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Pagliaro L, Chen SJ, Herranz D, Mecucci C, Harrison CJ, Mullighan CG, Zhang M, Chen Z, Boissel N, Winter SS, Roti G. Acute lymphoblastic leukaemia. Nat Rev Dis Primers 2024; 10:41. [PMID: 38871740 DOI: 10.1038/s41572-024-00525-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 05/01/2024] [Indexed: 06/15/2024]
Abstract
Acute lymphoblastic leukaemia (ALL) is a haematological malignancy characterized by the uncontrolled proliferation of immature lymphoid cells. Over past decades, significant progress has been made in understanding the biology of ALL, resulting in remarkable improvements in its diagnosis, treatment and monitoring. Since the advent of chemotherapy, ALL has been the platform to test for innovative approaches applicable to cancer in general. For example, the advent of omics medicine has led to a deeper understanding of the molecular and genetic features that underpin ALL. Innovations in genomic profiling techniques have identified specific genetic alterations and mutations that drive ALL, inspiring new therapies. Targeted agents, such as tyrosine kinase inhibitors and immunotherapies, have shown promising results in subgroups of patients while minimizing adverse effects. Furthermore, the development of chimeric antigen receptor T cell therapy represents a breakthrough in ALL treatment, resulting in remarkable responses and potential long-term remissions. Advances are not limited to treatment modalities alone. Measurable residual disease monitoring and ex vivo drug response profiling screening have provided earlier detection of disease relapse and identification of exceptional responders, enabling clinicians to adjust treatment strategies for individual patients. Decades of supportive and prophylactic care have improved the management of treatment-related complications, enhancing the quality of life for patients with ALL.
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Affiliation(s)
- Luca Pagliaro
- Department of Medicine and Surgery, University of Parma, Parma, Italy
- Translational Hematology and Chemogenomics (THEC), University of Parma, Parma, Italy
- Hematology and BMT Unit, Azienda Ospedaliero-Universitaria di Parma, Parma, Italy
| | - Sai-Juan Chen
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, China
| | - Daniel Herranz
- Rutgers Cancer Institute of New Jersey, Rutgers Robert Wood Johnson Medical School, Rutgers University, New Brunswick, NJ, USA
| | - Cristina Mecucci
- Department of Medicine, Hematology and Clinical Immunology, University of Perugia, Perugia, Italy
| | - Christine J Harrison
- Leukaemia Research Cytogenetics Group, Translational and Clinical Research Institute, Newcastle University Centre for Cancer, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Charles G Mullighan
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Ming Zhang
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, China
| | - Zhu Chen
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, China
| | - Nicolas Boissel
- Hôpital Saint-Louis, APHP, Institut de Recherche Saint-Louis, Université Paris Cité, Paris, France
| | - Stuart S Winter
- Children's Minnesota Cancer and Blood Disorders Program, Minneapolis, MN, USA
| | - Giovanni Roti
- Department of Medicine and Surgery, University of Parma, Parma, Italy.
- Translational Hematology and Chemogenomics (THEC), University of Parma, Parma, Italy.
- Hematology and BMT Unit, Azienda Ospedaliero-Universitaria di Parma, Parma, Italy.
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2
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Bhattarai KR, Mobley RJ, Barnett KR, Ferguson DC, Hansen BS, Diedrich JD, Bergeron BP, Yoshimura S, Yang W, Crews KR, Manring CS, Jabbour E, Paietta E, Litzow MR, Kornblau SM, Stock W, Inaba H, Jeha S, Pui CH, Cheng C, Pruett-Miller SM, Relling MV, Yang JJ, Evans WE, Savic D. Investigation of inherited noncoding genetic variation impacting the pharmacogenomics of childhood acute lymphoblastic leukemia treatment. Nat Commun 2024; 15:3681. [PMID: 38693155 PMCID: PMC11063049 DOI: 10.1038/s41467-024-48124-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Accepted: 04/18/2024] [Indexed: 05/03/2024] Open
Abstract
Defining genetic factors impacting chemotherapy failure can help to better predict response and identify drug resistance mechanisms. However, there is limited understanding of the contribution of inherited noncoding genetic variation on inter-individual differences in chemotherapy response in childhood acute lymphoblastic leukemia (ALL). Here we map inherited noncoding variants associated with treatment outcome and/or chemotherapeutic drug resistance to ALL cis-regulatory elements and investigate their gene regulatory potential and target gene connectivity using massively parallel reporter assays and three-dimensional chromatin looping assays, respectively. We identify 54 variants with transcriptional effects and high-confidence gene connectivity. Additionally, functional interrogation of the top variant, rs1247117, reveals changes in chromatin accessibility, PU.1 binding affinity and gene expression, and deletion of the genomic interval containing rs1247117 sensitizes cells to vincristine. Together, these data demonstrate that noncoding regulatory variants associated with diverse pharmacological traits harbor significant effects on allele-specific transcriptional activity and impact sensitivity to antileukemic agents.
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Affiliation(s)
- Kashi Raj Bhattarai
- Hematological Malignancies Program, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Robert J Mobley
- Hematological Malignancies Program, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Kelly R Barnett
- Hematological Malignancies Program, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Daniel C Ferguson
- Hematological Malignancies Program, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Baranda S Hansen
- Center for Advanced Genome Engineering, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
- Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Jonathan D Diedrich
- Hematological Malignancies Program, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Brennan P Bergeron
- Hematological Malignancies Program, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
- Graduate School of Biomedical Sciences, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Satoshi Yoshimura
- Hematological Malignancies Program, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
- Department of Advanced Pediatric Medicine, Tohoku University School of Medicine, Tokyo, Japan
| | - Wenjian Yang
- Hematological Malignancies Program, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Kristine R Crews
- Hematological Malignancies Program, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Christopher S Manring
- Alliance Hematologic Malignancy Biorepository; Clara D. Bloomfield Center for Leukemia Outcomes Research, Columbus, OH, 43210, USA
| | - Elias Jabbour
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | | | - Mark R Litzow
- Division of Hematology, Department of Medicine, Mayo Clinic, Rochester, MN, 55905, USA
| | - Steven M Kornblau
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Wendy Stock
- Comprehensive Cancer Center, University of Chicago Medicine, Chicago, IL, USA
| | - Hiroto Inaba
- Hematological Malignancies Program, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Sima Jeha
- Hematological Malignancies Program, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Ching-Hon Pui
- Hematological Malignancies Program, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Cheng Cheng
- Department of Biostatistics, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Shondra M Pruett-Miller
- Center for Advanced Genome Engineering, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
- Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Mary V Relling
- Hematological Malignancies Program, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Jun J Yang
- Hematological Malignancies Program, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
- Graduate School of Biomedical Sciences, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
- Integrated Biomedical Sciences Program, University of Tennessee Health Science Center, Memphis, TN, 38163, USA
| | - William E Evans
- Hematological Malignancies Program, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Daniel Savic
- Hematological Malignancies Program, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA.
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA.
- Graduate School of Biomedical Sciences, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA.
- Integrated Biomedical Sciences Program, University of Tennessee Health Science Center, Memphis, TN, 38163, USA.
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Rothschild SC, Lai G, Tombes RM, Clements WK. Constitutively active CaMKII Drives B lineage acute lymphoblastic leukemia/lymphoma in tp53 mutant zebrafish. PLoS Genet 2023; 19:e1011102. [PMID: 38117861 PMCID: PMC10766190 DOI: 10.1371/journal.pgen.1011102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 01/04/2024] [Accepted: 12/07/2023] [Indexed: 12/22/2023] Open
Abstract
Acute lymphoblastic leukemia/lymphoma (ALL) is the most common pediatric cancer and is a malignancy of T or B lineage lymphoblasts. Dysregulation of intracellular Ca2+ levels has been observed in patients with ALL, leading to improper activation of downstream signaling. Here we describe a new zebrafish model of B ALL, generated by expressing human constitutively active CaMKII (CA-CaMKII) in tp53 mutant lymphocytes. In this model, B cell hyperplasia in the kidney marrow and spleen progresses to overt leukemia/lymphoma, with only 29% of zebrafish surviving the first year of life. Leukemic fish have reduced productive genomic VDJ recombination in addition to reduced expression and improper splicing of ikaros1, a gene often deleted or mutated in patients with B ALL. Inhibiting CaMKII in human pre-B ALL cells induced cell death, further supporting a role for CaMKII in leukemogenesis. This research provides novel insight into the role of Ca2+-directed signaling in lymphoid malignancy and will be useful in understanding disease development and progression.
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Affiliation(s)
- Sarah C. Rothschild
- Life Sciences, Virginia Commonwealth University, Richmond, Virginia, United States of America
| | - Guanhua Lai
- Pathology, Virginia Commonwealth University, Richmond, Virginia, United States of America
| | - Robert M. Tombes
- Life Sciences, Virginia Commonwealth University, Richmond, Virginia, United States of America
| | - Wilson K. Clements
- Experimental Hematology, St. Jude Children’s Research Hospital, Memphis, Tennessee, United States of America
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4
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Ruan Y, Xie L, Zou A. Association of CDKN2A/B mutations, PD-1, and PD-L1 with the risk of acute lymphoblastic leukemia in children. J Cancer Res Clin Oncol 2023; 149:10841-10850. [PMID: 37314514 PMCID: PMC10423156 DOI: 10.1007/s00432-023-04974-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Accepted: 06/04/2023] [Indexed: 06/15/2023]
Abstract
PURPOSE Currently, the significance of CDKN2A/B mutations in the pathogenesis and prognosis of acute lymphoblastic leukemia (ALL) is inconclusive. In this study, we analyzed the genetic and clinical features of children with CDKN2A/B mutations in ALL. In addition, we evaluated the expression and significance of programmed cell death protein 1 (PD-1) and programmed cell death ligand 1 (PD-L1) in serum and explored their role in the susceptibility of childhood ALL. METHODS We sequenced CDKN2A/B in the peripheral blood of 120 children with ALL and 100 healthy children with physical examination. The levels of CD4+ T, CD8+ T, and NK cells were measured by flow cytometry (FCM). Furthermore, the expression of PD-1 and PD-L1 was detected by ELISA. RESULTS We found 32 cases of CDKN2A rs3088440 and 11 of CDKN2B rs2069426 in 120 ALL children. Children with ALL in the CDKN2A rs3088440 were more likely to have hepatosplenomegaly (P = 0.019) and high risk (P = 0.014) than the wild group. In contrast, CDKN2B rs2069426 was more likely to develop lymph node metastasis (P = 0.017). The level of PD-L1 in the serum of ALL children was significantly higher than that of the control group, and there was no significant difference in PD-1 (P < 0.001). Additionally, children with CDKN2A rs3088440 had reduced CD8+ T cell counts than the wild group (P = 0.039). CONCLUSION CDKN2A rs3088440 and CDKN2B rs2069426 may be related to the occurrence and development of ALL in Chinese children. Additionally, PD-1/PD-L1 may be involved in the immune escape process of ALL, which is expected to become a new target for the treatment of the disease.
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Affiliation(s)
- Yang Ruan
- Department of Laboratory Medicine, Hunan Children's Hospital, Changsha, 410007, China.
| | - Longlong Xie
- Pediatrics Research Institute of Hunan Province, Hunan Children's Hospital, Changsha, 410007, China
| | - Aijun Zou
- Department of Laboratory Medicine, Hunan Children's Hospital, Changsha, 410007, China
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5
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Pettersson H, Adamsson J, Johansson P, Nilsson S, Palmqvist L, Andréasson B, Asp J. The clinical relevance of broad mutational screening of myeloproliferative neoplasms at diagnosis. Front Oncol 2023; 13:1190305. [PMID: 37637067 PMCID: PMC10451068 DOI: 10.3389/fonc.2023.1190305] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 07/25/2023] [Indexed: 08/29/2023] Open
Abstract
Introduction Myeloproliferative neoplasm (MPN) is a heterogenous group of hematological malignancies including polycythemia vera (PV), essential thrombocythemia (ET) and primary myelofibrosis (PMF). JAK2V617F is the most frequent driver mutation in all three entities, but in PMF and ET mutations in CALR and MPL are also frequent. Mutations seen in additional genes are also often the same regardless of subtype of MPN. The aim of this study was to analyze a population based MPN cohort for genetic variants with prognostic value that can guide clinical decisions. Methods MPN patients from Western Sweden diagnosed between 2008-2013 (n=248) were screened for mutations in 54 genes associated with myeloid malignancy. Results Mutations in the genes SRSF2 and U2AF1 correlated significantly with impaired overall survival but did not correlate to increased risk for vascular events, neither before nor after diagnosis. Rather, mutations in these genes showed an association with disease transformation. Several recurrent gene variants with allele frequency close to 50% were confirmed to be germline. However, none of these variants was found to have an earlier onset of MPN. Discussion In conclusion, we identified gene mutations to be independent markers of impaired survival in MPN. This indicates the need for more individualized assessment and treatment of MPN patients and a wider gene mutation screening already at diagnosis. This could ensure the identification of patients with high-risk mutations early on. In addition, several genetic variants were also identified as germline in this study but gave no obvious clinical relevance. To avoid conclusions from non-informative genetic variants, a simultaneous analysis of normal cell DNA from patients at diagnosis should be considered.
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Affiliation(s)
- Helna Pettersson
- Hematology Section, Department of Medicine, NU Hospital Group, Uddevalla, Sweden
| | - Jenni Adamsson
- Department of Laboratory Medicine, University of Gothenburg, Gothenburg, Sweden
| | - Peter Johansson
- Hematology and Coagulation Section, Department of Medicine, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Staffan Nilsson
- Department of Laboratory Medicine, University of Gothenburg, Gothenburg, Sweden
| | - Lars Palmqvist
- Department of Laboratory Medicine, University of Gothenburg, Gothenburg, Sweden
- Department of Clinical Chemistry, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Björn Andréasson
- Hematology Section, Department of Medicine, NU Hospital Group, Uddevalla, Sweden
| | - Julia Asp
- Department of Laboratory Medicine, University of Gothenburg, Gothenburg, Sweden
- Department of Clinical Chemistry, Sahlgrenska University Hospital, Gothenburg, Sweden
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Svyatova G, Boranbayeva R, Berezina G, Manzhuova L, Murtazaliyeva A. Genes of Predisposition to Childhood Beta-Cell Acute Lymphoblastic Leukemia in the Kazakh Population. Asian Pac J Cancer Prev 2023; 24:2653-2666. [PMID: 37642051 PMCID: PMC10685230 DOI: 10.31557/apjcp.2023.24.8.2653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 08/09/2023] [Indexed: 08/31/2023] Open
Abstract
BACKGROUND Today, acute lymphoblastic leukemia is one of the most common malignant diseases of the hematopoietic system. The genetic predisposition to ALL is not fully explored in various ethnic populations. OBJECTIVE The study aimed to conduct a comparative analysis of the population frequencies of alleles and genotypes of polymorphic gene variants: immune regulation GATA3 (rs3824662); transcription and differentiation of B cells: ARID5B (rs7089424, rs10740055), IKZF1 (rs4132601); differentiation of hematopoietic cells: PIP4K2A (rs7088318); apoptosis: CEBPE (rs2239633), tumor suppressors: CDKN2A (rs3731249), TP53 (rs1042522); carcinogen metabolism: CBR3 (rs1056892), CYP1A1 (rs104894, rs4646903), according to genome-wide association studies analyses associated with the risk of developing pediatric beta-cell acute lymphoblastic leukemia (B-cell ALL), in an ethnically homogeneous population of Kazakhs with studied populations. METHODS The genomic database consists of 1800 conditionally healthy persons of Kazakh nationality, genotyped using OmniChip 2.5-8 Illumina chips at the deCODE genetics as part of the InterPregGen 7 project of the European Union (EU) framework program under Grant Agreement No. 282540. RESULTS High population frequencies of single nucleotide polymorphism (SNP) minor alleles identified for immune regulation genes - GATA3 rs3824662 - 42.5%; transcription and differentiation of B-cells genes - ARID5B rs7089424 - 33.1% and rs10740055 - 48.5%, which suggests their significant genetic contribution to the risk of development and prognosis of the effectiveness of B-cell ALL therapy in the Kazakh population. The significantly lower population frequency of the minor allele G rs1056892 CBR3 gene - 38.6% in the Kazakhs suggests its significant protective effect in reducing the risk of childhood B-cell ALL and the smaller number of cardiac complications after anthracycline therapy. CONCLUSION The obtained results will serve as a basis for developing effective methods for predicting the risk of development, early diagnosis, and effectiveness of treatment of B-cell ALL in children.
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Affiliation(s)
- Gulnara Svyatova
- Republican Medical Genetic Consultation, Scientific Center of Obstetrics, Gynecology and Perinatology, 050020, 125 Dostyk Ave., Almaty, Kazakhstan.
| | - Riza Boranbayeva
- Scientific Center of Pediatrics and Pediatric Surgery, 050060, 146 Al-Farabi Ave., Almaty, Kazakhstan.
| | - Galina Berezina
- Republican Medical Genetic Consultation, Scientific Center of Obstetrics, Gynecology and Perinatology, 050020, 125 Dostyk Ave., Almaty, Kazakhstan.
| | - Lyazat Manzhuova
- Scientific Center of Pediatrics and Pediatric Surgery, 050060, 146 Al-Farabi Ave., Almaty, Kazakhstan.
| | - Alexandra Murtazaliyeva
- Republican Medical Genetic Consultation, Scientific Center of Obstetrics, Gynecology and Perinatology, 050020, 125 Dostyk Ave., Almaty, Kazakhstan.
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Bhattarai KR, Mobley RJ, Barnett KR, Ferguson DC, Hansen BS, Diedrich JD, Bergeron BP, Yang W, Crews KR, Manring CS, Jabbour E, Paietta E, Litzow MR, Kornblau SM, Stock W, Inaba H, Jeha S, Pui CH, Cheng C, Pruett-Miller SM, Relling MV, Yang JJ, Evans WE, Savic D. Functional investigation of inherited noncoding genetic variation impacting the pharmacogenomics of childhood acute lymphoblastic leukemia treatment. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.02.10.23285762. [PMID: 36798219 PMCID: PMC9934807 DOI: 10.1101/2023.02.10.23285762] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/13/2023]
Abstract
Although acute lymphoblastic leukemia (ALL) is the most common childhood cancer, there is limited understanding of the contribution of inherited genetic variation on inter-individual differences in chemotherapy response. Defining genetic factors impacting therapy failure can help better predict response and identify drug resistance mechanisms. We therefore mapped inherited noncoding variants associated with chemotherapeutic drug resistance and/or treatment outcome to ALL cis-regulatory elements and investigated their gene regulatory potential and genomic connectivity using massively parallel reporter assays and promoter capture Hi-C, respectively. We identified 53 variants with reproducible allele-specific effects on transcription and high-confidence gene targets. Subsequent functional interrogation of the top variant (rs1247117) determined that it disrupted a PU.1 consensus motif and PU.1 binding affinity. Importantly, deletion of the genomic interval containing rs1247117 sensitized ALL cells to vincristine. Together, these data demonstrate that noncoding regulatory variation associated with diverse pharmacological traits harbor significant effects on allele-specific transcriptional activity and impact sensitivity to chemotherapeutic agents in ALL.
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Affiliation(s)
- Kashi Raj Bhattarai
- Hematological Malignancies Program, St. Jude Children's Research Hospital, Memphis, TN
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN
| | - Robert J. Mobley
- Hematological Malignancies Program, St. Jude Children's Research Hospital, Memphis, TN
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN
| | - Kelly R. Barnett
- Hematological Malignancies Program, St. Jude Children's Research Hospital, Memphis, TN
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN
| | - Daniel C. Ferguson
- Hematological Malignancies Program, St. Jude Children's Research Hospital, Memphis, TN
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN
| | - Baranda S. Hansen
- Center for Advanced Genome Engineering, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
- Department of Cell and Molecular Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Jonathan D. Diedrich
- Hematological Malignancies Program, St. Jude Children's Research Hospital, Memphis, TN
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN
| | - Brennan P. Bergeron
- Hematological Malignancies Program, St. Jude Children's Research Hospital, Memphis, TN
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN
- Graduate School of Biomedical Sciences, St. Jude Children's Research Hospital, Memphis, TN
| | - Wenjian Yang
- Hematological Malignancies Program, St. Jude Children's Research Hospital, Memphis, TN
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN
| | - Kristine R. Crews
- Hematological Malignancies Program, St. Jude Children's Research Hospital, Memphis, TN
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN
| | - Christopher S. Manring
- Alliance Hematologic Malignancy Biorepository; Clara D. Bloomfield Center for Leukemia Outcomes Research, Columbus, OH 43210, USA
| | - Elias Jabbour
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX
| | | | - Mark R. Litzow
- Division of Hematology, Department of Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | - Steven M. Kornblau
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Wendy Stock
- Comprehensive Cancer Center, University of Chicago Medicine, Chicago, IL
| | - Hiroto Inaba
- Hematological Malignancies Program, St. Jude Children's Research Hospital, Memphis, TN
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN
| | - Sima Jeha
- Hematological Malignancies Program, St. Jude Children's Research Hospital, Memphis, TN
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN
| | - Ching-Hon Pui
- Hematological Malignancies Program, St. Jude Children's Research Hospital, Memphis, TN
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN
| | - Cheng Cheng
- Department of Biostatistics, St. Jude Children's Research Hospital, Memphis, TN
| | - Shondra M. Pruett-Miller
- Center for Advanced Genome Engineering, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
- Department of Cell and Molecular Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Mary V. Relling
- Hematological Malignancies Program, St. Jude Children's Research Hospital, Memphis, TN
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN
| | - Jun J. Yang
- Hematological Malignancies Program, St. Jude Children's Research Hospital, Memphis, TN
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN
- Graduate School of Biomedical Sciences, St. Jude Children's Research Hospital, Memphis, TN
- Integrated Biomedical Sciences Program, University of Tennessee Health Science Center, Memphis, TN
| | - William E. Evans
- Hematological Malignancies Program, St. Jude Children's Research Hospital, Memphis, TN
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN
| | - Daniel Savic
- Hematological Malignancies Program, St. Jude Children's Research Hospital, Memphis, TN
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN
- Graduate School of Biomedical Sciences, St. Jude Children's Research Hospital, Memphis, TN
- Integrated Biomedical Sciences Program, University of Tennessee Health Science Center, Memphis, TN
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Berndt SI, Vijai J, Benavente Y, Camp NJ, Nieters A, Wang Z, Smedby KE, Kleinstern G, Hjalgrim H, Besson C, Skibola CF, Morton LM, Brooks-Wilson AR, Teras LR, Breeze C, Arias J, Adami HO, Albanes D, Anderson KC, Ansell SM, Bassig B, Becker N, Bhatti P, Birmann BM, Boffetta P, Bracci PM, Brennan P, Brown EE, Burdett L, Cannon-Albright LA, Chang ET, Chiu BCH, Chung CC, Clavel J, Cocco P, Colditz G, Conde L, Conti DV, Cox DG, Curtin K, Casabonne D, De Vivo I, Diepstra A, Diver WR, Dogan A, Edlund CK, Foretova L, Fraumeni JF, Gabbas A, Ghesquières H, Giles GG, Glaser S, Glenn M, Glimelius B, Gu J, Habermann TM, Haiman CA, Haioun C, Hofmann JN, Holford TR, Holly EA, Hutchinson A, Izhar A, Jackson RD, Jarrett RF, Kaaks R, Kane E, Kolonel LN, Kong Y, Kraft P, Kricker A, Lake A, Lan Q, Lawrence C, Li D, Liebow M, Link BK, Magnani C, Maynadie M, McKay J, Melbye M, Miligi L, Milne RL, Molina TJ, Monnereau A, Montalvan R, North KE, Novak AJ, Onel K, Purdue MP, Rand KA, Riboli E, Riby J, Roman E, Salles G, Sborov DW, Severson RK, Shanafelt TD, Smith MT, Smith A, Song KW, Song L, Southey MC, Spinelli JJ, Staines A, Stephens D, Sutherland HJ, Tkachuk K, Thompson CA, Tilly H, Tinker LF, Travis RC, Turner J, Vachon CM, Vajdic CM, Van Den Berg A, Van Den Berg DJ, Vermeulen RCH, Vineis P, Wang SS, Weiderpass E, Weiner GJ, Weinstein S, Doo NW, Ye Y, Yeager M, Yu K, Zeleniuch-Jacquotte A, Zhang Y, Zheng T, Ziv E, Sampson J, Chatterjee N, Offit K, Cozen W, Wu X, Cerhan JR, Chanock SJ, Slager SL, Rothman N. Distinct germline genetic susceptibility profiles identified for common non-Hodgkin lymphoma subtypes. Leukemia 2022; 36:2835-2844. [PMID: 36273105 PMCID: PMC10337695 DOI: 10.1038/s41375-022-01711-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 05/22/2022] [Accepted: 09/15/2022] [Indexed: 11/08/2022]
Abstract
Lymphoma risk is elevated for relatives with common non-Hodgkin lymphoma (NHL) subtypes, suggesting shared genetic susceptibility across subtypes. To evaluate the extent of mutual heritability among NHL subtypes and discover novel loci shared among subtypes, we analyzed data from eight genome-wide association studies within the InterLymph Consortium, including 10,629 cases and 9505 controls. We utilized Association analysis based on SubSETs (ASSET) to discover loci for subsets of NHL subtypes and evaluated shared heritability across the genome using Genome-wide Complex Trait Analysis (GCTA) and polygenic risk scores. We discovered 17 genome-wide significant loci (P < 5 × 10-8) for subsets of NHL subtypes, including a novel locus at 10q23.33 (HHEX) (P = 3.27 × 10-9). Most subset associations were driven primarily by only one subtype. Genome-wide genetic correlations between pairs of subtypes varied broadly from 0.20 to 0.86, suggesting substantial heterogeneity in the extent of shared heritability among subtypes. Polygenic risk score analyses of established loci for different lymphoid malignancies identified strong associations with some NHL subtypes (P < 5 × 10-8), but weak or null associations with others. Although our analyses suggest partially shared heritability and biological pathways, they reveal substantial heterogeneity among NHL subtypes with each having its own distinct germline genetic architecture.
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Affiliation(s)
- Sonja I Berndt
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Md, USA.
| | - Joseph Vijai
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Yolanda Benavente
- Cancer Epidemiology Research Programme, Catalan Institute of Oncology-IDIBELL, L'Hospitalet de Llobregat, Barcelona, Spain
- CIBER de Epidemiología y Salud Pública (CIBERESP), Barcelona, Spain
| | - Nicola J Camp
- Department of Internal Medicine and Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Alexandra Nieters
- Institute for Immunodeficiency, University Medical Center Freiburg, Freiburg, Germany
| | - Zhaoming Wang
- Department of Epidemiology and Cancer Control, St. Jude Children's Research Hospital, Memphis, TN, USA
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Karin E Smedby
- Department of Medicine, Solna, Karolinska Institutet, Stockholm, Sweden
- Hematology Center, Karolinska University Hospital, Stockholm, Sweden
| | | | - Henrik Hjalgrim
- Department of Epidemiology Research, Division of Health Surveillance and Research, Statens Serum Institut, Copenhagen, Denmark
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
- Department of Haematology, Rigshospitalet, Copenhagen, Denmark
- Danish Cancer Society Research Center, Danish Cancer Society, Copenhagen, Denmark
| | - Caroline Besson
- Centre Hospitalier de Versailles, Le Chesnay, France
- Université Paris-Saclay, UVSQ, Inserm, Équipe "Exposome et Hérédité", CESP, Villejuif, France
| | - Christine F Skibola
- Department of Hematology and Medical Oncology, Emory University School of Medicine, Atlanta, GA, USA
| | - Lindsay M Morton
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Md, USA
| | - Angela R Brooks-Wilson
- Genome Sciences Centre, BC Cancer Agency, Vancouver, BC, Canada
- Department of Biomedical Physiology and Kinesiology, Simon Fraser University, Burnaby, BC, Canada
| | - Lauren R Teras
- Department of Population Science, American Cancer Society, Atlanta, GA, USA
| | - Charles Breeze
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Md, USA
| | - Joshua Arias
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Md, USA
| | - Hans-Olov Adami
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Institute of Health and Society, Clinical Effectiveness Research Group, University of Oslo, Oslo, Norway
| | - Demetrius Albanes
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Md, USA
| | - Kenneth C Anderson
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Stephen M Ansell
- Department of Internal Medicine, Mayo Clinic, Rochester, MN, USA
| | - Bryan Bassig
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Md, USA
| | - Nikolaus Becker
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Baden-Württemberg, Germany
| | - Parveen Bhatti
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Brenda M Birmann
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Paolo Boffetta
- Stony Brook Cancer Center, Stony Brook University, Stony Brook, New York, 11794, NY, USA
- Department of Medical and Surgical Sciences, University of Bologna, Bologna, 41026, Italy
| | - Paige M Bracci
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA, USA
| | - Paul Brennan
- International Agency for Research on Cancer (IARC), Lyon, France
| | - Elizabeth E Brown
- Department of Pathology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Laurie Burdett
- Cancer Genomics Research Laboratory, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Gaithersburg, MA, USA
| | - Lisa A Cannon-Albright
- Department of Internal Medicine and Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT, USA
- George E. Wahlen Department of Veterans Affairs Medical Center, Salt Lake City, UT, USA
| | - Ellen T Chang
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA, USA
- Center for Health Sciences, Exponent, Inc., Menlo Park, CA, USA
| | - Brian C H Chiu
- Department of Public Health Sciences University of Chicago, Chicago, IL, USA
| | - Charles C Chung
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Md, USA
| | - Jacqueline Clavel
- CRESS, UMR1153, INSERM, Villejuif, France
- Université de Paris-Cité, Villejuif, France
| | - Pierluigi Cocco
- Centre for Occupational and Environmental Health, Division of Population Science, Health Services Research & Primary Care, University of Manchester, Manchester, United Kingdom
| | - Graham Colditz
- Division of Public Health Sciences, Department of Surgery, Washington University School of Medicine, St. Louis, MO, USA
| | - Lucia Conde
- Bill Lyons Informatics Centre, UCL Cancer Institute, University College London, London, United Kingdom
| | - David V Conti
- Department of Population and Public Health Sciences, USC Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - David G Cox
- INSERM U1052, Cancer Research Center of Lyon, Centre Léon Bérard, Lyon, France
| | - Karen Curtin
- Department of Internal Medicine and Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Delphine Casabonne
- Cancer Epidemiology Research Programme, Catalan Institute of Oncology-IDIBELL, L'Hospitalet de Llobregat, Barcelona, Spain
- CIBER de Epidemiología y Salud Pública (CIBERESP), Barcelona, Spain
| | - Immaculata De Vivo
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Arjan Diepstra
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - W Ryan Diver
- Department of Population Science, American Cancer Society, Atlanta, GA, USA
| | - Ahmet Dogan
- Departments of Laboratory Medicine and Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Christopher K Edlund
- Department of Population and Public Health Sciences, USC Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Lenka Foretova
- Department of Cancer Epidemiology and Genetics, Masaryk Memorial Cancer Institute, Brno, Czech Republic
| | - Joseph F Fraumeni
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Md, USA
| | - Attilio Gabbas
- Department of Public Health, Clinical and Molecular Medicine, University of Cagliari, Monserrato, Cagliari, Italy
| | - Hervé Ghesquières
- Department of Hematology, Hospices Civils de Lyon, Lyon Sud Hospital, Pierre Benite, France
- CIRI, Centre International de Recherche en Infectiologie, Team Lymphoma Immuno-Biology, Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, Lyon, France
| | - Graham G Giles
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, VC, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, University of Melbourne, Melbourne, VC, Australia
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, VC, Australia
| | - Sally Glaser
- Cancer Prevention Institute of California, Fremont, CA, USA
- Stanford Cancer Institute, Stanford, CA, USA
| | - Martha Glenn
- Department of Internal Medicine and Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Bengt Glimelius
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Jian Gu
- Department of Epidemiology, MD Anderson Cancer Center, Houston, TX, USA
| | | | - Christopher A Haiman
- Department of Population and Public Health Sciences, USC Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Corinne Haioun
- Lymphoid Malignancies Unit, Henri Mondor Hospital and University Paris Est, Créteil, France
| | - Jonathan N Hofmann
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Md, USA
| | - Theodore R Holford
- Department of Biostatistics, Yale School of Public Health, New Haven, CT, USA
| | - Elizabeth A Holly
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA, USA
| | - Amy Hutchinson
- Cancer Genomics Research Laboratory, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Gaithersburg, MA, USA
| | - Aalin Izhar
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Rebecca D Jackson
- Division of Endocrinology, Diabetes and Metabolism, The Ohio State University, Columbus, OH, USA
| | - Ruth F Jarrett
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Rudolph Kaaks
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Baden-Württemberg, Germany
| | - Eleanor Kane
- Department of Health Sciences, University of York, York, United Kingdom
| | - Laurence N Kolonel
- Cancer Epidemiology Program, University of Hawaii Cancer Center, Honolulu, HI, USA
| | - Yinfei Kong
- Information Systems and Decision Sciences, California State University, Fullerton, Fullerton, CA, USA
| | - Peter Kraft
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Anne Kricker
- Sydney School of Public Health, The University of Sydney, Sydney, NSW, Australia
| | - Annette Lake
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Qing Lan
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Md, USA
| | | | - Dalin Li
- F. Widjaja Family Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Mark Liebow
- Department of Internal Medicine, Mayo Clinic, Rochester, MN, USA
| | - Brian K Link
- Department of Internal Medicine, Carver College of Medicine, The University of Iowa, Iowa City, IA, USA
| | - Corrado Magnani
- CPO-Piemonte and Unit of Medical Statistics and Epidemiology, Department Translational Medicine, University of Piemonte Orientale, Novara, Italy
| | - Marc Maynadie
- INSERM U1231, EA 4184, Registre des Hémopathies Malignes de Côte d'Or, University of Burgundy and Dijon University Hospital, Dijon, France
| | - James McKay
- International Agency for Research on Cancer (IARC), Lyon, France
| | - Mads Melbye
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
- Jebsen Center for Genetic epidemiology, NTNU, Trondheim, Norway
- Danish Cancer Society Research Center, Copenhagen, Denmark
- Department of Genetics, Stanford University Medical School, Stanford, CA, USA
| | - Lucia Miligi
- Environmental and Occupational Epidemiology Unit, Cancer Prevention and Research Institute (ISPO), Florence, Italy
| | - Roger L Milne
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, VC, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, University of Melbourne, Melbourne, VC, Australia
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, VC, Australia
| | - Thierry J Molina
- Department of Pathology, APHP, Necker and Robert Debré, Université Paris Cité, Institut Imagine, INSERM U1163, Paris, France
| | - Alain Monnereau
- CRESS, UMR1153, INSERM, Villejuif, France
- Registre des hémopathies malignes de la Gironde, Institut Bergonié, Bordeaux, Cedex, France
| | | | - Kari E North
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Carolina Center for Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Anne J Novak
- Department of Internal Medicine, Mayo Clinic, Rochester, MN, USA
| | - Kenan Onel
- Donald and Barbara Zucker School of Medicine, Hofstra/Northwell, Hempstead, New York, NY, USA
| | - Mark P Purdue
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Md, USA
| | - Kristin A Rand
- Department of Population and Public Health Sciences, USC Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Elio Riboli
- School of Public Health, Imperial College London, London, United Kingdom
| | - Jacques Riby
- Department of Epidemiology, School of Public Health and Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, AL, USA
- Division of Environmental Health Sciences, University of California Berkeley School of Public Health, Berkeley, CA, USA
| | - Eve Roman
- Department of Health Sciences, University of York, York, United Kingdom
| | - Gilles Salles
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Douglas W Sborov
- Department of Internal Medicine and Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Richard K Severson
- Department of Family Medicine and Public Health Sciences, Wayne State University, Detroit, MI, USA
| | - Tait D Shanafelt
- Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Martyn T Smith
- Division of Environmental Health Sciences, University of California Berkeley School of Public Health, Berkeley, CA, USA
| | - Alexandra Smith
- Department of Health Sciences, University of York, York, United Kingdom
| | - Kevin W Song
- Leukemia/Bone Marrow Transplantation Program, BC Cancer Agency, Vancouver, BC, Canada
- Department of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Lei Song
- Center for Cancer Research, National Cancer Institute, Frederick, MA, USA
| | - Melissa C Southey
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, VC, Australia
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, VC, Australia
- Department of Clinical Pathology, Melbourne Medical School, The University of Melbourne, VC, 3010, Australia
| | - John J Spinelli
- Cancer Control Research, BC Cancer Agency, Vancouver, BC, Canada
- School of Population and Public Health, University of British Columbia, Vancouver, BC, Canada
| | - Anthony Staines
- School of Nursing, Psychotherapy and Community Health, Dublin City University, Dublin, Ireland
| | - Deborah Stephens
- Department of Internal Medicine and Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Heather J Sutherland
- Leukemia/Bone Marrow Transplantation Program, BC Cancer Agency, Vancouver, BC, Canada
- Department of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Kaitlyn Tkachuk
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | - Hervé Tilly
- Centre Henri Becquerel, Université de Rouen, Rouen, France
| | - Lesley F Tinker
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Ruth C Travis
- Cancer Epidemiology Unit, University of Oxford, Oxford, United Kingdom
| | - Jenny Turner
- Faculty of Medicine and Health Sciences, Macquarie University, Sydney, NSW, Australia
- Department of Histopathology, Douglass Hanly Moir Pathology, Sydney, NSW, Australia
| | - Celine M Vachon
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN, USA
| | - Claire M Vajdic
- The Kirby Institute, University of New South Wales, Sydney, NSW, Australia
| | - Anke Van Den Berg
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - David J Van Den Berg
- Department of Population and Public Health Sciences, USC Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Roel C H Vermeulen
- Institute for Risk Assessment Sciences, Utrecht University, Utrecht, The Netherlands
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Paolo Vineis
- MRC-PHE Centre for Environment and Health, School of Public Health, Imperial College London, London, United Kingdom
- Human Genetics Foundation, Turin, Italy
| | - Sophia S Wang
- Division of Health Analytics, City of Hope Beckman Research Institute, Duarte, CA, USA
| | | | - George J Weiner
- Department of Internal Medicine, Carver College of Medicine, The University of Iowa, Iowa City, IA, USA
| | - Stephanie Weinstein
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Md, USA
| | - Nicole Wong Doo
- Concord Clinical School, University of Sydney, Concord, NSW, Australia
| | - Yuanqing Ye
- Department of Epidemiology, MD Anderson Cancer Center, Houston, TX, USA
| | - Meredith Yeager
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Md, USA
- Cancer Genomics Research Laboratory, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Gaithersburg, MA, USA
| | - Kai Yu
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Md, USA
| | - Anne Zeleniuch-Jacquotte
- Department of Population Health, New York University School of Medicine, New York, NY, USA
- Department of Environmental Medicine, New York University School of Medicine, New York, NY, USA
- Perlmutter Cancer Center, NYU Langone Medical Center, New York, NY, USA
| | - Yawei Zhang
- Department of Environmental Health Sciences, Yale School of Public Health, New Haven, CT, USA
| | - Tongzhang Zheng
- Department of Epidemiology, Brown University, Providence, RI, USA
| | - Elad Ziv
- Division of General Internal Medicine, Department of Medicine, Institute of Human Genetics, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
| | - Joshua Sampson
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Md, USA
| | - Nilanjan Chatterjee
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Md, USA
- Department of Biostatistics, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MA, USA
- Department of Oncology, School of Medicine, Johns Hopkins University, Baltimore, MA, USA
| | - Kenneth Offit
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Wendy Cozen
- Chao Family Comprehensive Cancer Center, University of California, Irvine, Irvine, CA, USA
| | - Xifeng Wu
- Department of Epidemiology, MD Anderson Cancer Center, Houston, TX, USA
| | - James R Cerhan
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - Stephen J Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Md, USA
| | - Susan L Slager
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - Nathaniel Rothman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Md, USA
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Haas OA, Borkhardt A. Hyperdiploidy: the longest known, most prevalent, and most enigmatic form of acute lymphoblastic leukemia in children. Leukemia 2022; 36:2769-2783. [PMID: 36266323 PMCID: PMC9712104 DOI: 10.1038/s41375-022-01720-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 09/27/2022] [Accepted: 09/29/2022] [Indexed: 11/09/2022]
Abstract
Hyperdiploidy is the largest genetic entity B-cell precursor acute lymphoblastic leukemia in children. The diagnostic hallmark of its two variants that will be discussed in detail herein is a chromosome count between 52 and 67, respectively. The classical HD form consists of heterozygous di-, tri-, and tetrasomies, whereas the nonclassical one (usually viewed as "duplicated hyperhaploid") contains only disomies and tetrasomies. Despite their apparently different clinical behavior, we show that these two sub-forms can in principle be produced by the same chromosomal maldistribution mechanism. Moreover, their respective array, gene expression, and mutation patterns also indicate that they are biologically more similar than hitherto appreciated. Even though in-depth analyses of the genomic intricacies of classical HD leukemias are indispensable for the elucidation of the disease process, the ensuing results play at present surprisingly little role in treatment stratification, a fact that can be attributed to the overall good prognoses and low relapse rates of the concerned patients and, consequently, their excellent treatment outcome. Irrespective of this underutilization, however, the detailed genetic characterization of HD leukemias may, especially in planned treatment reduction trials, eventually become important for further treatment stratification, patient management, and the clinical elucidation of outcome data. It should therefore become an integral part of all upcoming treatment studies.
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Affiliation(s)
- Oskar A Haas
- St. Anna Children's Hospital, Pediatric Clinic, Medical University, Vienna, Austria.
- Labdia Labordiagnostik, Vienna, Austria.
| | - Arndt Borkhardt
- Department for Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty, Heinrich-Heine-University, Düsseldorf, Germany.
- German Cancer Consortium (DKTK), partnering site Essen/Düsseldorf, Düsseldorf, Germany.
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10
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Wang P, Sun X, Miao Q, Mi H, Cao M, Zhao S, Wang Y, Shu Y, Li W, Xu H, Bai D, Zhang Y. Novel genetic associations with five aesthetic facial traits: A genome-wide association study in the Chinese population. Front Genet 2022; 13:967684. [PMID: 36035146 PMCID: PMC9411802 DOI: 10.3389/fgene.2022.967684] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 06/27/2022] [Indexed: 11/17/2022] Open
Abstract
Background: The aesthetic facial traits are closely related to life quality and strongly influenced by genetic factors, but the genetic predispositions in the Chinese population remain poorly understood. Methods: A genome-wide association studies (GWAS) and subsequent validations were performed in 26,806 Chinese on five facial traits: widow’s peak, unibrow, double eyelid, earlobe attachment, and freckles. Functional annotation was performed based on the expression quantitative trait loci (eQTL) variants, genome-wide polygenic scores (GPSs) were developed to represent the combined polygenic effects, and single nucleotide polymorphism (SNP) heritability was presented to evaluate the contributions of the variants. Results: In total, 21 genetic associations were identified, of which ten were novel: GMDS-AS1 (rs4959669, p = 1.29 × 10−49) and SPRED2 (rs13423753, p = 2.99 × 10−14) for widow’s peak, a previously unreported trait; FARSB (rs36015125, p = 1.96 × 10−21) for unibrow; KIF26B (rs7549180, p = 2.41 × 10−15), CASC2 (rs79852633, p = 4.78 × 10−11), RPGRIP1L (rs6499632, p = 9.15 × 10−11), and PAX1 (rs147581439, p = 3.07 × 10−8) for double eyelid; ZFHX3 (rs74030209, p = 9.77 × 10−14) and LINC01107 (rs10211400, p = 6.25 × 10−10) for earlobe attachment; and SPATA33 (rs35415928, p = 1.08 × 10−8) for freckles. Functionally, seven identified SNPs tag the missense variants and six may function as eQTLs. The combined polygenic effect of the associations was represented by GPSs and contributions of the variants were evaluated using SNP heritability. Conclusion: These identifications may facilitate a better understanding of the genetic basis of features in the Chinese population and hopefully inspire further genetic research on facial development.
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Affiliation(s)
- Peiqi Wang
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, China
| | - Xinghan Sun
- Genomic & Phenomic Data Center, Chengdu 23Mofang Biotechnology Co., Ltd, Chengdu, China
- Department of Biobank, Chengdu 23Mofang Biotechnology Co., Ltd, Chengdu, China
| | - Qiang Miao
- Department of Laboratory Medicine/Research Center of Clinical Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, China
| | - Hao Mi
- Department of Biobank, Chengdu 23Mofang Biotechnology Co., Ltd, Chengdu, China
| | - Minyuan Cao
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, China
| | - Shan Zhao
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, China
| | - Yiyi Wang
- Department of Dermatology, Rare Disease Center, West China Hospital, Sichuan University, Chengdu, China
| | - Yang Shu
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, China
| | - Wei Li
- Department of Dermatology, Rare Disease Center, West China Hospital, Sichuan University, Chengdu, China
| | - Heng Xu
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, China
- Department of Laboratory Medicine/Research Center of Clinical Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, China
| | - Ding Bai
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
- *Correspondence: Ding Bai, ; Yan Zhang,
| | - Yan Zhang
- Lung Cancer Center, West China Hospital, Sichuan University, Chengdu, China
- State Key Laboratory of Biotherapy, Department of Thoracic Oncology, Cancer Center, West China Hospital, Sichuan University, Chengdu, China
- *Correspondence: Ding Bai, ; Yan Zhang,
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11
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Sattarzadeh Bardsiri M, Zehtab S, Karami N, Farsinejad A, Ehsan M, Fatemi A. Association of IKZF1 and CDKN2A gene polymorphisms with childhood acute lymphoblastic leukemia: a high-resolution melting analysis. BMC Med Genomics 2022; 15:171. [PMID: 35932035 PMCID: PMC9354342 DOI: 10.1186/s12920-022-01325-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 07/30/2022] [Indexed: 11/10/2022] Open
Abstract
Background Acute lymphoblastic leukemia is the most prevailing pediatric hematologic malignancy, and various factors such as environmental exposures and genetic variation affect ALL susceptibility and patients outcome. According to genome-wide association studies, several single nucleotide polymorphisms (SNPs) in IKZF1 (rs4132601) and CDKN2A (rs3731249 and rs3731217) genes are associated with ALL susceptibility. Hereupon, this study aimed to discover the association between these SNPs and the risk of childhood ALL among a sample of the Iranian population.
Methods A total of fifty children with ALL were included in this case–control study, along with an additional fifty healthy children, matched for age and gender. High-resolution melting (HRM) analysis was employed to genotyping rs4132601, rs3731249, and rs3731217.
Results In the patient group, the CT genotype and T allele frequency of rs3731249 were significantly greater than controls (p = 0.01 and p = 0.005, respectively). Moreover, the positive association of CT and dominant model (CT + TT) genotypes and T allele at rs3731249 with the risk of ALL was confirmed (OR = 9.56, OR = 10.76 and OR = 11.00, respectively). There was no significant relation between rs4132601 (IKZF1), rs3731217 (CDKN2A), and childhood ALL. Conclusion The present study indicates that CT genotype and T allele at rs3731249 (CDKN2A) can significantly increase the risk of ALL among children.
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Affiliation(s)
- Mahla Sattarzadeh Bardsiri
- Cell Therapy and Regenerative Medicine Comprehensive Center, Kerman University of Medical Sciences, Kerman, Iran.,Department of Hematology and Medical Laboratory Sciences, Faculty of Allied Medicine, Kerman University of Medical Sciences, Kerman, Iran
| | - Shahrzad Zehtab
- Department of Hematology and Medical Laboratory Sciences, Faculty of Allied Medicine, Kerman University of Medical Sciences, Kerman, Iran
| | - Najibe Karami
- Department of Hematology and Medical Laboratory Sciences, Faculty of Allied Medicine, Kerman University of Medical Sciences, Kerman, Iran
| | - Alireza Farsinejad
- Cell Therapy and Regenerative Medicine Comprehensive Center, Kerman University of Medical Sciences, Kerman, Iran.,Department of Hematology and Medical Laboratory Sciences, Faculty of Allied Medicine, Kerman University of Medical Sciences, Kerman, Iran
| | - Mohsen Ehsan
- Department of Hematology and Medical Laboratory Sciences, Faculty of Allied Medicine, Kerman University of Medical Sciences, Kerman, Iran.,Department of Hematology and Blood Banking, Faculty of Allied Medicine, Iran University of Medical Science, Tehran, Iran
| | - Ahmad Fatemi
- Department of Hematology and Medical Laboratory Sciences, Faculty of Allied Medicine, Kerman University of Medical Sciences, Kerman, Iran. .,Cellular and Molecular Research Center, Gerash University of Medical Sciences, Gerash, Iran.
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12
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Qian J, Li Z, Pei K, Li Z, Li C, Yan M, Qian M, Song Y, Zhang H, He Y. Effects of NRAS Mutations on Leukemogenesis and Targeting of Children With Acute Lymphoblastic Leukemia. Front Cell Dev Biol 2022; 10:712484. [PMID: 35211470 PMCID: PMC8861515 DOI: 10.3389/fcell.2022.712484] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Accepted: 01/04/2022] [Indexed: 12/12/2022] Open
Abstract
Through the advancements in recent decades, childhood acute lymphoblastic leukemia (ALL) is gradually becoming a highly curable disease. However, the truth is there remaining relapse in ∼15% of ALL cases with dismal outcomes. RAS mutations, in particular NRAS mutations, were predominant mutations affecting relapse susceptibility. KRAS mutations targeting has been successfully exploited, while NRAS mutation targeting remains to be explored due to its complicated and compensatory mechanisms. Using targeted sequencing, we profiled RAS mutations in 333 primary and 18 relapsed ALL patients and examined their impact on ALL leukemogenesis, therapeutic potential, and treatment outcome. Cumulative analysis showed that RAS mutations were associated with a higher relapse incidence in children with ALL. In vitro cellular assays revealed that about one-third of the NRAS mutations significantly transformed Ba/F3 cells as measured by IL3-independent growth. Meanwhile, we applied a high-throughput drug screening method to characterize variable mutation-related candidate targeted agents and uncovered that leukemogenic-NRAS mutations might respond to MEK, autophagy, Akt, EGFR signaling, Polo−like Kinase, Src signaling, and TGF−β receptor inhibition depending on the mutation profile.
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Affiliation(s)
- Jiabi Qian
- Guangzhou Women and Children's Medical Center, Institute of Pediatrics, Guangzhou, China.,Department of Hematology/Oncology, Guangzhou Women and Children's Medical Center, Guangzhou, China.,Department of Hematology and Oncology, The Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism, Institute of Pediatrics, Institutes of Biomedical Sciences, Children's Hospital of Fudan University, Ministry of Science and Technology, Fudan University, Shanghai, China
| | - Zifeng Li
- Department of Hematology and Oncology, National Children's Medical Center, Children's Hospital of Fudan University, Shanghai, China
| | - Kunlin Pei
- Department of Hematology/Oncology, Guangzhou Women and Children's Medical Center, Guangzhou, China
| | - Ziping Li
- Guangzhou Women and Children's Medical Center, Institute of Pediatrics, Guangzhou, China
| | - Chunjie Li
- Guangzhou Women and Children's Medical Center, Institute of Pediatrics, Guangzhou, China
| | - Muxia Yan
- Department of Hematology/Oncology, Guangzhou Women and Children's Medical Center, Guangzhou, China
| | - Maoxiang Qian
- Department of Hematology and Oncology, The Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism, Institute of Pediatrics, Institutes of Biomedical Sciences, Children's Hospital of Fudan University, Ministry of Science and Technology, Fudan University, Shanghai, China
| | - Yuanbin Song
- Department of Hematologic Oncology, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Hui Zhang
- Department of Hematology/Oncology, Guangzhou Women and Children's Medical Center, Guangzhou, China
| | - Yingyi He
- Department of Hematology/Oncology, Guangzhou Women and Children's Medical Center, Guangzhou, China
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13
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Li C, Zhao X, He Y, Li Z, Qian J, Zhang L, Ye Q, Qiu F, Lian P, Qian M, Zhang H. The functional role of inherited CDKN2A variants in childhood acute lymphoblastic leukemia. Pharmacogenet Genomics 2022; 32:43-50. [PMID: 34369425 PMCID: PMC8694244 DOI: 10.1097/fpc.0000000000000451] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Accepted: 07/13/2021] [Indexed: 11/18/2022]
Abstract
OBJECTIVE Genetic alterations in CDKN2A tumor suppressor gene on chromosome 9p21 confer a predisposition to childhood acute lymphoblastic leukemia (ALL). Genome-wide association studies have identified missense variants in CDKN2A associated with the development of ALL. This study systematically evaluated the effects of CDKN2A coding variants on ALL risk. METHODS We genotyped the CDKN2A coding region in 308 childhood ALL cases enrolled in CCCG-ALL-2015 clinical trials by Sanger Sequencing. Cell growth assay, cell cycle assay, MTT-based cell toxicity assay, and western blot were performed to assess the CDKN2A coding variants on ALL predisposition. RESULTS We identified 10 novel exonic germline variants, including 6 missense mutations (p.A21V, p.G45A and p.V115L of p16INK4A; p.T31R, p.R90G, and p.R129L of p14ARF) and 1 nonsense mutation and 1 heterozygous termination codon mutation in exon 2 (p16INK4A p.S129X). Functional studies indicate that five novel variants resulted in reduced tumor suppressor activity of p16INK4A, and increased the susceptibility to the leukemic transformation of hematopoietic progenitor cells. Compared to other variants, p.H142R contributes higher sensitivity to CDK4/6 inhibitors. CONCLUSION These findings provide direct insight into the influence of inherited genetic variants at the CDKN2A coding region on the development of ALL and the precise clinical application of CDK4/6 inhibitors.
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Affiliation(s)
- Chunjie Li
- Department of Hematology/Oncology
- Institute of Pediatrics, Affiliated Guangzhou Women and Children’s Medical Center, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou
| | - Xinying Zhao
- Department of Hematology/Oncology
- Institute of Pediatrics, Affiliated Guangzhou Women and Children’s Medical Center, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou
| | | | - Ziping Li
- Department of Hematology/Oncology
- Institute of Pediatrics, Affiliated Guangzhou Women and Children’s Medical Center, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou
| | - Jiabi Qian
- Department of Hematology/Oncology
- Institute of Pediatrics, Affiliated Guangzhou Women and Children’s Medical Center, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou
| | - Li Zhang
- Department of Hematology/Oncology
| | - Qian Ye
- Department of Hematology/Oncology
| | - Fei Qiu
- Bioinspired Engineering and Biomechanics Center, Xi’an Jiaotong University, Xi’an, China
| | - Peng Lian
- Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Maoxiang Qian
- Institute of Pediatrics and Department of Hematology and Oncology, Children’s Hospital of Fudan University, National Children’s Medical Center, the Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology), Institutes of Biomedical Sciences, Fudan University, Shanghai, China
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14
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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: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [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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15
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Moriyama T, Yang W, Smith C, Pui CH, Evans WE, Relling MV, Bhatia S, Yang JJ. Comprehensive characterization of pharmacogenetic variants in TPMT and NUDT15 in children with acute lymphoblastic leukemia. Pharmacogenet Genomics 2022; 32:60-66. [PMID: 34412101 PMCID: PMC8702453 DOI: 10.1097/fpc.0000000000000453] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Thiopurines [e.g. 6-mercaptopurine (6MP)] are essential for the cure of acute lymphoblastic leukemia (ALL) but can cause dose-limiting hematopoietic toxicity. Germline variants in drug-metabolizing enzyme genes TPMT and NUDT15 have been linked to the risk of thiopurine toxicity. However, the full spectrum of genetic polymorphism in these genes and their impact on the pharmacological effects of thiopurines remain unclear. Herein, we comprehensively sequenced the TPMT and NUDT15 genes in 685 children with ALL from the Children's Oncology Group AALL03N1 trial and evaluated their association with 6MP dose intensity. We identified 6 and 5 coding variants in TPMT and NUDT15 respectively, confirming the association at known pharmacogenetic variants. Importantly, we discovered a novel gain-of-function noncoding variants in TPMT associated with increased 6MP tolerance (rs12199316), with independent validation in 380 patients from the St. Jude Total Therapy XV protocol. Located adjacent to a regulatory DNA element, this intergenic variant was strongly associated TPMT transcription, with the variant allele linked to higher expression (P = 2.6 × 10-9). For NUDT15, one noncoding common variant, rs73189762, was identified as potentially related to 6MP intolerance. Collectively, we described pharmacogenetic variants in TPMT and NUDT15 associated with thiopurine sensitivity, providing further insights for implementing pharmacogenetics-based thiopurine individualization.
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Affiliation(s)
- Takaya Moriyama
- Department of Pharmaceutical Sciences, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | - Wenjian Yang
- Department of Pharmaceutical Sciences, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | - Colton Smith
- Department of Pharmaceutical Sciences, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | - Ching-Hon Pui
- Department of Oncology, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | - William E. Evans
- Department of Pharmaceutical Sciences, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | - Mary V. Relling
- Department of Pharmaceutical Sciences, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | - Smita Bhatia
- Institute for Cancer Outcomes and Survivorship and Division of Pediatric Hematology-Oncology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Jun J. Yang
- Department of Pharmaceutical Sciences, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
- Department of Oncology, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
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16
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Gargallo P, Oltra S, Yáñez Y, Juan-Ribelles A, Calabria I, Segura V, Lázaro M, Balaguer J, Tormo T, Dolz S, Fernández JM, Fuentes C, Torres B, Andrés M, Tasso M, Castel V, Font de Mora J, Cañete A. Germline Predisposition to Pediatric Cancer, from Next Generation Sequencing to Medical Care. Cancers (Basel) 2021; 13:5339. [PMID: 34771502 PMCID: PMC8582391 DOI: 10.3390/cancers13215339] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 10/18/2021] [Accepted: 10/21/2021] [Indexed: 11/16/2022] Open
Abstract
Knowledge about genetic predisposition to pediatric cancer is constantly expanding. The categorization and clinical management of the best-known syndromes has been refined over the years. Meanwhile, new genes for pediatric cancer susceptibility are discovered every year. Our current work shares the results of genetically studying the germline of 170 pediatric patients diagnosed with cancer. Patients were prospectively recruited and studied using a custom panel, OncoNano V2. The well-categorized predisposing syndromes incidence was 9.4%. Likely pathogenic variants for predisposition to the patient's tumor were identified in an additional 5.9% of cases. Additionally, a high number of pathogenic variants associated with recessive diseases was detected, which required family genetic counseling as well. The clinical utility of the Jongmans MC tool was evaluated, showing a high sensitivity for detecting the best-known predisposing syndromes. Our study confirms that the Jongmans MC tool is appropriate for a rapid assessment of patients; however, the updated version of Ripperger T criteria would be more accurate. Meaningfully, based on our findings, up to 9.4% of patients would present genetic alterations predisposing to cancer. Notably, up to 20% of all patients carry germline pathogenic or likely pathogenic variants in genes related to cancer and, thereby, they also require expert genetic counseling. The most important consideration is that the detection rate of genetic causality outside Jongmans MC et al. criteria was very low.
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Affiliation(s)
- Pablo Gargallo
- Pediatric Oncology Department, Hospital Universitario y Politécnico La Fe de Valencia, 46026 Valencia, Spain; (Y.Y.); (A.J.-R.); (V.S.); (J.B.); (T.T.); (J.M.F.); (C.F.); (B.T.); (M.A.); (V.C.); (A.C.)
- Imegen–Health in Code Group, Department of Oncology, Paterna, 46980 Valencia, Spain; (I.C.); (M.L.)
| | - Silvestre Oltra
- Genetics Unit, Hospital Universitario y Politécnico La Fe de Valencia, 46026 Valencia, Spain;
- Genetics Department, Universidad de Valencia, 46010 Valencia, Spain
| | - Yania Yáñez
- Pediatric Oncology Department, Hospital Universitario y Politécnico La Fe de Valencia, 46026 Valencia, Spain; (Y.Y.); (A.J.-R.); (V.S.); (J.B.); (T.T.); (J.M.F.); (C.F.); (B.T.); (M.A.); (V.C.); (A.C.)
| | - Antonio Juan-Ribelles
- Pediatric Oncology Department, Hospital Universitario y Politécnico La Fe de Valencia, 46026 Valencia, Spain; (Y.Y.); (A.J.-R.); (V.S.); (J.B.); (T.T.); (J.M.F.); (C.F.); (B.T.); (M.A.); (V.C.); (A.C.)
| | - Inés Calabria
- Imegen–Health in Code Group, Department of Oncology, Paterna, 46980 Valencia, Spain; (I.C.); (M.L.)
| | - Vanessa Segura
- Pediatric Oncology Department, Hospital Universitario y Politécnico La Fe de Valencia, 46026 Valencia, Spain; (Y.Y.); (A.J.-R.); (V.S.); (J.B.); (T.T.); (J.M.F.); (C.F.); (B.T.); (M.A.); (V.C.); (A.C.)
| | - Marián Lázaro
- Imegen–Health in Code Group, Department of Oncology, Paterna, 46980 Valencia, Spain; (I.C.); (M.L.)
| | - Julia Balaguer
- Pediatric Oncology Department, Hospital Universitario y Politécnico La Fe de Valencia, 46026 Valencia, Spain; (Y.Y.); (A.J.-R.); (V.S.); (J.B.); (T.T.); (J.M.F.); (C.F.); (B.T.); (M.A.); (V.C.); (A.C.)
| | - Teresa Tormo
- Pediatric Oncology Department, Hospital Universitario y Politécnico La Fe de Valencia, 46026 Valencia, Spain; (Y.Y.); (A.J.-R.); (V.S.); (J.B.); (T.T.); (J.M.F.); (C.F.); (B.T.); (M.A.); (V.C.); (A.C.)
| | - Sandra Dolz
- Laboratory of Cellular and Molecular Biology, Clinical and Translational Research in Cancer, Instituto de Investigación Sanitaria La Fe, 46026 Valencia, Spain; (S.D.); (J.F.d.M.)
| | - José María Fernández
- Pediatric Oncology Department, Hospital Universitario y Politécnico La Fe de Valencia, 46026 Valencia, Spain; (Y.Y.); (A.J.-R.); (V.S.); (J.B.); (T.T.); (J.M.F.); (C.F.); (B.T.); (M.A.); (V.C.); (A.C.)
| | - Carolina Fuentes
- Pediatric Oncology Department, Hospital Universitario y Politécnico La Fe de Valencia, 46026 Valencia, Spain; (Y.Y.); (A.J.-R.); (V.S.); (J.B.); (T.T.); (J.M.F.); (C.F.); (B.T.); (M.A.); (V.C.); (A.C.)
| | - Bárbara Torres
- Pediatric Oncology Department, Hospital Universitario y Politécnico La Fe de Valencia, 46026 Valencia, Spain; (Y.Y.); (A.J.-R.); (V.S.); (J.B.); (T.T.); (J.M.F.); (C.F.); (B.T.); (M.A.); (V.C.); (A.C.)
| | - Mara Andrés
- Pediatric Oncology Department, Hospital Universitario y Politécnico La Fe de Valencia, 46026 Valencia, Spain; (Y.Y.); (A.J.-R.); (V.S.); (J.B.); (T.T.); (J.M.F.); (C.F.); (B.T.); (M.A.); (V.C.); (A.C.)
| | - María Tasso
- Pediatric Oncology Department, Hospital General de Alicante, 03010 Alicante, Spain;
| | - Victoria Castel
- Pediatric Oncology Department, Hospital Universitario y Politécnico La Fe de Valencia, 46026 Valencia, Spain; (Y.Y.); (A.J.-R.); (V.S.); (J.B.); (T.T.); (J.M.F.); (C.F.); (B.T.); (M.A.); (V.C.); (A.C.)
| | - Jaime Font de Mora
- Laboratory of Cellular and Molecular Biology, Clinical and Translational Research in Cancer, Instituto de Investigación Sanitaria La Fe, 46026 Valencia, Spain; (S.D.); (J.F.d.M.)
| | - Adela Cañete
- Pediatric Oncology Department, Hospital Universitario y Politécnico La Fe de Valencia, 46026 Valencia, Spain; (Y.Y.); (A.J.-R.); (V.S.); (J.B.); (T.T.); (J.M.F.); (C.F.); (B.T.); (M.A.); (V.C.); (A.C.)
- Department of Pediatrics, Obstetrics and Gynecology, University of Valencia, 46010 Valencia, Spain
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17
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Hauer J, Fischer U, Borkhardt A. Toward prevention of childhood ALL by early-life immune training. Blood 2021; 138:1412-1428. [PMID: 34010407 PMCID: PMC8532195 DOI: 10.1182/blood.2020009895] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [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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Affiliation(s)
- Julia Hauer
- National Center for Tumor Diseases (NCT), Dresden, Germany
- Pediatric Hematology and Oncology, Department of Pediatrics, University Hospital Carl Gustav Carus, TU Dresden, Dresden, Germany
| | - Ute Fischer
- Department for Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty, Heinrich-Heine University, Düsseldorf, Germany; and
- German Cancer Consortium (DKTK), partnering site Essen/Düsseldorf, Germany
| | - Arndt Borkhardt
- Department for Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty, Heinrich-Heine University, Düsseldorf, Germany; and
- German Cancer Consortium (DKTK), partnering site Essen/Düsseldorf, Germany
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18
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Haas OA. Somatic Sex: On the Origin of Neoplasms With Chromosome Counts in Uneven Ploidy Ranges. Front Cell Dev Biol 2021; 9:631946. [PMID: 34422788 PMCID: PMC8373647 DOI: 10.3389/fcell.2021.631946] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2020] [Accepted: 06/22/2021] [Indexed: 01/09/2023] Open
Abstract
Stable aneuploid genomes with nonrandom numerical changes in uneven ploidy ranges define distinct subsets of hematologic malignancies and solid tumors. The idea put forward herein suggests that they emerge from interactions between diploid mitotic and G0/G1 cells, which can in a single step produce all combinations of mono-, di-, tri-, tetra- and pentasomic paternal/maternal homologue configurations that define such genomes. A nanotube-mediated influx of interphase cell cytoplasm into mitotic cells would thus be responsible for the critical nondisjunction and segregation errors by physically impeding the proper formation of the cell division machinery, whereas only a complete cell fusion can simultaneously generate pentasomies, uniparental trisomies as well as biclonal hypo- and hyperdiploid cell populations. The term "somatic sex" was devised to accentuate the similarities between germ cell and somatic cell fusions. A somatic cell fusion, in particular, recapitulates many processes that are also instrumental in the formation of an abnormal zygote that involves a diploid oocyte and a haploid sperm, which then may further develop into a digynic triploid embryo. Despite their somehow deceptive differences and consequences, the resemblance of these two routes may go far beyond of what has hitherto been appreciated. Based on the arguments put forward herein, I propose that embryonic malignancies of mesenchymal origin with these particular types of aneuploidies can thus be viewed as the kind of flawed somatic equivalent of a digynic triploid embryo.
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Affiliation(s)
- Oskar A Haas
- St. Anna Children's Cancer Research Institute, Vienna, Austria
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19
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Familial Melanoma and Susceptibility Genes: A Review of the Most Common Clinical and Dermoscopic Phenotypic Aspect, Associated Malignancies and Practical Tips for Management. J Clin Med 2021; 10:jcm10163760. [PMID: 34442055 PMCID: PMC8397216 DOI: 10.3390/jcm10163760] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2021] [Revised: 08/13/2021] [Accepted: 08/18/2021] [Indexed: 12/11/2022] Open
Abstract
A family history of melanoma greatly increases the risk of developing cutaneous melanoma, a highly aggressive skin cancer whose incidence has been steadily increasing worldwide. Familial melanomas account for about 10% of all malignant melanomas and display an inheritance pattern consistent with the presence of pathogenic germline mutations, among which those involving CDKN2A are the best characterized. In recent years, a growing number of genes, such as MC1R, MITF, CDK4, POT1, TERT, ACD, TERF2IP, and BAP1, have been implicated in familial melanoma. The fact that individuals harboring these germline mutations along with their close blood relatives have a higher risk of developing multiple primary melanomas as well as other internal organ malignancies, especially pancreatic cancer, makes cascade genetic testing and surveillance of these families of the utmost importance. Unfortunately, due to a polygenic inheritance mechanism involving multiple low-risk alleles, genetic modifiers, and environmental factors, it is still very difficult to predict the presence of these mutations. It is, however, known that germline mutation carriers can sometimes develop specific clinical traits, such as high atypical nevus counts and specific dermoscopic features, which could theoretically help clinicians predict the presence of these mutations in prone families. In this review, we provide a comprehensive overview of the high- and intermediate-penetrance genes primarily linked to familial melanoma, highlighting their most frequently associated non-cutaneous malignancies and clinical/dermoscopic phenotypes.
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20
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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] [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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21
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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] [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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22
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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] [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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23
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Nishii R, Baskin-Doerfler R, Yang W, Oak N, Zhao X, Yang W, Hoshitsuki K, Bloom M, Verbist K, Burns M, Li Z, Lin TN, Qian M, Moriyama T, Gastier-Foster JM, Rabin KR, Raetz E, Mullighan C, Pui CH, Yeoh AEJ, Zhang J, Metzger ML, Klco JM, Hunger SP, Newman S, Wu G, Loh ML, Nichols KE, Yang JJ. Molecular basis of ETV6-mediated predisposition to childhood acute lymphoblastic leukemia. Blood 2021; 137:364-373. [PMID: 32693409 PMCID: PMC7819760 DOI: 10.1182/blood.2020006164] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 07/03/2020] [Indexed: 12/24/2022] Open
Abstract
There is growing evidence supporting an inherited basis for susceptibility to acute lymphoblastic leukemia (ALL) in children. In particular, we and others reported recurrent germline ETV6 variants linked to ALL risk, which collectively represent a novel leukemia predisposition syndrome. To understand the influence of ETV6 variation on ALL pathogenesis, we comprehensively characterized a cohort of 32 childhood leukemia cases arising from this rare syndrome. Of 34 nonsynonymous germline ETV6 variants in ALL, we identified 22 variants with impaired transcription repressor activity, loss of DNA binding, and altered nuclear localization. Missense variants retained dimerization with wild-type ETV6 with potentially dominant-negative effects. Whole-transcriptome and whole-genome sequencing of this cohort of leukemia cases revealed a profound influence of germline ETV6 variants on leukemia transcriptional landscape, with distinct ALL subsets invoking unique patterns of somatic cooperating mutations. 70% of ALL cases with damaging germline ETV6 variants exhibited hyperdiploid karyotype with characteristic recurrent mutations in NRAS, KRAS, and PTPN11. In contrast, the remaining 30% cases had a diploid leukemia genome and an exceedingly high frequency of somatic copy-number loss of PAX5 and ETV6, with a gene expression pattern that strikingly mirrored that of ALL with somatic ETV6-RUNX1 fusion. Two ETV6 germline variants gave rise to both acute myeloid leukemia and ALL, with lineage-specific genetic lesions in the leukemia genomes. ETV6 variants compromise its tumor suppressor activity in vitro with specific molecular targets identified by assay for transposase-accessible chromatin sequencing profiling. ETV6-mediated ALL predisposition exemplifies the intricate interactions between inherited and acquired genomic variations in leukemia pathogenesis.
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Affiliation(s)
| | | | | | - Ninad Oak
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN
| | - Xujie Zhao
- Department of Pharmaceutical Sciences and
| | | | | | - Mackenzie Bloom
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN
| | - Katherine Verbist
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN
| | - Melissa Burns
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
| | - Zhenhua Li
- Department of Paediatrics, National University of Singapore, Singapore, Singapore
| | | | - Maoxiang Qian
- Department of Pharmaceutical Sciences and
- Children's Hospital of Fudan University, Shanghai, China
- Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | | | - Julie M Gastier-Foster
- Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH
- Department of Pathology and
- Department of Pediatrics, The Ohio State University, Columbus, OH
| | - Karen R Rabin
- Texas Children's Cancer Center, Baylor College of Medicine, Houston, TX
| | - Elizabeth Raetz
- Department of Pediatrics, NYU Langone Medical Center, New York, NY
| | - Charles Mullighan
- Department of Pathology and
- Hematological Malignancies Program, Comprehensive Cancer Center, St. Jude Children's Research Hospital, Memphis, TN
| | - Ching-Hon Pui
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN
- Hematological Malignancies Program, Comprehensive Cancer Center, St. Jude Children's Research Hospital, Memphis, TN
| | - Allen Eng-Juh Yeoh
- Khoo Teck Puat-National University Children's Medical Institute, National University Hospital, National University Health System, Singapore, Singapore
- VIVA-NUS Center for Translational Research in Acute Leukaemia, Department of Paediatrics, Yong Loo Lin School of Medicine, Singapore, Singapore
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | | | - Monika L Metzger
- Hematological Malignancies Program, Comprehensive Cancer Center, St. Jude Children's Research Hospital, Memphis, TN
- Department of Global Pediatric Medicine, St. Jude Children's Research Hospital, Memphis, TN
| | - Jeffery M Klco
- Department of Pathology and
- Hematological Malignancies Program, Comprehensive Cancer Center, St. Jude Children's Research Hospital, Memphis, TN
| | - Stephen P Hunger
- Department of Pediatrics and Center for Childhood Cancer Research, Children's Hospital of Philadelphia and the Perelman School of Medicine at The University of Pennsylvania, Philadelphia, PA
| | | | - Gang Wu
- Department of Computational Biology and
| | - Mignon L Loh
- Department of Pediatrics, Benioff Children's Hospital, San Francisco, CA; and
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA
| | - Kim E Nichols
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN
- Hematological Malignancies Program, Comprehensive Cancer Center, St. Jude Children's Research Hospital, Memphis, TN
| | - Jun J Yang
- Department of Pharmaceutical Sciences and
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN
- Hematological Malignancies Program, Comprehensive Cancer Center, St. Jude Children's Research Hospital, Memphis, TN
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24
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Yamashita T, Vollbrecht C, Hirsch B, Kleo K, Anagnostopoulos I, Hummel M. Integrative genomic analysis focused on cell cycle genes for MYC-driven aggressive mature B-cell lymphoma. J Clin Exp Hematop 2021; 60:87-96. [PMID: 32981916 PMCID: PMC7596913 DOI: 10.3960/jslrt.20021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
MYC is a transcriptional factor that regulates growth and proliferation through cell
cycle pathways. MYC alterations, in particular MYC rearrangements, are
important in assessing the prognosis of aggressive B-cell lymphoma. In this study, we
focused on the impact of nine major cell cycle genes for MYC-driven aggressive mature
B-cell lymphoma and analyzed the mutational status using targeted next generation
sequencing. Our 40 cases of aggressive mature B-cell lymphomas included 5 Burkitt
lymphomas, 17 high-grade B-cell lymphomas and 18 diffuse large B-cell lymphomas with MYC
breaks in 100%, 88% and 11%, respectively. Our data allowed a molecular classification
into four categories partially independent from the histopathological diagnosis but
correlating with the Ki-67 labelling index: (I) harboring TP53 and
CDKN2A mutations, being highly proliferative, (II) with
MYC rearrangement associated with MYC and/or
ID3 mutations, being highly proliferative, (III) with
MYC rearrangement combined with additional molecular changes, being
highly proliferative, and (IV) with a diverse pattern of molecular alterations, being less
proliferative. Taken together, we found that mutations of TP53,
CDKN2A, MYC and ID3 are associated
with highly proliferative B-cell lymphomas that could profit from novel therapeutic
strategies.
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Affiliation(s)
- Takahisa Yamashita
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Pathology, Berlin, Germany.,Department of Pathology, Saitama Medical Center, Saitama Medical University, Saitama, Japan
| | - Claudia Vollbrecht
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Pathology, Berlin, Germany.,German Cancer Consortium (DKTK), Berlin, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Burkhard Hirsch
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Pathology, Berlin, Germany
| | - Karsten Kleo
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Pathology, Berlin, Germany
| | - Ioannis Anagnostopoulos
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Pathology, Berlin, Germany
| | - Michael Hummel
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Pathology, Berlin, Germany
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25
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González-Gil C, Ribera J, Ribera JM, Genescà E. The Yin and Yang-Like Clinical Implications of the CDKN2A/ARF/CDKN2B Gene Cluster in Acute Lymphoblastic Leukemia. Genes (Basel) 2021; 12:genes12010079. [PMID: 33435487 PMCID: PMC7827355 DOI: 10.3390/genes12010079] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 01/04/2021] [Accepted: 01/05/2021] [Indexed: 12/13/2022] Open
Abstract
Acute lymphoblastic leukemia (ALL) is a malignant clonal expansion of lymphoid hematopoietic precursors that exhibit developmental arrest at varying stages of differentiation. Similar to what occurs in solid cancers, transformation of normal hematopoietic precursors is governed by a multistep oncogenic process that drives initiation, clonal expansion and metastasis. In this process, alterations in genes encoding proteins that govern processes such as cell proliferation, differentiation, and growth provide us with some of the clearest mechanistic insights into how and why cancer arises. In such a scenario, deletions in the 9p21.3 cluster involving CDKN2A/ARF/CDKN2B genes arise as one of the oncogenic hallmarks of ALL. Deletions in this region are the most frequent structural alteration in T-cell acute lymphoblastic leukemia (T-ALL) and account for roughly 30% of copy number alterations found in B-cell-precursor acute lymphoblastic leukemia (BCP-ALL). Here, we review the literature concerning the involvement of the CDKN2A/B genes as a prognosis marker of good or bad response in the two ALL subtypes (BCP-ALL and T-ALL). We compare frequencies observed in studies performed on several ALL cohorts (adult and child), which mainly consider genetic data produced by genomic techniques. We also summarize what we have learned from mouse models designed to evaluate the functional involvement of the gene cluster in ALL development and in relapse/resistance to treatment. Finally, we examine the range of possibilities for targeting the abnormal function of the protein-coding genes of this cluster and their potential to act as anti-leukemic agents in patients.
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Affiliation(s)
- Celia González-Gil
- Josep Carreras Leukaemia Research Institute (IJC), Campus ICO-Hospital Germans Trias i Pujol, Universitat Autònoma de Barcelona (UAB), 08916 Badalona, Spain; (C.G.-G.); (J.R.); (J.M.R.)
| | - Jordi Ribera
- Josep Carreras Leukaemia Research Institute (IJC), Campus ICO-Hospital Germans Trias i Pujol, Universitat Autònoma de Barcelona (UAB), 08916 Badalona, Spain; (C.G.-G.); (J.R.); (J.M.R.)
| | - Josep Maria Ribera
- Josep Carreras Leukaemia Research Institute (IJC), Campus ICO-Hospital Germans Trias i Pujol, Universitat Autònoma de Barcelona (UAB), 08916 Badalona, Spain; (C.G.-G.); (J.R.); (J.M.R.)
- Clinical Hematology Department, ICO-Hospital Germans Trias i Pujol, 08916 Badalona, Spain
| | - Eulàlia Genescà
- Josep Carreras Leukaemia Research Institute (IJC), Campus ICO-Hospital Germans Trias i Pujol, Universitat Autònoma de Barcelona (UAB), 08916 Badalona, Spain; (C.G.-G.); (J.R.); (J.M.R.)
- Correspondence: ; Tel.: +34-93-557-28-08
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26
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Miller JB, Ward E, Staley LA, Stevens J, Teerlink CC, Tavana JP, Cloward M, Page M, Dayton L, Cannon-Albright LA, Kauwe JSK. Identification and genomic analysis of pedigrees with exceptional longevity identifies candidate rare variants. Neurobiol Dis 2020; 143:104972. [PMID: 32574725 PMCID: PMC7461696 DOI: 10.1016/j.nbd.2020.104972] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 05/05/2020] [Accepted: 06/12/2020] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Longevity as a phenotype entails living longer than average and typically includes living without chronic age-related diseases. Recently, several common genetic components to longevity have been identified. This study aims to identify additional genetic variants associated with longevity using unique and powerful analyses of pedigrees with a statistical excess of healthy elderly individuals identified in the Utah Population Database (UPDB). METHODS From an existing biorepository of Utah pedigrees, six independent cousin pairs were selected from four extended pedigrees that exhibited an excess of healthy elderly individuals; whole exome sequencing (WES) was performed on two elderly individuals from each pedigree who were either first cousins or first cousins once removed. Rare (<.01 population frequency) variants shared by at least one elderly cousin pair in a region likely to be identical by descent were identified as candidates. Ingenuity Variant Analysis was used to prioritize putative causal variants based on quality control, frequency, and gain or loss of function. The variant frequency was compared in healthy cohorts and in an Alzheimer's disease cohort. Remaining variants were filtered based on their presence in genes reported to have an effect on the aging process, aging of cells, or the longevity process. Validation of these candidate variants included tests of segregation on other elderly relatives. RESULTS Fifteen rare candidate genetic variants spanning 17 genes shared within cousins were identified as having passed prioritization criteria. Of those variants, six were present in genes that are known or predicted to affect the aging process: rs78408340 (PAM), rs112892337 (ZFAT), rs61737629 (ESPL1), rs141903485 (CEBPE), rs144369314 (UTP4), and rs61753103 (NUP88 and RABEP1). ESPL1 rs61737629 and CEBPE rs141903485 show additional evidence of segregation with longevity in expanded pedigree analyses (p-values = .001 and .0001, respectively). DISCUSSION This unique pedigree analysis efficiently identified several novel rare candidate variants that may affect the aging process and added support to seven genes that likely contribute to longevity. Further analyses showed evidence for segregation for two rare variants, ESPL1 rs61737629 and CEBPE rs141903485, in the original longevity pedigrees in which they were initially observed. These candidate genes and variants warrant further investigation.
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Affiliation(s)
- Justin B Miller
- Department of Biology, Brigham Young University, Provo, UT 84602, USA
| | - Elizabeth Ward
- Department of Biology, Brigham Young University, Provo, UT 84602, USA
| | - Lyndsay A Staley
- Department of Biology, Brigham Young University, Provo, UT 84602, USA
| | - Jeffrey Stevens
- Genetic Epidemiology, Department of Internal Medicine, University of Utah, Salt Lake City, UT 84132, USA
| | - Craig C Teerlink
- Genetic Epidemiology, Department of Internal Medicine, University of Utah, Salt Lake City, UT 84132, USA
| | - Justina P Tavana
- Department of Biology, Brigham Young University, Provo, UT 84602, USA
| | - Matthew Cloward
- Department of Biology, Brigham Young University, Provo, UT 84602, USA
| | - Madeline Page
- Department of Biology, Brigham Young University, Provo, UT 84602, USA
| | - Louisa Dayton
- Department of Biology, Brigham Young University, Provo, UT 84602, USA
| | - Lisa A Cannon-Albright
- Genetic Epidemiology, Department of Internal Medicine, University of Utah, Salt Lake City, UT 84132, USA
| | - John S K Kauwe
- Department of Biology, Brigham Young University, Provo, UT 84602, USA.
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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] [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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28
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Wang P, Deng Y, Yan X, Zhu J, Yin Y, Shu Y, Bai D, Zhang S, Xu H, Lu X. The Role of ARID5B in Acute Lymphoblastic Leukemia and Beyond. Front Genet 2020; 11:598. [PMID: 32595701 PMCID: PMC7303299 DOI: 10.3389/fgene.2020.00598] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2020] [Accepted: 05/18/2020] [Indexed: 02/05/2023] Open
Abstract
Acute lymphoblastic leukemia (ALL) is the most common malignancy in children with distinct characteristics among different subtypes. Although the etiology of ALL has not been fully unveiled, initiation of ALL has been demonstrated to partly depend on genetic factors. As indicated by several genome wide association studies (GWASs) and candidate gene analyses, ARID5B, a member of AT-rich interactive domain (ARID) protein family, is associated with the occurrence and prognosis of ALL. However, the mechanisms by which ARID5B genotype impact on the susceptibility and treatment outcome remain vague. In this review, we outline developments in the understanding of ARID5B in the susceptibility of ALL and its therapeutic perspectives, and summarize the underlying mechanisms based on the limited functional studies, hoping to illustrate the possible mechanisms of ARID5B impact and highlight the potential treatment regimens.
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Affiliation(s)
- Peiqi Wang
- Department of Pediatric Hematology/Oncology, West China Second University Hospital, Sichuan University, Chengdu, China.,State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Yun Deng
- State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, China
| | - Xinyu Yan
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Jianhui Zhu
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Yuanyuan Yin
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Yang Shu
- State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, China
| | - Ding Bai
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Shouyue Zhang
- State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, China
| | - Heng Xu
- State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, China.,Department of Laboratory Medicine/Research Center of Clinical Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, China.,Precision Medicine Center, State Key Laboratory of Biotherapy and Precision Medicine, Key Laboratory of Sichuan Province, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, China
| | - Xiaoxi Lu
- Department of Pediatric Hematology/Oncology, West China Second University Hospital, Sichuan University, Chengdu, China
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29
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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] [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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30
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Yang C, Sun J, Yong L, Liang C, Liu T, Xu Y, Yang J, Liu X. Deficiency of PTEN and CDKN2A Tumor-Suppressor Genes in Conventional and Chondroid Chordomas: Molecular Characteristics and Clinical Relevance. Onco Targets Ther 2020; 13:4649-4663. [PMID: 32547095 PMCID: PMC7259488 DOI: 10.2147/ott.s252990] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2020] [Accepted: 05/11/2020] [Indexed: 12/03/2022] Open
Abstract
Introduction Chordoma is a malignant tumor predominantly involving the skull base and vertebral column. This study aimed to investigate the molecular characteristics of PTEN and CDKN2A in conventional and chondroid chordomas and their correlation with clinical prognosis. Materials and Methods A total of 42 patients were enrolled, including 26 patients with conventional chordoma and 16 patients with chondroid chordoma. Clinicopathological profiles and tissue specimens were collected. Gene sequencing and fluorescence in situ hybridization were performed to identify genetic alterations in the PTEN and CDKN2A genes. Immunohistochemical staining was used for semiquantitative evaluation of PTEN and CDKN2A expression. Results Gene sequencing revealed an intron SNP (c.80–96A>G) and a missense mutation (c.10G>A; p.Gly4Arg) in the PTEN gene and a missense mutation (c.442G>A; p.Ala148Thr) in the CDKN2A gene. Loss of the PTEN locus was identified in 25 (59.5%) cases, and loss of the CDKN2A locus was found in 28 (66.7%) cases. There was no significant correlation between progression-free survival (PFS)/overall survival (OS) and loss of PTEN or CDKN2A. The patients with lower PTEN expression showed significantly shorter PFS and OS than those with higher expression, while there was no significant difference in PFS or OS between patients with lower CDKN2A expression and those with higher CDKN2A expression. Conclusion Our findings delineated the genetic landscape and expression of PTEN and CDKN2A in chordomas. PTEN expression may serve as a prognostic and predictive biomarker for chordomas.
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Affiliation(s)
- Chenlong Yang
- Department of Orthopedics, Peking University Third Hospital, Beijing 100191, People's Republic of China
| | - Jianjun Sun
- Department of Neurosurgery, Peking University Third Hospital, Beijing 100191, People's Republic of China
| | - Lei Yong
- Department of Orthopedics, Peking University Third Hospital, Beijing 100191, People's Republic of China
| | - Chen Liang
- Department of Orthopedics, Peking University Third Hospital, Beijing 100191, People's Republic of China
| | - Tie Liu
- Department of Neurosurgery, China National Clinical Research Center for Neurological Diseases, Beijing Tiantan Hospital, Capital Medical University, Beijing 100070, People's Republic of China
| | - Yulun Xu
- Department of Neurosurgery, China National Clinical Research Center for Neurological Diseases, Beijing Tiantan Hospital, Capital Medical University, Beijing 100070, People's Republic of China
| | - Jun Yang
- Department of Neurosurgery, Peking University Third Hospital, Beijing 100191, People's Republic of China
| | - Xiaoguang Liu
- Department of Orthopedics, Peking University Third Hospital, Beijing 100191, People's Republic of China
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31
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Andréasson B, Pettersson H, Wasslavik C, Johansson P, Palmqvist L, Asp J. ASXL1 mutations, previous vascular complications and age at diagnosis predict survival in 85 WHO-defined polycythaemia vera patients. Br J Haematol 2020; 189:913-919. [PMID: 32066200 DOI: 10.1111/bjh.16450] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Revised: 10/15/2019] [Accepted: 10/15/2019] [Indexed: 12/17/2022]
Abstract
Polycythaemia vera (PV) patients have an overall comparatively favourable prognosis, but disease progression is very heterogeneous and life-threatening thrombosis and bleedings are frequent complications in untreated disease. Moreover, transformation to more severe secondary myelofibrosis and acute myeloid leukaemia can occur. The aim of this study was to identify gene mutations that could be used together with clinical data as prognostic markers to guide treatment decisions in PV patients. A well-characterized WHO-defined cohort of PV patients was used. Clinical data and blood values were evaluated and a myeloid sequencing panel was used to screen for additional mutations other than the diagnostic JAK2 V617F and JAK2 exon 12 mutations. In 78% of the PV patients, at least one mutation additional to JAK2 V617F was detected. Additional mutations in genes coding for epigenetic modifiers, like TET2, DNMT3A and ASXL1, were most frequent. When correlated to overall survival, mutations in ASXL1 were significantly associated with inferior survival. In an attempt to obtain prognostic guidance in a larger number of patients, the presence of ASXL1 mutations was combined with age and vascular complications prior to diagnosis. Based on these data we were able to define three risk groups that predicted survival.
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Affiliation(s)
- Björn Andréasson
- Hematology Section, Department of Medicine, NU Hospital Group, Uddevalla, Sweden
| | - Helna Pettersson
- Hematology Section, Department of Medicine, NU Hospital Group, Uddevalla, Sweden
| | - Carina Wasslavik
- Department of Clinical Chemistry, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Peter Johansson
- Haematology and Coagulation Section, Department of Medicine, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Lars Palmqvist
- Department of Clinical Chemistry, Sahlgrenska University Hospital, Gothenburg, Sweden.,Department of Laboratory Medicine, Institute of Biomedicine, the Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Julia Asp
- Department of Clinical Chemistry, Sahlgrenska University Hospital, Gothenburg, Sweden.,Department of Laboratory Medicine, Institute of Biomedicine, the Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
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32
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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] [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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33
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Movafagh A, Naji P, Sheikhpour M. Gene mutation of childhood B-acute lymphoblastic leukemia: A systematic review. CLINICAL CANCER INVESTIGATION JOURNAL 2020. [DOI: 10.4103/ccij.ccij_48_20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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34
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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: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [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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35
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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: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [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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36
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Williams LA, Richardson M, Marcotte EL, Poynter JN, Spector LG. Sex ratio among childhood cancers by single year of age. Pediatr Blood Cancer 2019; 66:e27620. [PMID: 30815990 PMCID: PMC6472964 DOI: 10.1002/pbc.27620] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Revised: 12/14/2018] [Accepted: 01/08/2019] [Indexed: 01/06/2023]
Abstract
BACKGROUND The male excess in childhood cancer incidence is well-established; however, the underlying biologic mechanisms remain unknown. Examining the association between male sex and childhood cancer by single year of age and tumor type may highlight important periods of risk such as variation in growth and hormonal changes, which will inform etiologic hypotheses. METHODS Using data from the Surveillance, Epidemiology, and End Results (SEER) 18 registries (2000-2015), incidence rate ratios (IRR) and 95% confidence intervals (95% CI) were estimated as the measure of association between male sex and childhood cancer by single year of age (0-19). RESULTS The IRR for male cancer overall was 1.19 (95% CI, 1.18-1.20) and was similar in magnitude at nearly every year of age. Burkitt lymphoma was strongly associated with male sex (IRRs ≥2 at each year of age). Increased incidence was observed among males for acute lymphoblastic leukemia, Hodgkin and non-Hodgkin lymphomas for nearly all years of age. Medulloblastoma was the only central nervous system tumor with a significant male predominance at nearly every age. Male sex displayed a consistent inverse association with nephroblastoma and thyroid carcinoma over the ages studied. CONCLUSIONS Male sex was positively associated with most cancers. The higher incidence rates observed in males remained consistent over the childhood and adolescent periods, suggesting that childhood and adolescent hormonal fluctuations may not be the primary driving factor for the sex disparities in childhood cancer. The observed incidence disparities may be due to sex differences in exposures, genetics, or immune responses.
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Affiliation(s)
- Lindsay A Williams
- Division of Epidemiology & Clinical Research, Department of Pediatrics, University of Minnesota, Minneapolis, Minnesota
| | - Michaela Richardson
- Division of Epidemiology & Clinical Research, Department of Pediatrics, University of Minnesota, Minneapolis, Minnesota
| | - Erin L. Marcotte
- Division of Epidemiology & Clinical Research, Department of Pediatrics, University of Minnesota, Minneapolis, Minnesota
| | - Jenny N Poynter
- 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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37
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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] [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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38
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Qian M, Xu H, Perez-Andreu V, Roberts KG, Zhang H, Yang W, Zhang S, Zhao X, Smith C, Devidas M, Gastier-Foster JM, Raetz E, Larsen E, Burchard EG, Winick N, Bowman WP, Martin PL, Borowitz M, Wood B, Antillon-Klussmann F, Pui CH, Mullighan CG, Evans WE, Hunger SP, Relling MV, Loh ML, Yang JJ. Novel susceptibility variants at the ERG locus for childhood acute lymphoblastic leukemia in Hispanics. Blood 2019; 133:724-729. [PMID: 30510082 PMCID: PMC6376278 DOI: 10.1182/blood-2018-07-862946] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Accepted: 11/13/2018] [Indexed: 02/05/2023] Open
Abstract
Acute lymphoblastic leukemia (ALL) is the most common malignancy in children. Characterized by high levels of Native American ancestry, Hispanics are disproportionally affected by this cancer with high incidence and inferior survival. However, the genetic basis for this disparity remains poorly understood because of a paucity of genome-wide investigation of ALL in Hispanics. Performing a genome-wide association study (GWAS) in 940 Hispanic children with ALL and 681 ancestry-matched non-ALL controls, we identified a novel susceptibility locus in the ERG gene (rs2836365; P = 3.76 × 10-8; odds ratio [OR] = 1.56), with independent validation (P = .01; OR = 1.43). Imputation analyses pointed to a single causal variant driving the association signal at this locus overlapping with putative regulatory DNA elements. The effect size of the ERG risk variant rose with increasing Native American genetic ancestry. The ERG risk genotype was underrepresented in ALL with the ETV6-RUNX1 fusion (P < .0005) but enriched in the TCF3-PBX1 subtype (P < .05). Interestingly, ALL cases with germline ERG risk alleles were significantly less likely to have somatic ERG deletion (P < .05). Our results provide novel insights into genetic predisposition to ALL and its contribution to racial disparity in this cancer.
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Affiliation(s)
- Maoxiang Qian
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN
- Children's Hospital and
- Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Heng Xu
- Department of Laboratory Medicine, Precision Medicine Center, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
| | - Virginia Perez-Andreu
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN
- Division of Internal Medicine, Graduate Medical Education, MountainView Hospital, University of Nevada, Reno, NV
| | - Kathryn G Roberts
- Department of Pathology, St Jude Children's Research Hospital, Memphis, TN
| | - Hui Zhang
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN
- Department of Pediatric Hematology/Oncology, Guangzhou Women and Children's Medical Center, Guangzhou, Guangdong, China
| | - Wenjian Yang
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN
| | - Shouyue Zhang
- Department of Laboratory Medicine, Precision Medicine Center, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
| | - Xujie Zhao
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN
| | - Colton Smith
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN
| | - Meenakshi Devidas
- Department of Biostatistics, College of Public Health and Health Professions and College of Medicine, University of Florida, Gainesville, FL
| | - Julie M Gastier-Foster
- Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH
- Department of Pathology and
- Department of Pediatrics, The Ohio State University, Columbus, OH
| | - Elizabeth Raetz
- Department of Pediatrics, NYU Langone Medical Center, New York, NY
| | - Eric Larsen
- Maine Children's Cancer Program, Scarborough, ME
| | - Esteban G Burchard
- Department of Bioengineering and Therapeutic Sciences, Schools of Pharmacy and Medicine, University of California San Francisco, San Francisco, CA
| | - Naomi Winick
- Department of Pediatric Hematology Oncology, University of Texas Southwestern Medical Center, Dallas, TX
| | | | - Paul L Martin
- Department of Pediatrics, Duke University, Durham, NC
| | | | - Brent Wood
- Division of Hematopathology, Department of Laboratory Medicine, University of Washington, Seattle, WA
| | | | - Ching-Hon Pui
- Department of Oncology and
- Hematological Malignancies Program, St. Jude Children's Research Hospital, Memphis, TN
| | - Charles G Mullighan
- Department of Pathology, St Jude Children's Research Hospital, Memphis, TN
- Hematological Malignancies Program, St. Jude Children's Research Hospital, Memphis, TN
| | - William E Evans
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN
- Hematological Malignancies Program, St. Jude Children's Research Hospital, Memphis, TN
| | - Stephen P Hunger
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
- Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Mary V Relling
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN
- Hematological Malignancies Program, St. Jude Children's Research Hospital, Memphis, TN
| | - Mignon L Loh
- Department of Pediatrics, Benioff Children's Hospital, San Francisco, CA; and
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA
| | - Jun J Yang
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN
- Department of Oncology and
- Hematological Malignancies Program, St. Jude Children's Research Hospital, Memphis, TN
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39
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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: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [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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40
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Abstract
Treatment outcomes for acute lymphoblastic leukemia (ALL), especially pediatric ALL, have greatly improved due to the risk-adapted therapy. Combination of drug development, clinical practice, as well as basic genetic researches has brought the survival rate of ALL from less than 10% to more than 90% today, not only increasing the treatment efficacy but also limiting adverse drug reactions (ADRs). In this review, we summarized the landscape identification of ALL genetic alterations, which provided the opportunity to increase the survival rate and especially minimize the relapse risk of ALL, and highlighted the importance of the development of new technologies of genomic investigation for translational medicine.
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41
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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] [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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42
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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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43
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Association of the independent polymorphisms in CDKN2A with susceptibility of acute lymphoblastic leukemia. Biosci Rep 2018; 38:BSR20180331. [PMID: 29654170 PMCID: PMC6019384 DOI: 10.1042/bsr20180331] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Revised: 04/04/2018] [Accepted: 04/09/2018] [Indexed: 02/05/2023] Open
Abstract
Acute lymphoblastic leukemia (ALL) is the most common cancer in children, and alterations in CDKN2A were considered to play an important role on leukemogenesis. Two single nucleotide polymorphisms (SNPs) at CDKN2A locus were identified to impact on ALL susceptibility via genome wide association studies, and followed by multiple subsequent replication studies at the specific hits. Here, we conducted a systematic review and meta-analysis to re-evaluate the association of both SNPs (rs3731217 and rs3731249) with ALL susceptibility by gathering the data from 24 independent studies, totally containing 7922 cases/21503 controls for rs3731217 and 6295 cases/24191 controls for rs3731249. Both SNPs were significantly associated with ALL risk (odds ratio [OR] = 0.72 and 2.26 respectively), however, exhibit race-specific pattern. In summary, our meta-analysis indicated that two SNPs at CDKN2A locus are associated with ALL susceptibility independently mainly in Caucasians. Future large-scale studies are required to validate the associations in other ethnicities.
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44
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Pui CH, Yang JJ, Bhakta N, Rodriguez-Galindo C. Global efforts toward the cure of childhood acute lymphoblastic leukaemia. THE LANCET. CHILD & ADOLESCENT HEALTH 2018; 2:440-454. [PMID: 30169285 PMCID: PMC6467529 DOI: 10.1016/s2352-4642(18)30066-x] [Citation(s) in RCA: 73] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Revised: 01/31/2018] [Accepted: 02/13/2018] [Indexed: 12/18/2022]
Abstract
Improvements in risk-directed treatment and supportive care, together with increased reliance on both national and international collaborative studies, have made childhood acute lymphoblastic leukaemia (ALL) one of the most curable human cancers. Next-generation sequencing studies of leukaemia cells and the host germline provide new opportunities for precision medicine and thus potential improvements in the cure rate and quality of life of patients. Efforts are underway to assess the global impact of childhood ALL and develop initiatives that can meet the long-term challenge of providing quality care to children with this disease worldwide and improving cure rates globally. This ambitious task will rely on increased collaborative research and international networking so that the therapeutic gains in high-income countries can be translated to patients in low-income and middle-income countries. Ultimately, the greatest obstacle to overcome will be to fully understand leukaemogenesis, enabling measures to decrease the risk of leukaemia development and thus close the last major gap in offering a cure to any child who might have the disease.
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Affiliation(s)
- Ching-Hon Pui
- Department of Oncology, St Jude Children's Research Hospital, University of Tennessee Health Science Center, Memphis, TN, USA.
| | - Jun J Yang
- Department of Pharmaceutical Science, St Jude Children's Research Hospital, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Nickhill Bhakta
- Department of Global Pediatric Medicine, St Jude Children's Research Hospital, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Carlos Rodriguez-Galindo
- Department of Global Pediatric Medicine, St Jude Children's Research Hospital, University of Tennessee Health Science Center, Memphis, TN, USA
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45
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Derkach A, Zhang H, Chatterjee N. Power Analysis for Genetic Association Test (PAGEANT) provides insights to challenges for rare variant association studies. Bioinformatics 2018; 34:1506-1513. [PMID: 29194474 PMCID: PMC5925788 DOI: 10.1093/bioinformatics/btx770] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Revised: 10/02/2017] [Accepted: 11/27/2017] [Indexed: 12/18/2022] Open
Abstract
Motivation Genome-wide association studies are now shifting focus from analysis of common to rare variants. As power for association testing for individual rare variants may often be low, various aggregate level association tests have been proposed to detect genetic loci. Typically, power calculations for such tests require specification of large number of parameters, including effect sizes and allele frequencies of individual variants, making them difficult to use in practice. We propose to approximate power to a varying degree of accuracy using a smaller number of key parameters, including the total genetic variance explained by multiple variants within a locus. Results We perform extensive simulation studies to assess the accuracy of the proposed approximations in realistic settings. Using these simplified power calculations, we develop an analytic framework to obtain bounds on genetic architecture of an underlying trait given results from genome-wide association studies with rare variants. Finally, we provide insights into the required quality of annotation/functional information for identification of likely causal variants to make meaningful improvement in power. Availability and implementation A shiny application that allows a variety of Power Analysis of GEnetic AssociatioN Tests (PAGEANT), in R is made publicly available at https://andrewhaoyu.shinyapps.io/PAGEANT/. Contact nilanjan@jhu.edu. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Andriy Derkach
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Haoyu Zhang
- Department of Biostatistics, Bloomberg School of Public Health, School of Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Nilanjan Chatterjee
- Department of Biostatistics, Bloomberg School of Public Health, School of Medicine, Johns Hopkins University, Baltimore, MD, USA
- Department of Oncology, School of Medicine, Johns Hopkins University, Baltimore, MD, USA
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46
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Hou Q, Liao F, Zhang S, Zhang D, Zhang Y, Zhou X, Xia X, Ye Y, Yang H, Li Z, Wang L, Wang X, Ma Z, Zhu Y, Ouyang L, Wang Y, Zhang H, Yang L, Xu H, Shu Y. Regulatory network of GATA3 in pediatric acute lymphoblastic leukemia. Oncotarget 2018; 8:36040-36053. [PMID: 28415601 PMCID: PMC5482637 DOI: 10.18632/oncotarget.16424] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Accepted: 03/11/2017] [Indexed: 02/05/2023] Open
Abstract
GATA3 polymorphisms were reported to be significantly associated with susceptibility of pediatric B-lineage acute lymphoblastic leukemia (ALL), by impacting on GATA3 expression. We noticed that ALL-related GATA3 polymorphism located around in the tissue-specific enhancer, and significantly associated with GATA3 expression. Although the regulatory network of GATA3 has been well reported in T cells, the functional status of GATA3 is poorly understood in B-ALL. We thus conducted genome-wide gene expression association analyses to reveal expression associated genes and pathways in nine independent B-ALL patient cohorts. In B-ALL patients, 173 candidates were identified to be significantly associated with GATA3 expression, including some reported GATA3-related genes (e.g., ITM2A) and well-known tumor-related genes (e.g., STAT4). Some of the candidates exhibit tissue-specific and subtype-specific association with GATA3. Through overexpression and down-regulation of GATA3 in leukemia cell lines, several reported and novel GATA3 regulated genes were validated. Moreover, association of GATA3 expression and its targets can be impacted by SNPs (e.g., rs4894953), which locate in the potential GATA3 binding motif. Our findings suggest that GATA3 may be involved in multiple tumor-related pathways (e.g., STAT/JAK pathway) in B-ALL to impact leukemogenesis through epigenetic regulation.
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Affiliation(s)
- 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, Sichuan, 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, Sichuan, China
| | - Shouyue 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, Sichuan, 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, Sichuan, China
| | - Yan Zhang
- Department of Thoracic Oncology, Cancer Center, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, 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, Sichuan, 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, Sichuan, China
| | - Yuanxin Ye
- Department of Laboratory Medicine, Research Center of Clinical Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Hanshuo Yang
- State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, Sichuan, China
| | - Zhaozhi Li
- 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, Sichuan, China
| | - Leiming Wang
- Department of Molecular Biology, Baylor College of Medicine, Houston, Texas, USA
| | - Xi Wang
- Department of Microbiology, Immunology and Molecular Genetics, University of California at Los Angles, Los Angles, California, USA
| | - Zhigui Ma
- Department of Pediatric Hematology/Oncology, West China Second Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Yiping Zhu
- Department of Pediatric Hematology/Oncology, West China Second Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Liang Ouyang
- State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, Sichuan, China
| | - Yuelan Wang
- 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, Sichuan, China
| | - Hui Zhang
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Li Yang
- State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, Sichuan, 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, Sichuan, China.,Department of Laboratory Medicine, Research Center of Clinical Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan, 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, Sichuan, China
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47
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Zhu Y, Yin D, Su Y, Xia X, Moriyama T, Nishii R, Liao F, Zhang S, Guo X, Hou Q, Ai Y, Zhou X, Sun S, Zhang D, Zhang Y, Lin C, Deng Y, Lu X, Wang Y, Ma Z, Wang H, Liu B, Yang L, Zhang W, Yang JJ, Shu Y, Gao J, Xu H. Combination of common and novel rare NUDT15 variants improves predictive sensitivity of thiopurine-induced leukopenia in children with acute lymphoblastic leukemia. Haematologica 2018. [PMID: 29519865 DOI: 10.3324/haematol.2018.187658] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Affiliation(s)
- Yiping Zhu
- Department of Pediatric Hematology/Oncology, West China Second Hospital, 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
| | - Yali Su
- Department of Pediatric Hematology/Oncology, West China Second Hospital, Sichuan University, 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
| | - Takaya Moriyama
- Department of Pharmaceutical Sciences and Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Rina Nishii
- Department of Pharmaceutical Sciences and Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - 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
| | - Shouyue 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
| | - Xia Guo
- Department of Pediatric Hematology/Oncology, West China Second Hospital, Sichuan University, 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
| | - Yuan Ai
- Department of Pediatric Hematology/Oncology, West China Second Hospital, Sichuan University, 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
| | - Shuwen Sun
- Department of Pediatric Hematology/Oncology, West China Second Hospital, Sichuan University, 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
| | - Yan Zhang
- Department of Thoracic Oncology, Cancer Center, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
| | - Chao Lin
- Department of Pediatric Hematology/Oncology, West China Second Hospital, Sichuan University, Chengdu, China
| | - Yiqi 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
| | - Xiaoxi Lu
- Department of Pediatric Hematology/Oncology, West China Second Hospital, Sichuan University, Chengdu, China
| | - Yuelan Wang
- 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
| | - Zhigui Ma
- Department of Pediatric Hematology/Oncology, West China Second Hospital, Sichuan University, Chengdu, China
| | - Heyao Wang
- Department of Precision Medicine, China-Japan Friendship Hospital, Beijing, China
| | - Bo Liu
- State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, China
| | - Li Yang
- State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, China
| | - Wei Zhang
- Department of Clinical Pharmacology, Hunan Key Laboratory of Pharmacogenetics, Xiangya Hospital, Central South University, Changsha, China
| | - Jun J Yang
- Department of Pharmaceutical Sciences and Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - 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
| | - Ju Gao
- Department of Pediatric Hematology/Oncology, West China Second Hospital, Sichuan University, 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
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48
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Wiemels JL, Walsh KM, de Smith AJ, Metayer C, Gonseth S, Hansen HM, Francis SS, Ojha J, Smirnov I, Barcellos L, Xiao X, Morimoto L, McKean-Cowdin R, Wang R, Yu H, Hoh J, DeWan AT, Ma X. GWAS in childhood acute lymphoblastic leukemia reveals novel genetic associations at chromosomes 17q12 and 8q24.21. Nat Commun 2018; 9:286. [PMID: 29348612 PMCID: PMC5773513 DOI: 10.1038/s41467-017-02596-9] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Accepted: 12/13/2017] [Indexed: 01/07/2023] Open
Abstract
Childhood acute lymphoblastic leukemia (ALL) (age 0-14 years) is 20% more common in Latino Americans than non-Latino whites. We conduct a genome-wide association study in a large sample of 3263 Californian children with ALL (including 1949 of Latino heritage) and 3506 controls matched on month and year of birth, sex, and ethnicity, and an additional 12,471 controls from the Kaiser Resource for Genetic Epidemiology Research on Aging Cohort. Replication of the strongest genetic associations is performed in two independent datasets from the Children's Oncology Group and the California Childhood Leukemia Study. Here we identify new risk loci on 17q12 near IKZF3/ZPBP2/GSDMB/ORMDL3, a locus encompassing a transcription factor important for lymphocyte development (IKZF3), and at an 8q24 region known for structural contacts with the MYC oncogene. These new risk loci may impact gene expression via local (four 17q12 genes) or long-range (8q24) interactions, affecting function of well-characterized hematopoietic and growth-regulation pathways.
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Affiliation(s)
- Joseph L Wiemels
- Department of Epidemiology and Biostatistics, University of California San Francisco, 1450 3rd Street, San Francisco, CA, 94158, USA.
- Department of Neurological Surgery, University of California San Francisco, 1450 3rd Street, San Francisco, CA, 94158, USA.
- Institute for Human Genetics, University of California San Francisco, 1450 3rd Street, San Francisco, CA, 94158, USA.
- Department of Preventative Medicine, University of Southern California, SSB 318D 2001 N. Soto Street, Los Angeles, CA, 90033, USA.
| | - Kyle M Walsh
- Department of Epidemiology and Biostatistics, University of California San Francisco, 1450 3rd Street, San Francisco, CA, 94158, USA
- Department of Neurological Surgery, University of California San Francisco, 1450 3rd Street, San Francisco, CA, 94158, USA
| | - Adam J de Smith
- Department of Epidemiology and Biostatistics, University of California San Francisco, 1450 3rd Street, San Francisco, CA, 94158, USA
| | - Catherine Metayer
- School of Public Health, University of California Berkeley, 1950 University Avenue, Suite 460, Berkeley, CA, 94720, USA
| | - Semira Gonseth
- Department of Epidemiology and Biostatistics, University of California San Francisco, 1450 3rd Street, San Francisco, CA, 94158, USA
- Department of Preventative Medicine, University of Southern California, SSB 318D 2001 N. Soto Street, Los Angeles, CA, 90033, USA
| | - Helen M Hansen
- Department of Neurological Surgery, University of California San Francisco, 1450 3rd Street, San Francisco, CA, 94158, USA
| | - Stephen S Francis
- Department of Epidemiology and Biostatistics, University of California San Francisco, 1450 3rd Street, San Francisco, CA, 94158, USA
- Department of Epidemiology, School of Community Health Sciences, University of Nevada Reno, 1664 N. Virginia Street, Reno, NV, 89557, USA
| | - Juhi Ojha
- Department of Epidemiology and Biostatistics, University of California San Francisco, 1450 3rd Street, San Francisco, CA, 94158, USA
| | - Ivan Smirnov
- Department of Neurological Surgery, University of California San Francisco, 1450 3rd Street, San Francisco, CA, 94158, USA
| | - Lisa Barcellos
- School of Public Health, University of California Berkeley, 1950 University Avenue, Suite 460, Berkeley, CA, 94720, USA
| | - Xiaorong Xiao
- School of Public Health, University of California Berkeley, 1950 University Avenue, Suite 460, Berkeley, CA, 94720, USA
| | - Libby Morimoto
- School of Public Health, University of California Berkeley, 1950 University Avenue, Suite 460, Berkeley, CA, 94720, USA
| | - Roberta McKean-Cowdin
- Department of Preventative Medicine, University of Southern California, SSB 318D 2001 N. Soto Street, Los Angeles, CA, 90033, USA
| | - Rong Wang
- Department of Chronic Diseases Epidemiology, School of Public Health, Yale University, 60 College Street, New Haven, CT, 06520, USA
| | - Herbert Yu
- University of Hawaii Cancer Center, 701 Ilalo Street, Honolulu, HI, 96813, USA
| | - Josephine Hoh
- Department of Chronic Diseases Epidemiology, School of Public Health, Yale University, 60 College Street, New Haven, CT, 06520, USA
| | - Andrew T DeWan
- Department of Chronic Diseases Epidemiology, School of Public Health, Yale University, 60 College Street, New Haven, CT, 06520, USA
| | - Xiaomei Ma
- Department of Chronic Diseases Epidemiology, School of Public Health, Yale University, 60 College Street, New Haven, CT, 06520, USA.
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49
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Urayama KY, Takagi M, Kawaguchi T, Matsuo K, Tanaka Y, Ayukawa Y, Arakawa Y, Hasegawa D, Yuza Y, Kaneko T, Noguchi Y, Taneyama Y, Ota S, Inukai T, Yanagimachi M, Keino D, Koike K, Toyama D, Nakazawa Y, Kurosawa H, Nakamura K, Moriwaki K, Goto H, Sekinaka Y, Morita D, Kato M, Takita J, Tanaka T, Inazawa J, Koh K, Ishida Y, Ohara A, Mizutani S, Matsuda F, Manabe A. Regional evaluation of childhood acute lymphoblastic leukemia genetic susceptibility loci among Japanese. Sci Rep 2018; 8:789. [PMID: 29335448 PMCID: PMC5768812 DOI: 10.1038/s41598-017-19127-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Accepted: 12/20/2017] [Indexed: 12/20/2022] Open
Abstract
Genome-wide association studies (GWAS) performed mostly in populations of European and Hispanic ancestry have confirmed an inherited genetic basis for childhood acute lymphoblastic leukemia (ALL), but these associations are less clear in other races/ethnicities. DNA samples from ALL patients (aged 0–19 years) previously enrolled onto a Tokyo Children’s Cancer Study Group trial were collected during 2013–2015, and underwent single nucleotide polymorphism (SNP) microarray genotyping resulting in 527 B-cell ALL for analysis. Cases and control data for 3,882 samples from the Nagahama Study Group and Aichi Cancer Center Study were combined, and association analyses across 10 previous GWAS-identified regions were performed after targeted SNP imputation. Linkage disequilibrium (LD) patterns in Japanese and other populations were evaluated using the varLD score based on 1000 Genomes data. Risk associations for ARID5B (rs10821936, OR = 1.84, P = 6 × 10−17) and PIP4K2A (rs7088318, OR = 0.76, P = 2 × 10−4) directly transferred to Japanese, and the IKZF1 association was detected by an alternate SNP (rs1451367, OR = 1.52, P = 2 × 10−6). Marked regional LD differences between Japanese and Europeans was observed for most of the remaining loci for which associations did not transfer, including CEBPE, CDKN2A, CDKN2B, and ELK3. This study represents a first step towards characterizing the role of genetic susceptibility in childhood ALL risk in Japanese.
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Affiliation(s)
- Kevin Y Urayama
- Department of Social Medicine, National Center for Child Health and Development, Tokyo, Japan. .,Graduate School of Public Health, St. Luke's International University, Tokyo, Japan.
| | - Masatoshi Takagi
- Department of Pediatrics and Developmental Biology, Tokyo Medical and Dental University, Tokyo, Japan
| | - Takahisa Kawaguchi
- Center for Genomic Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Keitaro Matsuo
- Division of Molecular and Clinical Epidemiology, Aichi Cancer Center Research Institute, Aichi, Japan
| | - Yoichi Tanaka
- Department of Clinical Pharmacy, Center for Clinical Pharmacy and Sciences, School of Pharmacy, Kitasato University, Tokyo, Japan
| | - Yoko Ayukawa
- Department of Social Medicine, National Center for Child Health and Development, Tokyo, Japan
| | - Yuki Arakawa
- Department of Hematology/Oncology, Saitama Children's Medical Center, Saitama, Japan
| | - Daisuke Hasegawa
- Department of Pediatrics, St. Luke's International Hospital, Tokyo, Japan
| | - Yuki Yuza
- Department of Hematology/Oncology, Tokyo Metropolitan Children's Medical Center, Tokyo, Japan
| | - Takashi Kaneko
- Department of Hematology/Oncology, Tokyo Metropolitan Children's Medical Center, Tokyo, Japan
| | - Yasushi Noguchi
- Department of Pediatrics, Japanese Red Cross Narita Hospital, Chiba, Japan
| | - Yuichi Taneyama
- Department of Hematology/Oncology, Chiba Children's Hospital, Chiba, Japan
| | - Setsuo Ota
- Department of Pediatrics, Teikyo University Chiba Medical Center, Chiba, Japan
| | - Takeshi Inukai
- Department of Pediatrics, University of Yamanashi, Yamanashi, Japan
| | - Masakatsu Yanagimachi
- Department of Pediatrics and Developmental Biology, Tokyo Medical and Dental University, Tokyo, Japan.,Department of Pediatrics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Dai Keino
- Department of Pediatrics, St. Marianna University School of Medicine, Kawasaki, Japan
| | - Kazutoshi Koike
- Division of Pediatric Hematology and Oncology, Ibaraki Children's Hospital, Mito, Japan
| | - Daisuke Toyama
- Division of Pediatrics, Showa University Fujigaoka Hospital, Yokohama, Japan
| | - Yozo Nakazawa
- Department of Pediatrics, Shinshu University School of Medicine, Matsumoto, Japan
| | | | - Kozue Nakamura
- Department of Pediatrics, Teikyo University Hospital, Tokyo, Japan
| | - Koichi Moriwaki
- Department of Pediatrics, Saitama Medical Center, Saitama Medical University, Saitama, Japan
| | - Hiroaki Goto
- Division of Hematology/Oncology & Regenerative Medicine, Kanagawa Children's Medical Center, Yokohama, Japan
| | - Yujin Sekinaka
- Department of Pediatrics, National Defense Medical College, Saitama, Japan
| | - Daisuke Morita
- Department of Pediatrics, Shinshu University School of Medicine, Matsumoto, Japan
| | - Motohiro Kato
- Children's Cancer Center, National Center for Child Health and Development, Tokyo, Japan
| | - Junko Takita
- Department of Pediatrics, The University of Tokyo Hospital, Tokyo, Japan
| | - Toshihiro Tanaka
- Department of Human Genetics and Disease Diversity, Tokyo Medical Dental University, Tokyo, Japan.,Bioresource Research Center, Tokyo Medical and Dental University, Tokyo, Japan
| | - Johji Inazawa
- Bioresource Research Center, Tokyo Medical and Dental University, Tokyo, Japan
| | - Katsuyoshi Koh
- Department of Hematology/Oncology, Saitama Children's Medical Center, Saitama, Japan
| | - Yasushi Ishida
- Pediatric Medical Center, Ehime Prefectural Central Hospital, Matsuyama, Japan
| | - Akira Ohara
- Department of Pediatrics, Toho University, Tokyo, Japan
| | - Shuki Mizutani
- Department of Pediatrics and Developmental Biology, Tokyo Medical and Dental University, Tokyo, Japan
| | - Fumihiko Matsuda
- Center for Genomic Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Atsushi Manabe
- Department of Pediatrics, St. Luke's International Hospital, Tokyo, Japan
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Qian M, Cao X, Devidas M, Yang W, Cheng C, Dai Y, Carroll A, Heerema NA, Zhang H, Moriyama T, Gastier-Foster JM, Xu H, Raetz E, Larsen E, Winick N, Bowman WP, Martin PL, Mardis ER, Fulton R, Zambetti G, Borowitz M, Wood B, Nichols KE, Carroll WL, Pui CH, Mullighan CG, Evans WE, Hunger SP, Relling MV, Loh ML, Yang JJ. TP53 Germline Variations Influence the Predisposition and Prognosis of B-Cell Acute Lymphoblastic Leukemia in Children. J Clin Oncol 2018; 36:591-599. [PMID: 29300620 DOI: 10.1200/jco.2017.75.5215] [Citation(s) in RCA: 104] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Purpose Germline TP53 variation is the genetic basis of Li-Fraumeni syndrome, a highly penetrant cancer predisposition condition. Recent reports of germline TP53 variants in childhood hypodiploid acute lymphoblastic leukemia (ALL) suggest that this type of leukemia is another manifestation of Li-Fraumeni syndrome; however, the pattern, prevalence, and clinical relevance of TP53 variants in childhood ALL remain unknown. Patients and Methods Targeted sequencing of TP53 coding regions was performed in 3,801 children from the Children's Oncology Group frontline ALL clinical trials, AALL0232 and P9900. TP53 variant pathogenicity was evaluated according to experimentally determined transcriptional activity, in silico prediction of damaging effects, and prevalence in non-ALL control populations. TP53 variants were analyzed for their association with ALL presenting features and treatment outcomes. Results We identified 49 unique nonsilent rare TP53 coding variants in 77 (2.0%) of 3,801 patients sequenced, of which 22 variants were classified as pathogenic. TP53 pathogenic variants were significantly over-represented in ALL compared with non-ALL controls (odds ratio, 5.2; P < .001). Children with TP53 pathogenic variants were significantly older at ALL diagnosis (median age, 15.5 years v 7.3 years; P < .001) and were more likely to have hypodiploid ALL (65.4% v 1.2%; P < .001). Carrying germline TP53 pathogenic variants was associated with inferior event-free survival and overall survival (hazard ratio, 4.2 and 3.9; P < .001 and .001, respectively). In particular, children with TP53 pathogenic variants were at a dramatically higher risk of second cancers than those without pathogenic variants, with 5-year cumulative incidence of 25.1% and 0.7% ( P < .001), respectively. Conclusion Loss-of-function germline TP53 variants predispose children to ALL and to adverse treatment outcomes with ALL therapy, particularly the risk of second malignant neoplasms.
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Affiliation(s)
- Maoxiang Qian
- Maoxiang Qian, Xueyuan Cao, Wenjian Yang, Cheng Cheng, Hui Zhang, Takaya Moriyama, Gerard Zambetti, Kim E. Nichols, Ching-Hon Pui, Charles G. Mullighan, William E. Evans, Mary V. Relling, and Jun J. Yang, St Jude Children's Research Hospital, Memphis, TN; Meenakshi Devidas and Yunfeng Dai, University of Florida, Gainesville, FL; Andrew Carroll, University of Alabama at Birmingham, Birmingham, AL; Nyla A. Heerema and Julie M. Gastier-Foster, The Ohio State University and Wexner Medical Center; Julie M. Gastier-Foster and Elaine R. Mardis, Nationwide Children's Hospital, Columbus, OH; Hui Zhang, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong; Heng Xu, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, China; Elizabeth Raetz, University of Utah, Salt Lake City, UT; Eric Larsen, Maine Children's Cancer Program, Scarborough, ME; Naomi Winick, University of Texas Southwestern Medical Center, Dallas; W. Paul Bowman, Cook Children's Medical Center, Fort Worth, TX; Paul L. Martin, Duke University, Durham, NC; Robert Fulton, Washington University School of Medicine, St Louis, MO; Michael Borowitz, Johns Hopkins Medical Institute, Baltimore, MD; Brent Wood, University of Washington, Seattle, WA; William L. Carroll, New York University, New York, NY; Stephen P. Hunger, Children's Hospital of Philadelphia and University of Pennsylvania, Philadelphia, PA; and Mignon L. Loh, Benioff Children's Hospital and University of California, San Francisco, San Francisco, CA
| | - Xueyuan Cao
- Maoxiang Qian, Xueyuan Cao, Wenjian Yang, Cheng Cheng, Hui Zhang, Takaya Moriyama, Gerard Zambetti, Kim E. Nichols, Ching-Hon Pui, Charles G. Mullighan, William E. Evans, Mary V. Relling, and Jun J. Yang, St Jude Children's Research Hospital, Memphis, TN; Meenakshi Devidas and Yunfeng Dai, University of Florida, Gainesville, FL; Andrew Carroll, University of Alabama at Birmingham, Birmingham, AL; Nyla A. Heerema and Julie M. Gastier-Foster, The Ohio State University and Wexner Medical Center; Julie M. Gastier-Foster and Elaine R. Mardis, Nationwide Children's Hospital, Columbus, OH; Hui Zhang, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong; Heng Xu, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, China; Elizabeth Raetz, University of Utah, Salt Lake City, UT; Eric Larsen, Maine Children's Cancer Program, Scarborough, ME; Naomi Winick, University of Texas Southwestern Medical Center, Dallas; W. Paul Bowman, Cook Children's Medical Center, Fort Worth, TX; Paul L. Martin, Duke University, Durham, NC; Robert Fulton, Washington University School of Medicine, St Louis, MO; Michael Borowitz, Johns Hopkins Medical Institute, Baltimore, MD; Brent Wood, University of Washington, Seattle, WA; William L. Carroll, New York University, New York, NY; Stephen P. Hunger, Children's Hospital of Philadelphia and University of Pennsylvania, Philadelphia, PA; and Mignon L. Loh, Benioff Children's Hospital and University of California, San Francisco, San Francisco, CA
| | - Meenakshi Devidas
- Maoxiang Qian, Xueyuan Cao, Wenjian Yang, Cheng Cheng, Hui Zhang, Takaya Moriyama, Gerard Zambetti, Kim E. Nichols, Ching-Hon Pui, Charles G. Mullighan, William E. Evans, Mary V. Relling, and Jun J. Yang, St Jude Children's Research Hospital, Memphis, TN; Meenakshi Devidas and Yunfeng Dai, University of Florida, Gainesville, FL; Andrew Carroll, University of Alabama at Birmingham, Birmingham, AL; Nyla A. Heerema and Julie M. Gastier-Foster, The Ohio State University and Wexner Medical Center; Julie M. Gastier-Foster and Elaine R. Mardis, Nationwide Children's Hospital, Columbus, OH; Hui Zhang, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong; Heng Xu, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, China; Elizabeth Raetz, University of Utah, Salt Lake City, UT; Eric Larsen, Maine Children's Cancer Program, Scarborough, ME; Naomi Winick, University of Texas Southwestern Medical Center, Dallas; W. Paul Bowman, Cook Children's Medical Center, Fort Worth, TX; Paul L. Martin, Duke University, Durham, NC; Robert Fulton, Washington University School of Medicine, St Louis, MO; Michael Borowitz, Johns Hopkins Medical Institute, Baltimore, MD; Brent Wood, University of Washington, Seattle, WA; William L. Carroll, New York University, New York, NY; Stephen P. Hunger, Children's Hospital of Philadelphia and University of Pennsylvania, Philadelphia, PA; and Mignon L. Loh, Benioff Children's Hospital and University of California, San Francisco, San Francisco, CA
| | - Wenjian Yang
- Maoxiang Qian, Xueyuan Cao, Wenjian Yang, Cheng Cheng, Hui Zhang, Takaya Moriyama, Gerard Zambetti, Kim E. Nichols, Ching-Hon Pui, Charles G. Mullighan, William E. Evans, Mary V. Relling, and Jun J. Yang, St Jude Children's Research Hospital, Memphis, TN; Meenakshi Devidas and Yunfeng Dai, University of Florida, Gainesville, FL; Andrew Carroll, University of Alabama at Birmingham, Birmingham, AL; Nyla A. Heerema and Julie M. Gastier-Foster, The Ohio State University and Wexner Medical Center; Julie M. Gastier-Foster and Elaine R. Mardis, Nationwide Children's Hospital, Columbus, OH; Hui Zhang, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong; Heng Xu, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, China; Elizabeth Raetz, University of Utah, Salt Lake City, UT; Eric Larsen, Maine Children's Cancer Program, Scarborough, ME; Naomi Winick, University of Texas Southwestern Medical Center, Dallas; W. Paul Bowman, Cook Children's Medical Center, Fort Worth, TX; Paul L. Martin, Duke University, Durham, NC; Robert Fulton, Washington University School of Medicine, St Louis, MO; Michael Borowitz, Johns Hopkins Medical Institute, Baltimore, MD; Brent Wood, University of Washington, Seattle, WA; William L. Carroll, New York University, New York, NY; Stephen P. Hunger, Children's Hospital of Philadelphia and University of Pennsylvania, Philadelphia, PA; and Mignon L. Loh, Benioff Children's Hospital and University of California, San Francisco, San Francisco, CA
| | - Cheng Cheng
- Maoxiang Qian, Xueyuan Cao, Wenjian Yang, Cheng Cheng, Hui Zhang, Takaya Moriyama, Gerard Zambetti, Kim E. Nichols, Ching-Hon Pui, Charles G. Mullighan, William E. Evans, Mary V. Relling, and Jun J. Yang, St Jude Children's Research Hospital, Memphis, TN; Meenakshi Devidas and Yunfeng Dai, University of Florida, Gainesville, FL; Andrew Carroll, University of Alabama at Birmingham, Birmingham, AL; Nyla A. Heerema and Julie M. Gastier-Foster, The Ohio State University and Wexner Medical Center; Julie M. Gastier-Foster and Elaine R. Mardis, Nationwide Children's Hospital, Columbus, OH; Hui Zhang, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong; Heng Xu, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, China; Elizabeth Raetz, University of Utah, Salt Lake City, UT; Eric Larsen, Maine Children's Cancer Program, Scarborough, ME; Naomi Winick, University of Texas Southwestern Medical Center, Dallas; W. Paul Bowman, Cook Children's Medical Center, Fort Worth, TX; Paul L. Martin, Duke University, Durham, NC; Robert Fulton, Washington University School of Medicine, St Louis, MO; Michael Borowitz, Johns Hopkins Medical Institute, Baltimore, MD; Brent Wood, University of Washington, Seattle, WA; William L. Carroll, New York University, New York, NY; Stephen P. Hunger, Children's Hospital of Philadelphia and University of Pennsylvania, Philadelphia, PA; and Mignon L. Loh, Benioff Children's Hospital and University of California, San Francisco, San Francisco, CA
| | - Yunfeng Dai
- Maoxiang Qian, Xueyuan Cao, Wenjian Yang, Cheng Cheng, Hui Zhang, Takaya Moriyama, Gerard Zambetti, Kim E. Nichols, Ching-Hon Pui, Charles G. Mullighan, William E. Evans, Mary V. Relling, and Jun J. Yang, St Jude Children's Research Hospital, Memphis, TN; Meenakshi Devidas and Yunfeng Dai, University of Florida, Gainesville, FL; Andrew Carroll, University of Alabama at Birmingham, Birmingham, AL; Nyla A. Heerema and Julie M. Gastier-Foster, The Ohio State University and Wexner Medical Center; Julie M. Gastier-Foster and Elaine R. Mardis, Nationwide Children's Hospital, Columbus, OH; Hui Zhang, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong; Heng Xu, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, China; Elizabeth Raetz, University of Utah, Salt Lake City, UT; Eric Larsen, Maine Children's Cancer Program, Scarborough, ME; Naomi Winick, University of Texas Southwestern Medical Center, Dallas; W. Paul Bowman, Cook Children's Medical Center, Fort Worth, TX; Paul L. Martin, Duke University, Durham, NC; Robert Fulton, Washington University School of Medicine, St Louis, MO; Michael Borowitz, Johns Hopkins Medical Institute, Baltimore, MD; Brent Wood, University of Washington, Seattle, WA; William L. Carroll, New York University, New York, NY; Stephen P. Hunger, Children's Hospital of Philadelphia and University of Pennsylvania, Philadelphia, PA; and Mignon L. Loh, Benioff Children's Hospital and University of California, San Francisco, San Francisco, CA
| | - Andrew Carroll
- Maoxiang Qian, Xueyuan Cao, Wenjian Yang, Cheng Cheng, Hui Zhang, Takaya Moriyama, Gerard Zambetti, Kim E. Nichols, Ching-Hon Pui, Charles G. Mullighan, William E. Evans, Mary V. Relling, and Jun J. Yang, St Jude Children's Research Hospital, Memphis, TN; Meenakshi Devidas and Yunfeng Dai, University of Florida, Gainesville, FL; Andrew Carroll, University of Alabama at Birmingham, Birmingham, AL; Nyla A. Heerema and Julie M. Gastier-Foster, The Ohio State University and Wexner Medical Center; Julie M. Gastier-Foster and Elaine R. Mardis, Nationwide Children's Hospital, Columbus, OH; Hui Zhang, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong; Heng Xu, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, China; Elizabeth Raetz, University of Utah, Salt Lake City, UT; Eric Larsen, Maine Children's Cancer Program, Scarborough, ME; Naomi Winick, University of Texas Southwestern Medical Center, Dallas; W. Paul Bowman, Cook Children's Medical Center, Fort Worth, TX; Paul L. Martin, Duke University, Durham, NC; Robert Fulton, Washington University School of Medicine, St Louis, MO; Michael Borowitz, Johns Hopkins Medical Institute, Baltimore, MD; Brent Wood, University of Washington, Seattle, WA; William L. Carroll, New York University, New York, NY; Stephen P. Hunger, Children's Hospital of Philadelphia and University of Pennsylvania, Philadelphia, PA; and Mignon L. Loh, Benioff Children's Hospital and University of California, San Francisco, San Francisco, CA
| | - Nyla A Heerema
- Maoxiang Qian, Xueyuan Cao, Wenjian Yang, Cheng Cheng, Hui Zhang, Takaya Moriyama, Gerard Zambetti, Kim E. Nichols, Ching-Hon Pui, Charles G. Mullighan, William E. Evans, Mary V. Relling, and Jun J. Yang, St Jude Children's Research Hospital, Memphis, TN; Meenakshi Devidas and Yunfeng Dai, University of Florida, Gainesville, FL; Andrew Carroll, University of Alabama at Birmingham, Birmingham, AL; Nyla A. Heerema and Julie M. Gastier-Foster, The Ohio State University and Wexner Medical Center; Julie M. Gastier-Foster and Elaine R. Mardis, Nationwide Children's Hospital, Columbus, OH; Hui Zhang, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong; Heng Xu, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, China; Elizabeth Raetz, University of Utah, Salt Lake City, UT; Eric Larsen, Maine Children's Cancer Program, Scarborough, ME; Naomi Winick, University of Texas Southwestern Medical Center, Dallas; W. Paul Bowman, Cook Children's Medical Center, Fort Worth, TX; Paul L. Martin, Duke University, Durham, NC; Robert Fulton, Washington University School of Medicine, St Louis, MO; Michael Borowitz, Johns Hopkins Medical Institute, Baltimore, MD; Brent Wood, University of Washington, Seattle, WA; William L. Carroll, New York University, New York, NY; Stephen P. Hunger, Children's Hospital of Philadelphia and University of Pennsylvania, Philadelphia, PA; and Mignon L. Loh, Benioff Children's Hospital and University of California, San Francisco, San Francisco, CA
| | - Hui Zhang
- Maoxiang Qian, Xueyuan Cao, Wenjian Yang, Cheng Cheng, Hui Zhang, Takaya Moriyama, Gerard Zambetti, Kim E. Nichols, Ching-Hon Pui, Charles G. Mullighan, William E. Evans, Mary V. Relling, and Jun J. Yang, St Jude Children's Research Hospital, Memphis, TN; Meenakshi Devidas and Yunfeng Dai, University of Florida, Gainesville, FL; Andrew Carroll, University of Alabama at Birmingham, Birmingham, AL; Nyla A. Heerema and Julie M. Gastier-Foster, The Ohio State University and Wexner Medical Center; Julie M. Gastier-Foster and Elaine R. Mardis, Nationwide Children's Hospital, Columbus, OH; Hui Zhang, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong; Heng Xu, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, China; Elizabeth Raetz, University of Utah, Salt Lake City, UT; Eric Larsen, Maine Children's Cancer Program, Scarborough, ME; Naomi Winick, University of Texas Southwestern Medical Center, Dallas; W. Paul Bowman, Cook Children's Medical Center, Fort Worth, TX; Paul L. Martin, Duke University, Durham, NC; Robert Fulton, Washington University School of Medicine, St Louis, MO; Michael Borowitz, Johns Hopkins Medical Institute, Baltimore, MD; Brent Wood, University of Washington, Seattle, WA; William L. Carroll, New York University, New York, NY; Stephen P. Hunger, Children's Hospital of Philadelphia and University of Pennsylvania, Philadelphia, PA; and Mignon L. Loh, Benioff Children's Hospital and University of California, San Francisco, San Francisco, CA
| | - Takaya Moriyama
- Maoxiang Qian, Xueyuan Cao, Wenjian Yang, Cheng Cheng, Hui Zhang, Takaya Moriyama, Gerard Zambetti, Kim E. Nichols, Ching-Hon Pui, Charles G. Mullighan, William E. Evans, Mary V. Relling, and Jun J. Yang, St Jude Children's Research Hospital, Memphis, TN; Meenakshi Devidas and Yunfeng Dai, University of Florida, Gainesville, FL; Andrew Carroll, University of Alabama at Birmingham, Birmingham, AL; Nyla A. Heerema and Julie M. Gastier-Foster, The Ohio State University and Wexner Medical Center; Julie M. Gastier-Foster and Elaine R. Mardis, Nationwide Children's Hospital, Columbus, OH; Hui Zhang, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong; Heng Xu, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, China; Elizabeth Raetz, University of Utah, Salt Lake City, UT; Eric Larsen, Maine Children's Cancer Program, Scarborough, ME; Naomi Winick, University of Texas Southwestern Medical Center, Dallas; W. Paul Bowman, Cook Children's Medical Center, Fort Worth, TX; Paul L. Martin, Duke University, Durham, NC; Robert Fulton, Washington University School of Medicine, St Louis, MO; Michael Borowitz, Johns Hopkins Medical Institute, Baltimore, MD; Brent Wood, University of Washington, Seattle, WA; William L. Carroll, New York University, New York, NY; Stephen P. Hunger, Children's Hospital of Philadelphia and University of Pennsylvania, Philadelphia, PA; and Mignon L. Loh, Benioff Children's Hospital and University of California, San Francisco, San Francisco, CA
| | - Julie M Gastier-Foster
- Maoxiang Qian, Xueyuan Cao, Wenjian Yang, Cheng Cheng, Hui Zhang, Takaya Moriyama, Gerard Zambetti, Kim E. Nichols, Ching-Hon Pui, Charles G. Mullighan, William E. Evans, Mary V. Relling, and Jun J. Yang, St Jude Children's Research Hospital, Memphis, TN; Meenakshi Devidas and Yunfeng Dai, University of Florida, Gainesville, FL; Andrew Carroll, University of Alabama at Birmingham, Birmingham, AL; Nyla A. Heerema and Julie M. Gastier-Foster, The Ohio State University and Wexner Medical Center; Julie M. Gastier-Foster and Elaine R. Mardis, Nationwide Children's Hospital, Columbus, OH; Hui Zhang, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong; Heng Xu, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, China; Elizabeth Raetz, University of Utah, Salt Lake City, UT; Eric Larsen, Maine Children's Cancer Program, Scarborough, ME; Naomi Winick, University of Texas Southwestern Medical Center, Dallas; W. Paul Bowman, Cook Children's Medical Center, Fort Worth, TX; Paul L. Martin, Duke University, Durham, NC; Robert Fulton, Washington University School of Medicine, St Louis, MO; Michael Borowitz, Johns Hopkins Medical Institute, Baltimore, MD; Brent Wood, University of Washington, Seattle, WA; William L. Carroll, New York University, New York, NY; Stephen P. Hunger, Children's Hospital of Philadelphia and University of Pennsylvania, Philadelphia, PA; and Mignon L. Loh, Benioff Children's Hospital and University of California, San Francisco, San Francisco, CA
| | - Heng Xu
- Maoxiang Qian, Xueyuan Cao, Wenjian Yang, Cheng Cheng, Hui Zhang, Takaya Moriyama, Gerard Zambetti, Kim E. Nichols, Ching-Hon Pui, Charles G. Mullighan, William E. Evans, Mary V. Relling, and Jun J. Yang, St Jude Children's Research Hospital, Memphis, TN; Meenakshi Devidas and Yunfeng Dai, University of Florida, Gainesville, FL; Andrew Carroll, University of Alabama at Birmingham, Birmingham, AL; Nyla A. Heerema and Julie M. Gastier-Foster, The Ohio State University and Wexner Medical Center; Julie M. Gastier-Foster and Elaine R. Mardis, Nationwide Children's Hospital, Columbus, OH; Hui Zhang, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong; Heng Xu, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, China; Elizabeth Raetz, University of Utah, Salt Lake City, UT; Eric Larsen, Maine Children's Cancer Program, Scarborough, ME; Naomi Winick, University of Texas Southwestern Medical Center, Dallas; W. Paul Bowman, Cook Children's Medical Center, Fort Worth, TX; Paul L. Martin, Duke University, Durham, NC; Robert Fulton, Washington University School of Medicine, St Louis, MO; Michael Borowitz, Johns Hopkins Medical Institute, Baltimore, MD; Brent Wood, University of Washington, Seattle, WA; William L. Carroll, New York University, New York, NY; Stephen P. Hunger, Children's Hospital of Philadelphia and University of Pennsylvania, Philadelphia, PA; and Mignon L. Loh, Benioff Children's Hospital and University of California, San Francisco, San Francisco, CA
| | - Elizabeth Raetz
- Maoxiang Qian, Xueyuan Cao, Wenjian Yang, Cheng Cheng, Hui Zhang, Takaya Moriyama, Gerard Zambetti, Kim E. Nichols, Ching-Hon Pui, Charles G. Mullighan, William E. Evans, Mary V. Relling, and Jun J. Yang, St Jude Children's Research Hospital, Memphis, TN; Meenakshi Devidas and Yunfeng Dai, University of Florida, Gainesville, FL; Andrew Carroll, University of Alabama at Birmingham, Birmingham, AL; Nyla A. Heerema and Julie M. Gastier-Foster, The Ohio State University and Wexner Medical Center; Julie M. Gastier-Foster and Elaine R. Mardis, Nationwide Children's Hospital, Columbus, OH; Hui Zhang, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong; Heng Xu, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, China; Elizabeth Raetz, University of Utah, Salt Lake City, UT; Eric Larsen, Maine Children's Cancer Program, Scarborough, ME; Naomi Winick, University of Texas Southwestern Medical Center, Dallas; W. Paul Bowman, Cook Children's Medical Center, Fort Worth, TX; Paul L. Martin, Duke University, Durham, NC; Robert Fulton, Washington University School of Medicine, St Louis, MO; Michael Borowitz, Johns Hopkins Medical Institute, Baltimore, MD; Brent Wood, University of Washington, Seattle, WA; William L. Carroll, New York University, New York, NY; Stephen P. Hunger, Children's Hospital of Philadelphia and University of Pennsylvania, Philadelphia, PA; and Mignon L. Loh, Benioff Children's Hospital and University of California, San Francisco, San Francisco, CA
| | - Eric Larsen
- Maoxiang Qian, Xueyuan Cao, Wenjian Yang, Cheng Cheng, Hui Zhang, Takaya Moriyama, Gerard Zambetti, Kim E. Nichols, Ching-Hon Pui, Charles G. Mullighan, William E. Evans, Mary V. Relling, and Jun J. Yang, St Jude Children's Research Hospital, Memphis, TN; Meenakshi Devidas and Yunfeng Dai, University of Florida, Gainesville, FL; Andrew Carroll, University of Alabama at Birmingham, Birmingham, AL; Nyla A. Heerema and Julie M. Gastier-Foster, The Ohio State University and Wexner Medical Center; Julie M. Gastier-Foster and Elaine R. Mardis, Nationwide Children's Hospital, Columbus, OH; Hui Zhang, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong; Heng Xu, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, China; Elizabeth Raetz, University of Utah, Salt Lake City, UT; Eric Larsen, Maine Children's Cancer Program, Scarborough, ME; Naomi Winick, University of Texas Southwestern Medical Center, Dallas; W. Paul Bowman, Cook Children's Medical Center, Fort Worth, TX; Paul L. Martin, Duke University, Durham, NC; Robert Fulton, Washington University School of Medicine, St Louis, MO; Michael Borowitz, Johns Hopkins Medical Institute, Baltimore, MD; Brent Wood, University of Washington, Seattle, WA; William L. Carroll, New York University, New York, NY; Stephen P. Hunger, Children's Hospital of Philadelphia and University of Pennsylvania, Philadelphia, PA; and Mignon L. Loh, Benioff Children's Hospital and University of California, San Francisco, San Francisco, CA
| | - Naomi Winick
- Maoxiang Qian, Xueyuan Cao, Wenjian Yang, Cheng Cheng, Hui Zhang, Takaya Moriyama, Gerard Zambetti, Kim E. Nichols, Ching-Hon Pui, Charles G. Mullighan, William E. Evans, Mary V. Relling, and Jun J. Yang, St Jude Children's Research Hospital, Memphis, TN; Meenakshi Devidas and Yunfeng Dai, University of Florida, Gainesville, FL; Andrew Carroll, University of Alabama at Birmingham, Birmingham, AL; Nyla A. Heerema and Julie M. Gastier-Foster, The Ohio State University and Wexner Medical Center; Julie M. Gastier-Foster and Elaine R. Mardis, Nationwide Children's Hospital, Columbus, OH; Hui Zhang, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong; Heng Xu, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, China; Elizabeth Raetz, University of Utah, Salt Lake City, UT; Eric Larsen, Maine Children's Cancer Program, Scarborough, ME; Naomi Winick, University of Texas Southwestern Medical Center, Dallas; W. Paul Bowman, Cook Children's Medical Center, Fort Worth, TX; Paul L. Martin, Duke University, Durham, NC; Robert Fulton, Washington University School of Medicine, St Louis, MO; Michael Borowitz, Johns Hopkins Medical Institute, Baltimore, MD; Brent Wood, University of Washington, Seattle, WA; William L. Carroll, New York University, New York, NY; Stephen P. Hunger, Children's Hospital of Philadelphia and University of Pennsylvania, Philadelphia, PA; and Mignon L. Loh, Benioff Children's Hospital and University of California, San Francisco, San Francisco, CA
| | - W Paul Bowman
- Maoxiang Qian, Xueyuan Cao, Wenjian Yang, Cheng Cheng, Hui Zhang, Takaya Moriyama, Gerard Zambetti, Kim E. Nichols, Ching-Hon Pui, Charles G. Mullighan, William E. Evans, Mary V. Relling, and Jun J. Yang, St Jude Children's Research Hospital, Memphis, TN; Meenakshi Devidas and Yunfeng Dai, University of Florida, Gainesville, FL; Andrew Carroll, University of Alabama at Birmingham, Birmingham, AL; Nyla A. Heerema and Julie M. Gastier-Foster, The Ohio State University and Wexner Medical Center; Julie M. Gastier-Foster and Elaine R. Mardis, Nationwide Children's Hospital, Columbus, OH; Hui Zhang, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong; Heng Xu, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, China; Elizabeth Raetz, University of Utah, Salt Lake City, UT; Eric Larsen, Maine Children's Cancer Program, Scarborough, ME; Naomi Winick, University of Texas Southwestern Medical Center, Dallas; W. Paul Bowman, Cook Children's Medical Center, Fort Worth, TX; Paul L. Martin, Duke University, Durham, NC; Robert Fulton, Washington University School of Medicine, St Louis, MO; Michael Borowitz, Johns Hopkins Medical Institute, Baltimore, MD; Brent Wood, University of Washington, Seattle, WA; William L. Carroll, New York University, New York, NY; Stephen P. Hunger, Children's Hospital of Philadelphia and University of Pennsylvania, Philadelphia, PA; and Mignon L. Loh, Benioff Children's Hospital and University of California, San Francisco, San Francisco, CA
| | - Paul L Martin
- Maoxiang Qian, Xueyuan Cao, Wenjian Yang, Cheng Cheng, Hui Zhang, Takaya Moriyama, Gerard Zambetti, Kim E. Nichols, Ching-Hon Pui, Charles G. Mullighan, William E. Evans, Mary V. Relling, and Jun J. Yang, St Jude Children's Research Hospital, Memphis, TN; Meenakshi Devidas and Yunfeng Dai, University of Florida, Gainesville, FL; Andrew Carroll, University of Alabama at Birmingham, Birmingham, AL; Nyla A. Heerema and Julie M. Gastier-Foster, The Ohio State University and Wexner Medical Center; Julie M. Gastier-Foster and Elaine R. Mardis, Nationwide Children's Hospital, Columbus, OH; Hui Zhang, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong; Heng Xu, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, China; Elizabeth Raetz, University of Utah, Salt Lake City, UT; Eric Larsen, Maine Children's Cancer Program, Scarborough, ME; Naomi Winick, University of Texas Southwestern Medical Center, Dallas; W. Paul Bowman, Cook Children's Medical Center, Fort Worth, TX; Paul L. Martin, Duke University, Durham, NC; Robert Fulton, Washington University School of Medicine, St Louis, MO; Michael Borowitz, Johns Hopkins Medical Institute, Baltimore, MD; Brent Wood, University of Washington, Seattle, WA; William L. Carroll, New York University, New York, NY; Stephen P. Hunger, Children's Hospital of Philadelphia and University of Pennsylvania, Philadelphia, PA; and Mignon L. Loh, Benioff Children's Hospital and University of California, San Francisco, San Francisco, CA
| | - Elaine R Mardis
- Maoxiang Qian, Xueyuan Cao, Wenjian Yang, Cheng Cheng, Hui Zhang, Takaya Moriyama, Gerard Zambetti, Kim E. Nichols, Ching-Hon Pui, Charles G. Mullighan, William E. Evans, Mary V. Relling, and Jun J. Yang, St Jude Children's Research Hospital, Memphis, TN; Meenakshi Devidas and Yunfeng Dai, University of Florida, Gainesville, FL; Andrew Carroll, University of Alabama at Birmingham, Birmingham, AL; Nyla A. Heerema and Julie M. Gastier-Foster, The Ohio State University and Wexner Medical Center; Julie M. Gastier-Foster and Elaine R. Mardis, Nationwide Children's Hospital, Columbus, OH; Hui Zhang, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong; Heng Xu, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, China; Elizabeth Raetz, University of Utah, Salt Lake City, UT; Eric Larsen, Maine Children's Cancer Program, Scarborough, ME; Naomi Winick, University of Texas Southwestern Medical Center, Dallas; W. Paul Bowman, Cook Children's Medical Center, Fort Worth, TX; Paul L. Martin, Duke University, Durham, NC; Robert Fulton, Washington University School of Medicine, St Louis, MO; Michael Borowitz, Johns Hopkins Medical Institute, Baltimore, MD; Brent Wood, University of Washington, Seattle, WA; William L. Carroll, New York University, New York, NY; Stephen P. Hunger, Children's Hospital of Philadelphia and University of Pennsylvania, Philadelphia, PA; and Mignon L. Loh, Benioff Children's Hospital and University of California, San Francisco, San Francisco, CA
| | - Robert Fulton
- Maoxiang Qian, Xueyuan Cao, Wenjian Yang, Cheng Cheng, Hui Zhang, Takaya Moriyama, Gerard Zambetti, Kim E. Nichols, Ching-Hon Pui, Charles G. Mullighan, William E. Evans, Mary V. Relling, and Jun J. Yang, St Jude Children's Research Hospital, Memphis, TN; Meenakshi Devidas and Yunfeng Dai, University of Florida, Gainesville, FL; Andrew Carroll, University of Alabama at Birmingham, Birmingham, AL; Nyla A. Heerema and Julie M. Gastier-Foster, The Ohio State University and Wexner Medical Center; Julie M. Gastier-Foster and Elaine R. Mardis, Nationwide Children's Hospital, Columbus, OH; Hui Zhang, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong; Heng Xu, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, China; Elizabeth Raetz, University of Utah, Salt Lake City, UT; Eric Larsen, Maine Children's Cancer Program, Scarborough, ME; Naomi Winick, University of Texas Southwestern Medical Center, Dallas; W. Paul Bowman, Cook Children's Medical Center, Fort Worth, TX; Paul L. Martin, Duke University, Durham, NC; Robert Fulton, Washington University School of Medicine, St Louis, MO; Michael Borowitz, Johns Hopkins Medical Institute, Baltimore, MD; Brent Wood, University of Washington, Seattle, WA; William L. Carroll, New York University, New York, NY; Stephen P. Hunger, Children's Hospital of Philadelphia and University of Pennsylvania, Philadelphia, PA; and Mignon L. Loh, Benioff Children's Hospital and University of California, San Francisco, San Francisco, CA
| | - Gerard Zambetti
- Maoxiang Qian, Xueyuan Cao, Wenjian Yang, Cheng Cheng, Hui Zhang, Takaya Moriyama, Gerard Zambetti, Kim E. Nichols, Ching-Hon Pui, Charles G. Mullighan, William E. Evans, Mary V. Relling, and Jun J. Yang, St Jude Children's Research Hospital, Memphis, TN; Meenakshi Devidas and Yunfeng Dai, University of Florida, Gainesville, FL; Andrew Carroll, University of Alabama at Birmingham, Birmingham, AL; Nyla A. Heerema and Julie M. Gastier-Foster, The Ohio State University and Wexner Medical Center; Julie M. Gastier-Foster and Elaine R. Mardis, Nationwide Children's Hospital, Columbus, OH; Hui Zhang, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong; Heng Xu, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, China; Elizabeth Raetz, University of Utah, Salt Lake City, UT; Eric Larsen, Maine Children's Cancer Program, Scarborough, ME; Naomi Winick, University of Texas Southwestern Medical Center, Dallas; W. Paul Bowman, Cook Children's Medical Center, Fort Worth, TX; Paul L. Martin, Duke University, Durham, NC; Robert Fulton, Washington University School of Medicine, St Louis, MO; Michael Borowitz, Johns Hopkins Medical Institute, Baltimore, MD; Brent Wood, University of Washington, Seattle, WA; William L. Carroll, New York University, New York, NY; Stephen P. Hunger, Children's Hospital of Philadelphia and University of Pennsylvania, Philadelphia, PA; and Mignon L. Loh, Benioff Children's Hospital and University of California, San Francisco, San Francisco, CA
| | - Michael Borowitz
- Maoxiang Qian, Xueyuan Cao, Wenjian Yang, Cheng Cheng, Hui Zhang, Takaya Moriyama, Gerard Zambetti, Kim E. Nichols, Ching-Hon Pui, Charles G. Mullighan, William E. Evans, Mary V. Relling, and Jun J. Yang, St Jude Children's Research Hospital, Memphis, TN; Meenakshi Devidas and Yunfeng Dai, University of Florida, Gainesville, FL; Andrew Carroll, University of Alabama at Birmingham, Birmingham, AL; Nyla A. Heerema and Julie M. Gastier-Foster, The Ohio State University and Wexner Medical Center; Julie M. Gastier-Foster and Elaine R. Mardis, Nationwide Children's Hospital, Columbus, OH; Hui Zhang, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong; Heng Xu, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, China; Elizabeth Raetz, University of Utah, Salt Lake City, UT; Eric Larsen, Maine Children's Cancer Program, Scarborough, ME; Naomi Winick, University of Texas Southwestern Medical Center, Dallas; W. Paul Bowman, Cook Children's Medical Center, Fort Worth, TX; Paul L. Martin, Duke University, Durham, NC; Robert Fulton, Washington University School of Medicine, St Louis, MO; Michael Borowitz, Johns Hopkins Medical Institute, Baltimore, MD; Brent Wood, University of Washington, Seattle, WA; William L. Carroll, New York University, New York, NY; Stephen P. Hunger, Children's Hospital of Philadelphia and University of Pennsylvania, Philadelphia, PA; and Mignon L. Loh, Benioff Children's Hospital and University of California, San Francisco, San Francisco, CA
| | - Brent Wood
- Maoxiang Qian, Xueyuan Cao, Wenjian Yang, Cheng Cheng, Hui Zhang, Takaya Moriyama, Gerard Zambetti, Kim E. Nichols, Ching-Hon Pui, Charles G. Mullighan, William E. Evans, Mary V. Relling, and Jun J. Yang, St Jude Children's Research Hospital, Memphis, TN; Meenakshi Devidas and Yunfeng Dai, University of Florida, Gainesville, FL; Andrew Carroll, University of Alabama at Birmingham, Birmingham, AL; Nyla A. Heerema and Julie M. Gastier-Foster, The Ohio State University and Wexner Medical Center; Julie M. Gastier-Foster and Elaine R. Mardis, Nationwide Children's Hospital, Columbus, OH; Hui Zhang, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong; Heng Xu, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, China; Elizabeth Raetz, University of Utah, Salt Lake City, UT; Eric Larsen, Maine Children's Cancer Program, Scarborough, ME; Naomi Winick, University of Texas Southwestern Medical Center, Dallas; W. Paul Bowman, Cook Children's Medical Center, Fort Worth, TX; Paul L. Martin, Duke University, Durham, NC; Robert Fulton, Washington University School of Medicine, St Louis, MO; Michael Borowitz, Johns Hopkins Medical Institute, Baltimore, MD; Brent Wood, University of Washington, Seattle, WA; William L. Carroll, New York University, New York, NY; Stephen P. Hunger, Children's Hospital of Philadelphia and University of Pennsylvania, Philadelphia, PA; and Mignon L. Loh, Benioff Children's Hospital and University of California, San Francisco, San Francisco, CA
| | - Kim E Nichols
- Maoxiang Qian, Xueyuan Cao, Wenjian Yang, Cheng Cheng, Hui Zhang, Takaya Moriyama, Gerard Zambetti, Kim E. Nichols, Ching-Hon Pui, Charles G. Mullighan, William E. Evans, Mary V. Relling, and Jun J. Yang, St Jude Children's Research Hospital, Memphis, TN; Meenakshi Devidas and Yunfeng Dai, University of Florida, Gainesville, FL; Andrew Carroll, University of Alabama at Birmingham, Birmingham, AL; Nyla A. Heerema and Julie M. Gastier-Foster, The Ohio State University and Wexner Medical Center; Julie M. Gastier-Foster and Elaine R. Mardis, Nationwide Children's Hospital, Columbus, OH; Hui Zhang, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong; Heng Xu, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, China; Elizabeth Raetz, University of Utah, Salt Lake City, UT; Eric Larsen, Maine Children's Cancer Program, Scarborough, ME; Naomi Winick, University of Texas Southwestern Medical Center, Dallas; W. Paul Bowman, Cook Children's Medical Center, Fort Worth, TX; Paul L. Martin, Duke University, Durham, NC; Robert Fulton, Washington University School of Medicine, St Louis, MO; Michael Borowitz, Johns Hopkins Medical Institute, Baltimore, MD; Brent Wood, University of Washington, Seattle, WA; William L. Carroll, New York University, New York, NY; Stephen P. Hunger, Children's Hospital of Philadelphia and University of Pennsylvania, Philadelphia, PA; and Mignon L. Loh, Benioff Children's Hospital and University of California, San Francisco, San Francisco, CA
| | - William L Carroll
- Maoxiang Qian, Xueyuan Cao, Wenjian Yang, Cheng Cheng, Hui Zhang, Takaya Moriyama, Gerard Zambetti, Kim E. Nichols, Ching-Hon Pui, Charles G. Mullighan, William E. Evans, Mary V. Relling, and Jun J. Yang, St Jude Children's Research Hospital, Memphis, TN; Meenakshi Devidas and Yunfeng Dai, University of Florida, Gainesville, FL; Andrew Carroll, University of Alabama at Birmingham, Birmingham, AL; Nyla A. Heerema and Julie M. Gastier-Foster, The Ohio State University and Wexner Medical Center; Julie M. Gastier-Foster and Elaine R. Mardis, Nationwide Children's Hospital, Columbus, OH; Hui Zhang, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong; Heng Xu, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, China; Elizabeth Raetz, University of Utah, Salt Lake City, UT; Eric Larsen, Maine Children's Cancer Program, Scarborough, ME; Naomi Winick, University of Texas Southwestern Medical Center, Dallas; W. Paul Bowman, Cook Children's Medical Center, Fort Worth, TX; Paul L. Martin, Duke University, Durham, NC; Robert Fulton, Washington University School of Medicine, St Louis, MO; Michael Borowitz, Johns Hopkins Medical Institute, Baltimore, MD; Brent Wood, University of Washington, Seattle, WA; William L. Carroll, New York University, New York, NY; Stephen P. Hunger, Children's Hospital of Philadelphia and University of Pennsylvania, Philadelphia, PA; and Mignon L. Loh, Benioff Children's Hospital and University of California, San Francisco, San Francisco, CA
| | - Ching-Hon Pui
- Maoxiang Qian, Xueyuan Cao, Wenjian Yang, Cheng Cheng, Hui Zhang, Takaya Moriyama, Gerard Zambetti, Kim E. Nichols, Ching-Hon Pui, Charles G. Mullighan, William E. Evans, Mary V. Relling, and Jun J. Yang, St Jude Children's Research Hospital, Memphis, TN; Meenakshi Devidas and Yunfeng Dai, University of Florida, Gainesville, FL; Andrew Carroll, University of Alabama at Birmingham, Birmingham, AL; Nyla A. Heerema and Julie M. Gastier-Foster, The Ohio State University and Wexner Medical Center; Julie M. Gastier-Foster and Elaine R. Mardis, Nationwide Children's Hospital, Columbus, OH; Hui Zhang, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong; Heng Xu, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, China; Elizabeth Raetz, University of Utah, Salt Lake City, UT; Eric Larsen, Maine Children's Cancer Program, Scarborough, ME; Naomi Winick, University of Texas Southwestern Medical Center, Dallas; W. Paul Bowman, Cook Children's Medical Center, Fort Worth, TX; Paul L. Martin, Duke University, Durham, NC; Robert Fulton, Washington University School of Medicine, St Louis, MO; Michael Borowitz, Johns Hopkins Medical Institute, Baltimore, MD; Brent Wood, University of Washington, Seattle, WA; William L. Carroll, New York University, New York, NY; Stephen P. Hunger, Children's Hospital of Philadelphia and University of Pennsylvania, Philadelphia, PA; and Mignon L. Loh, Benioff Children's Hospital and University of California, San Francisco, San Francisco, CA
| | - Charles G Mullighan
- Maoxiang Qian, Xueyuan Cao, Wenjian Yang, Cheng Cheng, Hui Zhang, Takaya Moriyama, Gerard Zambetti, Kim E. Nichols, Ching-Hon Pui, Charles G. Mullighan, William E. Evans, Mary V. Relling, and Jun J. Yang, St Jude Children's Research Hospital, Memphis, TN; Meenakshi Devidas and Yunfeng Dai, University of Florida, Gainesville, FL; Andrew Carroll, University of Alabama at Birmingham, Birmingham, AL; Nyla A. Heerema and Julie M. Gastier-Foster, The Ohio State University and Wexner Medical Center; Julie M. Gastier-Foster and Elaine R. Mardis, Nationwide Children's Hospital, Columbus, OH; Hui Zhang, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong; Heng Xu, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, China; Elizabeth Raetz, University of Utah, Salt Lake City, UT; Eric Larsen, Maine Children's Cancer Program, Scarborough, ME; Naomi Winick, University of Texas Southwestern Medical Center, Dallas; W. Paul Bowman, Cook Children's Medical Center, Fort Worth, TX; Paul L. Martin, Duke University, Durham, NC; Robert Fulton, Washington University School of Medicine, St Louis, MO; Michael Borowitz, Johns Hopkins Medical Institute, Baltimore, MD; Brent Wood, University of Washington, Seattle, WA; William L. Carroll, New York University, New York, NY; Stephen P. Hunger, Children's Hospital of Philadelphia and University of Pennsylvania, Philadelphia, PA; and Mignon L. Loh, Benioff Children's Hospital and University of California, San Francisco, San Francisco, CA
| | - William E Evans
- Maoxiang Qian, Xueyuan Cao, Wenjian Yang, Cheng Cheng, Hui Zhang, Takaya Moriyama, Gerard Zambetti, Kim E. Nichols, Ching-Hon Pui, Charles G. Mullighan, William E. Evans, Mary V. Relling, and Jun J. Yang, St Jude Children's Research Hospital, Memphis, TN; Meenakshi Devidas and Yunfeng Dai, University of Florida, Gainesville, FL; Andrew Carroll, University of Alabama at Birmingham, Birmingham, AL; Nyla A. Heerema and Julie M. Gastier-Foster, The Ohio State University and Wexner Medical Center; Julie M. Gastier-Foster and Elaine R. Mardis, Nationwide Children's Hospital, Columbus, OH; Hui Zhang, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong; Heng Xu, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, China; Elizabeth Raetz, University of Utah, Salt Lake City, UT; Eric Larsen, Maine Children's Cancer Program, Scarborough, ME; Naomi Winick, University of Texas Southwestern Medical Center, Dallas; W. Paul Bowman, Cook Children's Medical Center, Fort Worth, TX; Paul L. Martin, Duke University, Durham, NC; Robert Fulton, Washington University School of Medicine, St Louis, MO; Michael Borowitz, Johns Hopkins Medical Institute, Baltimore, MD; Brent Wood, University of Washington, Seattle, WA; William L. Carroll, New York University, New York, NY; Stephen P. Hunger, Children's Hospital of Philadelphia and University of Pennsylvania, Philadelphia, PA; and Mignon L. Loh, Benioff Children's Hospital and University of California, San Francisco, San Francisco, CA
| | - Stephen P Hunger
- Maoxiang Qian, Xueyuan Cao, Wenjian Yang, Cheng Cheng, Hui Zhang, Takaya Moriyama, Gerard Zambetti, Kim E. Nichols, Ching-Hon Pui, Charles G. Mullighan, William E. Evans, Mary V. Relling, and Jun J. Yang, St Jude Children's Research Hospital, Memphis, TN; Meenakshi Devidas and Yunfeng Dai, University of Florida, Gainesville, FL; Andrew Carroll, University of Alabama at Birmingham, Birmingham, AL; Nyla A. Heerema and Julie M. Gastier-Foster, The Ohio State University and Wexner Medical Center; Julie M. Gastier-Foster and Elaine R. Mardis, Nationwide Children's Hospital, Columbus, OH; Hui Zhang, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong; Heng Xu, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, China; Elizabeth Raetz, University of Utah, Salt Lake City, UT; Eric Larsen, Maine Children's Cancer Program, Scarborough, ME; Naomi Winick, University of Texas Southwestern Medical Center, Dallas; W. Paul Bowman, Cook Children's Medical Center, Fort Worth, TX; Paul L. Martin, Duke University, Durham, NC; Robert Fulton, Washington University School of Medicine, St Louis, MO; Michael Borowitz, Johns Hopkins Medical Institute, Baltimore, MD; Brent Wood, University of Washington, Seattle, WA; William L. Carroll, New York University, New York, NY; Stephen P. Hunger, Children's Hospital of Philadelphia and University of Pennsylvania, Philadelphia, PA; and Mignon L. Loh, Benioff Children's Hospital and University of California, San Francisco, San Francisco, CA
| | - Mary V Relling
- Maoxiang Qian, Xueyuan Cao, Wenjian Yang, Cheng Cheng, Hui Zhang, Takaya Moriyama, Gerard Zambetti, Kim E. Nichols, Ching-Hon Pui, Charles G. Mullighan, William E. Evans, Mary V. Relling, and Jun J. Yang, St Jude Children's Research Hospital, Memphis, TN; Meenakshi Devidas and Yunfeng Dai, University of Florida, Gainesville, FL; Andrew Carroll, University of Alabama at Birmingham, Birmingham, AL; Nyla A. Heerema and Julie M. Gastier-Foster, The Ohio State University and Wexner Medical Center; Julie M. Gastier-Foster and Elaine R. Mardis, Nationwide Children's Hospital, Columbus, OH; Hui Zhang, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong; Heng Xu, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, China; Elizabeth Raetz, University of Utah, Salt Lake City, UT; Eric Larsen, Maine Children's Cancer Program, Scarborough, ME; Naomi Winick, University of Texas Southwestern Medical Center, Dallas; W. Paul Bowman, Cook Children's Medical Center, Fort Worth, TX; Paul L. Martin, Duke University, Durham, NC; Robert Fulton, Washington University School of Medicine, St Louis, MO; Michael Borowitz, Johns Hopkins Medical Institute, Baltimore, MD; Brent Wood, University of Washington, Seattle, WA; William L. Carroll, New York University, New York, NY; Stephen P. Hunger, Children's Hospital of Philadelphia and University of Pennsylvania, Philadelphia, PA; and Mignon L. Loh, Benioff Children's Hospital and University of California, San Francisco, San Francisco, CA
| | - Mignon L Loh
- Maoxiang Qian, Xueyuan Cao, Wenjian Yang, Cheng Cheng, Hui Zhang, Takaya Moriyama, Gerard Zambetti, Kim E. Nichols, Ching-Hon Pui, Charles G. Mullighan, William E. Evans, Mary V. Relling, and Jun J. Yang, St Jude Children's Research Hospital, Memphis, TN; Meenakshi Devidas and Yunfeng Dai, University of Florida, Gainesville, FL; Andrew Carroll, University of Alabama at Birmingham, Birmingham, AL; Nyla A. Heerema and Julie M. Gastier-Foster, The Ohio State University and Wexner Medical Center; Julie M. Gastier-Foster and Elaine R. Mardis, Nationwide Children's Hospital, Columbus, OH; Hui Zhang, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong; Heng Xu, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, China; Elizabeth Raetz, University of Utah, Salt Lake City, UT; Eric Larsen, Maine Children's Cancer Program, Scarborough, ME; Naomi Winick, University of Texas Southwestern Medical Center, Dallas; W. Paul Bowman, Cook Children's Medical Center, Fort Worth, TX; Paul L. Martin, Duke University, Durham, NC; Robert Fulton, Washington University School of Medicine, St Louis, MO; Michael Borowitz, Johns Hopkins Medical Institute, Baltimore, MD; Brent Wood, University of Washington, Seattle, WA; William L. Carroll, New York University, New York, NY; Stephen P. Hunger, Children's Hospital of Philadelphia and University of Pennsylvania, Philadelphia, PA; and Mignon L. Loh, Benioff Children's Hospital and University of California, San Francisco, San Francisco, CA
| | - Jun J Yang
- Maoxiang Qian, Xueyuan Cao, Wenjian Yang, Cheng Cheng, Hui Zhang, Takaya Moriyama, Gerard Zambetti, Kim E. Nichols, Ching-Hon Pui, Charles G. Mullighan, William E. Evans, Mary V. Relling, and Jun J. Yang, St Jude Children's Research Hospital, Memphis, TN; Meenakshi Devidas and Yunfeng Dai, University of Florida, Gainesville, FL; Andrew Carroll, University of Alabama at Birmingham, Birmingham, AL; Nyla A. Heerema and Julie M. Gastier-Foster, The Ohio State University and Wexner Medical Center; Julie M. Gastier-Foster and Elaine R. Mardis, Nationwide Children's Hospital, Columbus, OH; Hui Zhang, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong; Heng Xu, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, China; Elizabeth Raetz, University of Utah, Salt Lake City, UT; Eric Larsen, Maine Children's Cancer Program, Scarborough, ME; Naomi Winick, University of Texas Southwestern Medical Center, Dallas; W. Paul Bowman, Cook Children's Medical Center, Fort Worth, TX; Paul L. Martin, Duke University, Durham, NC; Robert Fulton, Washington University School of Medicine, St Louis, MO; Michael Borowitz, Johns Hopkins Medical Institute, Baltimore, MD; Brent Wood, University of Washington, Seattle, WA; William L. Carroll, New York University, New York, NY; Stephen P. Hunger, Children's Hospital of Philadelphia and University of Pennsylvania, Philadelphia, PA; and Mignon L. Loh, Benioff Children's Hospital and University of California, San Francisco, San Francisco, CA
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