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de Smith AJ, Wahlster L, Jeon S, Kachuri L, Black S, Langie J, Cato LD, Nakatsuka N, Chan TF, Xia G, Mazumder S, Yang W, Gazal S, Eng C, Hu D, Burchard EG, Ziv E, Metayer C, Mancuso N, Yang JJ, Ma X, Wiemels JL, Yu F, Chiang CWK, Sankaran VG. A noncoding regulatory variant in IKZF1 increases acute lymphoblastic leukemia risk in Hispanic/Latino children. Cell Genom 2024; 4:100526. [PMID: 38537633 PMCID: PMC11019360 DOI: 10.1016/j.xgen.2024.100526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 12/11/2023] [Accepted: 02/27/2024] [Indexed: 04/04/2024]
Abstract
Hispanic/Latino children have the highest risk of acute lymphoblastic leukemia (ALL) in the US compared to other racial/ethnic groups, yet the basis of this remains incompletely understood. Through genetic fine-mapping analyses, we identified a new independent childhood ALL risk signal near IKZF1 in self-reported Hispanic/Latino individuals, but not in non-Hispanic White individuals, with an effect size of ∼1.44 (95% confidence interval = 1.33-1.55) and a risk allele frequency of ∼18% in Hispanic/Latino populations and <0.5% in European populations. This risk allele was positively associated with Indigenous American ancestry, showed evidence of selection in human history, and was associated with reduced IKZF1 expression. We identified a putative causal variant in a downstream enhancer that is most active in pro-B cells and interacts with the IKZF1 promoter. This variant disrupts IKZF1 autoregulation at this enhancer and results in reduced enhancer activity in B cell progenitors. Our study reveals a genetic basis for the increased ALL risk in Hispanic/Latino children.
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Affiliation(s)
- Adam J de Smith
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, University of Southern California Keck School of Medicine, Los Angeles, CA 90033, USA; USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90033, USA.
| | - Lara Wahlster
- Division of Hematology/Oncology, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Soyoung Jeon
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, University of Southern California Keck School of Medicine, Los Angeles, CA 90033, USA; USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90033, USA
| | - Linda Kachuri
- Department of Epidemiology and Population Health, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Susan Black
- Division of Hematology/Oncology, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Jalen Langie
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, University of Southern California Keck School of Medicine, Los Angeles, CA 90033, USA; USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90033, USA
| | - Liam D Cato
- Division of Hematology/Oncology, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | - Tsz-Fung Chan
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, University of Southern California Keck School of Medicine, Los Angeles, CA 90033, USA; USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90033, USA
| | - Guangze Xia
- GMU-GIBH Joint School of Life Sciences, The Guangdong-Hong Kong-Macau Joint Laboratory for Cell Fate Regulation and Diseases, Guangzhou National Laboratory, Guangzhou Medical University, Guangzhou, China
| | - Soumyaa Mazumder
- Division of Hematology/Oncology, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Wenjian Yang
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Steven Gazal
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, University of Southern California Keck School of Medicine, Los Angeles, CA 90033, USA; USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90033, USA
| | - Celeste Eng
- Department of Medicine, Institute for Human Genetics, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Bioengineering and Biotherapeutic Sciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Donglei Hu
- Department of Medicine, Institute for Human Genetics, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Esteban González Burchard
- Department of Medicine, Institute for Human Genetics, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Bioengineering and Biotherapeutic Sciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Elad Ziv
- Department of Medicine, Institute for Human Genetics, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Catherine Metayer
- School of Public Health, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Nicholas Mancuso
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, University of Southern California Keck School of Medicine, Los Angeles, CA 90033, USA; USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90033, USA
| | - Jun J Yang
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Xiaomei Ma
- Yale School of Public Health, New Haven, CT 06520, USA
| | - Joseph L Wiemels
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, University of Southern California Keck School of Medicine, Los Angeles, CA 90033, USA; USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90033, USA
| | - Fulong Yu
- Division of Hematology/Oncology, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; GMU-GIBH Joint School of Life Sciences, The Guangdong-Hong Kong-Macau Joint Laboratory for Cell Fate Regulation and Diseases, Guangzhou National Laboratory, Guangzhou Medical University, Guangzhou, China
| | - Charleston W K Chiang
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, University of Southern California Keck School of Medicine, Los Angeles, CA 90033, USA; USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90033, USA
| | - Vijay G Sankaran
- Division of Hematology/Oncology, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
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de Smith AJ, Jiménez-Morales S, Mejía-Aranguré JM. The genetic risk of acute lymphoblastic leukemia and its implications for children of Latin American origin. Front Oncol 2024; 13:1299355. [PMID: 38264740 PMCID: PMC10805326 DOI: 10.3389/fonc.2023.1299355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Accepted: 12/12/2023] [Indexed: 01/25/2024] Open
Abstract
Acute lymphoblastic leukemia (ALL) is the most common cancer in children, and disproportionately affects children of Hispanic/Latino ethnicity in the United States, who have the highest incidence of disease compared with other racial/ethnic groups. Incidence of childhood ALL is similarly high in several Latin American countries, notably in Mexico, and of concern is the rising incidence of childhood ALL in some Hispanic/Latino populations that may further widen this disparity. Prior studies have implicated common germline genetic variants in the increased risk of ALL among Hispanic/Latino children. In this review, we describe the known disparities in ALL incidence as well as patient outcomes that disproportionately affect Hispanic/Latino children across the Americas, and we focus on the role of genetic variation as well as Indigenous American ancestry in the etiology of these disparities. Finally, we discuss future avenues of research to further our understanding of the causes of the disparities in ALL incidence and outcomes in children of Latin American origin, which will be required for future precision prevention efforts.
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Affiliation(s)
- Adam J. de Smith
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, University of Southern California Keck School of Medicine, Los Angeles, CA, United States
- USC Norris Comprehensive Cancer Center, University of Southern California Keck School of Medicine, Los Angeles, CA, United States
| | - Silvia Jiménez-Morales
- Laboratorio de Innovación y Medicina de Precisión, Núcleo A, Instituto Nacional de Medicina Genómica, Ciudad de México, Mexico
| | - Juan Manuel Mejía-Aranguré
- Laboratorio de Genómica Funcional del Cáncer, Instituto Nacional de Medicina Genómica, Ciudad de México, Mexico
- Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
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Al-Zayan NR, Ashour MJ, Abuwarda HN, Sharif FA. ARID5B, IKZF1, GATA3, CEBPE, and CDKN2A germline polymorphisms and predisposition to childhood acute lymphoblastic leukemia. Pediatr Hematol Oncol 2023; 41:103-113. [PMID: 37578068 DOI: 10.1080/08880018.2023.2234946] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 04/10/2023] [Accepted: 06/21/2023] [Indexed: 08/15/2023]
Abstract
Acute lymphoblastic leukemia (ALL) is the most frequent type of pediatric cancer. Germline single nucleotide polymorphisms (SNPs), including ARID5B (rs10821936 T/C), IKZF1 (rs4132601 T/G), GATA3 (rs3824662 G/T), CEBPE (rs2239633 G/A), and CDKN2A (rs3731217 A/C) have been linked to pediatric ALL in different populations. Hitherto, no previous studies have tested the relationship between these SNPs and pediatric ALL in Gaza strip. Therefore, we investigated the association between these polymorphisms and the occurrence of childhood ALL in this part of Palestine. This case-control study recruited 100 healthy controls and 78 ALL patients. Allele-specific PCR (AS-PCR) technique was used for SNPs genotyping. Relevant statistical tests were used and the multifactor dimensionality reduction (MDR) approach was applied in the analysis of gene-gene interactions. Minor alleles of ARID5B rs10821936 T/C (p = 0.007) and IKZF1 rs4132601 T/G (p = 0.045) were significantly higher in ALL patients. The homozygous (TT) genotype of GATA3 rs3824662 G/T (p = 0.038), (CC) of ARID5B rs10821936 T/C (p = 0.008), and (AC and CC) genotypes of CDKN2A rs3731217 A/C (p < 0.0001) were significantly higher in ALL cases. On MDR analysis, the best model for ALL risk was the five-factor model combination of the examined SNPs (CVC = 10/10; TBA = 0.632; p < 0.0001). This work demonstrates the association of ARID5B rs10821936 T/C, IKZF1 rs4132601 T/G, GATA3 rs3824662 G/T, and CDKN2A rs3731217 A/C polymorphisms with increased risk of pediatric ALL among a patient cohort from Gaza Strip. Further studies with a larger sample size are needed in order to confirm these findings and test the value of these SNPs in prognosis and treatment sensitivity.
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Affiliation(s)
| | | | | | - Fadel A Sharif
- Department of Medical Laboratory Sciences-IUG, Gaza, Palestine
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4
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Zidane M, Haber M, Truong T, Rachédi F, Ory C, Chevillard S, Blanché H, Olaso R, Boland A, Conte É, Karimi M, Ren Y, Xhaard C, Souchard V, Gardon J, Taquet M, Bouville A, Deleuze JF, Drozdovitch V, de Vathaire F, Cazier JB. Genetic factors for differentiated thyroid cancer in French Polynesia: new candidate loci. Precis Clin Med 2023; 6:pbad015. [PMID: 37383672 PMCID: PMC10294640 DOI: 10.1093/pcmedi/pbad015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2023] [Accepted: 06/09/2023] [Indexed: 06/30/2023] Open
Abstract
Background Populations of French Polynesia (FP), where France performed atmospheric tests between 1966 and 1974, experience a high incidence of differentiated thyroid cancer (DTC). However, up to now, no sufficiently large study of DTC genetic factors in this population has been performed to reach definitive conclusion. This research aimed to analyze the genetic factors of DTC risk among the native FP populations. Methods We analyzed more than 300 000 single nucleotide polymorphisms (SNPs) genotyped in 283 DTC cases and 418 matched controls born in FP, most being younger than 15 years old at the time of the first nuclear tests. We analyzed the genetic profile of our cohort to identify population subgroups. We then completed a genome-wide analysis study on the whole population. Results We identified a specific genetic structure in the FP population reflecting admixture from Asian and European populations. We identified three regions associated with increased DTC risk at 6q24.3, 10p12.2, and 17q21.32. The lead SNPs at these loci showed respective p-values of 1.66 × 10-7, 2.39 × 10-7, and 7.19 × 10-7 and corresponding odds ratios of 2.02, 1.89, and 2.37. Conclusion Our study results suggest a role of the loci 6q24.3, 10p12.2 and 17q21.32 in DTC risk. However, a whole genome sequencing approach would be better suited to characterize these factors than genotyping with microarray chip designed for the Caucasian population. Moreover, the functional impact of these three new loci needs to be further explored and validated.
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Affiliation(s)
- Monia Zidane
- University Paris-Saclay, UVSQ, Inserm, Gustave Roussy, CESP, Team "Radiations Epidemiology", Villejuif 94805, France
| | - Marc Haber
- Centre for Computational Biology, University of Birmingham, Birmingham B152TT, UK
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham B152TT, UK
| | - Thérèse Truong
- University Paris-Saclay, UVSQ, Inserm, Gustave Roussy, CESP, Team "Exposome and Heredity", Villejuif 94805, France
| | - Frédérique Rachédi
- Endocrinology Unit, Territorial Hospital Taaone, F-98713, Papeete, Tahiti 98713, French Polynesia
| | - Catherine Ory
- CEA, Laboratoire de Cancérologie Fondamentale, Institut de Biologie François Jacob, iRCM, SREIT, Laboratoire de Cancérologie Expérimentale (LCE), Université Paris-Saclay, Fontenay aux Roses 92265, France
| | - Sylvie Chevillard
- CEA, Laboratoire de Cancérologie Fondamentale, Institut de Biologie François Jacob, iRCM, SREIT, Laboratoire de Cancérologie Expérimentale (LCE), Université Paris-Saclay, Fontenay aux Roses 92265, France
| | - Hélène Blanché
- Fondation Jean Dausset-Centre d'Etude du Polymorphisme Humain, Paris 75010, France
| | - Robert Olaso
- Université Paris-Saclay, CEA, Centre National de Recherche en Génomique Humaine, Evry 91057, France
| | - Anne Boland
- Université Paris-Saclay, CEA, Centre National de Recherche en Génomique Humaine, Evry 91057, France
| | - Éric Conte
- U.S.R. 2003 (CNRS / UPF), Faa'a, Tahiti 98702, France
| | - Mojgan Karimi
- University Paris-Saclay, UVSQ, Inserm, Gustave Roussy, CESP, Team "Exposome and Heredity", Villejuif 94805, France
| | - Yan Ren
- University Paris-Saclay, UVSQ, Inserm, Gustave Roussy, CESP, Team "Radiations Epidemiology", Villejuif 94805, France
| | - Constance Xhaard
- University of Lorraine, INSERM CIC 1433, Nancy CHRU, INSERM U1116, Nancy 54500, France
| | - Vincent Souchard
- University Paris-Saclay, UVSQ, Inserm, Gustave Roussy, CESP, Team "Radiations Epidemiology", Villejuif 94805, France
| | - Jacques Gardon
- Hydrosciences Montpellier, Research Institute for Development, CNRS, University of Montpellier, Montpellier 62307, France
| | - Marc Taquet
- Research Institute for Development, Center IRD on Tahiti, Arue, Tahiti 98713, French Polynesia
| | - André Bouville
- National Cancer Institute (retired), Bethesda, MD 20892, USA
| | - Jean-François Deleuze
- Fondation Jean Dausset-Centre d'Etude du Polymorphisme Humain, Paris 75010, France
- Université Paris-Saclay, CEA, Centre National de Recherche en Génomique Humaine, Evry 91057, France
| | - Vladimir Drozdovitch
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, DHHS, Bethesda, MD 20892, USA
| | | | - Jean-Baptiste Cazier
- Centre for Computational Biology, University of Birmingham, Birmingham B152TT, UK
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham B152TT, UK
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Liu X, Xiao M, Xing Z, Jiang H, Zhu C, Zhang X, Li W, Wang Z, Wu F, Chen Y. Contributions of ARID5B, IKZF1, PIP4K2A, and GATA3 Gene Polymorphisms to Childhood Acute Lymphoblastic Leukemia in a Chinese Population. J Pediatr Hematol Oncol 2023; 45:123-129. [PMID: 36952466 DOI: 10.1097/mph.0000000000002646] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Accepted: 01/16/2023] [Indexed: 03/25/2023]
Abstract
Various studies have shown that single nucleotide polymorphisms in the AT-rich interaction domain 5B (ARID5B), IKAROS family zinc finger 1 (IKZF1), phosphatidylinositol-5-phosphate 4-kinase type 2 alpha (PIP4K2A), and GATA binding protein 3 (GATA3) genes may be associated with the susceptibility and prognosis of childhood acute lymphoblastic leukemia (ALL). The present study aimed to investigate the association of ARID5B rs10821936, IKZF1 rs4132601, PIP4K2A rs7088318, and GATA3 rs3824662 gene polymorphisms with the susceptibility and prognosis of childhood ALL in China. We found that the C allele of rs10821936 (ARID5B) and the A allele of rs3824662 (GATA3) were associated with an increased risk of childhood ALL in the Chinese population. There was no significant difference in frequencies of rs4132601 (IKZF1) and rs7088318 (PIP4K2A) genotypes and alleles between the childhood ALL and control groups. We observed that CC genotype of rs10821936 (ARID5B) was associated with increased rates of high-risk and moderate-risk childhood ALL. The rs10821936 (ARID5B) could serve as a potential biomarker for assessing the risk of childhood ALL in Chinese children.
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Affiliation(s)
| | - Min Xiao
- Department of Laboratory, Cancer Hospital Chinese Academy of Medical Science, Shenzhen Center, Shenzhen, Guangdong People's Republic of China
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Junk SV, Schaeffeler E, Zimmermann M, Möricke A, Beier R, Schütte P, Fedders B, Alten J, Hinze L, Klein N, Kulozik A, Muckenthaler MU, Koehler R, Borkhardt A, Vijayakrishnan J, Ellinghaus D, Forster M, Franke A, Wintering A, Kratz CP, Schrappe M, Schwab M, Houlston RS, Cario G, Stanulla M. Chemotherapy-related hyperbilirubinemia in pediatric acute lymphoblastic leukemia: a genome-wide association study from the AIEOP-BFM ALL study group. J Exp Clin Cancer Res 2023; 42:21. [PMID: 36639636 PMCID: PMC9838013 DOI: 10.1186/s13046-022-02585-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 12/26/2022] [Indexed: 01/15/2023]
Abstract
BACKGROUND Characterization of clinical phenotypes in context with tumor and host genomic information can aid in the development of more effective and less toxic risk-adapted and targeted treatment strategies. To analyze the impact of therapy-related hyperbilirubinemia on treatment outcome and to identify contributing genetic risk factors of this well-recognized adverse effect we evaluated serum bilirubin levels in 1547 pediatric patients with acute lymphoblastic leukemia (ALL) and conducted a genome-wide association study (GWAS). PATIENTS AND METHODS Patients were treated in multicenter trial AIEOP-BFM ALL 2000 for pediatric ALL. Bilirubin toxicity was graded 0 to 4 according to the Common Toxicity Criteria (CTC) of the National Cancer Institute. In the GWAS discovery cohort, including 650 of the 1547 individuals, genotype frequencies of 745,895 single nucleotide variants were compared between 435 patients with hyperbilirubinemia (CTC grades 1-4) during induction/consolidation treatment and 215 patients without it (grade 0). Replication analyses included 224 patients from the same trial. RESULTS Compared to patients with no (grade 0) or moderate hyperbilirubinemia (grades 1-2) during induction/consolidation, patients with grades 3-4 had a poorer 5-year event free survival (76.6 ± 3% versus 87.7 ± 1% for grades 1-2, P = 0.003; 85.2 ± 2% for grade 0, P < 0.001) and a higher cumulative incidence of relapse (15.6 ± 3% versus 9.0 ± 1% for grades 1-2, P = 0.08; 11.1 ± 1% for grade 0, P = 0.007). GWAS identified a strong association of the rs6744284 variant T allele in the UGT1A gene cluster with risk of hyperbilirubinemia (allelic odds ratio (OR) = 2.1, P = 7 × 10- 8). TT-homozygotes had a 6.5-fold increased risk of hyperbilirubinemia (grades 1-4; 95% confidence interval (CI) = 2.9-14.6, P = 7 × 10- 6) and a 16.4-fold higher risk of grade 3-4 hyperbilirubinemia (95% CI 6.1-43.8, P = 2 × 10- 8). Replication analyses confirmed these associations with joint analysis yielding genome-wide significance (allelic OR = 2.1, P = 6 × 10- 11; 95% CI 1.7-2.7). Moreover, rs6744284 genotypes were strongly linked to the Gilbert's syndrome-associated UGT1A1*28/*37 allele (r2 = 0.70), providing functional support for study findings. Of clinical importance, the rs6744284 TT genotype counterbalanced the adverse prognostic impact of high hyperbilirubinemia on therapy outcome. CONCLUSIONS Chemotherapy-related hyperbilirubinemia is a prognostic factor for treatment outcome in pediatric ALL and genetic variation in UGT1A aids in predicting the clinical impact of hyperbilirubinemia. TRIAL REGISTRATION http://www. CLINICALTRIALS gov ; #NCT00430118.
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Affiliation(s)
- Stefanie V. Junk
- grid.10423.340000 0000 9529 9877Department of Pediatric Hematology and Oncology, Hannover Medical School, Carl-Neuberg-Str. 1, 30625 Hannover, Germany
| | - Elke Schaeffeler
- Margarete-Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart, Germany
| | - Martin Zimmermann
- grid.10423.340000 0000 9529 9877Department of Pediatric Hematology and Oncology, Hannover Medical School, Carl-Neuberg-Str. 1, 30625 Hannover, Germany
| | - Anja Möricke
- grid.412468.d0000 0004 0646 2097Department of Pediatrics, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Rita Beier
- grid.10423.340000 0000 9529 9877Department of Pediatric Hematology and Oncology, Hannover Medical School, Carl-Neuberg-Str. 1, 30625 Hannover, Germany
| | - Peter Schütte
- grid.10423.340000 0000 9529 9877Department of Pediatric Hematology and Oncology, Hannover Medical School, Carl-Neuberg-Str. 1, 30625 Hannover, Germany
| | - Birthe Fedders
- grid.412468.d0000 0004 0646 2097Department of Pediatrics, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Julia Alten
- grid.412468.d0000 0004 0646 2097Department of Pediatrics, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Laura Hinze
- grid.10423.340000 0000 9529 9877Department of Pediatric Hematology and Oncology, Hannover Medical School, Carl-Neuberg-Str. 1, 30625 Hannover, Germany
| | - Norman Klein
- grid.10423.340000 0000 9529 9877Department of Pediatric Hematology and Oncology, Hannover Medical School, Carl-Neuberg-Str. 1, 30625 Hannover, Germany
| | - Andreas Kulozik
- grid.7700.00000 0001 2190 4373Department of Pediatric Hematology, Oncology and Immunology, University of Heidelberg, Heidelberg, Germany
| | - Martina U. Muckenthaler
- grid.7700.00000 0001 2190 4373Department of Pediatric Hematology, Oncology and Immunology, University of Heidelberg, Heidelberg, Germany
| | - Rolf Koehler
- grid.7700.00000 0001 2190 4373Department of Human Genetics, University of Heidelberg, Heidelberg, Germany
| | - Arndt Borkhardt
- grid.411327.20000 0001 2176 9917Clinic for Pediatric Oncology, Hematology, and Clinical Immunology, Medical Faculty, Heinrich-Heine-University, Düsseldorf, Germany
| | - Jayaram Vijayakrishnan
- grid.18886.3fDivision of Genetics and Epidemiology, The Institute of Cancer Research, Sutton, Surrey, UK
| | - David Ellinghaus
- grid.9764.c0000 0001 2153 9986Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany
| | - Michael Forster
- grid.9764.c0000 0001 2153 9986Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany
| | - Andre Franke
- grid.9764.c0000 0001 2153 9986Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany
| | - Astrid Wintering
- grid.10423.340000 0000 9529 9877Department of Pediatric Hematology and Oncology, Hannover Medical School, Carl-Neuberg-Str. 1, 30625 Hannover, Germany
| | - Christian P. Kratz
- grid.10423.340000 0000 9529 9877Department of Pediatric Hematology and Oncology, Hannover Medical School, Carl-Neuberg-Str. 1, 30625 Hannover, Germany
| | - Martin Schrappe
- grid.412468.d0000 0004 0646 2097Department of Pediatrics, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Matthias Schwab
- Margarete-Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart, Germany ,grid.10392.390000 0001 2190 1447Departments of Clinical Pharmacology, and of Biochemistry and Pharmacy, University of Tuebingen, Tuebingen, Germany ,grid.10392.390000 0001 2190 1447Cluster of Excellence iFIT (EXC 2180) “Image-Guided and Functionally Instructed Tumor Therapies”, University of Tuebingen, Tuebingen, Germany ,German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ) Partner Site Tübingen, Tübingen, Germany
| | - Richard S. Houlston
- grid.18886.3fDivision of Genetics and Epidemiology, The Institute of Cancer Research, Sutton, Surrey, UK
| | - Gunnar Cario
- grid.412468.d0000 0004 0646 2097Department of Pediatrics, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Martin Stanulla
- grid.10423.340000 0000 9529 9877Department of Pediatric Hematology and Oncology, Hannover Medical School, Carl-Neuberg-Str. 1, 30625 Hannover, Germany
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Llorente A, Arora GK, Grenier SF, Emerling BM. PIP kinases: A versatile family that demands further therapeutic attention. Adv Biol Regul 2023; 87:100939. [PMID: 36517396 PMCID: PMC9992244 DOI: 10.1016/j.jbior.2022.100939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Accepted: 11/29/2022] [Indexed: 12/12/2022]
Abstract
Phosphoinositides are membrane-localized phospholipids that regulate a plethora of essential cellular processes. These lipid signaling molecules are critical for cell homeostasis and therefore their levels are strictly regulated by the coordinated action of several families of lipid kinases and phosphatases. In this review, we provide a focused perspective on the phosphatidylinositol phosphate kinase (PIPK) family and the three subfamilies that compose it: Type I PIPKs or phosphatidylinositol-4-phosphate 5-kinases (PI4P5Ks), Type II PIPKs or phosphatidylinositol-5-phosphate 4-kinases (PI5P4Ks), and Type III PIPKs or phosphatidylinositol-3-phosphate 5-kinases (PIKfyve). Each subfamily is responsible for catalyzing a hydroxyl phosphorylation on specific phosphoinositide species to generate a double phosphorylated lipid, therefore regulating the levels of both substrate and product. Here, we summarize our current knowledge about the functions and regulation of each PIPK subfamily. Further, we highlight the roles of these kinases in various in vivo genetic models and give an overview of their involvement in multiple pathological conditions. The phosphoinositide field has been long focused on targeting PI3K signaling, but growing evidence suggests that it is time to draw attention to the other phosphoinositide kinases. The discovery of the involvement of PIPKs in the pathogenesis of multiple diseases has prompted substantial efforts to turn these enzymes into pharmacological targets. An increasingly refined knowledge of the biology of PIPKs in a variety of in vitro and in vivo models will facilitate the development of effective approaches for therapeutic intervention with the potential to translate into meaningful clinical benefits for patients suffering from cancer, immunological and infectious diseases, and neurodegenerative disorders.
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Affiliation(s)
- Alicia Llorente
- Cell and Molecular Biology of Cancer Program, Sanford Burnham Prebys, La Jolla, CA, 92037, USA
| | - Gurpreet K Arora
- Cell and Molecular Biology of Cancer Program, Sanford Burnham Prebys, La Jolla, CA, 92037, USA
| | - Shea F Grenier
- Cell and Molecular Biology of Cancer Program, Sanford Burnham Prebys, La Jolla, CA, 92037, USA
| | - Brooke M Emerling
- Cell and Molecular Biology of Cancer Program, Sanford Burnham Prebys, La Jolla, CA, 92037, USA.
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8
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Zhao X, Qian M, Goodings C, Zhang Y, Yang W, Wang P, Xu B, Tian C, Pui CH, Hunger SP, Raetz EA, Devidas M, Relling MV, Loh ML, Savic D, Li C, Yang JJ. Molecular Mechanisms of ARID5B-Mediated Genetic Susceptibility to Acute Lymphoblastic Leukemia. J Natl Cancer Inst 2022; 114:1287-1295. [PMID: 35575404 PMCID: PMC9468286 DOI: 10.1093/jnci/djac101] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 04/05/2022] [Accepted: 05/09/2022] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND There is growing evidence for the inherited basis of susceptibility to childhood acute lymphoblastic leukemia (ALL). Genome-wide association studies have identified non-coding ALL risk variants at the ARID5B gene locus, but their exact functional effects and the molecular mechanism linking ARID5B to B-cell ALL leukemogenesis remain largely unknown. METHODS We performed targeted sequencing of ARID5B in germline DNA of 5008 children with ALL. Variants were evaluated for association with ALL susceptibility using 3644 patients from the UK10K cohort as non-ALL controls, under an additive model. Cis-regulatory elements in ARID5B were systematically identified using dCas9-KRAB-mediated enhancer interference system enhancer screen in ALL cells. Disruption of transcription factor binding by ARID5B variant was predicted informatically and then confirmed using chromatin immunoprecipitation and coimmunoprecipitation. ARID5B variant association with hematological traits was examined using UK Biobank dataset. All statistical tests were 2-sided. RESULTS We identified 54 common variants in ARID5B statistically significantly associated with leukemia risk, all of which were noncoding. Six cis-regulatory elements at the ARID5B locus were discovered using CRISPR-based high-throughput enhancer screening. Strikingly, the top ALL risk variant (rs7090445, P = 5.57 × 10-45) is located precisely within the strongest enhancer element, which is also distally tethered to the ARID5B promoter. The variant allele disrupts the MEF2C binding motif sequence, resulting in reduced MEF2C affinity and decreased local chromosome accessibility. MEF2C influences ARID5B expression in ALL, likely via a transcription factor complex with RUNX1. Using the UK Biobank dataset (n = 349 861), we showed that rs7090445 was also associated with lymphocyte percentage and count in the general population (P = 8.6 × 10-22 and 2.1 × 10-18, respectively). CONCLUSIONS Our results indicate that ALL risk variants in ARID5B function by modulating cis-regulatory elements at this locus.
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Affiliation(s)
- Xujie Zhao
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Maoxiang Qian
- Institute of Pediatrics and Department of Hematology and Oncology, Children's Hospital of Fudan University, National Children's Medical Center, and the Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Charnise Goodings
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Yang Zhang
- Department of Tumor Cell Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Wenjian Yang
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Ping Wang
- Department of Genome Technologies, The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Beisi Xu
- Center for Applied Bioinformatics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Cheng Tian
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Ching-Hon Pui
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Stephen P Hunger
- Department of Pediatrics and The Center for Childhood Cancer Research, The Children's Hospital of Philadelphia and The Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Elizabeth A Raetz
- Department of Pediatrics and Perlmutter Cancer Center, New York University Langone Medical Center, New York, NY, USA
| | - Meenakshi Devidas
- Department of Global Pediatric Medicine, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Mary V Relling
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Mignon L Loh
- Department of Pediatrics, Benioff Children's Hospital and the Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Daniel Savic
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Chunliang Li
- Department of Tumor Cell Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Jun J Yang
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA.,Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, USA
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9
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Goodings C, Zhao X, McKinney-Freeman S, Zhang H, Yang JJ. ARID5B influences B-cell development and function in mouse. Haematologica 2022; 108:502-512. [PMID: 35924577 PMCID: PMC9890020 DOI: 10.3324/haematol.2022.281157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Indexed: 02/03/2023] Open
Abstract
There is growing evidence for an inherited basis of susceptibility to childhood acute lymphoblastic leukemia. Genomewide association studies by us and others have identified non-coding acute lymphoblastic leukemia risk variants at the ARID5B gene locus, but the molecular mechanisms linking ARID5B to normal and malignant hematopoiesis remain largely unknown. Using a Vav1-driven transgenic mouse model, we characterized the role of Arid5b in hematopoiesis in vivo. Arid5b overexpression resulted in a dramatic reduction in the proportion of circulating B cells, immature, and mature Bcell fractions in the peripheral blood and the bone marrow, and also a decrease of follicular B cells in the spleen. There were significant defects in B-cell activation upon Arid5b overexpression in vitro with hyperactivation of B-cell receptor signaling at baseline. In addition, increased mitochondrial oxygen consumption rate of naïve or stimulated B cells of Arid5b-overexpressing mice was observed, compared to the rate of wild-type counterparts. Taken together, our results indicate that ARID5B may play an important role in B-cell development and function.
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Affiliation(s)
- Charnise Goodings
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA,*CG and XZ contributed equally as co-first authors
| | - Xujie Zhao
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA,*CG and XZ contributed equally as co-first authors
| | | | - Hui Zhang
- Department of Hematology/Oncology, Shanghai Children’s Medical Center, Shanghai, China
| | - Jun J. Yang
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA,Department of Oncology, St. Jude Children’s Research Hospital, Memphis, TN, USA,J. J. Yang
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10
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Yang H, Zhang H, Luan Y, Liu T, Yang W, Roberts KG, Qian MX, Zhang B, Yang W, Perez-Andreu V, Xu J, Iyyanki S, Kuang D, Stasiak LA, Reshmi SC, Gastier-Foster J, Smith C, Pui CH, Evans WE, Hunger SP, Platanias LC, Relling MV, Mullighan CG, Loh ML, Yue F, Yang JJ. Noncoding genetic variation in GATA3 increases acute lymphoblastic leukemia risk through local and global changes in chromatin conformation. Nat Genet 2022; 54:170-179. [PMID: 35115686 PMCID: PMC9794680 DOI: 10.1038/s41588-021-00993-x] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Accepted: 11/29/2021] [Indexed: 12/31/2022]
Abstract
Inherited noncoding genetic variants confer significant disease susceptibility to childhood acute lymphoblastic leukemia (ALL) but the molecular processes linking germline polymorphisms with somatic lesions in this cancer are poorly understood. Through targeted sequencing in 5,008 patients, we identified a key regulatory germline variant in GATA3 associated with Philadelphia chromosome-like ALL (Ph-like ALL). Using CRISPR-Cas9 editing and samples from patients with Ph-like ALL, we showed that this variant activated a strong enhancer that upregulated GATA3 transcription. This, in turn, reshaped global chromatin accessibility and three-dimensional genome organization, including regions proximal to the ALL oncogene CRLF2. Finally, we showed that GATA3 directly regulated CRLF2 and potentiated the JAK-STAT oncogenic effects during leukemogenesis. Taken together, we provide evidence for a distinct mechanism by which a germline noncoding variant contributes to oncogene activation, epigenetic regulation and three-dimensional genome reprogramming.
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Affiliation(s)
- Hongbo Yang
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine Northwestern University, Chicago, IL, USA
- Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, IL, USA
- Obstetrics and Gynecology Hospital, Institute of Reproduction and Development, Fudan University, Shanghai, China
| | - Hui Zhang
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
- Department of Hematology/Oncology, Guangzhou Women and Children's Medical Center, Guangzhou, China
- Department of Hematology/Oncology, Shanghai Children's Medical Center, Shanghai, China
| | - Yu Luan
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine Northwestern University, Chicago, IL, USA
| | - Tingting Liu
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine Northwestern University, Chicago, IL, USA
| | - Wentao Yang
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Kathryn G Roberts
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Mao-Xiang Qian
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Bo Zhang
- Bioinformatics and Genomics Program, The Pennsylvania State University, University Park, PA, USA
| | - Wenjian Yang
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Virginia Perez-Andreu
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
- Internal Medicine Department, MountainView Hospital, University of Reno, Las Vegas, NV, USA
| | - Jie Xu
- Department of Biochemistry and Molecular Biology, Penn State School of Medicine, Hershey, PA, USA
| | - Sriranga Iyyanki
- Department of Biochemistry and Molecular Biology, Penn State School of Medicine, Hershey, PA, USA
| | - Da Kuang
- Department of Computer and Information Science, University of Pennsylvania, Philadelphia, PA, USA
| | - Lena A Stasiak
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine Northwestern University, Chicago, IL, USA
| | - Shalini C Reshmi
- Department of Pathology and Laboratory Medicine, Nationwide Children's Hospital, Columbus, OH, USA
- Department of Pediatrics, Ohio State University School of Medicine, Columbus, OH, USA
| | - Julie Gastier-Foster
- Department of Pathology and Laboratory Medicine, Nationwide Children's Hospital, Columbus, OH, USA
- Department of Pediatrics, Ohio State University School of Medicine, Columbus, OH, USA
| | - Colton Smith
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Ching-Hon Pui
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - William E Evans
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Stephen P Hunger
- Division of Oncology and the Center for Childhood Cancer Research, Children's Hospital of Philadelphia and the Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Leonidas C Platanias
- Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, IL, USA
| | - Mary V Relling
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Charles G Mullighan
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Mignon L Loh
- Department of Pediatrics, Benioff Children's Hospital and the Helen Diller Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
| | - Feng Yue
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine Northwestern University, Chicago, IL, USA.
- Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, IL, USA.
| | - Jun J Yang
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA.
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11
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Arora GK, Palamiuc L, Emerling BM. Expanding role of PI5P4Ks in cancer: A promising druggable target. FEBS Lett 2021; 596:3-16. [PMID: 34822164 DOI: 10.1002/1873-3468.14237] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 11/04/2021] [Accepted: 11/15/2021] [Indexed: 12/14/2022]
Abstract
Cancer cells are challenged by a myriad of microenvironmental stresses, and it is their ability to efficiently adapt to the constantly changing nutrient, energy, oxidative, and/or immune landscape that allows them to survive and proliferate. Such adaptations, however, result in distinct vulnerabilities that are attractive therapeutic targets. Phosphatidylinositol 5-phosphate 4-kinases (PI5P4Ks) are a family of druggable stress-regulated phosphoinositide kinases that become conditionally essential as a metabolic adaptation, paving the way to targeting cancer cell dependencies. Further, PI5P4Ks have a synthetic lethal interaction with the tumor suppressor p53, the loss of which is one of the most prevalent genetic drivers of malignant transformation. PI5P4K's emergence as a crucial axis in the expanding landscape of phosphoinositide signaling in cancer has already stimulated the development of specific inhibitors. Thus, a better understanding of the biology of the PI5P4Ks will allow for targeted and effective therapeutic interventions. Here, we attempt to summarize the mounting roles of the PI5P4Ks in cancer, including evidence that targeting them is a therapeutic vulnerability and promising next-in-line treatment for multiple cancer subtypes.
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Affiliation(s)
- Gurpreet K Arora
- Cell and Molecular Biology of Cancer Program, Sanford Burnham Prebys, La Jolla, CA, USA
| | - Lavinia Palamiuc
- Cell and Molecular Biology of Cancer Program, Sanford Burnham Prebys, La Jolla, CA, USA
| | - Brooke M Emerling
- Cell and Molecular Biology of Cancer Program, Sanford Burnham Prebys, La Jolla, CA, USA
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12
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Yang T, Mills LJ, Xue H, Raduski A, Williams LA, Spector LG. Impact of fetal expression quantitative trait loci on transcriptome-wide association study of childhood leukemia. Hum Mol Genet 2021; 31:3207-3215. [PMID: 34791233 DOI: 10.1093/hmg/ddab336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 10/08/2021] [Accepted: 11/07/2021] [Indexed: 11/12/2022] Open
Abstract
Transcriptome-wide association studies increase the yield of loci associated with disease phenotypes by focusing on expression quantitative trait loci (eQTL). The major source of eQTL data for is the Gene and Tissue Expression (GTEx) project, which is comprised entirely of adults, mainly those > 50 years of age at death. Since gene expression levels differ by developmental stage, it is not clear whether eQTLs derived from adult data sources are best suited for use in young-onset diseases such as pediatric cancers. To fill in this knowledge gap, we performed a large-scale eQTL mapping analysis in the GenCord study with newborn samples and compared it with GTEx. Under matched conditions, we found around 80% of the eQTLs in one study can be replicated in the other. However, among all eQTLs identified in GenCord (GTEx), 584 (1045) showed statistically significant differences in effect sizes in GTEx (GenCord). We further investigated how using fetal eQTL data can facilitate the genetic association study of acute lymphoblastic leukemia. GenCord and GTEx identified the same genetic loci with statistical significance; however, the overall association pattern was only weakly correlated. Our paper demonstrates age-differential eQTLs and shows their potential influence on childhood leukemia research.
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Affiliation(s)
- Tianzhong Yang
- Department of Biostatistics, School of Public Health, University of Minnesota, MN, USA.,Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
| | - Lauren J Mills
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA.,Division of Epidemiology and Clinical Research, Department of Pediatrics, University of Minnesota School of Medicine, Minneapolis, MN, USA
| | - Haoran Xue
- Department of Statistics, University of Minnesota, MN, USA
| | - Andrew Raduski
- Division of Epidemiology and Clinical Research, Department of Pediatrics, University of Minnesota School of Medicine, Minneapolis, MN, USA
| | - Lindsay A Williams
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA.,Division of Epidemiology and Clinical Research, Department of Pediatrics, University of Minnesota School of Medicine, Minneapolis, MN, USA.,Brain Tumor Program, University of Minnesota, Minneapolis, MN, USA
| | - Logan G Spector
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA.,Division of Epidemiology and Clinical Research, Department of Pediatrics, University of Minnesota School of Medicine, Minneapolis, MN, USA
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13
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Kachuri L, Jeon S, DeWan AT, Metayer C, Ma X, Witte JS, Chiang CWK, Wiemels JL, de Smith AJ. Genetic determinants of blood-cell traits influence susceptibility to childhood acute lymphoblastic leukemia. Am J Hum Genet 2021; 108:1823-1835. [PMID: 34469753 PMCID: PMC8546033 DOI: 10.1016/j.ajhg.2021.08.004] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 08/06/2021] [Indexed: 01/07/2023] Open
Abstract
Acute lymphoblastic leukemia (ALL) is the most common childhood cancer. Despite overlap between genetic risk loci for ALL and hematologic traits, the etiological relevance of dysregulated blood-cell homeostasis remains unclear. We investigated this question in a genome-wide association study (GWAS) of childhood ALL (2,666 affected individuals, 60,272 control individuals) and a multi-trait GWAS of nine blood-cell indices in the UK Biobank. We identified 3,000 blood-cell-trait-associated (p < 5.0 × 10-8) variants, explaining 4.0% to 23.9% of trait variation and including 115 loci associated with blood-cell ratios (LMR, lymphocyte-to-monocyte ratio; NLR, neutrophil-to-lymphocyte ratio; PLR, platelet-to-lymphocyte ratio). ALL susceptibility was genetically correlated with lymphocyte counts (rg = 0.088, p = 4.0 × 10-4) and PLR (rg = -0.072, p = 0.0017). In Mendelian randomization analyses, genetically predicted increase in lymphocyte counts was associated with increased ALL risk (odds ratio [OR] = 1.16, p = 0.031) and strengthened after accounting for other cell types (OR = 1.43, p = 8.8 × 10-4). We observed positive associations with increasing LMR (OR = 1.22, p = 0.0017) and inverse effects for NLR (OR = 0.67, p = 3.1 × 10-4) and PLR (OR = 0.80, p = 0.002). Our study shows that a genetically induced shift toward higher lymphocyte counts, overall and in relation to monocytes, neutrophils, and platelets, confers an increased susceptibility to childhood ALL.
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Affiliation(s)
- Linda Kachuri
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Soyoung Jeon
- Center for Genetic Epidemiology, Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Andrew T DeWan
- Center for Perinatal, Pediatric, and Environmental Epidemiology, Yale School of Public Health, New Haven, CT 06510, USA; Department of Chronic Disease Epidemiology, Yale School of Public Health, New Haven, CT 06510, USA
| | - Catherine Metayer
- Division of Epidemiology and Biostatistics, School of Public Health, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Xiaomei Ma
- Department of Chronic Disease Epidemiology, Yale School of Public Health, New Haven, CT 06510, USA
| | - John S Witte
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA 94158, USA; Institute for Human Genetics, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Urology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Charleston W K Chiang
- Center for Genetic Epidemiology, Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA; Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA 90089, USA
| | - Joseph L Wiemels
- Center for Genetic Epidemiology, Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA; Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90033, USA
| | - Adam J de Smith
- Center for Genetic Epidemiology, Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA; Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90033, USA.
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14
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Cobaleda C, Vicente-Dueñas C, Sanchez-Garcia I. Infectious triggers and novel therapeutic opportunities in childhood B cell leukaemia. Nat Rev Immunol 2021; 21:570-581. [PMID: 33558682 DOI: 10.1038/s41577-021-00505-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/08/2021] [Indexed: 01/30/2023]
Abstract
B cell acute lymphoblastic leukaemia (B-ALL) is the most common form of childhood cancer. Although treatment has advanced remarkably in the past 50 years, it still fails in ~20% of patients. Recent studies revealed that more than 5% of healthy newborns carry preleukaemic clones that originate in utero, but only a small percentage of these carriers will progress to overt B-ALL. The drivers of progression are unclear, but B-ALL incidence seems to be increasing in parallel with the adoption of modern lifestyles. Emerging evidence shows that a major driver for the conversion from the preleukaemic state to the B-ALL state is exposure to immune stressors, such as infection. Here, we discuss our current understanding of the environmental triggers and genetic predispositions that may lead to B-ALL, highlighting lessons from epidemiology, the clinic and animal models, and identifying priority areas for future research.
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Affiliation(s)
- Cesar Cobaleda
- Immune System Development and Function Unit, Centro de Biología Molecular Severo Ochoa, CSIC and Universidad Autónoma de Madrid, Madrid, Spain.
| | | | - Isidro Sanchez-Garcia
- Institute for Biomedical Research of Salamanca (IBSAL), Salamanca, Spain. .,Experimental Therapeutics and Translational Oncology Program, Instituto de Biología Molecular y Celular del Cáncer, CSIC and Universidad de Salamanca, Salamanca, Spain.
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15
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Li Y, Yang W, Devidas M, Winter SS, Kesserwan C, Yang W, Dunsmore KP, Smith C, Qian M, Zhao X, Zhang R, Gastier-Foster JM, Raetz EA, Carroll WL, Li C, Liu PP, Rabin KR, Sanda T, Mullighan CG, Nichols KE, Evans WE, Pui CH, Hunger SP, Teachey DT, Relling MV, Loh ML, Yang JJ. Germline RUNX1 variation and predisposition to childhood acute lymphoblastic leukemia. J Clin Invest 2021; 131:147898. [PMID: 34166225 PMCID: PMC8409579 DOI: 10.1172/jci147898] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Accepted: 06/22/2021] [Indexed: 12/31/2022] Open
Abstract
Genetic alterations in the RUNX1 gene are associated with benign and malignant blood disorders, particularly of megakaryocyte and myeloid lineages. The role of RUNX1 in acute lymphoblastic leukemia (ALL) is less clear, particularly how germline genetic variation influences the predisposition to this type of leukemia. Sequencing 4,836 children with B-ALL and 1,354 cases of T-ALL, we identified 31 and 18 germline RUNX1 variants, respectively. RUNX1 variants in B-ALL consistently showed minimal damaging effects. By contrast, 6 T-ALL-related variants result in drastic loss of RUNX1 activity as a transcription activator in vitro. Ectopic expression of dominant-negative RUNX1 variants in human CD34+ cells repressed differentiation into erythroid, megakaryocytes, and T cells, while promoting myeloid cell development. Chromatin immunoprecipitation sequencing of T-ALL models showed distinctive patterns of RUNX1 binding by variant proteins. Further whole genome sequencing identified JAK3 mutation as the most frequent somatic genomic abnormality in T-ALL with germline RUNX1 variants. Co-introduction of RUNX1 variant and JAK3 mutation in hematopoietic stem and progenitor cells in mice gave rise to T-ALL with early T-cell precursor phenotype. Taken together, these results indicated that RUNX1 is an important predisposition gene for T-ALL and pointed to novel biology of RUNX1-mediated leukemogenesis in the lymphoid lineages.
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Affiliation(s)
- Yizhen Li
- Department of Pharmaceutical Sciences and
| | | | - Meenakshi Devidas
- Department of Global Pediatric Medicine, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | - Stuart S. Winter
- Children’s Minnesota Research Institute, Children’s Minnesota, Minneapolis, Minnesota, USA
| | - Chimene Kesserwan
- Center for Cancer Research, Genetics Branch, National Cancer Institute, Bethesda, Maryland, USA
| | | | - Kimberly P. Dunsmore
- Children’s Hematology and Oncology, Carilion Clinic and Virginia Tech Carilion School of Medicine, Roanoke, Virginia, USA
| | | | - Maoxiang Qian
- Institute of Pediatrics and Department of Hematology and Oncology, Children’s Hospital of Fudan University, Institutes of Biomedical Sciences, Shanghai, China
| | - Xujie Zhao
- Department of Pharmaceutical Sciences and
| | | | | | - Elizabeth A. Raetz
- Division of Pediatric Hematology and Oncology, Perlmutter Cancer Center, New York University Langone Health, New York, New York, USA
| | - William L. Carroll
- Division of Pediatric Hematology and Oncology, Perlmutter Cancer Center, New York University Langone Health, New York, New York, USA
| | - Chunliang Li
- Tumor Cell Biology, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | - Paul P. Liu
- Oncogenesis and Development Section, National Human Genome Research Institute, NIH, Bethesda, Maryland, USA
| | - Karen R. Rabin
- Texas Children’s Cancer and Hematology Centers, Baylor College of Medicine, Houston, Texas, USA
| | - Takaomi Sanda
- Cancer Science Institute of Singapore, and
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | | | | | - William E. Evans
- Department of Pharmaceutical Sciences and
- Hematological Malignancies Program, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | - Ching-Hon Pui
- Department of Oncology, and
- Hematological Malignancies Program, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | - Stephen P. Hunger
- Department of Pediatrics and Center for Childhood Cancer Research, Children’s Hospital of Philadelphia and Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - David T. Teachey
- Department of Pediatrics and Center for Childhood Cancer Research, Children’s Hospital of Philadelphia and Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Mary V. Relling
- Department of Pharmaceutical Sciences and
- Hematological Malignancies Program, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | - Mignon L. Loh
- Department of Pediatrics, Benioff Children’s Hospital and the Helen Diller Family Comprehensive Cancer Center, UCSF, San Francisco, California, USA
| | - Jun J. Yang
- Department of Pharmaceutical Sciences and
- Department of Oncology, and
- Hematological Malignancies Program, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
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16
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Ratti S, Evangelisti C, Mongiorgi S, De Stefano A, Fazio A, Bonomini F, Follo MY, Faenza I, Manzoli L, Sheth B, Vidalle MC, Kimber ST, Divecha N, Cocco L, Fiume R. "Modulating Phosphoinositide Profiles as a Roadmap for Treatment in Acute Myeloid Leukemia". Front Oncol 2021; 11:678824. [PMID: 34109125 PMCID: PMC8181149 DOI: 10.3389/fonc.2021.678824] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Accepted: 05/04/2021] [Indexed: 12/12/2022] Open
Abstract
Polyphosphoinositides (PPIns) and their modulating enzymes are involved in regulating many important cellular functions including proliferation, differentiation or gene expression, and their deregulation is involved in human diseases such as metabolic syndromes, neurodegenerative disorders and cancer, including Acute Myeloid Leukemia (AML). Given that PPIns regulating enzymes are highly druggable targets, several studies have recently highlighted the potential of targeting them in AML. For instance many inhibitors targeting the PI3K pathway are in various stages of clinical development and more recently other novel enzymes such as PIP4K2A have been implicated as AML targets. PPIns have distinct subcellular organelle profiles, in part driven by the specific localisation of enzymes that metabolise them. In particular, in the nucleus, PPIns are regulated in response to various extracellular and intracellular pathways and interact with specific nuclear proteins to control epigenetic cell state. While AML does not normally manifest with as many mutations as other cancers, it does appear in large part to be a disease of dysregulation of epigenetic signalling and many novel therapeutics are aimed at reprogramming AML cells toward a differentiated cell state or to one that is responsive to alternative successful but limited AML therapies such as ATRA. Here, we propose that by combining bioinformatic analysis with inhibition of PPIns pathways, especially within the nucleus, we might discover new combination therapies aimed at reprogramming transcriptional output to attenuate uncontrolled AML cell growth. Furthermore, we outline how different part of a PPIns signalling unit might be targeted to control selective outputs that might engender more specific and therefore less toxic inhibitory outcomes.
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Affiliation(s)
- Stefano Ratti
- Cellular Signalling Laboratory, Department of Biomedical Sciences (DIBINEM), University of Bologna, Bologna, Italy
| | - Camilla Evangelisti
- Cellular Signalling Laboratory, Department of Biomedical Sciences (DIBINEM), University of Bologna, Bologna, Italy
| | - Sara Mongiorgi
- Cellular Signalling Laboratory, Department of Biomedical Sciences (DIBINEM), University of Bologna, Bologna, Italy
| | - Alessia De Stefano
- Cellular Signalling Laboratory, Department of Biomedical Sciences (DIBINEM), University of Bologna, Bologna, Italy
| | - Antonietta Fazio
- Cellular Signalling Laboratory, Department of Biomedical Sciences (DIBINEM), University of Bologna, Bologna, Italy
| | - Francesca Bonomini
- Cellular Signalling Laboratory, Department of Biomedical Sciences (DIBINEM), University of Bologna, Bologna, Italy
| | - Matilde Y Follo
- Cellular Signalling Laboratory, Department of Biomedical Sciences (DIBINEM), University of Bologna, Bologna, Italy
| | - Irene Faenza
- Cellular Signalling Laboratory, Department of Biomedical Sciences (DIBINEM), University of Bologna, Bologna, Italy
| | - Lucia Manzoli
- Cellular Signalling Laboratory, Department of Biomedical Sciences (DIBINEM), University of Bologna, Bologna, Italy
| | - Bhavwanti Sheth
- Inositide Laboratory, School of Biological Sciences, Faculty of Environmental and Life Sciences, University of Southampton, Southampton, United Kingdom
| | - Magdalena C Vidalle
- Inositide Laboratory, School of Biological Sciences, Faculty of Environmental and Life Sciences, University of Southampton, Southampton, United Kingdom
| | - Scott T Kimber
- Inositide Laboratory, School of Biological Sciences, Faculty of Environmental and Life Sciences, University of Southampton, Southampton, United Kingdom
| | - Nullin Divecha
- Inositide Laboratory, School of Biological Sciences, Faculty of Environmental and Life Sciences, University of Southampton, Southampton, United Kingdom
| | - Lucio Cocco
- Cellular Signalling Laboratory, Department of Biomedical Sciences (DIBINEM), University of Bologna, Bologna, Italy
| | - Roberta Fiume
- Cellular Signalling Laboratory, Department of Biomedical Sciences (DIBINEM), University of Bologna, Bologna, Italy
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17
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Hauer J, Fischer U, Borkhardt A. Towards prevention of childhood ALL by early-life immune training. Blood 2021:blood. [PMID: 34010407 DOI: 10.1182/blood.2020009895] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 04/21/2021] [Indexed: 11/21/2022] Open
Abstract
B-cell precursor acute lymphoblastic leukemia (BCP-ALL) is the most common form of childhood cancer. Chemotherapy is associated with life-long health sequelae and fails in ∼20% of cases. Thus, prevention of leukemia would be preferable to treatment. Childhood leukemia frequently starts before birth, during fetal hematopoiesis. A first genetic hit (eg, the ETV6-RUNX1 gene fusion) leads to the expansion of preleukemic B-cell clones, which are detectable in healthy newborn cord blood (up to 5%). These preleukemic clones give rise to clinically overt leukemia in only ∼0.2% of carriers. Experimental evidence suggests that a major driver of conversion from the preleukemic to the leukemic state is exposure to immune challenges. Novel insights have shed light on immune host responses and how they shape the complex interplay between (1) inherited or acquired genetic predispositions, (2) exposure to infection, and (3) abnormal cytokine release from immunologically untrained cells. Here, we integrate the recently emerging concept of “trained immunity” into existing models of childhood BCP-ALL and suggest future avenues toward leukemia prevention.
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18
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Hao Q, Cao M, Zhang C, Yin D, Wang Y, Ye Y, Zhao S, Yang Y, Chen KL, Ying B, Wang L, Zhang Y, Xu C, Zhu Y, Wu Y, Gao J, Zhao JN, Zhang Y, Lu X. Age-related differences of genetic susceptibility to patients with acute lymphoblastic leukemia. Aging (Albany NY) 2021; 13:12456-12465. [PMID: 33891562 PMCID: PMC8148462 DOI: 10.18632/aging.202903] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Accepted: 03/05/2021] [Indexed: 02/05/2023]
Abstract
Inherited predispositions to acute lymphoblastic leukemia have been well investigated in pediatric patients, but studies on adults, particularly Chinese patients, are limited. In this study, we conducted a genome-wide association study in 466 all-age Chinese patients with Acute lymphoblastic leukemia (ALL) and 1,466 non-ALL controls to estimate the impact of age on ALL susceptibility in the Chinese population. Among the 17 reported loci, 8 have been validated in pediatric and 1 in adult patients. The strongest association signal was identified at ARID5B locus and gradually decreased with age, while the signal at GATA3 exhibited the opposite trend and significantly impact on adult patients. With genome-wide approaches, germline variants at 2q14.3 rank as the top inherited predisposition to adult patients (e.g., rs73956024, P = 4.3 × 10-5) and separate the genetic risk of pediatric vs. adult patients (P = 3.6 × 10-6), whereas variants at 15q25.3 (e.g., rs11638062) have a similar impact on patients in different age groups (overall P = 2.9 × 10-7). Our analysis highlights the impact of age on genetic susceptibility to ALL in Chinese patients.
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Affiliation(s)
- Qing Hao
- Department of Thoracic Oncology, Cancer Center, West China Hospital, Sichuan University, Chengdu, China.,College of Pharmaceutical Sciences, Southwest Medical University, Luzhou, China.,Sichuan Center for Translational Medicine of Traditional Chinese Medicine, Institute of Translational Pharmacology, Sichuan Academy of Chinese Medicine Sciences, Chengdu, China
| | - Minyuan Cao
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, China
| | - Chunlan Zhang
- Department of Hematology, West China Hospital, Sichuan University, Chengdu, China
| | - Dandan Yin
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, China
| | - Yuelan Wang
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, China
| | - Yuanxin Ye
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, China
| | - Shan Zhao
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, China
| | - Yunfan Yang
- Department of Hematology, West China Hospital, Sichuan University, Chengdu, China
| | - Ke-Ling Chen
- Digestive Surgery Institute, West China Hospital, Sichuan University, Chengdu, China
| | - Binwu Ying
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, China
| | - Lanlan Wang
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, China
| | - Yiguan Zhang
- Sichuan Center for Translational Medicine of Traditional Chinese Medicine, Institute of Translational Pharmacology, Sichuan Academy of Chinese Medicine Sciences, Chengdu, China
| | - Caigang Xu
- Department of Hematology, West China Hospital, Sichuan University, Chengdu, China
| | - Yiping Zhu
- Department of Hematology/Oncology, West China Second Hospital, Sichuan University, Chengdu, China
| | - Yu Wu
- Department of Hematology, West China Hospital, Sichuan University, Chengdu, China
| | - Ju Gao
- Department of Hematology/Oncology, West China Second Hospital, Sichuan University, Chengdu, China
| | - Jun-Ning Zhao
- Sichuan Center for Translational Medicine of Traditional Chinese Medicine, Institute of Translational Pharmacology, Sichuan Academy of Chinese Medicine Sciences, Chengdu, China
| | - Yan Zhang
- Department of Thoracic Oncology, Cancer Center, West China Hospital, Sichuan University, Chengdu, China
| | - Xiaoxi Lu
- Department of Hematology/Oncology, West China Second Hospital, Sichuan University, Chengdu, China
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19
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Zhang H, Liu APY, Devidas M, Lee S, Cao X, Pei D, Borowitz M, Wood B, Gastier-Foster JM, Dai Y, Raetz E, Larsen E, Winick N, Bowman WP, Karol S, Yang W, Martin PL, Carroll WL, Pui CH, Mullighan CG, Evans WE, Cheng C, Hunger SP, Relling MV, Loh ML, Yang JJ. Association of GATA3 Polymorphisms With Minimal Residual Disease and Relapse Risk in Childhood Acute Lymphoblastic Leukemia. J Natl Cancer Inst 2021; 113:408-417. [PMID: 32894760 PMCID: PMC8680540 DOI: 10.1093/jnci/djaa138] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Revised: 06/17/2020] [Accepted: 08/26/2020] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Minimal residual disease (MRD) after induction therapy is one of the strongest prognostic factors in childhood acute lymphoblastic leukemia (ALL), and MRD-directed treatment intensification improves survival. Little is known about the effects of inherited genetic variants on interpatient variability in MRD. METHODS A genome-wide association study was performed on 2597 children on the Children's Oncology Group AALL0232 trial for high-risk B-cell ALL. Association between genotype and end-of-induction MRD levels was evaluated for 863 370 single nucleotide polymorphisms (SNPs), adjusting for genetic ancestry and treatment strata. Top variants were further evaluated in a validation cohort of 491 patients from the Children's Oncology Group P9905 and 6 ALL trials. The independent prognostic value of single nucleotide polymorphisms was determined in multivariable analyses. All statistical tests were 2-sided. RESULTS In the discovery genome-wide association study, we identified a genome-wide significant association at the GATA3 locus (rs3824662, odds ratio [OR] = 1.58, 95% confidence interval [CI] = 1.35 to 1.84; P = 1.15 × 10-8 as a dichotomous variable). This association was replicated in the validation cohort (P = .003, MRD as a dichotomous variable). The rs3824662 risk allele independently predicted ALL relapse after adjusting for age, white blood cell count, and leukemia DNA index (P = .04 and .007 in the discovery and validation cohort, respectively) and remained prognostic when the analyses were restricted to MRD-negative patients (P = .04 and .03 for the discovery and validation cohorts, respectively). CONCLUSION Inherited GATA3 variant rs3824662 strongly influences ALL response to remission induction therapy and is associated with relapse. This work highlights the potential utility of germline variants in upfront risk stratification in ALL.
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Affiliation(s)
- Hui Zhang
- Department of Pharmaceutical Sciences, St Jude
Children’s Research Hospital, Memphis, TN, USA
- Department of Hematology & Oncology,
Guangzhou Women and Children’s Medical Center, Guangzhou,
China
| | - Anthony Pak-Yin Liu
- Department of Oncology, St Jude Children’s
Research Hospital, Memphis, TN, USA
| | - Meenakshi Devidas
- Department of Global Pediatric Medicine, St Jude
Children’s Research Hospital, Memphis, TN, USA
- Department of Biostatistics, University of
Florida, Gainesville, FL, USA
| | - Shawn HR Lee
- Department of Pharmaceutical Sciences, St Jude
Children’s Research Hospital, Memphis, TN, USA
- Division of Paediatric Hematology-Oncology, Khoo
Teck Puat-National University Children’s Medical Institute, National
University Health System, Singapore
| | - Xueyuan Cao
- Preventive Medicine, University of Tennessee Health
Science Center, Memphis, TN, USA
| | - Deqing Pei
- Department of Biostatistics, St Jude
Children’s Research Hospital, Memphis, TN, USA
| | - Michael Borowitz
- Division of Hematologic Pathology, Department of
Pathology, Johns Hopkins Medical Institute, Baltimore, MD,
USA
| | - Brent Wood
- Department of Laboratory Medicine, University of
Washington, Seattle, WA, USA
| | | | - Yunfeng Dai
- Department of Biostatistics, University of
Florida, Gainesville, FL, USA
| | - Elizabeth Raetz
- Division of Pediatric Hematology/Oncology,
Department of Pediatrics, Stephen D. Hassenfeld Children’s Center for
Cancer & Blood Disorders, New York, NY, USA
| | - Eric Larsen
- Maine Children’s Cancer
Program, Scarborough, ME, USA
| | - Naomi Winick
- Department of Pediatrics, University of Texas
Southwestern Medical Center, Dallas, TX, USA
| | - W Paul Bowman
- Department of Pediatrics, Cook Children’s
Medical Center, Fort Worth, TX, USA
| | - Seth Karol
- Department of Oncology, St Jude Children’s
Research Hospital, Memphis, TN, USA
| | - Wenjian Yang
- Department of Pharmaceutical Sciences, St Jude
Children’s Research Hospital, Memphis, TN, USA
| | - Paul L Martin
- Department of Pediatrics, Duke
University, Durham, NC, USA
| | - William L Carroll
- Division of Pediatric Hematology/Oncology,
Department of Pediatrics, Stephen D. Hassenfeld Children’s Center for
Cancer & Blood Disorders, New York, NY, USA
| | - Ching-Hon Pui
- Department of Oncology, St Jude Children’s
Research Hospital, Memphis, TN, USA
| | - Charles G Mullighan
- Department of Pathology, St Jude Children’s
Research Hospital, Memphis, TN, USA
| | - William E Evans
- Department of Pharmaceutical Sciences, St Jude
Children’s Research Hospital, Memphis, TN, USA
| | - Cheng Cheng
- Department of Biostatistics, St Jude
Children’s Research Hospital, Memphis, TN, USA
| | - Stephen P Hunger
- Division of Oncology and the Center for Childhood
Cancer Research, Department of Pediatrics, Children’s Hospital of
Philadelphia and the Perelman School of Medicine at the University of
Pennsylvania, Philadelphia, PA, USA
| | - Mary V Relling
- Department of Pharmaceutical Sciences, St Jude
Children’s Research Hospital, Memphis, TN, USA
| | - Mignon L Loh
- Division of Hematology Oncology, Department of
Pediatrics, Benioff Children’s Hospital and University of
California, San Francisco, San Francisco, CA, USA
| | - Jun J Yang
- Department of Pharmaceutical Sciences, St Jude
Children’s Research Hospital, Memphis, TN, USA
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20
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Abstract
Although much work has focused on the elucidation of somatic alterations that drive the development of acute leukaemias and other haematopoietic diseases, it has become increasingly recognized that germline mutations are common in many of these neoplasms. In this Review, we highlight the different genetic pathways impacted by germline mutations that can ultimately lead to the development of familial and sporadic haematological malignancies, including acute lymphoblastic leukaemia, acute myeloid leukaemia (AML) and myelodysplastic syndrome (MDS). Many of the genes disrupted by somatic mutations in these diseases (for example, TP53, RUNX1, IKZF1 and ETV6) are the same as those that harbour germline mutations in children and adolescents who develop these malignancies. Moreover, the presumption that familial leukaemias only present in childhood is no longer true, in large part due to the numerous studies demonstrating germline DDX41 mutations in adults with MDS and AML. Lastly, we highlight how different cooperating events can influence the ultimate phenotype in these different familial leukaemia syndromes.
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Affiliation(s)
- Jeffery M Klco
- Department of Pathology and the Hematological Malignancies Program, St. Jude Children's Research Hospital, Memphis, TN, USA.
| | - Charles G Mullighan
- Department of Pathology and the Hematological Malignancies Program, St. Jude Children's Research Hospital, Memphis, TN, USA.
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21
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Gant VU, Junco JJ, Terrell M, Rashid R, Rabin KR. Enhancer polymorphisms at the IKZF1 susceptibility locus for acute lymphoblastic leukemia impact B-cell proliferation and differentiation in both Down syndrome and non-Down syndrome genetic backgrounds. PLoS One 2021; 16:e0244863. [PMID: 33411777 DOI: 10.1371/journal.pone.0244863] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2020] [Accepted: 12/17/2020] [Indexed: 12/26/2022] Open
Abstract
Children with Down syndrome have an approximately 10-fold increased risk of developing acute lymphoblastic leukemia and this risk is influenced by inherited genetic variation. Genome-wide association studies have identified IKZF1 as a strong acute lymphoblastic leukemia susceptibility locus in children both with and without Down syndrome, with association signals reported at rs4132601 in non-Down syndrome and rs58923657 in individuals with Down syndrome (r2 = 0.98 for these two loci). Expression quantitative trait locus analysis in non-Down syndrome lymphoblastoid cell lines has demonstrated an association between the rs4132601 risk allele and decreased IKZF1 mRNA levels. In this study, we provide further mechanistic evidence linking the region encompassing IKZF1-associated polymorphisms to pro-leukemogenic effects in both human lymphoblastoid cell lines and murine hematopoietic stem cells. CRISPR/Cas9-mediated deletion of the region encompassing the rs17133807 major allele (r2 with rs58923657 = 0.97) resulted in significant reduction of IKZF1 mRNA levels in lymphoblastoid cell lines, with a greater effect in Down syndrome versus non-Down syndrome cells. Since rs17133807 is highly conserved in mammals, we also evaluated the orthologous murine locus at rs263378223, in hematopoietic stem cells from the Dp16(1)Yey mouse model of Down syndrome as well as non-Down syndrome control mice. Homozygous deletion of the region encompassing rs263378223 resulted in significantly reduced Ikzf1 mRNA, confirming that this polymorphism maps to a strong murine Ikzf1 enhancer, and resulted in increased B-lymphoid colony growth and decreased B-lineage differentiation. Our results suggest that both the region encompassing rs17133807 and its conserved orthologous mouse locus have functional effects that may mediate increased leukemia susceptibility in both the Down syndrome and non-Down syndrome genetic backgrounds.
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22
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Gutierrez-Camino A, Richer C, St-Onge P, Lopez-Lopez E, Bañeres AC, de Andoin NG, Sastre A, Astigarraga I, Martin-Guerrero I, Sinnett D, Garcia-Orad A. Role of rs10406069 in miR-5196 in hyperdiploid childhood acute lymphoblastic leukemia. Epigenomics 2020; 12:1949-1955. [PMID: 33245684 DOI: 10.2217/epi-2020-0152] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Aim: To determine the role of single nucleotide polymorphisms (SNPs) in noncoding RNAs in childhood acute lymphoblastic leukemia (ALL) subtypes. Materials & methods: We screened all SNPs in 130 pre-miRNA genes to assess their role in the susceptibility of the most common subtypes of ALL: hyperdiploid and ETV6-RUNX1. Results: In two independent cohorts, we found a significant association between rs10406069 in miR-5196 and the risk of developing hyperdiploid ALL. This observation could be explained by the impact of the SNP on miR-5196 expression and in turn, in its target genes. Indeed, rs10406069 was associated with expression changes in SMC1A, a gene involved in sister chromatin cohesion. Conclusion: rs10406069 in miR-5196 may have a relevant role in hyperdiploid ALL risk.
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Affiliation(s)
- Angela Gutierrez-Camino
- Department of Genetics, Physical Anthropology & Animal Physiology, Faculty of Medicine & Nursing, University of the Basque Country, UPV/EHU, Leioa, Spain.,Pediatric Oncology Group, BioCruces Bizkaia Health Research Institute, Barakaldo, Spain.,Division of Hematology-Oncology, CHU Sainte-Justine Research Center, Montreal, QC H3T 1C5, Canada
| | - Chantal Richer
- Division of Hematology-Oncology, CHU Sainte-Justine Research Center, Montreal, QC H3T 1C5, Canada
| | - Pascal St-Onge
- Division of Hematology-Oncology, CHU Sainte-Justine Research Center, Montreal, QC H3T 1C5, Canada
| | - Elixabet Lopez-Lopez
- Department of Genetics, Physical Anthropology & Animal Physiology, Faculty of Medicine & Nursing, University of the Basque Country, UPV/EHU, Leioa, Spain.,Pediatric Oncology Group, BioCruces Bizkaia Health Research Institute, Barakaldo, Spain
| | - Ana Carbone Bañeres
- Department of Paediatrics, University Hospital Miguel Servet, Zaragoza, Spain
| | - Nagore Garcia de Andoin
- Department of Paediatrics, University Hospital Donostia, San Sebastian, Spain.,Unit of Pediatric Oncohematology, BioDonostia Health Research Institute, San Sebastian, Spain.,Department of Pediatrics, University of the Basque Country, UPV/EHU, Leioa, Spain
| | - Ana Sastre
- Department of Oncohematology, University Hospital La Paz, Madrid, Spain
| | - Itziar Astigarraga
- Pediatric Oncology Group, BioCruces Bizkaia Health Research Institute, Barakaldo, Spain.,Department of Pediatrics, University of the Basque Country, UPV/EHU, Leioa, Spain.,Department of Paediatrics, University Hospital Cruces, Barakaldo, Spain
| | - Idoia Martin-Guerrero
- Department of Genetics, Physical Anthropology & Animal Physiology, Faculty of Medicine & Nursing, University of the Basque Country, UPV/EHU, Leioa, Spain.,Pediatric Oncology Group, BioCruces Bizkaia Health Research Institute, Barakaldo, Spain
| | - Daniel Sinnett
- Division of Hematology-Oncology, CHU Sainte-Justine Research Center, Montreal, QC H3T 1C5, Canada.,Department of Pediatrics, Faculty of Medicine, University of Montreal, Montreal, QC H3T 1C5, Canada
| | - Africa Garcia-Orad
- Department of Genetics, Physical Anthropology & Animal Physiology, Faculty of Medicine & Nursing, University of the Basque Country, UPV/EHU, Leioa, Spain.,Pediatric Oncology Group, BioCruces Bizkaia Health Research Institute, Barakaldo, Spain
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23
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Liao F, Ye Y, Yin D, Qin Y, Zhao J, Zhang W, Zhang Y, Deng Z, Wang Y, Ying B, Wang L, Gao J, Shu Y, Zhu Y, Lu X. Validations of Top and Novel Susceptibility Variants in All-Age Chinese Patients With Acute Lymphoblastic Leukemia. Front Genet 2020; 11:1004. [PMID: 33193587 PMCID: PMC7477633 DOI: 10.3389/fgene.2020.01004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Accepted: 08/06/2020] [Indexed: 02/05/2023] Open
Abstract
Through genome-wide association studies (GWAS), multiple inherited predispositions to acute lymphoblastic leukemia (ALL) have been identified in children. Most recently, a novel susceptibility locus at ERG was localized, exhibiting Hispanic-specific manner. In this study, we conducted a replication study to in all-age Chinese patients (N = 451), not only validating the novel ERG locus, but also systematically determining the impact of age on association status of the top GWAS signals. We found that single nucleotide polymorphisms at ARID5B, IKZF1, CEBPE, PIP4K2A were only significantly associated with ALL susceptibility in childhood patients with no BCR-ABL fusion, while GATA3 signal exhibited its significance in adults no matter carrying BCR-ABL fusion or not. Moreover, the novel ERG SNP can be validated in pediatric patients without both BCR-ABL and ETV6-RUNX1 fusion. Our finding suggests the modifying effects of age on genetic predisposition to ALL, and highlights the impact of ERG SNP in Chinese patients.
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Affiliation(s)
- Fei Liao
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Department of Pediatric Hematology/Oncology, West China Second Hospital, Sichuan University, Ministry of Education, Chengdu, China.,State Key Laboratory of Biotherapy, Department of Laboratory Medicine, Precision Medicine Center, West China Hospital, Sichuan University, Chengdu, China
| | - Yuanxin Ye
- State Key Laboratory of Biotherapy, Department of Laboratory Medicine, Precision Medicine Center, West China Hospital, Sichuan University, Chengdu, China
| | - Dandan Yin
- State Key Laboratory of Biotherapy, Department of Laboratory Medicine, Precision Medicine Center, West China Hospital, Sichuan University, Chengdu, China
| | - Yun Qin
- Department of Radiology, West China Hospital, Sichuan University, Chengdu, China
| | - Jiangyan Zhao
- State Key Laboratory of Biotherapy, Department of Laboratory Medicine, Precision Medicine Center, West China Hospital, Sichuan University, Chengdu, China
| | - Wanhua Zhang
- Department of Hematology and Hematology Research Laboratory, West China Hospital, Sichuan University, Chengdu, China
| | - Yan Zhang
- State Key Laboratory of Biotherapy, Department of Thoracic Oncology, Cancer Center, West China Hospital, Sichuan University, Chengdu, China
| | - Zhujun Deng
- State Key Laboratory of Biotherapy, Department of Laboratory Medicine, Precision Medicine Center, West China Hospital, Sichuan University, Chengdu, China
| | - Yuelan Wang
- State Key Laboratory of Biotherapy, Department of Laboratory Medicine, Precision Medicine Center, West China Hospital, Sichuan University, Chengdu, China
| | - Binwu Ying
- State Key Laboratory of Biotherapy, Department of Laboratory Medicine, Precision Medicine Center, West China Hospital, Sichuan University, Chengdu, China
| | - Lanlan Wang
- State Key Laboratory of Biotherapy, Department of Laboratory Medicine, Precision Medicine Center, West China Hospital, Sichuan University, Chengdu, China
| | - Ju Gao
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Department of Pediatric Hematology/Oncology, West China Second Hospital, Sichuan University, Ministry of Education, Chengdu, China
| | - Yang Shu
- State Key Laboratory of Biotherapy, Department of Laboratory Medicine, Precision Medicine Center, West China Hospital, Sichuan University, Chengdu, China
| | - Yiping Zhu
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Department of Pediatric Hematology/Oncology, West China Second Hospital, Sichuan University, Ministry of Education, Chengdu, China
| | - Xiaoxi Lu
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Department of Pediatric Hematology/Oncology, West China Second Hospital, Sichuan University, Ministry of Education, Chengdu, China
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24
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Mei E, Wei X, Gao J, Tian X, Li W, Liu L, Qian C. Association of TLX1 gene polymorphisms with the risk of acute lymphoblastic leukemia and B lineage acute lymphoblastic leukemia in Han Chinese children. J Clin Lab Anal 2020; 34:e23414. [PMID: 32488880 PMCID: PMC7521250 DOI: 10.1002/jcla.23414] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Revised: 05/03/2020] [Accepted: 05/05/2020] [Indexed: 12/12/2022] Open
Abstract
Background Studies on gene polymorphism association are centered on childhood acute lymphoblastic leukemia (ALL), a common hematological malignancy in children younger than 16 years. Single‐nucleotide polymorphisms (SNPs) in some genes, such as ARID5B and CDKN2B, are associated with the risk of childhood ALL. T‐cell leukemia homeobox 1 (TLX1), a member of the HOX gene family, was identified based on its abnormal expression in T‐lineage leukemia. This study aimed to determine whether TLX1 is associated with B‐ALL and which SNP plays a significant role in ALL. Methods A total of 217 cases of ALL and 241 controls were included in this study. Six tag SNPs (rs75329544, rs946328, rs12415670, rs2075879, rs17113735, and rs1051723) were selected, and genotyping was carried out on Sequenom MassARRAY platform. Results Rs17113735 was possibly the risk locus associated with increased risk for ALL, whereas rs946328 was possibly associated with decreased risk for ALL. Moreover, rs17113735 was likely to be the risk locus for B‐cell ALL (B‐ALL), and rs2075879 was associated with decreased risk for B‐ALL (P < .05). All SNPs in the two sample types (ALL and B‐ALL samples) demonstrated linkage disequilibrium except between rs75329544 and rs2075879. Haplotype analysis showed no significant difference between the cases and controls in the two sample types. Conclusion TLX1 gene polymorphisms are associated with ALL (rs17113735 and rs946328) and possibly play a significant role in B‐ALL (rs17113735 and rs2075879). This work provides a reference for the diagnosis and therapy of this disease.
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Affiliation(s)
- Endian Mei
- School of Life Sciences and Medicine, Zhejiang Sci-Tech University. Hangzhou, Zhejiang, China
| | - Xubin Wei
- School of Life Sciences and Medicine, Zhejiang Sci-Tech University. Hangzhou, Zhejiang, China
| | - Jiadong Gao
- School of Life Sciences and Medicine, Zhejiang Sci-Tech University. Hangzhou, Zhejiang, China
| | - Xiaolong Tian
- School of Life Sciences and Medicine, Zhejiang Sci-Tech University. Hangzhou, Zhejiang, China
| | - Wei Li
- Department of Clinical Laboratory, School of Medicine, Children's Hospital, Zhejiang University, Hangzhou, China
| | - Li Liu
- School of Life Sciences and Medicine, Zhejiang Sci-Tech University. Hangzhou, Zhejiang, China
| | - Cheng Qian
- School of Life Sciences and Medicine, Zhejiang Sci-Tech University. Hangzhou, Zhejiang, China
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25
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Sbirkov Y, Burnusuzov H, Sarafian V. Metabolic reprogramming in childhood acute lymphoblastic leukemia. Pediatr Blood Cancer 2020; 67:e28255. [PMID: 32293782 DOI: 10.1002/pbc.28255] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Revised: 02/04/2020] [Accepted: 02/25/2020] [Indexed: 12/12/2022]
Abstract
The first observations of altered metabolism in malignant cells were made nearly 100 years ago and therapeutic strategies targeting cell metabolism have been in clinical use for several decades. In this review, we summarize our current understanding of cell metabolism dysregulation in childhood acute lymphoblastic leukemia (cALL). Reprogramming of cellular bioenergetic processes can be expected in the three distinct stages of cALL: at diagnosis, during standard chemotherapy, and in cases of relapse. Upregulation of glycolysis, dependency on anaplerotic energy sources, and activation of the electron transport chain have all been observed in cALL. While the current treatment strategies are tackling some of these aberrations, cALL cells are likely to be able to rewire their metabolism in order to escape therapy, which may contribute to a refractory disease and relapse. Finally, here we focus on novel therapeutic approaches emerging from our evolving understanding of the alterations of different metabolic networks in lymphoblasts.
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Affiliation(s)
- Yordan Sbirkov
- Department of Medical Biology, Medical University of Plovdiv, Plovdiv, Bulgaria.,Research Institute at Medical University- Plovdiv, Plovdiv, Bulgaria
| | - Hasan Burnusuzov
- Research Institute at Medical University- Plovdiv, Plovdiv, Bulgaria.,Department of Pediatrics and Medical Genetics, Medical University of Plovdiv, Plovdiv, Bulgaria
| | - Victoria Sarafian
- Department of Medical Biology, Medical University of Plovdiv, Plovdiv, Bulgaria.,Research Institute at Medical University- Plovdiv, Plovdiv, Bulgaria
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26
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Semmes EC, Vijayakrishnan J, Zhang C, Hurst JH, Houlston RS, Walsh KM. Leveraging Genome and Phenome-Wide Association Studies to Investigate Genetic Risk of Acute Lymphoblastic Leukemia. Cancer Epidemiol Biomarkers Prev 2020; 29:1606-1614. [PMID: 32467347 DOI: 10.1158/1055-9965.epi-20-0113] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Revised: 03/23/2020] [Accepted: 05/06/2020] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Genome-wide association studies (GWAS) of childhood cancers remain limited, highlighting the need for novel analytic strategies. We describe a hybrid GWAS and phenome-wide association study (PheWAS) approach to uncover genotype-phenotype relationships and candidate risk loci, applying it to acute lymphoblastic leukemia (ALL). METHODS PheWAS was performed for 12 ALL SNPs identified by prior GWAS and two control SNP-sets using UK Biobank data. PheWAS-traits significantly associated with ALL SNPs compared with control SNPs were assessed for association with ALL risk (959 cases, 2,624 controls) using polygenic score and Mendelian randomization analyses. Trait-associated SNPs were tested for association with ALL risk in single-SNP analyses, with replication in an independent case-control dataset (1,618 cases, 9,409 controls). RESULTS Platelet count was the trait most enriched for association with known ALL risk loci. A polygenic score for platelet count (223 SNPs) was not associated with ALL risk (P = 0.82) and Mendelian randomization did not suggest a causal relationship. However, twelve platelet count-associated SNPs were nominally associated with ALL risk in COG data and three were replicated in UK data (rs10058074, rs210142, rs2836441). CONCLUSIONS In our hybrid GWAS-PheWAS approach, we identify pleiotropic genetic variation contributing to ALL risk and platelet count. Three SNPs known to influence platelet count were reproducibly associated with ALL risk, implicating genomic regions containing IRF1, proapoptotic protein BAK1, and ERG in platelet production and leukemogenesis. IMPACT Incorporating PheWAS data into association studies can leverage genetic pleiotropy to identify cancer risk loci, highlighting the utility of our novel approach.
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Affiliation(s)
- Eleanor C Semmes
- Medical Scientist Training Program, Duke University, Durham, North Carolina.,Children's Health and Discovery Initiative, Department of Pediatrics, Duke University, Durham, North Carolina
| | - Jayaram Vijayakrishnan
- Division of Genetics and Epidemiology, The Institute of Cancer Research, Sutton, Surrey, United Kingdom
| | - Chenan Zhang
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, California
| | - Jillian H Hurst
- Children's Health and Discovery Initiative, Department of Pediatrics, Duke University, Durham, North Carolina
| | - Richard S Houlston
- Division of Genetics and Epidemiology, The Institute of Cancer Research, Sutton, Surrey, United Kingdom
| | - Kyle M Walsh
- Children's Health and Discovery Initiative, Department of Pediatrics, Duke University, Durham, North Carolina. .,Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, California.,Department of Neurosurgery, Duke University, Durham, North Carolina.,Duke Cancer Institute, Duke University, Durham, North Carolina
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27
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Shu X, Long J, Cai Q, Kweon SS, Choi JY, Kubo M, Park SK, Bolla MK, Dennis J, Wang Q, Yang Y, Shi J, Guo X, Li B, Tao R, Aronson KJ, Chan KYK, Chan TL, Gao YT, Hartman M, Kee Ho W, Ito H, Iwasaki M, Iwata H, John EM, Kasuga Y, Soon Khoo U, Kim MK, Kong SY, Kurian AW, Kwong A, Lee ES, Li J, Lophatananon A, Low SK, Mariapun S, Matsuda K, Matsuo K, Muir K, Noh DY, Park B, Park MH, Shen CY, Shin MH, Spinelli JJ, Takahashi A, Tseng C, Tsugane S, Wu AH, Xiang YB, Yamaji T, Zheng Y, Milne RL, Dunning AM, Pharoah PDP, García-Closas M, Teo SH, Shu XO, Kang D, Easton DF, Simard J, Zheng W. Identification of novel breast cancer susceptibility loci in meta-analyses conducted among Asian and European descendants. Nat Commun 2020; 11:1217. [PMID: 32139696 PMCID: PMC7057957 DOI: 10.1038/s41467-020-15046-w] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Accepted: 02/10/2020] [Indexed: 02/08/2023] Open
Abstract
Known risk variants explain only a small proportion of breast cancer heritability, particularly in Asian women. To search for additional genetic susceptibility loci for breast cancer, here we perform a meta-analysis of data from genome-wide association studies (GWAS) conducted in Asians (24,206 cases and 24,775 controls) and European descendants (122,977 cases and 105,974 controls). We identified 31 potential novel loci with the lead variant showing an association with breast cancer risk at P < 5 × 10-8. The associations for 10 of these loci were replicated in an independent sample of 16,787 cases and 16,680 controls of Asian women (P < 0.05). In addition, we replicated the associations for 78 of the 166 known risk variants at P < 0.05 in Asians. These findings improve our understanding of breast cancer genetics and etiology and extend previous findings from studies of European descendants to Asian women.
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Affiliation(s)
- Xiang Shu
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Jirong Long
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Qiuyin Cai
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Sun-Seog Kweon
- Department of Preventive Medicine, Chonnam National University Medical School, Hwasun, Korea
- Jeonnam Regional Cancer Center, Chonnam National University Hwasun Hospital, Hwasun, Korea
| | - Ji-Yeob Choi
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Korea
- Department of Preventive Medicine, Seoul National University College of Medicine, Seoul, Korea
- Cancer Research Institute, Seoul National University College of Medicine, Seoul, Korea
| | - Michiaki Kubo
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Sue K Park
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Korea
- Department of Preventive Medicine, Seoul National University College of Medicine, Seoul, Korea
- Cancer Research Institute, Seoul National University College of Medicine, Seoul, Korea
| | - Manjeet K Bolla
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Joe Dennis
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Qin Wang
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Yaohua Yang
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Jiajun Shi
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Xingyi Guo
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Bingshan Li
- Department of Molecular Physiology & Biophysics, Vanderbilt Genetics Institute, Vanderbilt University, Nashville, TN, USA
| | - Ran Tao
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN, USA
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Kristan J Aronson
- Department of Public Health Sciences and Queen's Cancer Research Institute, Queen's University, Kingston, ON, Canada
| | - Kelvin Y K Chan
- Department of Pathology, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong SAR, China
- Department of Obstetrics & Gynaecology, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong SAR, China
| | - Tsun L Chan
- Hong Kong Hereditary Breast Cancer Family Registry, Hong Kong SAR, China
- Department of Molecular Pathology, Hong Kong Sanatorium & Hospital, Hong Kong SAR, China
| | - Yu-Tang Gao
- State Key Laboratory of Oncogene and Related Genes & Department of Epidemiology, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Mikael Hartman
- Department of Surgery, National University Hospital, Singapore, Singapore
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore, Singapore
- Department of Surgery, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Weang Kee Ho
- Department of Applied Mathematics, Faculty of Engineering, University of Nottingham Malaysia Campus, Semenyih, Selangor, Malaysia
| | - Hidemi Ito
- Division of Cancer Information and Control, Aichi Cancer Center Research Institute, Nagoya, Japan
- Department of Descriptive Cancer Epidemiology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Motoki Iwasaki
- Division of Epidemiology, Center for Public Health Sciences, National Cancer Center, Tokyo, Japan
| | - Hiroji Iwata
- Department of Breast Oncology, Aichi Cancer Center, Nagoya, Aichi, Japan
| | - Esther M John
- Department of Epidemiology, Cancer Prevention Institute of California, Fremont, CA, USA
- Departments of Health Research and Policy, School of Medicine, Stanford University, California, CA, USA
- Stanford Cancer Institute, Stanford University School of Medicine, California, CA, USA
| | - Yoshio Kasuga
- Department of Surgery, Nagano Matsushiro General Hospital, Nagano, Japan
| | - Ui Soon Khoo
- Department of Pathology, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong SAR, China
| | - Mi-Kyung Kim
- Division of Cancer Epidemiology and Management, National Cancer Center, Goyang, Korea
| | - Sun-Young Kong
- National Cancer Center Graduate School of Cancer Science and Policy, Goyang, Republic of Korea
- Hospital, National Cancer Center, Goyang, Republic of Korea
- Research Institute, National Cancer Center, Goyang, Republic of Korea
| | - Allison W Kurian
- Departments of Health Research and Policy, School of Medicine, Stanford University, California, CA, USA
| | - Ava Kwong
- Hong Kong Hereditary Breast Cancer Family Registry, Hong Kong SAR, China
- Department of Surgery, University of Hong Kong, Hong Kong SAR, China
- Department of Surgery, Hong Kong Sanatorium & Hospital, Hong Kong SAR, China
| | - Eun-Sook Lee
- National Cancer Center Graduate School of Cancer Science and Policy, Goyang, Republic of Korea
- Hospital, National Cancer Center, Goyang, Republic of Korea
- Research Institute, National Cancer Center, Goyang, Republic of Korea
| | - Jingmei Li
- Department of Surgery, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Human Genetics, Genome Institute of Singapore, Singapore, Singapore
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Artitaya Lophatananon
- Division of Health Sciences, Warwick Medical School, Warwick University, Coventry, UK
- Institute of Population Health, University of Manchester, Manchester, UK
| | - Siew-Kee Low
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | | | - Koichi Matsuda
- Laboratory of Clinical Genome Sequencing, Graduate School of Frontier Sciences, University of Tokyo, Tokyo, Japan
| | - Keitaro Matsuo
- Division of Cancer Epidemiology and Prevention, Aichi Cancer Center Research Institute, Nagoya, Japan
- Division of Cancer Epidemiology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Kenneth Muir
- Division of Health Sciences, Warwick Medical School, Warwick University, Coventry, UK
- Institute of Population Health, University of Manchester, Manchester, UK
| | - Dong-Young Noh
- Cancer Research Institute, Seoul National University College of Medicine, Seoul, Korea
- Department of Surgery, Seoul National University Hospital, Seoul, South Korea
| | - Boyoung Park
- Department of Medicine, Hanyang University College of Medicine, Seoul, Korea
| | - Min-Ho Park
- Department of Surgery, Chonnam National University Medical School, Seoul, Korea
| | - Chen-Yang Shen
- College of Public Health, China Medical University, Taichong, Taiwan
- Taiwan Biobank, Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Min-Ho Shin
- Department of Preventive Medicine, Chonnam National University Medical School, Hwasun, Korea
| | - John J Spinelli
- Population Oncology, BC Cancer, Vancouver, BC, Canada
- School of Population and Public Health, University of British Columbia, Vancouver, BC, Canada
| | - Atsushi Takahashi
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Department of Genomic Medicine, Research Institute, National Cerebral and Cardiovascular Center, Suita, Osaka, Japan
| | - Chiuchen Tseng
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Shoichiro Tsugane
- Center for Public Health Sciences, National Cancer Center, Tokyo, Japan
| | - Anna H Wu
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Yong-Bing Xiang
- State Key Laboratory of Oncogene and Related Genes & Department of Epidemiology, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Taiki Yamaji
- Division of Epidemiology, Center for Public Health Sciences, National Cancer Center, Tokyo, Japan
| | - Ying Zheng
- Shanghai Municipal Center for Disease Control and Prevention, Shanghai, China
| | - Roger L Milne
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, University of Melbourne, Parkville, Victoria, Australia
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, Victoria, Australia
| | - Alison M Dunning
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Paul D P Pharoah
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | | | - Soo-Hwang Teo
- Cancer Research Malaysia, Subang Jaya, Selangor, Malaysia
- Department of Surgery, Faculty of Medicine, University Malaya, Kuala Lumpar, Malaysia
| | - Xiao-Ou Shu
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Daehee Kang
- Department of Preventive Medicine, Seoul National University College of Medicine, Seoul, Korea
- Cancer Research Institute, Seoul National University College of Medicine, Seoul, Korea
- Department of Biomedical Sciences, Seoul National University Graduate School, Seoul, Korea
- Institute of Environmental Medicine, Seoul National University Medical Research Center, Seoul, Korea
| | - Douglas F Easton
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Jacques Simard
- Genomics Center, Centre Hospitalier Universitaire de Québec - Université Laval, Research Center, Québec City, QC, Canada
| | - Wei Zheng
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA.
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28
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Bloom M, Maciaszek JL, Clark ME, Pui CH, Nichols KE. Recent advances in genetic predisposition to pediatric acute lymphoblastic leukemia. Expert Rev Hematol 2020; 13:55-70. [PMID: 31657974 PMCID: PMC10576863 DOI: 10.1080/17474086.2020.1685866] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2019] [Accepted: 10/24/2019] [Indexed: 12/11/2022]
Abstract
Introduction: Historically, the majority of childhood cancers, including acute lymphoblastic leukemia (ALL), were not thought to have a hereditary basis. However, recent germline genomic studies have revealed that at least 5 - 10% of children with cancer (and approximately 3 - 4% of children with ALL) develop the disease due to an underlying genetic predisposition.Areas covered: This review discusses several recently identified ALL predisposing conditions and provides updates on other more well-established syndromes. It also covers topics related to the evaluation and management of children and family members at increased ALL risk.Expert opinion: Germline predisposition is gaining recognition as an important risk factor underlying the development of pediatric ALL. The challenge now lies in how best to capitalize on germline genetic information to improve ALL diagnosis, treatment, and perhaps even prevention.
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Affiliation(s)
- Mackenzie Bloom
- Department of Oncology, St. Jude Children’s Research Hospital, Memphis, TN, USA
- Graduate School of Biomedical Sciences, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Jamie L. Maciaszek
- Department of Oncology, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Mary Egan Clark
- Department of Oncology, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Ching-Hon Pui
- Department of Oncology, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Kim E. Nichols
- Department of Oncology, St. Jude Children’s Research Hospital, Memphis, TN, USA
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29
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Qian M, Zhao X, Devidas M, Yang W, Gocho Y, Smith C, Gastier-Foster JM, Li Y, Xu H, Zhang S, Jeha S, Zhai X, Sanda T, Winter SS, Dunsmore KP, Raetz EA, Carroll WL, Winick NJ, Rabin KR, Zweidler-Mckay PA, Wood B, Pui CH, Evans WE, Hunger SP, Mullighan CG, Relling MV, Loh ML, Yang JJ. Genome-Wide Association Study of Susceptibility Loci for T-Cell Acute Lymphoblastic Leukemia in Children. J Natl Cancer Inst 2019; 111:1350-1357. [PMID: 30938820 PMCID: PMC6910193 DOI: 10.1093/jnci/djz043] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Revised: 01/04/2019] [Accepted: 03/25/2019] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Acute lymphoblastic leukemia (ALL) is the most common cancer in children and can arise in B or T lymphoid lineages. Although risk loci have been identified for B-ALL, the inherited basis of T-ALL is mostly unknown, with a particular paucity of genome-wide investigation of susceptibility variants in large patient cohorts. METHODS We performed a genome-wide association study (GWAS) in 1191 children with T-ALL and 12 178 controls, with independent replication using 117 cases and 5518 controls. The associations were tested using an additive logistic regression model. Top risk variants were tested for effects on enhancer activity using luciferase assay. All statistical tests were two sided. RESULTS A novel risk locus in the USP7 gene (rs74010351, odds ratio [OR] = 1.44, 95% confidence interval [CI] = 1.27 to 1.65, P = 4.51 × 10-8) reached genome-wide significance in the discovery cohort, with independent validation (OR = 1.51, 95% CI = 1.03 to 2.22, P = .04). The USP7 risk allele was overrepresented in individuals of African descent, thus contributing to the higher incidence of T-ALL in this race/ethnic group. Genetic changes in USP7 (germline variants or somatic mutations) were observed in 56.4% of T-ALL with TAL1 overexpression, statistically significantly higher than in any other subtypes. Functional analyses suggested this T-ALL risk allele is located in a putative cis-regulatory DNA element with negative effects on USP7 transcription. Finally, comprehensive comparison of 14 susceptibility loci in T- vs B-ALL pointed to distinctive etiology of these leukemias. CONCLUSIONS These findings indicate strong associations between inherited genetic variation and T-ALL susceptibility in children and shed new light on the molecular etiology of ALL, particularly commonalities and differences in the biology of the two major subtypes (B- vs T-ALL).
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Jun J Yang
- Correspondence to: Jun J. Yang, PhD, Hematologic Malignancies Program, Comprehensive Cancer Center, St. Jude Children’s Research Hospital, 262 Danny Thomas Pl, MS313, Memphis, TN 38105 (e-mail: )
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30
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Vijayakrishnan J, Qian M, Studd JB, Yang W, Kinnersley B, Law PJ, Broderick P, Raetz EA, Allan J, Pui CH, Vora A, Evans WE, Moorman A, Yeoh A, Yang W, Li C, Bartram CR, Mullighan CG, Zimmerman M, Hunger SP, Schrappe M, Relling MV, Stanulla M, Loh ML, Houlston RS, Yang JJ. Identification of four novel associations for B-cell acute lymphoblastic leukaemia risk. Nat Commun 2019; 10:5348. [PMID: 31767839 PMCID: PMC6877561 DOI: 10.1038/s41467-019-13069-6] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Accepted: 10/17/2019] [Indexed: 12/12/2022] Open
Abstract
There is increasing evidence for a strong inherited genetic basis of susceptibility to acute lymphoblastic leukaemia (ALL) in children. To identify new risk variants for B-cell ALL (B-ALL) we conducted a meta-analysis with four GWAS (genome-wide association studies), totalling 5321 cases and 16,666 controls of European descent. We herein describe novel risk loci for B-ALL at 9q21.31 (rs76925697, P = 2.11 × 10-8), for high-hyperdiploid ALL at 5q31.1 (rs886285, P = 1.56 × 10-8) and 6p21.31 (rs210143 in BAK1, P = 2.21 × 10-8), and ETV6-RUNX1 ALL at 17q21.32 (rs10853104 in IGF2BP1, P = 1.82 × 10-8). Particularly notable are the pleiotropic effects of the BAK1 variant on multiple haematological malignancies and specific effects of IGF2BP1 on ETV6-RUNX1 ALL evidenced by both germline and somatic genomic analyses. Integration of GWAS signals with transcriptomic/epigenomic profiling and 3D chromatin interaction data for these leukaemia risk loci suggests deregulation of B-cell development and the cell cycle as central mechanisms governing genetic susceptibility to ALL.
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Affiliation(s)
- Jayaram Vijayakrishnan
- Division of Genetics and Epidemiology, The Institute of Cancer Research, 15 Cotswold Road, Sutton, Surrey, SM2 5NG, UK
| | - Maoxiang Qian
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
- Children's Hospital and Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - James B Studd
- Division of Genetics and Epidemiology, The Institute of Cancer Research, 15 Cotswold Road, Sutton, Surrey, SM2 5NG, UK
| | - Wenjian Yang
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Ben Kinnersley
- Division of Genetics and Epidemiology, The Institute of Cancer Research, 15 Cotswold Road, Sutton, Surrey, SM2 5NG, UK
| | - Philip J Law
- Division of Genetics and Epidemiology, The Institute of Cancer Research, 15 Cotswold Road, Sutton, Surrey, SM2 5NG, UK
| | - Peter Broderick
- Division of Genetics and Epidemiology, The Institute of Cancer Research, 15 Cotswold Road, Sutton, Surrey, SM2 5NG, UK
| | - Elizabeth A Raetz
- Division of Pediatric Hematology and Oncology, New York University Langone Health, New York, New York, USA
| | - James Allan
- Northern Institute for Cancer Research, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Ching-Hon Pui
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
- Hematological Malignancies Program, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | | | - William E Evans
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
- Hematological Malignancies Program, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Anthony Moorman
- Wolfson Childhood Cancer Research Centre, Northern Institute for Cancer Research, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
| | - Allen Yeoh
- Centre for Translational Research in Acute Leukaemia, Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- VIVA-University Children's Cancer Centre, Khoo Teck Puat-National University Children's Medical Institute, National University Hospital, National University Health System, Singapore, Singapore
| | - Wentao Yang
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Chunliang Li
- Department of Tumor Cell Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Claus R Bartram
- Institute of Human Genetics, University Hospital, Heidelberg, Germany
| | - Charles G Mullighan
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
- Hematological Malignancies Program, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Martin Zimmerman
- Department of Paediatric Haematology and Oncology, Hannover Medical School, 30625, Hannover, Germany
| | - Stephen P Hunger
- Department of Paediatrics and Centre for Childhood Cancer Research, Children's Hospital of Philadelphia and the Perelman School of Medicine at The University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Martin Schrappe
- Department of Paediatrics, University Medical Centre Schleswig-Holstein, Kiel, Germany
| | - Mary V Relling
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
- Hematological Malignancies Program, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Martin Stanulla
- Department of Paediatric Haematology and Oncology, Hannover Medical School, 30625, Hannover, Germany
| | - Mignon L Loh
- Department of Pediatrics, Benioff Children's Hospital and the Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California, USA
| | - Richard S Houlston
- Division of Genetics and Epidemiology, The Institute of Cancer Research, 15 Cotswold Road, Sutton, Surrey, SM2 5NG, UK.
| | - Jun J Yang
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee, USA.
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA.
- Hematological Malignancies Program, St. Jude Children's Research Hospital, Memphis, Tennessee, USA.
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31
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Yang X, Wu X, Fang N, Liu X, Liu X, Yang L, Huang K, Luo A, Cai M, Wu F, Jiang H, Xu L. FOXO3 gene polymorphisms influence the risk of acute lymphoblastic leukemia in Chinese children. J Cell Biochem 2019; 121:2019-2026. [PMID: 31691337 DOI: 10.1002/jcb.29436] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Accepted: 10/10/2019] [Indexed: 12/22/2022]
Abstract
Acute lymphoblastic leukemia (ALL) is the most frequently diagnosed cancer in children and single-nucleotide polymorphisms (SNPs) in certain genes influence risk of ALL. Although FOXO3 had been demonstrated to be involved leukemia, the role of FOXO3 polymorphisms was still not clear. In the present study, we explored the association of FOXO3 SNPs with ALL risk in Chinese children. We genotyped four polymorphisms (rs17069665 A>G, rs4945816 T>C, rs4946936 C>T, and rs9400241 A>C) of FOXO3 in 425 ALL cases and 1339 health controls. The associations were estimated by odds ratios (ORs) with their 95% confidence intervals (CIs). Further analyses were performed to explore associations of rs17069665 and rs9400241 with ALL susceptibility in terms of age, gender, immunophenotype, minimal residual disease (MRD), and other clinical characteristics. We found rs17069665 related to the increased ALL risk (OR = 1.76; 95% CI = 1.02-3.04), rs9400241 related to decreased ALL risk (OR = 0.80; 95% CI = 0.64-0.99). The effects of rs17069665 on ALL risk were more predominant in males and children < 10 years, and patients with lower rates of platelet or neutrophil. As for rs9400241, the effects were more predominant in children < 10 years, and in patients with pre B ALL, positive MRD, anemia, or hepatomegaly. In conclusion, FOXO3 gene polymorphisms influence the risk of ALL in children and might be a potential biomarker for ALL susceptibility.
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Affiliation(s)
- Xu Yang
- Department of Hematology, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Xuedong Wu
- Department of Pediatrics, Nanfang Hospital, Guangzhou, Guangdong, China
| | - Na Fang
- Guangdong Provincial Bioengineering Institute (Guangzhou Sugarcane Industry Research Institute), Guangzhou, Guangdong, China
| | - Xiaoping Liu
- Department of Hematology, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Xiaodan Liu
- Division of Birth Cohort Study, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Lihua Yang
- Pediatric Center of Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Ke Huang
- Department of Pediatrics, The Second Affiliated Hospital of Sun Yat-Sen University (Sun Yat-sen Memorial Hospital), Guangzhou, Guangdong, China
| | - Ailing Luo
- Department of Hematology, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Mansi Cai
- Department of Hematology, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Fan Wu
- Department of Hematology, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Hua Jiang
- Department of Hematology, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Ling Xu
- Department of Hematology, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, Guangdong, China
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32
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Brown AL, de Smith AJ, Gant VU, Yang W, Scheurer ME, Walsh KM, Chernus JM, Kallsen NA, Peyton SA, Davies GE, Ehli EA, Winick N, Heerema NA, Carroll AJ, Borowitz MJ, Wood BL, Carroll WL, Raetz EA, Feingold E, Devidas M, Barcellos LF, Hansen HM, Morimoto L, Kang AY, Smirnov I, Healy J, Laverdière C, Sinnett D, Taub JW, Birch JM, Thompson P, Spector LG, Pombo-de-Oliveira MS, DeWan AT, Mullighan CG, Hunger SP, Pui CH, Loh ML, Zwick ME, Metayer C, Ma X, Mueller BA, Sherman SL, Wiemels JL, Relling MV, Yang JJ, Lupo PJ, Rabin KR. Inherited genetic susceptibility to acute lymphoblastic leukemia in Down syndrome. Blood 2019; 134:1227-1237. [PMID: 31350265 PMCID: PMC6788009 DOI: 10.1182/blood.2018890764] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Accepted: 07/14/2019] [Indexed: 02/07/2023] Open
Abstract
Children with Down syndrome (DS) have a 20-fold increased risk of acute lymphoblastic leukemia (ALL) and distinct somatic features, including CRLF2 rearrangement in ∼50% of cases; however, the role of inherited genetic variation in DS-ALL susceptibility is unknown. We report the first genome-wide association study of DS-ALL, comprising a meta-analysis of 4 independent studies, with 542 DS-ALL cases and 1192 DS controls. We identified 4 susceptibility loci at genome-wide significance: rs58923657 near IKZF1 (odds ratio [OR], 2.02; Pmeta = 5.32 × 10-15), rs3731249 in CDKN2A (OR, 3.63; Pmeta = 3.91 × 10-10), rs7090445 in ARID5B (OR, 1.60; Pmeta = 8.44 × 10-9), and rs3781093 in GATA3 (OR, 1.73; Pmeta = 2.89 × 10-8). We performed DS-ALL vs non-DS ALL case-case analyses, comparing risk allele frequencies at these and other established susceptibility loci (BMI1, PIP4K2A, and CEBPE) and found significant association with DS status for CDKN2A (OR, 1.58; Pmeta = 4.1 × 10-4). This association was maintained in separate regression models, both adjusting for and stratifying on CRLF2 overexpression and other molecular subgroups, indicating an increased penetrance of CDKN2A risk alleles in children with DS. Finally, we investigated functional significance of the IKZF1 risk locus, and demonstrated mapping to a B-cell super-enhancer, and risk allele association with decreased enhancer activity and differential protein binding. IKZF1 knockdown resulted in significantly higher proliferation in DS than non-DS lymphoblastoid cell lines. Our findings demonstrate a higher penetrance of the CDKN2A risk locus in DS and serve as a basis for further biological insights into DS-ALL etiology.
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Affiliation(s)
- Austin L Brown
- Department of Pediatrics, Section of Hematology-Oncology, Baylor College of Medicine, Houston, TX
| | - Adam J de Smith
- Department of Epidemiology & Biostatistics, University of California, San Francisco, San Francisco, CA
- Center for Genetic Epidemiology, University of Southern California, Los Angeles, CA
| | - Vincent U Gant
- Department of Pediatrics, Section of Hematology-Oncology, Baylor College of Medicine, Houston, TX
| | - Wenjian Yang
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN
| | - Michael E Scheurer
- Department of Pediatrics, Section of Hematology-Oncology, Baylor College of Medicine, Houston, TX
| | - Kyle M Walsh
- Division of Neuro-epidemiology, Department of Neurosurgery, Duke University, Durham, NC
| | - Jonathan M Chernus
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA
| | | | | | | | - Erik A Ehli
- Avera Institute for Human Genetics, Sioux Falls, SD
| | - Naomi Winick
- Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX
| | - Nyla A Heerema
- Department of Pathology, The Ohio State University, Columbus, OH
| | - Andrew J Carroll
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL
| | - Michael J Borowitz
- Department of Pathology and
- Department of Oncology, Johns Hopkins Hospital, Baltimore, MD;
| | - Brent L Wood
- Department of Pathology and
- Department of Medicine, University of Washington Medical Center, Seattle, WA
| | - William L Carroll
- Department of Pediatrics, Perlmutter Cancer Center, New York University, New York, NY
| | - Elizabeth A Raetz
- Department of Pediatrics, Perlmutter Cancer Center, New York University, New York, NY
| | - Eleanor Feingold
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA
| | - Meenakshi Devidas
- Department of Biostatistics, College of Medicine, Public Health and Health Professions, University of Florida, Gainesville, FL
| | - Lisa F Barcellos
- Division of Epidemiology, School of Public Health, University of California, Berkeley, Berkeley, CA
| | - Helen M Hansen
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA
| | - Libby Morimoto
- Division of Epidemiology, School of Public Health, University of California, Berkeley, Berkeley, CA
| | - Alice Y Kang
- Division of Epidemiology, School of Public Health, University of California, Berkeley, Berkeley, CA
| | - Ivan Smirnov
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA
| | - Jasmine Healy
- Division of Hematology-Oncology, Sainte-Justine University Health Center, Montreal, QC, Canada
| | - Caroline Laverdière
- Division of Hematology-Oncology, Sainte-Justine University Health Center, Montreal, QC, Canada
| | - Daniel Sinnett
- Division of Hematology-Oncology, Sainte-Justine University Health Center, Montreal, QC, Canada
| | - Jeffrey W Taub
- Division of Hematology Oncology, Department of Oncology, Wayne State University, Detroit, MI
| | - Jillian M Birch
- Department of Paediatric and Adolescent Oncology, University of Manchester, Manchester, United Kingdom
| | - Pamela Thompson
- Department of Paediatric and Adolescent Oncology, University of Manchester, Manchester, United Kingdom
| | - Logan G Spector
- Division of Epidemiology & Clinical Research, Department of Pediatrics, University of Minnesota, Minneapolis, MN
| | | | - Andrew T DeWan
- Department of Chronic Disease Epidemiology, Yale School of Public Health, New Haven, CT
| | | | - Stephen P Hunger
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Ching-Hon Pui
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN
| | - Mignon L Loh
- Department of Pediatrics, Benioff Children's Hospital, University of California, San Francisco, San Francisco, CA
| | - Michael E Zwick
- Department of Human Genetics, Emory University, Atlanta, GA; and
| | - Catherine Metayer
- Division of Epidemiology, School of Public Health, University of California, Berkeley, Berkeley, CA
| | - Xiaomei Ma
- Department of Chronic Disease Epidemiology, Yale School of Public Health, New Haven, CT
| | - Beth A Mueller
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA
| | | | - Joseph L Wiemels
- Department of Epidemiology & Biostatistics, University of California, San Francisco, San Francisco, CA
- Center for Genetic Epidemiology, University of Southern California, Los Angeles, CA
| | - Mary V Relling
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN
| | - Jun J Yang
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN
| | - Philip J Lupo
- Department of Pediatrics, Section of Hematology-Oncology, Baylor College of Medicine, Houston, TX
| | - Karen R Rabin
- Department of Pediatrics, Section of Hematology-Oncology, Baylor College of Medicine, Houston, TX
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33
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Xu H, Zhao X, Bhojwani D, E S, Goodings C, Zhang H, Seibel NL, Yang W, Li C, Carroll WL, Evans WE, Yang JJ. ARID5B Influences Antimetabolite Drug Sensitivity and Prognosis of Acute Lymphoblastic Leukemia. Clin Cancer Res 2019; 26:256-264. [PMID: 31573954 DOI: 10.1158/1078-0432.ccr-19-0190] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Revised: 06/13/2019] [Accepted: 09/26/2019] [Indexed: 02/07/2023]
Abstract
PURPOSE Treatment outcomes for childhood acute lymphoblastic leukemia (ALL) have improved steadily, but a significant proportion of patients still experience relapse due to drug resistance, which is partly explained by inherited and/or somatic genetic alternations. Recently, we and others have identified genetic variants in the ARID5B gene associated with susceptibility to ALL and also with relapse. In this study, we sought to characterize the molecular pathway by which ARID5B affects antileukemic drug response in patients with ALL. EXPERIMENTAL DESIGN We analyzed association of ARID5B expression in primary human ALL blasts with molecular subtypes and treatment outcome. Subsequent mechanistic studies were performed in ALL cell lines by manipulating ARID5B expression isogenically, in which we evaluated drug sensitivity, metabolism, and molecular signaling events. RESULTS ARID5B expression varied substantially by ALL subtype, with the highest level being observed in hyperdiploid ALL. Lower ARID5B expression at diagnosis was associated with the risk of ALL relapse, and further reduction was noted at ALL relapse. In isogenic ALL cell models in vitro, ARID5B knockdown led to resistance specific to antimetabolite drugs (i.e., 6-mercaptopurine and methotrexate), without significantly affecting sensitivity to other antileukemic agents. ARID5B downregulation significantly inhibited ALL cell proliferation and caused partial cell-cycle arrest. At the molecular level, the cell-cycle checkpoint regulator p21 (encoded by CDKN1A) was most consistently modulated by ARID5B, plausibly as its direct transcription regulation target. CONCLUSIONS Our data indicate that ARID5B is an important molecular determinant of antimetabolite drug sensitivity in ALL, in part, through p21-mediated effects on cell-cycle progression.
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Affiliation(s)
- Heng Xu
- Department of Laboratory Medicine, Precision Medicine Center, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Xujie Zhao
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Deepa Bhojwani
- Division of Hematology, Oncology, Blood and Marrow Transplantation, Children's Hospital Los Angeles, Los Angeles, California
| | - Shuyu E
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Charnise Goodings
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Hui Zhang
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee.,Department of Pediatric Hematology and Oncology, Guangzhou Women and Children's Medical Center, Guangzhou, Guangdong, China
| | - Nita L Seibel
- Cancer Therapy Evaluation Program, National Cancer Institute, Bethesda, Maryland
| | - Wentao Yang
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Chunliang Li
- Department of Tumor Cell Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - William L Carroll
- Departments of Pediatrics and Pathology, New York University Langone Medical Center, New York, New York
| | - William E Evans
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee.,Hematological Malignancies Program, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Jun J Yang
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee. .,Hematological Malignancies Program, St. Jude Children's Research Hospital, Memphis, Tennessee
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34
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Abstract
Developments over the past five years have significantly advanced our ability to use genome-scale analyses—including high-density genotyping, transcriptome sequencing, exome sequencing, and genome sequencing—to identify the genetic basis of childhood cancer. This article reviews several key results from an expanding number of genomic studies of pediatric cancer: ( a) Histopathologic subtypes of cancers can be associated with a high incidence of germline predisposition, ( b) neurodevelopmental disorders or highly penetrant cancer predisposition syndromes can result from specific patterns of variation in genes encoding the SMARC family of chromatin remodelers, ( c) genome-wide association studies with relatively small pediatric cancer cohorts have successfully identified single-nucleotide polymorphisms with large effect sizes and provided insight into population differences in cancer risk, and ( d) multiple exome or genome analyses of unselected childhood cancer cohorts have yielded a 7–10% incidence of pathogenic variants in cancer predisposition genes. This work supports the increasing use of genomic sequencing in the care of pediatric cancer patients and at-risk family members.
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Affiliation(s)
- Sharon E. Plon
- Section of Hematology-Oncology, Department of Pediatrics, Baylor College of Medicine, Houston, Texas 77030, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
- Texas Children's Cancer Center, Texas Children's Hospital, Houston, Texas 77030, USA
- Dan L Duncan Cancer Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Philip J. Lupo
- Section of Hematology-Oncology, Department of Pediatrics, Baylor College of Medicine, Houston, Texas 77030, USA
- Texas Children's Cancer Center, Texas Children's Hospital, Houston, Texas 77030, USA
- Dan L Duncan Cancer Center, Baylor College of Medicine, Houston, Texas 77030, USA
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35
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Gocho Y, Yang JJ. Genetic defects in hematopoietic transcription factors and predisposition to acute lymphoblastic leukemia. Blood 2019; 134:793-7. [PMID: 31311817 DOI: 10.1182/blood.2018852400] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2018] [Accepted: 06/10/2019] [Indexed: 01/01/2023] Open
Abstract
Recent genome-wide studies have revealed a plethora of germline variants that significantly influence the susceptibility to acute lymphoblastic leukemia (ALL), thus providing compelling evidence for genetic inheritance of this blood cancer. In particular, hematopoietic transcription factors (eg, ETV6, PAX5, IKZF1) are most frequently implicated in familial ALL, and germline variants in these genes confer strong predisposition (albeit with incomplete penetrance). Studies of germline risk factors for ALL provide unique insights into the molecular etiology of this leukemia.
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36
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Noë M, Hackeng WM, de Leng WWJ, Vergeer M, Vleggaar FP, Morsink FHM, Wood LD, Hruban RH, Offerhaus GJA, Brosens LAA. Well-differentiated Pancreatic Neuroendocrine Tumor in a Patient With Familial Atypical Multiple Mole Melanoma Syndrome (FAMMM). Am J Surg Pathol 2019; 43:1297-302. [PMID: 31261289 DOI: 10.1097/PAS.0000000000001314] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Germline mutations in CDKN2A result in Familial Atypical Multiple Mole Melanoma Syndrome (FAMMM), which is associated with an increased risk for pancreatic ductal adenocarcinoma and melanoma. CDKN2A is somatically inactivated in multiple neoplasms, raising the possibility that, although the data are not conclusive, germline CDKN2A mutation may also impose an increased risk for other neoplasms. We present a patient with a CDKN2A germline mutation (p16-Leiden mutation) and mosaicism for neurofibromatosis type 2, who presented with a small asymptomatic pancreatic lesion, detected during endoscopic ultrasound screening of the pancreas. After resection, the lesion was found to be a well-differentiated pancreatic neuroendocrine tumor (PanNET). Molecular analysis of the tumor showed somatic loss of the second allele, supporting a causal relation of the PanNET to the underlying FAMMM syndrome. Recent data, showing the association between certain single-nucleotide polymorphisms in the CDKN2A gene and an increased incidence for PanNET, further support a role for germline CDKN2A alterations in PanNET risk. We conclude that PanNETs can be a phenotypic expression of FAMMM syndrome. This can have implications for screening and for the diagnosis of pancreatic neoplasms in carriers of germline CDKN2A mutations.
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37
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Reyes-León A, Ramírez-Martínez M, Fernández-García D, Amaro-Muñoz D, Velázquez-Aragón JA, Salas-Labadía C, Zapata-Tarrés M, Velasco-Hidalgo L, López-Santiago N, López-Ruiz MI, Malavar-Guadarrama MA, Cárdenas-Cardós R, Paredes-Aguilera R, Rivera-Luna R, Dean M, Pérez-Vera P. Variants in ARID5B gene are associated with the development of acute lymphoblastic leukemia in Mexican children. Ann Hematol 2019; 98:2379-2388. [DOI: 10.1007/s00277-019-03730-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Accepted: 06/10/2019] [Indexed: 11/29/2022]
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38
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Coccaro N, Anelli L, Zagaria A, Specchia G, Albano F. Next-Generation Sequencing in Acute Lymphoblastic Leukemia. Int J Mol Sci 2019; 20:ijms20122929. [PMID: 31208040 PMCID: PMC6627957 DOI: 10.3390/ijms20122929] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Revised: 06/04/2019] [Accepted: 06/14/2019] [Indexed: 12/25/2022] Open
Abstract
Acute lymphoblastic leukemia (ALL) is the most common childhood cancer and accounts for about a quarter of adult acute leukemias, and features different outcomes depending on the age of onset. Improvements in ALL genomic analysis achieved thanks to the implementation of next-generation sequencing (NGS) have led to the recent discovery of several novel molecular entities and to a deeper understanding of the existing ones. The purpose of our review is to report the most recent discoveries obtained by NGS studies for ALL diagnosis, risk stratification, and treatment planning. We also report the first efforts at NGS use for minimal residual disease (MRD) assessment, and early studies on the application of third generation sequencing in cancer research. Lastly, we consider the need for the integration of NGS analyses in clinical practice for genomic patients profiling from the personalized medicine perspective.
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Affiliation(s)
- Nicoletta Coccaro
- Department of Emergency and Organ Transplantation (D.E.T.O.), Hematology Section, University of Bari, 70124 Bari, Italy.
| | - Luisa Anelli
- Department of Emergency and Organ Transplantation (D.E.T.O.), Hematology Section, University of Bari, 70124 Bari, Italy.
| | - Antonella Zagaria
- Department of Emergency and Organ Transplantation (D.E.T.O.), Hematology Section, University of Bari, 70124 Bari, Italy.
| | - Giorgina Specchia
- Department of Emergency and Organ Transplantation (D.E.T.O.), Hematology Section, University of Bari, 70124 Bari, Italy.
| | - Francesco Albano
- Department of Emergency and Organ Transplantation (D.E.T.O.), Hematology Section, University of Bari, 70124 Bari, Italy.
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39
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de Smith AJ, Lavoie G, Walsh KM, Aujla S, Evans E, Hansen HM, Smirnov I, Kang AY, Zenker M, Ceremsak JJ, Stieglitz E, Muskens IS, Roberts W, McKean-Cowdin R, Metayer C, Roux PP, Wiemels JL. Predisposing germline mutations in high hyperdiploid acute lymphoblastic leukemia in children. Genes Chromosomes Cancer 2019; 58:723-730. [PMID: 31102422 DOI: 10.1002/gcc.22765] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Revised: 05/13/2019] [Accepted: 05/13/2019] [Indexed: 12/24/2022] Open
Abstract
High hyperdiploidy (HD) is the most common cytogenetic subtype of childhood acute lymphoblastic leukemia (ALL), and a higher incidence of HD has been reported in ALL patients with congenital cancer syndromes. We assessed the frequency of predisposing germline mutations in 57 HD-ALL patients from the California Childhood Leukemia Study via targeted sequencing of cancer-relevant genes. Three out of 57 patients (5.3%) harbored confirmed germline mutations that were likely causal, in NBN, ETV6, and FLT3, with an additional six patients (10.5%) harboring putative predisposing mutations that were rare in unselected individuals (<0.01% allele frequency in the Exome Aggregation Consortium, ExAC) and predicted functional (scaled CADD score ≥ 20) in known or potential ALL predisposition genes (SH2B3, CREBBP, PMS2, MLL, ABL1, and MYH9). Three additional patients carried rare and predicted damaging germline mutations in GAB2, a known activator of the ERK/MAPK and PI3K/AKT pathways and binding partner of PTPN11-encoded SHP2. The frequency of rare and predicted functional germline GAB2 mutations was significantly higher in our patients (2.6%) than in ExAC (0.28%, P = 4.4 × 10-3 ), an observation that was replicated in ALL patients from the TARGET project (P = .034). We cloned patient GAB2 mutations and expressed mutant proteins in HEK293 cells and found that frameshift mutation P621fs led to reduced SHP2 binding and ERK1/2 phosphorylation but significantly increased AKT phosphorylation, suggesting possible RAS-independent leukemogenic effects. Our results support a significant contribution of rare, high penetrance germline mutations to HD-ALL etiology, and pinpoint GAB2 as a putative novel ALL predisposition gene.
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Affiliation(s)
- Adam J de Smith
- Center for Genetic Epidemiology, Department of Preventive Medicine, USC Keck School of Medicine, Los Angeles, California.,Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, California
| | - Geneviève Lavoie
- Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montreal, Quebec, Canada
| | - Kyle M Walsh
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, California.,Department of Neurosurgery, Duke University, Durham, North Carolina.,Children's Health and Discovery Institute, Duke University, Durham, North Carolina
| | - Sumeet Aujla
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, California
| | - Erica Evans
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, California
| | - Helen M Hansen
- Department of Neurological Surgery, University of California San Francisco, San Francisco, California
| | - Ivan Smirnov
- Department of Neurological Surgery, University of California San Francisco, San Francisco, California
| | - Alice Y Kang
- School of Public Health, University of California, Berkeley, Berkeley, California
| | - Martin Zenker
- University Hospital Magdeburg, Institute of Human Genetics, Magdeburg, Germany
| | - John J Ceremsak
- Department of Pediatrics, University of California San Francisco, San Francisco, California
| | - Elliot Stieglitz
- Department of Pediatrics, University of California San Francisco, San Francisco, California
| | - Ivo S Muskens
- Center for Genetic Epidemiology, Department of Preventive Medicine, USC Keck School of Medicine, Los Angeles, California
| | - William Roberts
- Division of Pediatric Hematology/Oncology, Department of Pediatrics, University of California San Diego, San Diego, California.,Rady Children's Hospital San Diego, San Diego, California
| | - Roberta McKean-Cowdin
- Department of Preventive Medicine, USC Keck School of Medicine, Los Angeles, California
| | - Catherine Metayer
- School of Public Health, University of California, Berkeley, Berkeley, California
| | - Philippe P Roux
- Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montreal, Quebec, Canada.,Department of Pathology and Cell Biology, Faculty of Medicine, Université de Montréal, Montreal, Quebec, Canada
| | - Joseph L Wiemels
- Center for Genetic Epidemiology, Department of Preventive Medicine, USC Keck School of Medicine, Los Angeles, California.,Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, California
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40
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Madzio J, Pastorczak A, Sedek L, Braun M, Taha J, Wypyszczak K, Trelinska J, Lejman M, Muszynska-Roslan K, Tomasik B, Derwich K, Koltan A, Kazanowska B, Irga-Jaworska N, Badowska W, Matysiak M, Kowalczyk J, Styczynski J, Fendler W, Szczepanski T, Mlynarski W. GATA3 germline variant is associated with CRLF2 expression and predicts outcome in pediatric B-cell precursor acute lymphoblastic leukemia. Genes Chromosomes Cancer 2019; 58:619-626. [PMID: 30859636 DOI: 10.1002/gcc.22748] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Revised: 03/04/2019] [Accepted: 03/05/2019] [Indexed: 12/13/2022] Open
Abstract
The germline variant at rs3824662 in GATA3 is a risk locus for Philadelphia-like acute lymphoblastic leukemia (Ph-like ALL), the biological subtype of B-cell precursor (BCP)-ALL defined by a distinct gene expression profile and the presence of specific somatic aberrations including rearrangements of CRLF2. In this study, we investigated whether rs3824662 in GATA3 associates with CRLF2 expression in leukemic cells and predicts prognosis in pediatric BCP-ALL patients treated according to the ALL Intercontinental Berlin-Frankfurt-Münster (IC BFM) 2009 (n = 645) and the ALL IC BFM 2002 (n = 216) protocols. High expression of CRLF2 was observed at both protein and mRNA levels (fourfold higher in AA than in CA + CC) among GATA3 AA variant carriers, independent of the presence of P2RY8-CRLF2 fusion. Additionally, the AA variant at rs3824662 was a significant factor affecting minimal residual disease level at the end of induction phase and overall survival regardless of the risk group and the protocol. The germline variant at rs3824662 in GATA3 is a prognostic factor which associates with CRLF2 expression in leukemic cells supporting the hypothesis that GATA3 may have a regulatory effect on the CRLF2 pathway in pediatric BCP-ALL.
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Affiliation(s)
- Joanna Madzio
- Department of Pediatrics, Oncology and Hematology, Medical University of Lodz, Lodz, Poland.,Postgraduate School of Molecular Medicine, Medical University of Warsaw, Warsaw, Poland
| | - Agata Pastorczak
- Department of Pediatrics, Oncology and Hematology, Medical University of Lodz, Lodz, Poland
| | - Lukasz Sedek
- Department of Microbiology and Immunology, Medical University of Silesia, Katowice, Poland
| | - Marcin Braun
- Department of Pediatrics, Oncology and Hematology, Medical University of Lodz, Lodz, Poland.,Postgraduate School of Molecular Medicine, Medical University of Warsaw, Warsaw, Poland.,Department of Pathology, Medical University of Lodz, Lodz, Poland
| | - Joanna Taha
- Department of Pediatrics, Oncology and Hematology, Medical University of Lodz, Lodz, Poland
| | - Kamila Wypyszczak
- Department of Pediatrics, Oncology and Hematology, Medical University of Lodz, Lodz, Poland
| | - Joanna Trelinska
- Department of Pediatrics, Oncology and Hematology, Medical University of Lodz, Lodz, Poland
| | - Monika Lejman
- Department of Pediatric Hematology and Oncology, Medical University of Lublin, Lublin, Poland
| | | | - Bartlomiej Tomasik
- Department of Pediatrics, Oncology and Hematology, Medical University of Lodz, Lodz, Poland.,Postgraduate School of Molecular Medicine, Medical University of Warsaw, Warsaw, Poland.,Department of Biostatistics & Translational Medicine, Medical University of Lodz, Lodz, Poland
| | - Katarzyna Derwich
- Department of Pediatric Hematology, Oncology and Transplantology, University of Medical Sciences, Poznan, Poland
| | - Andrzej Koltan
- Department of Pediatric Hematology and Oncology, Collegium Medicum, Nicolaus Copernicus University, Torun, Poland
| | - Bernarda Kazanowska
- Department of Pediatric Hematology, Oncology and Transplantology, Medical University of Wroclaw, Wroclaw, Poland
| | - Nina Irga-Jaworska
- Department of Pediatric Hematology, Gdansk Medical University, Gdansk, Poland
| | - Wanda Badowska
- Department of Pediatric Hematology and Oncology, University of Warmia and Mazury, Olsztyn, Poland
| | - Michal Matysiak
- Department of Pediatric Hematology and Oncology, Medical University of Warsaw, Warsaw, Poland
| | - Jerzy Kowalczyk
- Department of Pediatric Hematology and Oncology, Medical University of Lublin, Lublin, Poland
| | - Jan Styczynski
- Department of Pediatric Hematology and Oncology, Collegium Medicum, Nicolaus Copernicus University, Torun, Poland
| | - Wojciech Fendler
- Department of Biostatistics & Translational Medicine, Medical University of Lodz, Lodz, Poland.,Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Tomasz Szczepanski
- Department of Pediatric Hematology and Oncology, Zabrze Medical University of Silesia, Katowice, Poland
| | - Wojciech Mlynarski
- Department of Pediatrics, Oncology and Hematology, Medical University of Lodz, Lodz, Poland
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Larsen V, Barlow WE, Yang JJ, Zhu Q, Liu S, Kwan ML, Ergas IJ, Roh JM, Hutchins LF, Kadlubar SA, Albain KS, Rae JM, Yeh IT, Ravdin PM, Martino S, Lyss AP, Osborne CK, Hortobagyi GN, Kushi LH, Hayes DF, Ambrosone CB, Yao S. Germline Genetic Variants in GATA3 and Breast Cancer Treatment Outcomes in SWOG S8897 Trial and the Pathways Study. Clin Breast Cancer 2019; 19:225-235.e2. [PMID: 30928413 DOI: 10.1016/j.clbc.2019.02.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Revised: 12/05/2018] [Accepted: 02/20/2019] [Indexed: 12/15/2022]
Abstract
INTRODUCTION GATA3 is a critical transcription factor in maintaining the differentiated state of luminal mammary epithelial cells. We sought to determine the prognostic and predictive roles of GATA3 genotypes for breast cancer. PATIENTS AND METHODS Twelve single nucleotide polymorphisms (SNPs) were genotyped in 2 breast cancer cohorts, including the SWOG S8897 trial where patients were treated with adjuvant chemotherapy (CAF [cyclophosphamide, doxorubicin, 5-fluorouracil] vs. CMF [cyclophosphamide, methotrexate, 5-fluorouracil]) or untreated, and the observational Pathways Study. RESULTS In the S8897 trial, rs3802604 and rs568727 were associated with disease-free survival and overall survival in the treated group, regardless of chemotherapy regimen. The GG genotype of rs3802604 conferred poorer overall survival (adjusted hazard ratio, 2.45; 95% confidence interval, 1.48-4.05) and disease-free survival (adjusted hazard ratio, 1.95; 95% confidence interval, 1.27-2.99) compared with the AA genotype. Similar associations were found for rs568727. In contrast, no association with either SNP was found in the untreated group. Subgroup analyses indicated that these 2 SNPs more strongly influenced outcomes in the patients who also received tamoxifen. However, the associations in the subgroup with tamoxifen treatment were not replicated in the Pathways Study, possibly owing to substantial differences between the 2 patient cohorts, such as chemotherapy regimen and length of follow-up. Results from joint analyses across these 2 cohorts were marginally significant, driven by the results in S8897. Bioinformatic analyses support potential functional disruption of the GATA3 SNPs in breast tissue. CONCLUSIONS The present study provides some evidence for the predictive value of GATA3 genotypes for breast cancer adjuvant therapies. Future replication studies in appropriate patient populations are warranted.
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Haas OA. Primary Immunodeficiency and Cancer Predisposition Revisited: Embedding Two Closely Related Concepts Into an Integrative Conceptual Framework. Front Immunol 2019; 9:3136. [PMID: 30809233 PMCID: PMC6379258 DOI: 10.3389/fimmu.2018.03136] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Accepted: 12/19/2018] [Indexed: 12/13/2022] Open
Abstract
Common understanding suggests that the normal function of a "healthy" immune system safe-guards and protects against the development of malignancies, whereas a genetically impaired one might increase the likelihood of their manifestation. This view is primarily based on and apparently supported by an increased incidence of such diseases in patients with specific forms of immunodeficiencies that are caused by high penetrant gene defects. As I will review and discuss herein, such constellations merely represent the tip of an iceberg. The overall situation is by far more varied and complex, especially if one takes into account the growing difficulties to define what actually constitutes an immunodeficiency and what defines a cancer predisposition. The enormous advances in genome sequencing, in bioinformatic analyses and in the functional in vitro and in vivo assessment of novel findings together with the availability of large databases provide us with a wealth of information that steadily increases the number of sequence variants that concur with clinically more or less recognizable immunological problems and their consequences. Since many of the newly identified hard-core defects are exceedingly rare, their tumor predisposing effect is difficult to ascertain. The analyses of large data sets, on the other hand, continuously supply us with low penetrant variants that, at least in statistical terms, are clearly tumor predisposing, although their specific relevance for the respective carriers still needs to be carefully assessed on an individual basis. Finally, defects and variants that affect the same gene families and pathways in both a constitutional and somatic setting underscore the fact that immunodeficiencies and cancer predisposition can be viewed as two closely related errors of development. Depending on the particular genetic and/or environmental context as well as the respective stage of development, the same changes can have either a neutral, predisposing and, in some instances, even a protective effect. To understand the interaction between the immune system, be it "normal" or "deficient" and tumor predisposition and development on a systemic level, one therefore needs to focus on the structure and dynamic functional organization of the entire immune system rather than on its isolated individual components alone.
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Affiliation(s)
- Oskar A. Haas
- Department of Clinical Genetics, Children's Cancer Research Institute, Vienna, Austria
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44
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Zhang S, Li Z, Yan X, Bao L, Deng Y, Zeng F, Wang P, Zhu J, Yin D, Liao F, Zhou X, Zhang D, Xia X, Wang H, Yang X, Zhang W, Gao H, Zhang W, Yang L, Hou Q, Xu H, Zhang Y, Shu Y, Wang Y. Regulatory Network and Prognostic Effect Investigation of PIP4K2A in Leukemia and Solid Cancers. Front Genet 2019; 9:721. [PMID: 30697230 PMCID: PMC6341070 DOI: 10.3389/fgene.2018.00721] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Accepted: 12/21/2018] [Indexed: 02/05/2023] Open
Abstract
Germline variants of PIP4K2A impact susceptibility of acute lymphoblastic leukemia (ALL) through inducing its overexpression. Although limited reports suggested the oncogenic role of PIP4K2A in cancers, regulatory network and prognostic effect of this gene remains poorly understood in tumorigenesis and leukemogenesis. In this study, we conducted genome-wide gene expression association analyses in pediatric B-ALL cohorts to discover expression associated genes and pathways, which is followed by the bioinformatics analyses to investigate the prognostic role of PIP4K2A and its related genes in multiple cancer types. 214 candidates were identified to be significantly associated with PIP4K2A expression in ALL patients, with known cancer-related genes rankings the top (e.g., RAC2, RBL2, and TFDP1). These candidates do not only tend to be clustered in the same types of leukemia, but can also separate the patients into novel molecular subtypes. PIP4K2A is noticed to be frequently overexpressed in multiple other types of leukemia and solid cancers from cancer cohorts including TCGA, and associated with its candidates in subtype-specific and cancer-specific manners. Interestingly, the association status varied in tumors compared to their matched normal tissues. Moreover, PIP4K2A and its related candidates exhibit stage-independent prognostic effects in multiple cancers, mostly with its lower expression significantly associated with longer overall survival (p < 0.05). Our findings reveal the transcriptional regulatory network of PIP4K2A in leukemia, and suggest its potentially important role on molecular subtypes of multiple cancers and subsequent treatment outcomes.
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Affiliation(s)
- Shouyue Zhang
- Department of Thoracic Oncology, Cancer Center, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China.,Department of Laboratory Medicine, 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
| | - Zhaozhi Li
- Key Laboratory of Bio-Resources and Eco-Environment, College of Life Sciences, Sichuan University, Chengdu, China
| | - Xinyu Yan
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Li Bao
- Key Laboratory of Bio-Resources and Eco-Environment, College of Life Sciences, Sichuan University, Chengdu, China
| | - Yun Deng
- Department of Laboratory Medicine, 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
| | - Feier Zeng
- Department of Laboratory Medicine, 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
| | - Peiqi Wang
- 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
| | - Dandan Yin
- Department of Laboratory Medicine, 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
| | - Fei Liao
- Department of Laboratory Medicine, 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
| | - Xueyan Zhou
- Department of Laboratory Medicine, 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
| | - Duyu Zhang
- Department of Laboratory Medicine, 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
| | - Xuyang Xia
- Department of Laboratory Medicine, 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
| | - Hong Wang
- Integrated Biomedical Sciences Program, University of Tennessee Health Science Center, Memphis, TN, United States
| | - Xue Yang
- Integrated Biomedical Sciences Program, University of Tennessee Health Science Center, Memphis, TN, United States
| | - Wanhua Zhang
- Department of Hematology and Hematology Research Laboratory, Sichuan University, Chengdu, China
| | - Hu Gao
- Department of Emergency, West China Second University Hospital, Sichuan University, Chengdu
| | - Wei Zhang
- Department of Clinical Pharmacology, Hunan Key Laboratory of Pharmacogenetics, Xiangya Hospital, Central South University, Changsha, China
| | - Li Yang
- Department of Laboratory Medicine, 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
| | - Qianqian Hou
- Department of Laboratory Medicine, 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
| | - Heng Xu
- Department of Laboratory Medicine, 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
| | - Yan Zhang
- Department of Thoracic Oncology, Cancer Center, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
| | - Yang Shu
- Department of Laboratory Medicine, 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
| | - Yuelan Wang
- Department of Thoracic Oncology, Cancer Center, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China.,Department of Laboratory Medicine, 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
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45
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de Smith AJ, Walsh KM, Francis SS, Zhang C, Hansen HM, Smirnov I, Morimoto L, Whitehead TP, Kang A, Shao X, Barcellos LF, McKean-Cowdin R, Zhang L, Fu C, Wang R, Yu H, Hoh J, Dewan AT, Metayer C, Ma X, Wiemels JL. BMI1 enhancer polymorphism underlies chromosome 10p12.31 association with childhood acute lymphoblastic leukemia. Int J Cancer 2018; 143:2647-2658. [PMID: 29923177 PMCID: PMC6235695 DOI: 10.1002/ijc.31622] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Revised: 05/10/2018] [Accepted: 05/14/2018] [Indexed: 01/07/2023]
Abstract
Genome-wide association studies of childhood acute lymphoblastic leukemia (ALL) have identified regions of association at PIP4K2A and upstream of BMI1 at chromosome 10p12.31-12.2. The contribution of both loci to ALL risk and underlying functional variants remain to be elucidated. We carried out single nucleotide polymorphism (SNP) imputation across chromosome 10p12.31-12.2 in Latino and non-Latino white ALL cases and controls from two independent California childhood leukemia studies, and additional Genetic Epidemiology Research on Aging study controls. Ethnicity-stratified association analyses were performed using logistic regression, with meta-analysis including 3,133 cases (1,949 Latino, 1,184 non-Latino white) and 12,135 controls (8,584 Latino, 3,551 non-Latino white). SNP associations were identified at both BMI1 and PIP4K2A. After adjusting for the lead PIP4K2A SNP, genome-wide significant associations remained at BMI1, and vice-versa (pmeta < 10-10 ), supporting independent effects. Lead SNPs differed by ethnicity at both peaks. We sought functional variants in tight linkage disequilibrium with both the lead Latino SNP among Admixed Americans and lead non-Latino white SNP among Europeans. This pinpointed rs11591377 (pmeta = 2.1 x 10-10 ) upstream of BMI1, residing within a hematopoietic stem cell enhancer of BMI1, and which showed significant preferential binding of the risk allele to MYBL2 (p = 1.73 x 10-5 ) and p300 (p = 1.55 x 10-3 ) transcription factors using binomial tests on ChIP-Seq data from a SNP heterozygote. At PIP4K2A, we identified rs4748812 (pmeta = 1.3 x 10-15 ), which alters a RUNX1 binding motif and demonstrated chromosomal looping to the PIP4K2A promoter. Fine-mapping chromosome 10p12 in a multi-ethnic ALL GWAS confirmed independent associations and identified putative functional variants upstream of BMI1 and at PIP4K2A.
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Affiliation(s)
- Adam J. de Smith
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA 94158
- Center for Genetic Epidemiology, Department of Preventive Medicine, Keck School of Medicine, University of Southern California, CA 90033
| | - Kyle M. Walsh
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA 94158
- Department of Neurosurgery, Duke University, Durham, NC 27710
| | - Stephen S. Francis
- Department of Epidemiology, School of Community Health Sciences, University of Nevada Reno, Reno, NV 89557
| | - Chenan Zhang
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA 94158
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA 94158
| | - Helen M. Hansen
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA 94158
| | - Ivan Smirnov
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA 94158
| | - Libby Morimoto
- School of Public Health, University of California Berkeley, Berkeley, CA 94720
| | - Todd P. Whitehead
- School of Public Health, University of California Berkeley, Berkeley, CA 94720
| | - Alice Kang
- School of Public Health, University of California Berkeley, Berkeley, CA 94720
| | - Xiaorong Shao
- School of Public Health, University of California Berkeley, Berkeley, CA 94720
| | - Lisa F. Barcellos
- School of Public Health, University of California Berkeley, Berkeley, CA 94720
| | - Roberta McKean-Cowdin
- Center for Genetic Epidemiology, Department of Preventive Medicine, Keck School of Medicine, University of Southern California, CA 90033
| | - Luoping Zhang
- School of Public Health, University of California Berkeley, Berkeley, CA 94720
| | - Cecilia Fu
- Children’s Hospital of Los Angeles, Los Angeles, CA 90027
| | - Rong Wang
- Department of Chronic Diseases Epidemiology, School of Public Health, Yale University, New Haven, CT 06520
| | - Herbert Yu
- University of Hawaii Cancer Center, Honolulu, HI 96813
| | - Josephine Hoh
- Department of Chronic Diseases Epidemiology, School of Public Health, Yale University, New Haven, CT 06520
| | - Andrew T. Dewan
- Department of Chronic Diseases Epidemiology, School of Public Health, Yale University, New Haven, CT 06520
| | - Catherine Metayer
- School of Public Health, University of California Berkeley, Berkeley, CA 94720
| | - Xiaomei Ma
- Department of Chronic Diseases Epidemiology, School of Public Health, Yale University, New Haven, CT 06520
| | - Joseph L. Wiemels
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA 94158
- Center for Genetic Epidemiology, Department of Preventive Medicine, Keck School of Medicine, University of Southern California, CA 90033
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA 94158
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Mosaad YM, Hammad A, Elghzaly AA, Tawhid ZME, Hammad EM, Showma A, Abdelsalam R, Elmoughy A, Fawzy IM, Anber N. GATA3 rs3824662 gene polymorphism as possible risk factor for systemic lupus erythematosus. Lupus 2018; 27:2112-2119. [DOI: 10.1177/0961203318804894] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Background There is no report about the association between GATA3 rs3824662 polymorphism and systemic lupus erythematosus (SLE). Objective To investigate the possible role of GATA3 rs3824662 polymorphism as a susceptibility risk factor for either adult SLE (aSLE) or pediatric SLE (pSLE) and to evaluate its role in the development of lupus nephritis (LN) in pSLE. Methods Typing of GATA3 rs3824662 polymorphism was done using real-time polymerase chain reaction for three groups; 104 pSLE patients, 140 aSLE patients and 436 age- and sex-matched healthy controls. Results Non-significant differences were found between SLE patients and healthy controls for the allele and genotype frequencies of GATA3 rs3824662 ( p > 0.05). In pSLE; the AC genotype was associated with LN ( p = 0.04); the A allele and AC genotype were associated with persistent proteinuria ( p = 0.036 and 0.01, respectively) and both the A allele and AA genotype were associated with higher chronicity index ( p = 0.031 and 0.04, respectively). In aSLE; the C allele was associated with cellular cast ( p = 0.03) and thrombocytopenia ( p = 0.01). Logistic regression analysis revealed significant association between the AC+AA genotypes and the prediction of LN and renal active disease in pSLE ( p = 0.04 and 0.01, respectively). Conclusion GATA3 rs3824662 is not associated with susceptibility to SLE either in adult or in pediatric patients; however, in pSLE patients, the heterozygous AC genotype could be considered a risk factor for LN. At the same time, the AC and AA genotypes could be considered as predictors for LN and active renal disease. However, the small sample size is a limiting factor of the present study when interpreting the positive association.
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Affiliation(s)
- Y M Mosaad
- Clinical Immunology Unit, Clinical Pathology Department, Faculty of Medicine, Mansoura University, Mansoura, Egypt
| | - A Hammad
- Pediatric Nephrology Unit, Mansoura University Children's Hospital, Faculty of Medicine, Mansoura University, Mansoura, Egypt
| | - A A Elghzaly
- Clinical Immunology Unit, Clinical Pathology Department, Faculty of Medicine, Mansoura University, Mansoura, Egypt
| | - Z M E Tawhid
- Clinical Immunology Unit, Clinical Pathology Department, Faculty of Medicine, Mansoura University, Mansoura, Egypt
| | - E M Hammad
- Rheumatology and Rehabilitation Department, Mansoura University Hospital, Faculty of Medicine, Mansoura University, Mansoura, Egypt
| | - A Showma
- Pediatric Nephrology Unit, Mansoura University Children's Hospital, Faculty of Medicine, Mansoura University, Mansoura, Egypt
| | - R Abdelsalam
- Rheumatology and Rehabilitation Department, Mansoura University Hospital, Faculty of Medicine, Mansoura University, Mansoura, Egypt
| | - A Elmoughy
- Pediatric Nephrology Unit, Mansoura University Children's Hospital, Faculty of Medicine, Mansoura University, Mansoura, Egypt
| | - I M Fawzy
- Laboratory Medicine Department, Mansoura Fever Hospital, Ministry of Health, Mansoura, Egypt
| | - N Anber
- Emergency Hospital, Mansoura University, Mansoura, Egypt
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González-Quezada BA, Flores-Aguilar H, Olaya-Vargas A, Salazar-Rosales H, Pérez-García M, Valero-Saldaña LM, Acosta-Maldonado BL, Ovilla-Martínez R, Gorodezky C. IFNG +874 A/T is associated with acute lymphoblastic leukemia in Mexican Mestizos. Cytokine 2018; 111:265-271. [PMID: 30212785 DOI: 10.1016/j.cyto.2018.08.014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Revised: 08/10/2018] [Accepted: 08/13/2018] [Indexed: 01/02/2023]
Abstract
Acute lymphoblastic leukemia (ALL), the most common type of cancer in children worldwide, has one of the highest incidence rates in Mexico. It is a multifactorial disease and different cytokine single nucleotide polymorphisms (SNP), have been associated with ALL expression. Few studies have been published analyzing IFNG +874 T/A and IL2 -330 G/T in this type of leukemia. These SNPs are involved in high or low expression, and are central to cellular immunity, influencing greatly tumor growth. The purpose of this work was to explore the association of IFNG +874 A/T (rs2430561) and IL2 -330 G/T (rs2069762) SNPs with ALL susceptibility and/or protection in 488 Mexican Mestizos patients, as compared to 950 Mexican Mestizo healthy controls. The results demonstrated that IFNG +874 T allele (pc = 0.00004, OR = 0.673) and the TT genotype (pc = 0.00015, OR = 0.349), protect against ALL expression with no specific gender association; however, the TT homozygote genotype (vs. TA+AA) seems more protective in males (pc = 0.00683). IL2 -330 G/T does not contribute to the development of ALL. In healthy Mexicans, the most common genotypes for IL2 and IFNG, are the low cytokine producers, suggesting that the genetic background in this ethnic group, may be partly responsible for the high incidence of ALL. These results show for the first time in Mexicans, the relevant role that IFNG SNP has in the genetic etiology of ALL. Thus, a large group of patients belonging to different ethnicities will be very helpful to study in order to demonstrate if these SNPs contribute to the genetic etiology of ALL, as shown here in Mexican Mestizos.
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Affiliation(s)
- Betsy Annel González-Quezada
- Department of Immunology and Immunogenetics, InDRE, Secretary of Health, Francisco P. Miranda #177, col. Lomas de Plateros, Del. Álvaro Obregón, CP 01480 Mexico City, Mexico; Fundación Comparte Vida, A.C. Galileo #92, col. Polanco, Del. Miguel Hidalgo, CP 11550 Mexico City, Mexico.
| | - Hilario Flores-Aguilar
- Department of Immunology and Immunogenetics, InDRE, Secretary of Health, Francisco P. Miranda #177, col. Lomas de Plateros, Del. Álvaro Obregón, CP 01480 Mexico City, Mexico; Fundación Comparte Vida, A.C. Galileo #92, col. Polanco, Del. Miguel Hidalgo, CP 11550 Mexico City, Mexico.
| | - Alberto Olaya-Vargas
- Instituto Nacional de Pediatría, Secretary of Health, Insurgentes Sur #3700, Letra C, Delegación Coyoacán, CP. 04530 Mexico City, Mexico
| | - Haydee Salazar-Rosales
- Instituto Nacional de Pediatría, Secretary of Health, Insurgentes Sur #3700, Letra C, Delegación Coyoacán, CP. 04530 Mexico City, Mexico
| | - Martín Pérez-García
- Instituto Nacional de Pediatría, Secretary of Health, Insurgentes Sur #3700, Letra C, Delegación Coyoacán, CP. 04530 Mexico City, Mexico
| | - Luis Manuel Valero-Saldaña
- Instituto Nacional de Cancerología, Secretary of Health, Av. San Fernando #22, Col. Sección 16, C.P. 14080 Mexico City, Mexico
| | - Brenda Lizeth Acosta-Maldonado
- Instituto Nacional de Cancerología, Secretary of Health, Av. San Fernando #22, Col. Sección 16, C.P. 14080 Mexico City, Mexico
| | - Roberto Ovilla-Martínez
- Hospital Ángeles Lomas, Hacienda de las Palmas, Col. Valle de las Palmas, CP 52763 State of Mexico, Mexico
| | - Clara Gorodezky
- Department of Immunology and Immunogenetics, InDRE, Secretary of Health, Francisco P. Miranda #177, col. Lomas de Plateros, Del. Álvaro Obregón, CP 01480 Mexico City, Mexico; Fundación Comparte Vida, A.C. Galileo #92, col. Polanco, Del. Miguel Hidalgo, CP 11550 Mexico City, Mexico.
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Abstract
In this Review, I present evidence supporting a multifactorial causation of childhood acute lymphoblastic leukaemia (ALL), a major subtype of paediatric cancer. ALL evolves in two discrete steps. First, in utero initiation by fusion gene formation or hyperdiploidy generates a covert, pre-leukaemic clone. Second, in a small fraction of these cases, the postnatal acquisition of secondary genetic changes (primarily V(D)J recombination-activating protein (RAG) and activation-induced cytidine deaminase (AID)-driven copy number alterations in the case of ETS translocation variant 6 (ETV6)-runt-related transcription factor 1 (RUNX1)+ ALL) drives conversion to overt leukaemia. Epidemiological and modelling studies endorse a dual role for common infections. Microbial exposures earlier in life are protective but, in their absence, later infections trigger the critical secondary mutations. Risk is further modified by inherited genetics, chance and, probably, diet. Childhood ALL can be viewed as a paradoxical consequence of progress in modern societies, where behavioural changes have restrained early microbial exposure. This engenders an evolutionary mismatch between historical adaptations of the immune system and contemporary lifestyles. Childhood ALL may be a preventable cancer.
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Affiliation(s)
- Mel Greaves
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK.
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Huda N, Hosen MI, Yasmin T, Sarkar PK, Hasan AKMM, Nabi AHMN. Genetic variation of the transcription factor GATA3, not STAT4, is associated with the risk of type 2 diabetes in the Bangladeshi population. PLoS One 2018; 13:e0198507. [PMID: 30044774 PMCID: PMC6059405 DOI: 10.1371/journal.pone.0198507] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Accepted: 05/21/2018] [Indexed: 12/20/2022] Open
Abstract
Type 2 diabetes mellitus is a multifactorial metabolic disorder caused by environmental factors and has a strong association with hereditary issues. These hereditary issues result in an imbalance in CD4+T cells and a decreased level of naïve CD4+T cells, which may be critical in the pathogenesis of type 2 diabetes. Transcription factors GATA3 and STAT4 mediate the cytokine-induced development of naïve T cells into Th1 or Th2 types. In the present study, genetic analyses of GATA3 SNP rs3824662 and STAT4 SNP rs10181656 were performed to investigate the association of allelic and genotypic variations with the risk of T2D in the Bangladeshi population. A total of 297 unrelated Bangladeshi patients with type 2 diabetes and 247 healthy individuals were included in the study. The allelic and genotypic frequencies of rs10181656 located in the STAT4 gene were not found to be associated with risk of type 2 diabetes. The GATA3 rs3824662 T allele and mutant TT genotype had a significant association with the risk of T2D [OR: 1.52 (1.15–2.02), X2 = 8.66, p = 0.003 and OR: 2.98 (1.36–6.55), X2 = 7.98, p = 0.04, respectively]. Thus, the present study postulates that the genetic variation of the transcription factor GATA3, not STAT4, is associated with the risk of type 2 diabetes in the Bangladeshi population.
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Affiliation(s)
- Nafiul Huda
- Laboratory of Population Genetics, Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka, Bangladesh
| | - Md. Ismail Hosen
- Laboratory of Population Genetics, Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka, Bangladesh
| | - Tahirah Yasmin
- Laboratory of Population Genetics, Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka, Bangladesh
| | | | - A. K. M. Mahbub Hasan
- Laboratory of Population Genetics, Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka, Bangladesh
| | - A. H. M. Nurun Nabi
- Laboratory of Population Genetics, Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka, Bangladesh
- * E-mail:
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Studd JB, Yang M, Li Z, Vijayakrishnan J, Lu Y, Yeoh AE, Paulsson K, Houlston RS. Genetic predisposition to B-cell acute lymphoblastic leukemia at 14q11.2 is mediated by a CEBPE promoter polymorphism. Leukemia 2019; 33:1-14. [PMID: 29977016 DOI: 10.1038/s41375-018-0184-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Revised: 05/21/2018] [Accepted: 05/30/2018] [Indexed: 01/08/2023]
Abstract
Acute lymphoblastic leukaemia (ALL) is the most common paediatric malignancy. Genome-wide association studies have shown variation at 14q11.2 influences ALL risk. We sought to decipher causal variant(s) at 14q11.2 and the mechanism of tumorigenesis. We show rs2239630 G>A resides in the promoter of the CCAT enhancer-binding protein epsilon (CEBPE) gene. The rs2239630-A risk allele is associated with increased promotor activity and CEBPE expression. Depletion of CEBPE in ALL cells reduces cell growth, correspondingly CEBPE binds to the promoters of electron transport and energy generation genes. RNA-seq in CEBPE depleted cells demonstrates CEBPE regulates the expression of genes involved in B-cell development (IL7R), apoptosis (BCL2), and methotrexate resistance (RASS4L). CEBPE regulated genes significantly overlapped in CEBPE depleted cells, ALL blasts and IGH-CEBPE translocated ALL. This suggests CEBPE regulates a similar set of genes in each, consistent with a common biological mechanism of leukemogenesis for rs2239630 associated and CEBPE translocated ALL. Finally, we map IGH-CEBPE translocation breakpoints in two cases, implicating RAG recombinase activity in their formation.
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