGROUND Genome-wide and candidate gene association studies have previously revealed links between a predisposition to acute lymphoblastic leukemia (ALL) and genetic polymorphisms in the following genes: IKZF1 (7p12.2; ID: 10320), DDC (7p12.2; ID: 1644), CDKN2A (9p21.3; ID: 1029), CEBPE (14q11.2; ID: 1053), and LMO1 (11p15; ID: 4004). In this study, we aimed to conduct an investigation into the possible association between polymorphisms in these genes and ALL within a sample of Yemeni children of Arab-Asian descent. METHODS Seven single-nucleotide polymorphisms (SNPs) in IKZF1, three SNPs in DDC, two SNPs in CDKN2A, two SNPs in CEBPE, and three SNPs in LMO1 were genotyped in 289 Yemeni children (136 cases and 153 controls), using the nanofluidic Dynamic Array (Fluidigm 192.24 Dynamic Array). Logistic regression analyses were used to estimate ALL risk, and the strength of association was expressed as odds ratios with 95% confidence intervals. RESULTS We found that the IKZF1 SNP rs10235796 C allele (p = 0.002), the IKZF1 rs6964969 A>G polymorphism (p = 0.048, GG vs. AA), the CDKN2A rs3731246 G>C polymorphism (p = 0.047, GC+CC vs. GG), and the CDKN2A SNP rs3731246 C allele (p = 0.007) were significantly associated with ALL in Yemenis of Arab-Asian descent. In addition, a borderline association was found between IKZF1 rs4132601 T>G variant and ALL risk. No associations were found between the IKZF1 SNPs (rs11978267; rs7789635), DDC SNPs (rs3779084; rs880028; rs7809758), CDKN2A SNP (rs3731217), the CEBPE SNPs (rs2239633; rs12434881) and LMO1 SNPs (rs442264; rs3794012; rs4237770) with ALL in Yemeni children. CONCLUSION The IKZF1 SNPs, rs10235796 and rs6964969, and the CDKN2A SNP rs3731246 (previously unreported) could serve as risk markers for ALL susceptibility in Yemeni children.
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Affiliation(s)
- Boshra Al-Absi
- 1 Department of Molecular Medicine, University of Malaya , Kuala Lumpur, Malaysia
| | - Muhammad F M Razif
- 1 Department of Molecular Medicine, University of Malaya , Kuala Lumpur, Malaysia
| | - Suzita M Noor
- 2 Department of Biomedical Science, Faculty of Medicine, University of Malaya , Kuala Lumpur, Malaysia
| | - Riyadh Saif-Ali
- 3 Department of Biochemistry and Molecular Biology, Faculty of Medicine, Sana'a University , Sana'a, Yemen
| | - Mohammed Aqlan
- 4 Department of Pediatrics, Al-Kuwait University Hospital , Sana'a, Yemen
| | - Sameer D Salem
- 3 Department of Biochemistry and Molecular Biology, Faculty of Medicine, Sana'a University , Sana'a, Yemen
| | - Radwan H Ahmed
- 1 Department of Molecular Medicine, University of Malaya , Kuala Lumpur, Malaysia
| | - Sekaran Muniandy
- 5 Department of Biochemistry, Faculty of Medicine, MAHSA University , Kuala Lumpur, Malaysia
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15
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Kutszegi N, Yang X, Gézsi A, Schermann G, Erdélyi DJ, Semsei ÁF, Gábor KM, Sági JC, Kovács GT, Falus A, Zhang H, Szalai C. HLA-DRB1*07:01-HLA-DQA1*02:01-HLA-DQB1*02:02 haplotype is associated with a high risk of asparaginase hypersensitivity in acute lymphoblastic leukemia. Haematologica 2017; 102:1578-1586. [PMID: 28596278 PMCID: PMC5685222 DOI: 10.3324/haematol.2017.168211] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Accepted: 05/30/2017] [Indexed: 01/24/2023] Open
Abstract
Hypersensitivity reactions are the most frequent dose-limiting adverse reactions to Escherichia coli-derived asparaginase in pediatric acute lymphoblastic leukemia (ALL) patients. The aim of the present study was to identify associations between sequence-based Human Leukocyte Antigen Class II region alleles and asparaginase hypersensitivity in a Hungarian ALL population. Four-digit typing of HLA-DRB1 and HLA-DQB1 loci was performed in 359 pediatric ALL patients by using next-generation sequencing method. Based on genotypic data of the two loci, haplotype reconstruction was carried out. In order to investigate the possible role of the HLA-DQ complex, the HLA-DQA1 alleles were also inferred. Multivariate logistic regression analysis and a Bayesian network-based approach were applied to identify relevant genetic risk factors of asparaginase hypersensitivity. Patients with HLA-DRB1*07:01 and HLA-DQB1*02:02 alleles had significantly higher risk of developing asparaginase hypersensitivity compared to non-carriers [P=4.56×10−5; OR=2.86 (1.73–4.75) and P=1.85×10−4; OR=2.99 (1.68–5.31); n=359, respectively]. After haplotype reconstruction, the HLA-DRB1*07:01-HLA-DQB1*02:02 haplotype was associated with an increased risk. After inferring the HLA-DQA1 alleles the HLA-DRB1*07:01–HLA-DQA1*02:01–HLA-DQB1*02:02 haplotype was associated with the highest risk of asparaginase hypersensitivity [P=1.22×10−5; OR=5.00 (2.43–10.29); n=257]. Significantly fewer T-cell ALL patients carried the HLA-DQB1*02:02 allele and the associated haplotype than did pre-B-cell ALL patients (6.5%; vs. 19.2%, respectively; P=0.047). In conclusion, we identified a haplotype in the Human Leukocyte Antigen Class II region associated with a higher risk of asparaginase hypersensitivity. Our results confirm that variations in HLA-D region might influence the development of asparaginase hypersensitivity.
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Affiliation(s)
- Nóra Kutszegi
- Department of Genetics, Cell- and Immunobiology, Semmelweis University, Budapest, Hungary.,2 Department of Paediatrics, Semmelweis University, Budapest, Hungary
| | | | - András Gézsi
- Department of Genetics, Cell- and Immunobiology, Semmelweis University, Budapest, Hungary
| | - Géza Schermann
- Department of Genetics, Cell- and Immunobiology, Semmelweis University, Budapest, Hungary
| | - Dániel J Erdélyi
- 2 Department of Paediatrics, Semmelweis University, Budapest, Hungary
| | - Ágnes F Semsei
- Department of Genetics, Cell- and Immunobiology, Semmelweis University, Budapest, Hungary
| | - Krisztina M Gábor
- Department of Pediatrics and Pediatric Health Care Center, Faculty of Medicine, University of Szeged, Szeged, Hungary
| | - Judit C Sági
- Department of Genetics, Cell- and Immunobiology, Semmelweis University, Budapest, Hungary
| | - Gábor T Kovács
- 2 Department of Paediatrics, Semmelweis University, Budapest, Hungary
| | - András Falus
- Department of Genetics, Cell- and Immunobiology, Semmelweis University, Budapest, Hungary
| | | | - Csaba Szalai
- Department of Genetics, Cell- and Immunobiology, Semmelweis University, Budapest, Hungary .,Central Laboratory, Heim Pal Children Hospital, Budapest, Hungary
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16
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Al-Absi B, Noor SM, Saif-Ali R, Salem SD, Ahmed RH, Razif MF, Muniandy S. Association of ARID5B gene variants with acute lymphoblastic leukemia in Yemeni children. Tumour Biol 2017; 39:1010428317697573. [PMID: 28381164 DOI: 10.1177/1010428317697573] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Studies have shown an association between ARID5B gene polymorphisms and childhood acute lymphoblastic leukemia. However, the association between ARID5B variants and acute lymphoblastic leukemia among the Arab population still needs to be studied. The aim of this study was to investigate the association between ARID5B variants with acute lymphoblastic leukemia in Yemeni children. A total of 14 ARID5B gene single nucleotide polymorphisms (SNPs) were genotyped in 289 Yemeni children, of whom 136 had acute lymphoblastic leukemia and 153 were controls, using the nanofluidic Dynamic Array (Fluidigm 192.24 Dynamic Array). Using logistic regression adjusted for age and gender, the risks of acute lymphoblastic leukemia were presented as odds ratios and 95% confidence intervals. We found that nine SNPs were associated with acute lymphoblastic leukemia under additive genetic models: rs7073837, rs10740055, rs7089424, rs10821936, rs4506592, rs10994982, rs7896246, rs10821938, and rs7923074. Furthermore, the recessive models revealed that six SNPs were risk factors for acute lymphoblastic leukemia: rs10740055, rs7089424, rs10994982, rs7896246, rs10821938, and rs7923074. The gender-specific impact of these SNPs under the recessive genetic model revealed that SNPs rs10740055, rs10994982, and rs6479779 in females, and rs10821938 and rs7923074 in males were significantly associated with acute lymphoblastic leukemia risk. Under the dominant model, SNPs rs7073837, rs10821936, rs7896246, and rs6479778 in males only showed striking association with acute lymphoblastic leukemia. The additive model revealed that SNPs with significant association with acute lymphoblastic leukemia were rs10821936 (both males and females); rs7073837, rs10740055, rs10994982, and rs4948487 (females only); and rs7089424, rs7896246, rs10821938, and rs7923074 (males only). In addition, the ARID5B haplotype block (CGAACACAA) showed a higher risk for acute lymphoblastic leukemia. The haplotype (CCCGACTGC) was associated with protection against acute lymphoblastic leukemia. In conclusion, our study has shown that ARID5B variants are associated with acute lymphoblastic leukemia in Yemeni children with several gender biases of ARID5B single nucleotide polymorphisms reported.
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Affiliation(s)
- Boshra Al-Absi
- 1 Department of Molecular Medicine, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Suzita M Noor
- 2 Department of Biomedical Science, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Riyadh Saif-Ali
- 3 Department of Biochemistry and Molecular Biology, Faculty of Medicine, Sana'a University, Sana'a, Yemen
| | - Sameer D Salem
- 3 Department of Biochemistry and Molecular Biology, Faculty of Medicine, Sana'a University, Sana'a, Yemen
| | - Radwan H Ahmed
- 1 Department of Molecular Medicine, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Muhammad Fm Razif
- 1 Department of Molecular Medicine, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Sekaran Muniandy
- 1 Department of Molecular Medicine, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
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17
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Bashash M, Connors JM, Gascoyne RD, Meissner B, Schuetz JM, Leach S, Slack GW, Berry BR, Hu H, Sehn LH, Brooks-Wilson AR, Spinelli JJ. Genetic polymorphism at BCL2 as a predictor for rituximab, cyclophosphamide, doxorubicin, vincristine and prednisone efficacy in patients with diffuse large B-cell lymphoma. Haematologica 2017; 102:e199-e202. [PMID: 28154089 DOI: 10.3324/haematol.2016.159087] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Affiliation(s)
- Morteza Bashash
- Department of Cancer Control Research, BC Cancer Agency, Vancouver, BC, Canada.,Dalla Lana School of Public Health, University of Toronto, ON, Canada
| | - Joseph M Connors
- Division of Medical Oncology, BC Cancer Agency, Vancouver, BC, Canada.,Department of Lymphoid Cancer Research, BC Cancer Agency, Vancouver, BC, Canada
| | - Randy D Gascoyne
- Department of Pathology, BC Cancer Agency, Vancouver, BC, Canada.,Department of Lymphoid Cancer Research, BC Cancer Agency, Vancouver, BC, Canada
| | - Barbara Meissner
- Department of Lymphoid Cancer Research, BC Cancer Agency, Vancouver, BC, Canada
| | - Johanna M Schuetz
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC, Canada
| | - Stephen Leach
- Department of Cancer Control Research, BC Cancer Agency, Vancouver, BC, Canada
| | - Graham W Slack
- Department of Pathology, BC Cancer Agency, Vancouver, BC, Canada.,Department of Lymphoid Cancer Research, BC Cancer Agency, Vancouver, BC, Canada
| | - Brian R Berry
- Department of Pathology, Royal Jubilee Hospital, Victoria, BC, Canada
| | - Howard Hu
- Dalla Lana School of Public Health, University of Toronto, ON, Canada
| | - Laurie H Sehn
- Division of Medical Oncology, BC Cancer Agency, Vancouver, BC, Canada.,Department of Lymphoid Cancer Research, BC Cancer Agency, Vancouver, BC, Canada
| | - Angela R Brooks-Wilson
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC, Canada.,Department of Pathology, Royal Jubilee Hospital, Victoria, BC, Canada.,Department of Biomedical Physiology and Kinesiology, Simon Fraser University, Burnaby, BC, Canada
| | - John J Spinelli
- Department of Cancer Control Research, BC Cancer Agency, Vancouver, BC, Canada .,School of Population and Public Health, University of British Columbia, Vancouver, BC, Canada
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18
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Zeng H, Wang XB, Cui NH, Nam S, Zeng T, Long X. Associations between AT-rich interactive domain 5B gene polymorphisms and risk of childhood acute lymphoblastic leukemia: a meta-analysis. Asian Pac J Cancer Prev 2017; 15:6211-7. [PMID: 25124600 DOI: 10.7314/apjcp.2014.15.15.6211] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Previous genome-wide association studies (GWAS) have implicated several single nucleotide polymorphisms (SNPs) in the AT-rich interactive domain 5B (ARID5B) gene with childhood acute lymphoblastic leukemia (ALL). However, replicated studies reported some inconsistent results in different populations. Using meta-analysis, we here aimed to clarify the nature of the genetic risks contributed by the two polymorphisms (rs10994982, rs7089424) for developing childhood ALL. Through searches of PubMed, EMBASE, and manually searching relevant references, a total of 14 articles with 16 independent studies were included. Odds ratios (ORs) with 95% confidence intervals (95%CI) were calculated to assess the associations. Both SNPs rs10994982 and rs7089424 showed significant associations with childhood ALL risk in all genetic models after Bonferroni correction. Furthermore, subtype analyses of B-lineage ALL provided strong evidence that SNP rs10994982 is highly associated with the risk of developing B-hyperdiploid ALL. These results indicate that SNPs rs10994982 and rs7089424 are indeed significantly associated with increased risk of childhood ALL.
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Affiliation(s)
- Hui Zeng
- Center for Gene Diagnosis, Zhongnan Hospital of Wuhan University, Wuhan, China E-mail :
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19
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Fodor LE, Gézsi A, Ungvári L, Semsei AF, Gál Z, Nagy A, Gálffy G, Tamási L, Kiss A, Antal P, Szalai C. Investigation of the Possible Role of the Hippo/YAP1 Pathway in Asthma and Allergy. ALLERGY, ASTHMA & IMMUNOLOGY RESEARCH 2017; 9:247-256. [PMID: 28293931 PMCID: PMC5352576 DOI: 10.4168/aair.2017.9.3.247] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Revised: 11/09/2016] [Accepted: 11/16/2016] [Indexed: 01/29/2023]
Abstract
Purpose Several lines of evidence indicate that the Hippo/Yes-associated protein 1 (YAP1) pathways might play a role in the pathogenesis of asthma. To investigate the possible role of the Hippo/YAP1 pathway in the pathogenesis of asthma or its phenotypes. Methods The levels of gene expressions of the members of the Hippo/YAP1 were compared. The presence of the proteins of the YAP1 and FRMD6 were analyzed with Western blot in induced sputum of 18 asthmatic subjects and 10 control subjects. Fourteen single nucleotide polymorphisms (SNPs) in the YAP1 gene were genotyped in 522 asthmatic subjects and 711 healthy controls. The results were evaluated with traditional frequentist methods and with Bayesian network-based Bayesian multilevel analysis of relevance (BN-BMLA). Results The mRNA of all the members of the Hippo/YAP1 pathway could be detected in the induced sputum of both controls and cases. A correlation was found between YAP1 mRNA levels and sputum bronchial epithelial cells (r=0.575, P=0.003). The signal for the FRMD6 protein could be detected in all sputum samples while the YAP1 protein could not be detected in the sputum samples, of the healthy controls and severe asthmatics, but it was detectable in mild asthmatics. The rs2846836 SNP of the YAP1 gene was significantly associated with exercise-induced asthma (odds ratio [OR]=2.1 [1.3-3.4]; P=0.004). The distribution of genotypes of rs11225138 and certain haplotypes of the YAP1 gene showed significant differences between different asthma severity statuses. With BN-BMLA, 2 SNPs, genetic variations in the FRMD6 gene proved to be the most relevant to exercise-induced asthma and allergic rhinitis. These 2 SNPs through allergic rhinitis and exercise-induced asthma were in epistatic interaction with each other. Conclusions Our results provided additional evidence that the FRMD6/Hippo/YAP1 pathway plays a role in the pathogenesis of asthma. If additional studies can confirm these findings, this pathway can be a potential novel therapeutic target in asthma and other inflammatory airway diseases.
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Affiliation(s)
- Lili E Fodor
- Department of Genetics, Cell- and Immunobiology, Semmelweis University, Budapest, Hungary
| | - András Gézsi
- Department of Genetics, Cell- and Immunobiology, Semmelweis University, Budapest, Hungary
| | - Ldikó Ungvári
- Department of Genetics, Cell- and Immunobiology, Semmelweis University, Budapest, Hungary
| | - Agnes F Semsei
- Department of Genetics, Cell- and Immunobiology, Semmelweis University, Budapest, Hungary
| | - Zsófia Gál
- Department of Genetics, Cell- and Immunobiology, Semmelweis University, Budapest, Hungary
| | | | - Gabriella Gálffy
- Department of Pulmonology, Semmelweis University, Budapest, Hungary
| | - Lilla Tamási
- Department of Pulmonology, Semmelweis University, Budapest, Hungary
| | - András Kiss
- Heim, Pal Children Hospital, Budapest, Hungary
| | - Péter Antal
- Department of Measurement and Information Systems, University of Technology and Economics, Budapest, Hungary
| | - Csaba Szalai
- Department of Genetics, Cell- and Immunobiology, Semmelweis University, Budapest, Hungary.,Heim, Pal Children Hospital, Budapest, Hungary.
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20
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Yoon J, Choi YJ, Lee E, Cho HJ, Yang SI, Kim YH, Jung YH, Seo JH, Kwon JW, Kim HB, Lee SY, Kim BS, Shim JY, Kim EJ, Lee JS, Hong SJ. Allergic Rhinitis in Preschool Children and the Clinical Utility of FeNO. ALLERGY, ASTHMA & IMMUNOLOGY RESEARCH 2017; 9:314-321. [PMID: 28497918 PMCID: PMC5446946 DOI: 10.4168/aair.2017.9.4.314] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/02/2016] [Revised: 10/31/2016] [Accepted: 12/19/2016] [Indexed: 12/27/2022]
Abstract
PURPOSE The nature of allergic rhinitis (AR) in preschool aged children remains incompletely characterized. This study aimed to investigate the prevalence of AR and its associated risk factors in preschool-aged children and to assess the clinical utility of fractional exhaled nitric oxide (FeNO). METHODS This general population-based, cross-sectional survey included 933 preschool-aged (3- to 7-year-old) children from Korea. Current AR was defined as having nasal symptoms within the last 12 months and physician-diagnosed AR. RESULTS The prevalence of current AR in preschool children was 17.0% (156/919). Mold exposure (adjusted odds ratio [aOR], 1.67; 95% confidence interval [CI], 1.15-2.43) and the use of antibiotics (aOR, 1.97; 95% CI, 1.33-2.90) during infancy were associated with an increased risk of current AR, whereas having an older sibling (aOR, 0.52; 95% CI, 0.35-0.75) reduced the risk. Children with current atopic AR had significantly higher geometric mean levels of FeNO compared to those with non-atopic rhinitis (12.43; range of 1standard deviation [SD], 7.31-21.14 vs 8.25; range of 1SD, 5.62-12.10, P=0.001) or non-atopic healthy children (8.58; range of 1SD, 5.51-13.38, P<0.001). The FeNO levels were higher in children with current atopic AR compared with atopic healthy children (9.78; range of 1SD, 5.97-16.02, P=0.083). CONCLUSIONS Mold exposure and use of antibiotics during infancy increases the risk of current AR, whereas having an older sibling reduces it. Children with current atopic AR exhibit higher levels of FeNO compared with non-atopic rhinitis cases, suggesting that FeNO levels may be a useful discriminatory marker for subtypes of AR in preschool children.
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Affiliation(s)
- Jisun Yoon
- Department of Pediatrics, Childhood Asthma Atopy Center, Research Center for the Standardization of Allergic Diseases, University of Ulsan College of Medicine, Asan Medical Center, Seoul, Korea
| | - Yean Jung Choi
- Department of Pediatrics, Childhood Asthma Atopy Center, Research Center for the Standardization of Allergic Diseases, University of Ulsan College of Medicine, Asan Medical Center, Seoul, Korea
| | - Eun Lee
- Department of Pediatrics, Chonnam National University Hospital, Gwangju, Korea
| | - Hyun Ju Cho
- Department of Pediatrics, Childhood Asthma Atopy Center, Research Center for the Standardization of Allergic Diseases, University of Ulsan College of Medicine, Asan Medical Center, Seoul, Korea
| | - Song I Yang
- Department of Pediatrics, Hallym University Sacred Heart Hospital, Hallym University College of Medicine, Anyang, Korea
| | - Young Ho Kim
- Department of Pediatrics, Gyeongsang National University Changwon Hospital, Gyeongsang, Korea
| | - Young Ho Jung
- Department of Pediatrics, CHA Bundang Medical Center, College of Medicine, CHA University, Seongnam, Korea
| | - Ju Hee Seo
- Department of Pediatrics, Dankook University Hospital, Cheonan, Korea
| | - Ji Won Kwon
- Department of Pediatrics, Seoul National University Bundang Hospital, Seongnam, Korea
| | - Hyo Bin Kim
- Department of Pediatrics, Inje University Sanggye Paik Hospital, Inje University College of Medicine, Seoul, Korea
| | - So Yeon Lee
- Department of Pediatrics, Hallym University Sacred Heart Hospital, Hallym University College of Medicine, Anyang, Korea
| | - Bong Seong Kim
- Department of Pediatrics, Gangneung Asan Hospital, Gangneung, Korea
| | - Jung Yeon Shim
- Department of Pediatrics, Kangbuk Samsung Hospital, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Eun Jin Kim
- Division of Allergy and Chronic Respiratory Diseases, Center for Biomedical Sciences, Korea National Institute of Health, Korea Center for Disease Control and Prevention, Cheongju, Korea
| | - Joo Shil Lee
- Division of Allergy and Chronic Respiratory Diseases, Center for Biomedical Sciences, Korea National Institute of Health, Korea Center for Disease Control and Prevention, Cheongju, Korea
| | - Soo Jong Hong
- Department of Pediatrics, Childhood Asthma Atopy Center, Research Center for the Standardization of Allergic Diseases, University of Ulsan College of Medicine, Asan Medical Center, Seoul, Korea.
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Gharbi H, Ben Hassine I, Soltani I, Safra I, Ouerhani S, Bel Haj Othmen H, Teber M, Farah A, Amouri H, Toumi NH, Abdennebi S, Abbes S, Menif S. Association of genetic variation in IKZF1, ARID5B, CDKN2A, and CEBPE with the risk of acute lymphoblastic leukemia in Tunisian children and their contribution to racial differences in leukemia incidence. Pediatr Hematol Oncol 2016; 33:157-67. [PMID: 27184773 DOI: 10.3109/08880018.2016.1161685] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Recent genome-wide association studies (GWAS) focusing on pediatric acute lymphoblastic leukemia (ALL), the most common malignancy in children younger than 15 years old, have found evidence that single-nucleotide polymorphisms (SNPs) in IKZF1 (7p12.2), ARID5B (10q21.2), CDKN2A (9p21.3), and CEBPE (14q11.2) are strongly associated to the risk of developing pediatric ALL. These studies have been conducted in European and Thai populations, and it is unclear whether these observations generalize to other populations with a lower incidence of pediatric ALL. In order to explore the impact of these variants on pediatric ALL risk in the Tunisian population, we genotyped 58 cases of pediatric ALL and 150 controls for SNPs rs4132601 (7p12.2), rs7089424 (10q21.2), rs3731217 (9p21.3), and rs2239633 (14q11.2). Our results, which are consistent with findings in European populations, show that 3 SNPs, i.e., rs4132601 (P = .00116, odds ratio [OR] = 2.78, 95% confidence interval [CI] = [1.42, 5.87]), rs7089424 (P = .0022, OR = 0.49, 95% CI = [0.31, 0.79]), and rs2239633 (P = .0010, OR = 0.47, 95% CI = [0.29, 0.75]) are significantly associated with a higher risk of developing pediatric ALL (P < .05). Furthermore, we show differences in allele frequencies in SNPs between Tunisian and Caucasian and/or Thai populations (e.g., CEBPE, rs2239633; population attributable risk [PAR] ∼15-fold the PAR of Thai population). These differences, combined with differences in linkage disequilibrium structure between populations and differences in size between populations, may contribute to racial differences in pediatric ALL incidence.
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Affiliation(s)
- Hanene Gharbi
- a Laboratory of Molecular and Cellular Hematology , Pasteur Institute of Tunis, University of Tunis El Manar , Tunis , Tunisia
| | - Islem Ben Hassine
- a Laboratory of Molecular and Cellular Hematology , Pasteur Institute of Tunis, University of Tunis El Manar , Tunis , Tunisia
| | - Ismail Soltani
- a Laboratory of Molecular and Cellular Hematology , Pasteur Institute of Tunis, University of Tunis El Manar , Tunis , Tunisia
| | - Ines Safra
- a Laboratory of Molecular and Cellular Hematology , Pasteur Institute of Tunis, University of Tunis El Manar , Tunis , Tunisia
| | - Slah Ouerhani
- a Laboratory of Molecular and Cellular Hematology , Pasteur Institute of Tunis, University of Tunis El Manar , Tunis , Tunisia
| | - Hind Bel Haj Othmen
- a Laboratory of Molecular and Cellular Hematology , Pasteur Institute of Tunis, University of Tunis El Manar , Tunis , Tunisia
| | - Mouheb Teber
- a Laboratory of Molecular and Cellular Hematology , Pasteur Institute of Tunis, University of Tunis El Manar , Tunis , Tunisia
| | - Ahlem Farah
- a Laboratory of Molecular and Cellular Hematology , Pasteur Institute of Tunis, University of Tunis El Manar , Tunis , Tunisia
| | - Hassiba Amouri
- a Laboratory of Molecular and Cellular Hematology , Pasteur Institute of Tunis, University of Tunis El Manar , Tunis , Tunisia
| | | | | | - Salem Abbes
- a Laboratory of Molecular and Cellular Hematology , Pasteur Institute of Tunis, University of Tunis El Manar , Tunis , Tunisia
| | - Samia Menif
- a Laboratory of Molecular and Cellular Hematology , Pasteur Institute of Tunis, University of Tunis El Manar , Tunis , Tunisia
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Zhang XX, Du YF, Zhai YJ, Gao F, Yang YJ, Ma XC, Lu J, Zheng J. A common genetic variation in CEBPE and acute lymphoblastic leukemia: a meta-analysis of the available evidence. Onco Targets Ther 2015; 8:2443-51. [PMID: 26388693 PMCID: PMC4571986 DOI: 10.2147/ott.s89661] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Acute lymphoblastic leukemia (ALL) has been studied intensively for decades, but the details of its etiology and underlying mechanisms have yet to be fully elucidated. It is now generally acknowledged that genetic factors contribute greatly to the development of this disease. The gene encoding CCAAT/enhancer-binding protein ε (CEBPE) is involved in the development of leukemia, and in particular the rs2239633 single nucleotide polymorphism (SNP) of CEBPE. The association between rs2239633 and risk of ALL has been well studied, but remains unclear. Therefore, a meta-analysis was performed in this study to establish a more precise estimation of that relationship. A comprehensive literature search of the PubMed electronic database was conducted, and relevant studies published up to February 20, 2015 were selected for analysis. The references of the retrieved articles were also screened. The extracted data were analyzed statistically, and pooled odds ratios with 95% confidence intervals were calculated using Review Manager (version 5.2) to estimate the association strength. Finally, eleven studies were included in the meta-analysis. The pooled analyses revealed that rs2239633 was associated with an increased risk of childhood ALL in Caucasians under any contrast models (P<0.01). However, this SNP did not affect the risk of ALL in adulthood among Caucasians, or in childhood among East Asians. In conclusion, these findings confirm that the CEBPE rs2239633 SNP could be considered a good marker of pediatric ALL risk in Caucasians, but not in East Asians; it is not a good marker of adult ALL risk in Caucasians.
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Affiliation(s)
- Xiao-Xia Zhang
- Department of Pharmacy, The First Affiliated Hospital, Xi'an Jiaotong University, Xi'an, Shaanxi, People's Republic of China
| | - Yue-Feng Du
- Department of Urology, The First Affiliated Hospital, Xi'an Jiaotong University, Xi'an, Shaanxi, People's Republic of China
| | - Ya-Jing Zhai
- Department of Pharmacy, The First Affiliated Hospital, Xi'an Jiaotong University, Xi'an, Shaanxi, People's Republic of China
| | - Fan Gao
- Clinical Research Center, The First Affiliated Hospital, Xi'an Jiaotong University, Xi'an, Shaanxi, People's Republic of China
| | - Yu-Juan Yang
- The Third Department of Cardiology, Shaanxi Provincial People's Hospital, Xi'an, Shaanxi, People's Republic of China
| | - Xian-Cang Ma
- Clinical Research Center, The First Affiliated Hospital, Xi'an Jiaotong University, Xi'an, Shaanxi, People's Republic of China
| | - Jun Lu
- Clinical Research Center, The First Affiliated Hospital, Xi'an Jiaotong University, Xi'an, Shaanxi, People's Republic of China
| | - Jie Zheng
- Clinical Research Center, The First Affiliated Hospital, Xi'an Jiaotong University, Xi'an, Shaanxi, People's Republic of China
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Brisson GD, Alves LR, Pombo-de-Oliveira MS. Genetic susceptibility in childhood acute leukaemias: a systematic review. Ecancermedicalscience 2015; 9:539. [PMID: 26045716 PMCID: PMC4448992 DOI: 10.3332/ecancer.2015.539] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2015] [Indexed: 11/06/2022] Open
Abstract
Acute leukaemias (AL) correspond to 25-35% of all cancer cases in children. The aetiology is still sheltered, although several factors are implicated in causality of AL subtypes. Childhood acute leukaemias are associated with genetic syndromes (5%) and ionising radiation as risk factors. Somatic genomic alterations occur during fetal life and are initiating events to childhood leukaemia. Genetic susceptibility has been explored as a risk factor, since environmental exposure of the child to xenobiotics, direct or indirectly, can contribute to the accumulation of somatic mutations. Hence, a systematic review was conducted in order to understand the association between gene polymorphisms and childhood leukaemia risk. The search was performed in the electronic databases PubMed, Lilacs, and Scielo, selecting articles published between 1995 and 2013. This review included 90 case-control publications, which were classified into four groups: xenobiotic system (n = 50), DNA repair (n = 16), regulatory genes (n = 15), and genome wide association studies (GWAS) (n = 9). We observed that the most frequently investigated genes were: NQO1, GSTM1, GSTT1, GSTP1, CYP1A1, NAT2, CYP2D6, CYP2E1, MDR1 (ABCB1), XRCC1, ARID5B, and IKZF1. The collected evidence suggests that genetic polymorphisms in CYP2E1, GSTM1, NQO1, NAT2, MDR1, and XRCC1 are capable of modulating leukaemia risk, mainly when associated with environmental exposures, such as domestic pesticides and insecticides, smoking, trihalomethanes, alcohol consumption, and x-rays. More recently, genome wide association studies identified significant associations between genetic polymorphisms in ARID5B e IKZF1 and acute lymphoblastic leukaemia, but only a few studies have replicated these results until now. In conclusion, genetic susceptibility contributes to the risk of childhood leukaemia through the effects of gene-gene and gene-environment interactions.
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Affiliation(s)
- Gisele D Brisson
- Paediatric Haematology-Oncology Programme, Research Centre, Instituto Nacional de Câncer, Rio de Janeiro, Brazil, 20231050
| | - Liliane R Alves
- Pharmacy Service, Multiprofessional Residency Programme, Instituto Nacional de Câncer, Rio de Janeiro, Brazil, 20231050
| | - Maria S Pombo-de-Oliveira
- Paediatric Haematology-Oncology Programme, Research Centre, Instituto Nacional de Câncer, Rio de Janeiro, Brazil, 20231050
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Gabor KM, Schermann G, Lautner-Csorba O, Rarosi F, Erdelyi DJ, Endreffy E, Berek K, Bartyik K, Bereczki C, Szalai C, Semsei AF. Impact of single nucleotide polymorphisms of cytarabine metabolic genes on drug toxicity in childhood acute lymphoblastic leukemia. Pediatr Blood Cancer 2015; 62:622-8. [PMID: 25557962 DOI: 10.1002/pbc.25379] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/07/2014] [Accepted: 11/05/2014] [Indexed: 11/05/2022]
Abstract
BACKGROUND Cytarabine (cytosine arabinoside, ara-C) is a chemotherapeutical agent used in the treatment of pediatric acute lymphoblastic leukemia (ALL). Adverse drug reactions, such as interpatient variability in sensitivity to ara-C, are considerable and may cause difficulties during chemotherapy. Single nucleotide polymorphisms (SNPs) can play a significant role in modifying nucleoside-drug pharmacokinetics and pharmacodynamics and thus the development of adverse effects. Our aim was to determine whether polymorphisms in genes encoding transporters and enzymes responsible for the metabolism of ara-C are associated with toxicity and clinical outcome in a patient population with childhood ALL. PROCEDURE We studied 8 SNPs in the CDA, DCK, DCTD, SLC28A3, and SLC29A1 genes in 144 patients with childhood acute lymphoblastic leukemia treated according to ALLIC BFM 1990, 1995 and 2002 protocols. RESULTS DCK rs12648166 and DCK rs4694362 SNPs were associated with hematologic toxicity (OR = 2.63, CI 95% = 1.37-5.04, P = 0.0036 and OR = 2.53, CI 95% = 1.34-4.80, P = 0.0044, respectively). CONCLUSIONS Our results indicate that DCK polymorphisms might be important genetic risk factors for hematologic toxicity during ALL treatment with ara-C. Individualized chemotherapy based on genetic profiling may help to optimize ara-C dosing, leading to improvements in clinical outcome and reduced toxicity.
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Affiliation(s)
- Krisztina Mita Gabor
- Department of Pediatrics and Pediatric Health Care Center, Faculty of Medicine, University of Szeged, Hungary
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Pan Y, Chen H, Liang H, Wang X, Wang L. Meta-analysis of the association between CCAAT/enhancer binding protein-ε polymorphism and the risk of childhood acute lymphoblastic leukemia. Int J Clin Exp Med 2014; 7:5553-5557. [PMID: 25664070 PMCID: PMC4307517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2014] [Accepted: 11/24/2014] [Indexed: 06/04/2023]
Abstract
CEBPE rs2239633 polymorphism has been implicated in susceptibility to childhood acute lymphoblastic leukemia (ALL) risk. Several studies investigated the association of this polymorphism with ALL in different populations. However, the results were contradictory. A meta-analysis was conducted to assess the association between CEBPE rs2239633 polymorphism and ALL susceptibility. Databases including Pubmed, EMBASE, Chinese National Knowledge Infrastructure (CNKI) and Wangfang were searched to find relevant studies. Odds ratios (ORs) with 95% confidence intervals (CIs) were used to assess the strength of associations. A random-effects model was used. A significant association was found between CEBPE rs2239633 polymorphism and childhood ALL (OR = 1.19, 95% CI, 1.11-1.28). In the subgroup analyses by ethnicity, the significant association was found among Caucasians (OR = 1.19, 95% CI, 1.09-1.30) and Hispanics (OR = 1.39, 95% CI, 1.18-1.63), but not in Asians (OR = 1.05, 95% CI, 0.90-1.22). In the subgroup analysis by histology, B-cell ALL risk (OR = 1.29, 95% CI, 1.15-1.44) and B hyperdiploid ALL risk (OR = 1.84, 95% CI, 1.40-2.43) were increased. Our results suggested that CEBPE rs2239633 polymorphism conferred a risk factor of childhood ALL.
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Affiliation(s)
- Yangqiong Pan
- Department of Emergency, Children’s Hospital of ZhengzhouZhengzhou 450052, Henan, China
| | - Hao Chen
- Department of pediatrics, The Third Affiliated Hospital of Zhengzhou UniversityZhengzhou 450052, Henan, China
| | - Hong Liang
- Department of Emergency, Children’s Hospital of ZhengzhouZhengzhou 450052, Henan, China
| | - Xiaowen Wang
- Department of Emergency, Children’s Hospital of ZhengzhouZhengzhou 450052, Henan, China
| | - Lingling Wang
- Department of Emergency, Children’s Hospital of ZhengzhouZhengzhou 450052, Henan, China
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26
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Dai YE, Tang L, Healy J, Sinnett D. Contribution of polymorphisms in IKZF1 gene to childhood acute leukemia: a meta-analysis of 33 case-control studies. PLoS One 2014; 9:e113748. [PMID: 25423013 PMCID: PMC4244140 DOI: 10.1371/journal.pone.0113748] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2014] [Accepted: 10/28/2014] [Indexed: 11/23/2022] Open
Abstract
Objective Two common polymorphisms in the IKZF1 gene (rs4132601 and rs11978267 variants) have been reported to be associated with childhood acute leukemia (AL) risk, however the results were inconsistent. Here, we conducted a meta-analysis to generate large-scale evidence on whether IKZF1 variants are risk factors for childhood AL. Methods The PubMed, Embase, EBSCO, and Web of Science were searched up to June 2, 2014 for studies on the association of IKZF1 polymorphisms with childhood AL risk. Data were extracted and the odd ratios (ORs) and95% confidence intervals (95% CIs) were calculated by a fixed-effects orrandom-effects model. Subgroup analysis by ethnicity and leukemia subtype, sensitivity and cumulative meta-analyses were performed. Moreover, publication bias was assessed by Begg's and Egger's tests. Results In total, 33 case control studies were finally included in this meta-analysis. For rs4132601 polymorphism, significantly increased AL risk was observed in all genetic models (the association was still significant when the p value was Bonferroni adjusted to 0.025). In the subgroup analysis by tumor type, statistical association was observed in B-cell precursor ALL (BCP-ALL). Additionally, when stratified by ethnicity, significantly increased AL risk was only observed in European subgroup, but not among African or mixed population subgroups. Finally, similar results were found forrs11978267 polymorphism. Conclusion In summary, this meta-analysis provides evidence that rs4132601 and rs11978267 polymorphisms in the IKZF1 gene mightcontribute to the occurrence of BCP-ALL, especially in European populations. Moreover, further studies with large sample size are required to clarify possibleroles of IKZF1 variants in other ethnic groups (e.g., Asians and Africans).
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Affiliation(s)
- Yue-e Dai
- Nanjing Children's Hospital, Nanjing Medical University, Nanjing, China
- * E-mail:
| | - Linjun Tang
- Department of Neurosurgery, Tongling People's Hospital, Tongling, Anhui, China
| | - Jasmine Healy
- Sainte-Justine University Hospital Research Center, Montreal, Quebec, Canada
| | - Daniel Sinnett
- Sainte-Justine University Hospital Research Center, Montreal, Quebec, Canada
- Department of Pediatrics, Faculty of Medicine, University of Montreal, Montreal, Quebec, Canada
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27
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Gézsi A, Lautner-Csorba O, Erdélyi DJ, Hullám G, Antal P, Semsei ÁF, Kutszegi N, Hegyi M, Csordás K, Kovács G, Szalai C. In interaction with gender a common CYP3A4 polymorphism may influence the survival rate of chemotherapy for childhood acute lymphoblastic leukemia. THE PHARMACOGENOMICS JOURNAL 2014; 15:241-7. [PMID: 25266680 DOI: 10.1038/tpj.2014.60] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2014] [Revised: 07/24/2014] [Accepted: 08/21/2014] [Indexed: 11/09/2022]
Abstract
CYP3A4 has an important role in the metabolisms of many drugs used in acute lymphoblastic leukemia (ALL) therapy; still, there are practically no publications about the role of CYP3A4 polymorphisms in ALL pharmacogenomics. We genotyped eight common single-nucleotide polymorphisms (SNPs) in the CYP3A4 and CYP3A5 genes in 511 children with ALL and investigated whether they influenced the survival of the patients. We involved additional 127 SNPs in 34 candidate genes and searched for interactions with respect to the survival rates. Significant association between the survival rates and the common rs2246709 SNP in the CYP3A4 gene was observed. The gender of the patients and the rs1076991 in the MTHFD1 gene strongly influenced this effect. We calculated new risk assessments involving the gender-rs2246709 interaction and showed that they significantly outperformed the earlier risk-group assessments at every time point. If this finding is confirmed in other populations, it can have a considerable prognostic significance.
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Affiliation(s)
- A Gézsi
- Department of Genetics, Cell- and Immunobiology, Semmelweis University, Budapest, Hungary
| | - O Lautner-Csorba
- Department of Genetics, Cell- and Immunobiology, Semmelweis University, Budapest, Hungary
| | - D J Erdélyi
- 2nd Department of Pediatrics, Semmelweis University, Budapest, Hungary
| | - G Hullám
- Department of Measurement and Information Systems, University of Technology and Economics, Budapest, Hungary
| | - P Antal
- Department of Measurement and Information Systems, University of Technology and Economics, Budapest, Hungary
| | - Á F Semsei
- Department of Genetics, Cell- and Immunobiology, Semmelweis University, Budapest, Hungary
| | - N Kutszegi
- Department of Genetics, Cell- and Immunobiology, Semmelweis University, Budapest, Hungary
| | - M Hegyi
- 2nd Department of Pediatrics, Semmelweis University, Budapest, Hungary
| | - K Csordás
- 2nd Department of Pediatrics, Semmelweis University, Budapest, Hungary
| | - G Kovács
- 2nd Department of Pediatrics, Semmelweis University, Budapest, Hungary
| | - C Szalai
- 1] Department of Genetics, Cell- and Immunobiology, Semmelweis University, Budapest, Hungary [2] Heim Pal Children Hospital, Budapest, Hungary [3] Csertex Research Laboratory, Budapest, Hungary
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28
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CEBPE polymorphism confers an increased risk of childhood acute lymphoblastic leukemia: a meta-analysis of 11 case-control studies with 5,639 cases and 10,036 controls. Ann Hematol 2014; 94:181-5. [PMID: 25195121 DOI: 10.1007/s00277-014-2186-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2014] [Accepted: 08/04/2014] [Indexed: 10/24/2022]
Abstract
The association between CCAAT/enhancer binding protein-ε (CEBPE) rs2239633 polymorphism and acute lymphoblastic leukemia (ALL) risk has been reported, but results of previous studies remain controversial and ambiguous. To assess the association between CEBPE rs2239633 polymorphism and childhood ALL risk, a meta-analysis was performed. Based on comprehensive searches of the PubMed, Embase, Chinese National Knowledge Infrastructure (CNKI), and Chinese Biomedical Literature Database (CBM), we identified outcome data from all articles estimating the association between CEBPE rs2239633 polymorphism and childhood ALL risk. The pooled odds ratio (OR) with 95 % confidence intervals (CIs) were calculated. A significant association between CEBPE rs2239633 polymorphism with childhood ALL was found (OR = 1.19, 95 % CI 1.11-1.28, P < 0.01). Subgroup analysis stratified by ethnicity also suggested a significant association between this polymorphism and childhood ALL in the Caucasian subgroup (OR = 1.19, 95 % CI 1.09-1.30, P < 0.01) and Hispanic subgroup (OR = 1.39, 95 % CI 1.18-1.63, P < 0.01). No significant association was observed in the Asian subgroup (OR = 1.05, 95 % CI 0.90-1.22, P = 0.53). The CEBPE rs2239633 polymorphism increased B cell ALL risk (OR = 1.29, 95 % CI 1.15-1.44, P < 0.01) and B hyperdiploid ALL risk (OR = 1.84, 95 % CI 1.40-2.43, P < 0.01). This meta-analysis demonstrated that the CEBPE rs2239633 polymorphism was significantly associated with childhood ALL risk.
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29
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Li S, Ren L, Fan L, Wang G. IKZF1rs4132601 polymorphism and acute lymphoblastic leukemia susceptibility: a meta-analysis. Leuk Lymphoma 2014; 56:978-82. [DOI: 10.3109/10428194.2014.939965] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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30
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Kennedy AE, Kamdar KY, Lupo PJ, Okcu MF, Scheurer ME, Dorak MT. Genetic markers in a multi-ethnic sample for childhood acute lymphoblastic leukemia risk. Leuk Lymphoma 2014; 56:169-74. [DOI: 10.3109/10428194.2014.910662] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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31
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Csordas K, Lautner-Csorba O, Semsei AF, Harnos A, Hegyi M, Erdelyi DJ, Eipel OT, Szalai C, Kovacs GT. Associations of novel genetic variations in the folate-related andARID5Bgenes with the pharmacokinetics and toxicity of high-dose methotrexate in paediatric acute lymphoblastic leukaemia. Br J Haematol 2014; 166:410-20. [DOI: 10.1111/bjh.12886] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2013] [Accepted: 03/04/2014] [Indexed: 11/29/2022]
Affiliation(s)
- Katalin Csordas
- 2nd Department of Paediatrics; Semmelweis University; Budapest Hungary
| | | | - Agnes F. Semsei
- Deparment of Genetics, Cell- and Immunbiology; Semmelweis University; Budapest Hungary
| | - Andrea Harnos
- Department of Biomathematics and Informatics; Faculty of Veterinary Science; Szent Istvan University; Budapest Hungary
| | - Marta Hegyi
- 2nd Department of Paediatrics; Semmelweis University; Budapest Hungary
| | - Daniel J. Erdelyi
- 2nd Department of Paediatrics; Semmelweis University; Budapest Hungary
| | - Oliver T. Eipel
- 2nd Department of Paediatrics; Semmelweis University; Budapest Hungary
| | - Csaba Szalai
- Deparment of Genetics, Cell- and Immunbiology; Semmelweis University; Budapest Hungary
| | - Gabor T. Kovacs
- 2nd Department of Paediatrics; Semmelweis University; Budapest Hungary
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Bayesian systems-based genetic association analysis with effect strength estimation and omic wide interpretation: a case study in rheumatoid arthritis. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2014; 1142:143-76. [PMID: 24706282 DOI: 10.1007/978-1-4939-0404-4_14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Rich dependency structures are often formed in genetic association studies between the phenotypic, clinical, and environmental descriptors. These descriptors may not be standardized, and may encompass various disease definitions and clinical endpoints which are only weakly influenced by various (e.g., genetic) factors. Such loosely defined complex intermediate clinical phenotypes are typically used in follow-up candidate gene association studies, e.g., after genome-wide analysis, to deepen the understanding of the associations and to estimate effect strength. This chapter discusses a solid methodology, which is useful in such a scenario, by using probabilistic graphical models, namely, Bayesian networks in the Bayesian statistical framework. This method offers systematically scalable, comprehensive hierarchical hypotheses about multivariate relevance. We discuss its workflow: from data engineering to semantic publication of the results. We overview the construction, visualization, and interpretation of complex hypotheses related to the structural analysis of relevance. Furthermore, we illustrate the use of a dependency model-based relevance measure, which takes into account the structural properties of the model, for quantifying the effect strength. Finally, we discuss the "interpretational" or translational challenge of a genetic association study, with a focus on the fusion of heterogeneous omic knowledge to reintegrate the results into a genome-wide context.
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Emerenciano M, Barbosa TC, Lopes BA, Blunck CB, Faro A, Andrade C, Meyer C, Marschalek R, Pombo-de-Oliveira MS. ARID5B polymorphism confers an increased risk to acquire specific MLL rearrangements in early childhood leukemia. BMC Cancer 2014; 14:127. [PMID: 24564228 PMCID: PMC3948138 DOI: 10.1186/1471-2407-14-127] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2013] [Accepted: 02/12/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Acute leukemia in early age (EAL) is characterized by acquired genetic alterations such as MLL rearrangements (MLL-r). The aim of this case-controlled study was to investigate whether single nucleotide polymorphisms (SNPs) of IKZF1, ARID5B, and CEBPE could be related to the onset of EAL cases (<24 months-old at diagnosis). METHODS The SNPs (IKZF1 rs11978267, ARID5B rs10821936 and rs10994982, CEBPE rs2239633) were genotyped in 265 cases [169 acute lymphoblastic leukemia (ALL) and 96 acute myeloid leukaemia (AML)] and 505 controls by Taqman allelic discrimination assay. Logistic regression was used to evaluate the association between SNPs of cases and controls, adjusted on skin color and/or age. The risk was determined by calculating odds ratios (ORs) with 95% confidence interval (CI). RESULTS Children with the IKZF1 SNP had an increased risk of developing MLL-germline ALL in white children. The heterozygous/mutant genotype in ARID5B rs10994982 significantly increased the risk for MLL-germline leukemia in white and non-white children (OR 2.60, 95% CI: 1.09-6.18 and OR 3.55, 95% CI: 1.57-8.68, respectively). The heterozygous genotype in ARID5B rs10821936 increased the risk for MLL-r leukemia in both white and non-white (OR 2.06, 95% CI: 1.12-3.79 and OR 2.36, 95% CI: 1.09-5.10, respectively). Furthermore, ARID5B rs10821936 conferred increased risk for MLL-MLLT3 positive cases (OR 7.10, 95% CI:1.54-32.68). Our data do not show evidence that CEBPE rs2239633 confers increased genetic susceptibility to EAL. CONCLUSIONS IKZF1 and CEBPE variants seem to play a minor role in genetic susceptibility to EAL, while ARID5B rs10821936 increased the risk of MLL-MLLT3. This result shows that genetic susceptibility could be associated with the differences regarding MLL breakpoints and partner genes.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Maria S Pombo-de-Oliveira
- Pediatric Hematology-Oncology Program, Research Center, Instituto Nacional de Câncer, Rua André Cavalcanti 37, Rio de Janeiro/RJ 20231-050, Brasil.
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Gutiérrez-Camino Á, López-López E, Martín-Guerrero I, Sánchez-Toledo J, García de Andoin N, Carboné Bañeres A, García-Miguel P, Navajas A, García-Orad Á. Intron 3 of the ARID5B gene: a hot spot for acute lymphoblastic leukemia susceptibility. J Cancer Res Clin Oncol 2013; 139:1879-86. [PMID: 24013273 DOI: 10.1007/s00432-013-1512-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2013] [Accepted: 08/30/2013] [Indexed: 11/30/2022]
Abstract
PURPOSE Single-nucleotide polymorphisms (SNPs) in AT-rich interactive domain 5B (ARID5B) have been associated with risk for pediatric acute lymphoblastic leukemia (ALL). After reviewing previous studies, we realized that the most significant associations were restricted to intron 3, but the mechanism(s) by which those SNPs affect ALL risk remain to be elucidated. Therefore, the aim of this study was to analyze the association between genetic variants of the intron 3 region of ARID5B and the incidence of B-ALL in a Spanish population. We also aimed to find a functional explanation for the association, searching for copy number variations (CNVs), and changes in ARID5B expression associated with the genotypes of the SNPs. METHODS We analyzed 10 SNPs in intron 3 of ARID5B in a Spanish population of 219 B-ALL patients and 397 unrelated controls with the Taqman Open Array platform. CNVs were analyzed in 23 patients and 17 controls using the Cytogenetics Whole-genome 2.7 M platform. Expression of ARID5B transcript 1 was quantified by qPCR and related to SNPs genotype in seven ALL cell lines. RESULTS Association between intron 3 and B-ALL risk was confirmed for all of the SNPs evaluated in our Spanish population. We could not explain this association by the presence of CNVs. We neither detected changes in the expression of ARID5B isoform associated with the genotype of the SNPs. CONCLUSIONS The intron 3 of ARID5B gene was found to be strongly associated with B-ALL risk in the Spanish population examined. However, neither CNVs nor changes in mRNA expression were found to be responsible for this association.
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Affiliation(s)
- Ángela Gutiérrez-Camino
- Department of Genetics, Physical Anthropology and Animal Physiology, Faculty of Medicine and Dentistry, University of the Basque Country (UPV/EHU), Barrio Sarriena s/n, 48940, Leioa, Spain
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ARID5B gene rs10821936 polymorphism is associated with childhood acute lymphoblastic leukemia: a meta-analysis based on 39,116 subjects. Tumour Biol 2013; 35:709-13. [PMID: 23975371 DOI: 10.1007/s13277-013-1097-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2013] [Accepted: 08/07/2013] [Indexed: 10/26/2022] Open
Abstract
Childhood acute lymphoblastic leukemia (ALL) is the leading cause of cancer-related deaths among children. Two recent genome-wide association studies and several replicated studies have provided convincing evidence that inherited genetic variation in ARID5B contributes to childhood ALL predisposition. In the present study, we performed a meta-analysis to systematically summarize the association between ARID5B genetic polymorphism and the risk for ALL. We conducted a search of case-control studies on the association of ARID5B genetic polymorphisms with susceptibility to ALL in PubMed, EMBASE, Wanfang database in China, and Chinese National Knowledge Infrastructure databases. Data from eligible studies were extracted for meta-analysis. ALL risk associated with ARID5B genetic polymorphism was estimated by pooled odds ratios (ORs) and 95% confidence intervals (95% CIs). Nine articles including 13 case-control studies were included in the present meta-analysis. We found that rs10821936 polymorphism in ARID5B gene was associated with increased risk for ALL (P < 0.0001; OR = 1.27; 95%CI, 1.17-1.37). This meta-analysis suggests that ARID5B genetic polymorphism was associated with the increased risk of ALL.
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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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Vereczkei A, Demetrovics Z, Szekely A, Sarkozy P, Antal P, Szilagyi A, Sasvari-Szekely M, Barta C. Multivariate analysis of dopaminergic gene variants as risk factors of heroin dependence. PLoS One 2013; 8:e66592. [PMID: 23840506 PMCID: PMC3696122 DOI: 10.1371/journal.pone.0066592] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2013] [Accepted: 05/08/2013] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Heroin dependence is a debilitating psychiatric disorder with complex inheritance. Since the dopaminergic system has a key role in rewarding mechanism of the brain, which is directly or indirectly targeted by most drugs of abuse, we focus on the effects and interactions among dopaminergic gene variants. OBJECTIVE To study the potential association between allelic variants of dopamine D2 receptor (DRD2), ANKK1 (ankyrin repeat and kinase domain containing 1), dopamine D4 receptor (DRD4), catechol-O-methyl transferase (COMT) and dopamine transporter (SLC6A3) genes and heroin dependence in Hungarian patients. METHODS 303 heroin dependent subjects and 555 healthy controls were genotyped for 7 single nucleotide polymorphisms (SNPs) rs4680 of the COMT gene; rs1079597 and rs1800498 of the DRD2 gene; rs1800497 of the ANKK1 gene; rs1800955, rs936462 and rs747302 of the DRD4 gene. Four variable number of tandem repeats (VNTRs) were also genotyped: 120 bp duplication and 48 bp VNTR in exon 3 of DRD4 and 40 bp VNTR and intron 8 VNTR of SLC6A3. We also perform a multivariate analysis of associations using Bayesian networks in Bayesian multilevel analysis (BN-BMLA). FINDINGS AND CONCLUSIONS In single marker analysis the TaqIA (rs1800497) and TaqIB (rs1079597) variants were associated with heroin dependence. Moreover, -521 C/T SNP (rs1800955) of the DRD4 gene showed nominal association with a possible protective effect of the C allele. After applying the Bonferroni correction TaqIB was still significant suggesting that the minor (A) allele of the TaqIB SNP is a risk component in the genetic background of heroin dependence. The findings of the additional multiple marker analysis are consistent with the results of the single marker analysis, but this method was able to reveal an indirect effect of a promoter polymorphism (rs936462) of the DRD4 gene and this effect is mediated through the -521 C/T (rs1800955) polymorphism in the promoter.
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Affiliation(s)
- Andrea Vereczkei
- Department of Medical Chemistry, Molecular Biology and Pathobiochemistry, Semmelweis University, Budapest, Hungary
| | - Zsolt Demetrovics
- Institute of Psychology, Eötvös Loránd University, Budapest, Hungary
| | - Anna Szekely
- Institute of Psychology, Eötvös Loránd University, Budapest, Hungary
| | - Peter Sarkozy
- Technical University of Budapest, Measurement and Information Systems, Budapest, Hungary
| | - Peter Antal
- Technical University of Budapest, Measurement and Information Systems, Budapest, Hungary
| | - Agnes Szilagyi
- 3rd Department of Internal Medicine, Research Laboratory, Semmelweis University, Budapest, Hungary
| | - Maria Sasvari-Szekely
- Department of Medical Chemistry, Molecular Biology and Pathobiochemistry, Semmelweis University, Budapest, Hungary
| | - Csaba Barta
- Department of Medical Chemistry, Molecular Biology and Pathobiochemistry, Semmelweis University, Budapest, Hungary
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Relling MV, Ramsey LB. Pharmacogenomics of acute lymphoid leukemia: new insights into treatment toxicity and efficacy. HEMATOLOGY. AMERICAN SOCIETY OF HEMATOLOGY. EDUCATION PROGRAM 2013; 2013:126-130. [PMID: 24319173 DOI: 10.1182/asheducation-2013.1.126] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Childhood acute lymphoblastic leukemia (ALL) provides an outstanding model for pharmacogenomic research: it is a drug-responsive disseminated cancer that is cured with medications alone in ∼ 85% of patients, but relapse remains unacceptably high for some subgroups. Inherited genomic variation contributes to the risk of relapse and to the risk of short- and long-term serious adverse effects of therapy. Our goal is to identify the inherited genomic variants that contribute to interindividual differences in response in patients with ALL. We discuss results of whole-genome interrogations of germline DNA in ALL.
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