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Farrokhi A, Atre T, Rever J, Fidanza M, Duey W, Salitra S, Myung J, Guo M, Jo S, Uzozie A, Baharvand F, Rolf N, Auer F, Hauer J, Grupp SA, Eydoux P, Lange PF, Seif AE, Maxwell CA, Reid GSD. The Eμ-Ret mouse is a novel model of hyperdiploid B-cell acute lymphoblastic leukemia. Leukemia 2024; 38:969-980. [PMID: 38519798 PMCID: PMC11073968 DOI: 10.1038/s41375-024-02221-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: 07/03/2023] [Revised: 02/27/2024] [Accepted: 03/05/2024] [Indexed: 03/25/2024]
Abstract
The presence of supernumerary chromosomes is the only abnormality shared by all patients diagnosed with high-hyperdiploid B cell acute lymphoblastic leukemia (HD-ALL). Despite being the most frequently diagnosed pediatric leukemia, the lack of clonal molecular lesions and complete absence of appropriate experimental models have impeded the elucidation of HD-ALL leukemogenesis. Here, we report that for 23 leukemia samples isolated from moribund Eμ-Ret mice, all were characterized by non-random chromosomal gains, involving combinations of trisomy 9, 12, 14, 15, and 17. With a median gain of three chromosomes, leukemia emerged after a prolonged latency from a preleukemic B cell precursor cell population displaying more diverse aneuploidy. Transition from preleukemia to overt disease in Eμ-Ret mice is associated with acquisition of heterogeneous genomic abnormalities affecting the expression of genes implicated in pediatric B-ALL. The development of abnormal centrosomes in parallel with aneuploidy renders both preleukemic and leukemic cells sensitive to inhibitors of centrosome clustering, enabling targeted in vivo depletion of leukemia-propagating cells. This study reveals the Eμ-Ret mouse to be a novel tool for investigating HD-ALL leukemogenesis, including supervision and selection of preleukemic aneuploid clones by the immune system and identification of vulnerabilities that could be targeted to prevent relapse.
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Affiliation(s)
- Ali Farrokhi
- Michael Cuccione Childhood Cancer Research Program, BC Children's Hospital Research Institute, Vancouver, BC, Canada
| | - Tanmaya Atre
- Michael Cuccione Childhood Cancer Research Program, BC Children's Hospital Research Institute, Vancouver, BC, Canada
| | - Jenna Rever
- Michael Cuccione Childhood Cancer Research Program, BC Children's Hospital Research Institute, Vancouver, BC, Canada
| | - Mario Fidanza
- Michael Cuccione Childhood Cancer Research Program, BC Children's Hospital Research Institute, Vancouver, BC, Canada
| | - Wendy Duey
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Samuel Salitra
- Michael Cuccione Childhood Cancer Research Program, BC Children's Hospital Research Institute, Vancouver, BC, Canada
| | - Junia Myung
- Michael Cuccione Childhood Cancer Research Program, BC Children's Hospital Research Institute, Vancouver, BC, Canada
| | - Meiyun Guo
- Michael Cuccione Childhood Cancer Research Program, BC Children's Hospital Research Institute, Vancouver, BC, Canada
| | - Sumin Jo
- Michael Cuccione Childhood Cancer Research Program, BC Children's Hospital Research Institute, Vancouver, BC, Canada
| | - Anuli Uzozie
- Michael Cuccione Childhood Cancer Research Program, BC Children's Hospital Research Institute, Vancouver, BC, Canada
| | - Fatemeh Baharvand
- Michael Cuccione Childhood Cancer Research Program, BC Children's Hospital Research Institute, Vancouver, BC, Canada
| | - Nina Rolf
- Michael Cuccione Childhood Cancer Research Program, BC Children's Hospital Research Institute, Vancouver, BC, Canada
| | - Franziska Auer
- Department of Pediatrics, Children's Cancer Research Center, Kinderklinik München Schwabing, School of Medicine, Technical University of Munich, Munich, Germany
| | - Julia Hauer
- Department of Pediatrics, Children's Cancer Research Center, Kinderklinik München Schwabing, School of Medicine, Technical University of Munich, Munich, Germany
| | - Stephan A Grupp
- Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, PA, USA
| | - Patrice Eydoux
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Philipp F Lange
- Michael Cuccione Childhood Cancer Research Program, BC Children's Hospital Research Institute, Vancouver, BC, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Alix E Seif
- Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, PA, USA
| | - Christopher A Maxwell
- Michael Cuccione Childhood Cancer Research Program, BC Children's Hospital Research Institute, Vancouver, BC, Canada
- Department of Pediatrics, University of British Columbia, Vancouver, BC, Canada
| | - Gregor S D Reid
- Michael Cuccione Childhood Cancer Research Program, BC Children's Hospital Research Institute, Vancouver, BC, Canada.
- Department of Pediatrics, University of British Columbia, Vancouver, BC, Canada.
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2
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Panuciak K, Nowicka E, Mastalerczyk A, Zawitkowska J, Niedźwiecki M, Lejman M. Overview on Aneuploidy in Childhood B-Cell Acute Lymphoblastic Leukemia. Int J Mol Sci 2023; 24:ijms24108764. [PMID: 37240110 DOI: 10.3390/ijms24108764] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 05/04/2023] [Accepted: 05/10/2023] [Indexed: 05/28/2023] Open
Abstract
Recent years have brought significant progress in the treatment of B-cell acute lymphoblastic leukemia (ALL). This was influenced by both the improved schemes of conventionally used therapy, as well as the development of new forms of treatment. As a consequence, 5-year survival rates have increased and now exceed 90% in pediatric patients. For this reason, it would seem that everything has already been explored in the context of ALL. However, delving into its pathogenesis at the molecular level shows that there are many variations that still need to be analyzed in more detail. One of them is aneuploidy, which is among the most common genetic changes in B-cell ALL. It includes both hyperdiploidy and hypodiploidy. Knowledge of the genetic background is important already at the time of diagnosis, because the first of these forms of aneuploidy is characterized by a good prognosis, in contrast to the second, which is in favor of an unfavorable course. In our work, we will focus on summarizing the current state of knowledge on aneuploidy, along with an indication of all the consequences that may be correlated with it in the context of the treatment of patients with B-cell ALL.
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Affiliation(s)
- Kinga Panuciak
- Student Scientific Society, Independent Laboratory of Genetic Diagnostics, Medical University of Lublin, 20-093 Lublin, Poland
| | - Emilia Nowicka
- Student Scientific Society, Independent Laboratory of Genetic Diagnostics, Medical University of Lublin, 20-093 Lublin, Poland
| | - Angelika Mastalerczyk
- Student Scientific Society, Independent Laboratory of Genetic Diagnostics, Medical University of Lublin, 20-093 Lublin, Poland
| | - Joanna Zawitkowska
- Department of Pediatric Hematology, Oncology and Transplantology, Medical University of Lublin, Gębali 6, 20-093 Lublin, Poland
| | - Maciej Niedźwiecki
- Department of Pediatrics, Hematology and Oncology, Medical University of Gdansk, Debinki 7, 80-211 Gdansk, Poland
| | - Monika Lejman
- Independent Laboratory of Genetic Diagnostics, Medical University of Lublin, 20-093 Lublin, Poland
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3
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Shen D, Liu L, Xu X, Song H, Zhang J, Xu W, Zhao F, Liang J, Liao C, Wang Y, Xia T, Wang C, Lou F, Cao S, Qin J, Tang Y. Spectrum and clinical features of gene mutations in Chinese pediatric acute lymphoblastic leukemia. BMC Pediatr 2023; 23:62. [PMID: 36739388 PMCID: PMC9898934 DOI: 10.1186/s12887-023-03856-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 01/19/2023] [Indexed: 02/06/2023] Open
Abstract
PURPOSE The 5-year survival rate of children with acute lymphoblastic leukemia (ALL) is 85-90%, with a 10-15% rate of treatment failure. Next-generation sequencing (NGS) identified recurrent mutated genes in ALL that might alter the diagnosis, classification, prognostic stratification, treatment, and response to ALL. Few studies on gene mutations in Chinese pediatric ALL have been identified. Thus, an in-depth understanding of the biological characteristics of these patients is essential. The present study aimed to characterize the spectrum and clinical features of recurrent driver gene mutations in a single-center cohort of Chinese pediatric ALL. METHODS We enrolled 219 patients with pediatric ALL in our single center. Targeted sequencing based on NGS was used to detect gene mutations in patients. The correlation was analyzed between gene mutation and clinical features, including patient characteristics, cytogenetics, genetic subtypes, risk stratification and treatment outcomes using χ2-square test or Fisher's exact test for categorical variables. RESULTS A total of 381 gene mutations were identified in 66 different genes in 152/219 patients. PIK3R1 mutation was more common in infants (P = 0.021). KRAS and FLT3 mutations were both more enriched in patients with hyperdiploidy (both P < 0.001). NRAS, PTPN11, FLT3, and KMT2D mutations were more common in patients who did not carry the fusion genes (all P < 0.050). PTEN mutation was significantly associated with high-risk ALL patients (P = 0.011), while NOTCH1 mutation was common in middle-risk ALL patients (P = 0.039). Patients with ETV6 or PHF6 mutations were less sensitive to steroid treatment (P = 0.033, P = 0.048, respectively). CONCLUSION This study depicted the specific genomic landscape of Chinese pediatric ALL and revealed the relevance between mutational spectrum and clinical features of Chinese pediatric ALL, which highlights the need for molecular classification, risk stratification, and prognosis evaluation.
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Affiliation(s)
- Diying Shen
- grid.13402.340000 0004 1759 700XPediatric Hematology-Oncology Center, Zhejiang Provincial Center for Childhood Leukemia Diagnosis and Treatment, The Children’s Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, China
| | - Lixia Liu
- Acornmed Biotechnology Co., Ltd, Tianjin, China
| | - Xiaojun Xu
- grid.13402.340000 0004 1759 700XPediatric Hematology-Oncology Center, Zhejiang Provincial Center for Childhood Leukemia Diagnosis and Treatment, The Children’s Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, China
| | - Hua Song
- grid.13402.340000 0004 1759 700XPediatric Hematology-Oncology Center, Zhejiang Provincial Center for Childhood Leukemia Diagnosis and Treatment, The Children’s Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, China
| | - Jingying Zhang
- grid.13402.340000 0004 1759 700XPediatric Hematology-Oncology Center, Zhejiang Provincial Center for Childhood Leukemia Diagnosis and Treatment, The Children’s Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, China
| | - Weiqun Xu
- grid.13402.340000 0004 1759 700XPediatric Hematology-Oncology Center, Zhejiang Provincial Center for Childhood Leukemia Diagnosis and Treatment, The Children’s Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, China
| | - Fenying Zhao
- grid.13402.340000 0004 1759 700XPediatric Hematology-Oncology Center, Zhejiang Provincial Center for Childhood Leukemia Diagnosis and Treatment, The Children’s Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, China
| | - Juan Liang
- grid.13402.340000 0004 1759 700XPediatric Hematology-Oncology Center, Zhejiang Provincial Center for Childhood Leukemia Diagnosis and Treatment, The Children’s Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, China
| | - Chan Liao
- grid.13402.340000 0004 1759 700XPediatric Hematology-Oncology Center, Zhejiang Provincial Center for Childhood Leukemia Diagnosis and Treatment, The Children’s Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, China
| | - Yan Wang
- grid.13402.340000 0004 1759 700XPediatric Hematology-Oncology Center, Zhejiang Provincial Center for Childhood Leukemia Diagnosis and Treatment, The Children’s Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, China
| | - Tian Xia
- grid.13402.340000 0004 1759 700XPediatric Hematology-Oncology Center, Zhejiang Provincial Center for Childhood Leukemia Diagnosis and Treatment, The Children’s Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, China
| | | | - Feng Lou
- Acornmed Biotechnology Co., Ltd, Tianjin, China
| | - Shanbo Cao
- Acornmed Biotechnology Co., Ltd, Tianjin, China
| | - Jiayue Qin
- Acornmed Biotechnology Co., Ltd, Tianjin, China
| | - Yongmin Tang
- Pediatric Hematology-Oncology Center, Zhejiang Provincial Center for Childhood Leukemia Diagnosis and Treatment, The Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, China.
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4
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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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5
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Davidow K, Mumanachit S, Mangum DS. The two-hit hypothesis in practice: Monozygotic twins with simultaneous hyperdiploid acute lymphoblastic leukemia. Pediatr Blood Cancer 2022; 69:e29885. [PMID: 35856567 DOI: 10.1002/pbc.29885] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 06/23/2022] [Accepted: 06/26/2022] [Indexed: 11/12/2022]
Abstract
Approximately 25% of B-cell acute lymphoblastic leukemia (B-ALL) cases are defined by hyperdiploidy, with RAS mutations occurring in 30% of hyperdiploid B-ALL patients. It is believed that hyperdiploidy is an in utero event with RAS mutations occurring postnatally, but clinical evidence of this is based on relatively few patients. We present a case of monozygotic, monochorionic twins who developed concordant hyperdiploid B-ALL with identical chromosomal gains but different RAS mutations, adding further evidence that hyperdiploidy is occurring prenatally, with RAS mutations developing postnatally. Environmental exposures were reviewed with the family without identification of a clear association.
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Affiliation(s)
- Kimberly Davidow
- Division of Pediatric Hematology/Oncology, Nemours Center for Cancer and Blood Disorders, Nemours Children's Hospital - Delaware, Wilmington, Delaware, USA
| | - Sarah Mumanachit
- Division of Pediatrics, Nemours Children's Hospital - Delaware, Wilmington, Delaware, USA
| | - David Spencer Mangum
- Division of Pediatric Hematology/Oncology, Nemours Center for Cancer and Blood Disorders, Nemours Children's Hospital - Delaware, Wilmington, Delaware, USA
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6
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Matsukawa T, Yin M, Baslan T, Chung YJ, Cao D, Bertoli R, Zhu YJ, Walker RL, Freeland A, Knudsen E, Lowe SW, Meltzer PS, Aplan PD. Mcm2 hypomorph leads to acute leukemia or hematopoietic stem cell failure, dependent on genetic context. FASEB J 2022; 36:e22430. [PMID: 35920299 PMCID: PMC9377154 DOI: 10.1096/fj.202200061rr] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 06/07/2022] [Accepted: 06/13/2022] [Indexed: 11/11/2022]
Abstract
Minichromosome maintenance proteins (Mcm2-7) form a hexameric complex that unwinds DNA ahead of a replicative fork. The deficiency of Mcm proteins leads to replicative stress and consequent genomic instability. Mice with a germline insertion of a Cre cassette into the 3'UTR of the Mcm2 gene (designated Mcm2Cre ) have decreased Mcm2 expression and invariably develop precursor T-cell lymphoblastic leukemia/lymphoma (pre-T LBL), due to 100-1000 kb deletions involving important tumor suppressor genes. To determine whether mice that were protected from pre-T LBL would develop non-T-cell malignancies, we used two approaches. Mice engrafted with Mcm2Cre/Cre Lin- Sca-1+ Kit+ hematopoietic stem/progenitor cells did not develop hematologic malignancy; however, these mice died of hematopoietic stem cell failure by 6 months of age. Placing the Mcm2Cre allele onto an athymic nu/nu background completely prevented pre-T LBL and extended survival of these mice three-fold (median 296.5 vs. 80.5 days). Ultimately, most Mcm2Cre/Cre ;nu/nu mice developed B-cell precursor acute lymphoblastic leukemia (BCP-ALL). We identified recurrent deletions of 100-1000 kb that involved genes known or suspected to be involved in BCP-ALL, including Pax5, Nf1, Ikzf3, and Bcor. Moreover, whole-exome sequencing identified recurrent mutations of genes known to be involved in BCP-ALL progression, such as Jak1/Jak3, Ptpn11, and Kras. These findings demonstrate that an Mcm2Cre/Cre hypomorph can induce hematopoietic dysfunction via hematopoietic stem cell failure as well as a "deletor" phenotype affecting known or suspected tumor suppressor genes.
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Affiliation(s)
- Toshihiro Matsukawa
- Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
- These authors contributed equally to this work
| | - Mianmian Yin
- Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
- These authors contributed equally to this work
| | - Timour Baslan
- Cancer Biology and Genetics Program, Sloan-Kettering Institute, NY, USA
| | - Yang Jo Chung
- Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Dengchao Cao
- Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Ryan Bertoli
- Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Yuelin J. Zhu
- Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Robert L. Walker
- Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Amy Freeland
- Department of Molecular and Cellular Biology, Roswell Park Cancer Institute, Buffalo, NY, USA
| | - Erik Knudsen
- Department of Molecular and Cellular Biology, Roswell Park Cancer Institute, Buffalo, NY, USA
| | - Scott W. Lowe
- Cancer Biology and Genetics Program, Sloan-Kettering Institute, NY, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Paul S. Meltzer
- Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Peter D. Aplan
- Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
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7
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Resistance Mechanisms in Pediatric B-Cell Acute Lymphoblastic Leukemia. Int J Mol Sci 2022; 23:ijms23063067. [PMID: 35328487 PMCID: PMC8950780 DOI: 10.3390/ijms23063067] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 03/09/2022] [Accepted: 03/10/2022] [Indexed: 02/01/2023] Open
Abstract
Despite the rapid development of medicine, even nowadays, acute lymphoblastic leukemia (ALL) is still a problem for pediatric clinicians. Modern medicine has reached a limit of curability even though the recovery rate exceeds 90%. Relapse occurs in around 20% of treated patients and, regrettably, 10% of diagnosed ALL patients are still incurable. In this article, we would like to focus on the treatment resistance and disease relapse of patients with B-cell leukemia in the context of prognostic factors of ALL. We demonstrate the mechanisms of the resistance to steroid therapy and Tyrosine Kinase Inhibitors and assess the impact of genetic factors on the treatment resistance, especially TCF3::HLF translocation. We compare therapeutic protocols and decipher how cancer cells become resistant to innovative treatments—including CAR-T-cell therapies and monoclonal antibodies. The comparisons made in our article help to bring closer the main factors of resistance in hematologic malignancies in the context of ALL.
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8
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Studd JB, Cornish AJ, Hoang PH, Law P, Kinnersley B, Houlston R. Cancer drivers and clonal dynamics in acute lymphoblastic leukaemia subtypes. Blood Cancer J 2021; 11:177. [PMID: 34753926 PMCID: PMC8578656 DOI: 10.1038/s41408-021-00570-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 10/25/2021] [Accepted: 10/27/2021] [Indexed: 12/17/2022] Open
Abstract
To obtain a comprehensive picture of composite genetic driver events and clonal dynamics in subtypes of paediatric acute lymphoblastic leukaemia (ALL) we analysed tumour-normal whole genome sequencing and expression data from 361 newly diagnosed patients. We report the identification of both structural drivers, as well as recurrent non-coding variation in promoters. Additionally we found the transcriptional profile of histone gene cluster 1 and CTCF altered tumours shared hallmarks of hyperdiploid ALL suggesting a 'hyperdiploid like' subtype. ALL subtypes are driven by distinct mutational processes with AID mutagenesis being confined to ETV6-RUNX1 tumours. Subclonality is a ubiquitous feature of ALL, consistent with Darwinian evolution driving selection and expansion of tumours. Driver mutations in B-cell developmental genes (IKZF1, PAX5, ZEB2) tend to be clonal and RAS/RTK mutations subclonal. In addition to identifying new avenues for therapeutic exploitation, this analysis highlights that targeted therapies should take into account composite mutational profile and clonality.
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Affiliation(s)
- James B Studd
- Division of Genetics and Epidemiology, The Institute of Cancer Research, Sutton, SM2 5NG, UK.
| | - Alex J Cornish
- Division of Genetics and Epidemiology, The Institute of Cancer Research, Sutton, SM2 5NG, UK
| | - Phuc H Hoang
- Division of Genetics and Epidemiology, The Institute of Cancer Research, Sutton, SM2 5NG, UK
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, ML, USA
| | - Philip Law
- Division of Genetics and Epidemiology, The Institute of Cancer Research, Sutton, SM2 5NG, UK
| | - Ben Kinnersley
- Division of Genetics and Epidemiology, The Institute of Cancer Research, Sutton, SM2 5NG, UK
| | - Richard Houlston
- Division of Genetics and Epidemiology, The Institute of Cancer Research, Sutton, SM2 5NG, UK
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9
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A systematic analysis of genetic interactions and their underlying biology in childhood cancer. Commun Biol 2021; 4:1139. [PMID: 34615983 PMCID: PMC8494736 DOI: 10.1038/s42003-021-02647-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Accepted: 09/08/2021] [Indexed: 02/08/2023] Open
Abstract
Childhood cancer is a major cause of child death in developed countries. Genetic interactions between mutated genes play an important role in cancer development. They can be detected by searching for pairs of mutated genes that co-occur more (or less) often than expected. Co-occurrence suggests a cooperative role in cancer development, while mutual exclusivity points to synthetic lethality, a phenomenon of interest in cancer treatment research. Little is known about genetic interactions in childhood cancer. We apply a statistical pipeline to detect genetic interactions in a combined dataset comprising over 2,500 tumors from 23 cancer types. The resulting genetic interaction map of childhood cancers comprises 15 co-occurring and 27 mutually exclusive candidates. The biological explanation of most candidates points to either tumor subtype, pathway epistasis or cooperation while synthetic lethality plays a much smaller role. Thus, other explanations beyond synthetic lethality should be considered when interpreting genetic interaction test results.
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10
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Akram AM, Chaudhary A, Kausar H, Althobaiti F, Abbas AS, Hussain Z, Fatima N, Zafar E, Asif W, Afzal U, Yousaf Z, Zafar A, Harakeh SM, Qamer S. Analysis of RAS gene mutations in cytogenetically normal de novo acute myeloid leukemia patients reveals some novel alterations. Saudi J Biol Sci 2021; 28:3735-3740. [PMID: 34220225 PMCID: PMC8241590 DOI: 10.1016/j.sjbs.2021.04.089] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Revised: 04/20/2021] [Accepted: 04/28/2021] [Indexed: 11/26/2022] Open
Abstract
Rat sarcoma gene (RAS) holds great importance in pathogenesis of acute myeloid leukemia (AML). The activated mutations in Neuroblastoma rat sarcoma viral oncogene homolog (NRAS) and Kirsten rat sarcoma viral oncogene homolog (KRAS) confers proliferative and survival signals, deliberating numerous effects on overall survival and progression free survival in AML patients. In this study thirty one (31) blood samples of adult newly diagnosed AML patients were collected to identify possible incidence of mutations through amplification of KRAS (exon 1 and 2) and NRAS gene (exon 1 and 2) using polymerase chain reaction (PCR). Amplicons were then subjected to sequencing and were analyzed through Geneious Prime 2019. Five of thirty one (16.12%) patients had altered sites in either NRAS or KRAS. The NRAS mutations were observed in three AML patients (N = 3, 9.67%). A novel missense mutation NRAS-I36R (239 T > G) representing a substitution of single nucleotide basepair found in NRAS exon 1 while exon 2 was detected with heterozygous mutation NRAS-E63X (318G > T) and insertion (A), resulting in frameshift of the amino acid sequence and insertion of two nucleotide basepairs (TA) in two of the patients. KRAS mutations (N = 2, 6.45%) were found in exon 1 whereas no mutations in KRAS exon 2 were detected in our patient cohort. Mutation in KRAS Exon 1, KRAS-D30N (280G > A) was observed in two patients and one of them also had a novel heterozygous mutation KRAS-L16N (240G > C). In addition there was no statistically significant association of mutRAS gene of AML patients with several prognostic markers including age, gender, karyotyping, CD34 positivity, cytogenetic abnormalities, total leukocyte count, white blood cell count and French-American-British (FAB) classification. However, the presence of mutRAS gene were strongly associated (p = 0.001) with increased percentage of bone marrow blasts. The prevalence of mutations in correlation with clinical and hematological parameter is useful for risk stratification in AML patients.
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Affiliation(s)
- Afia Muhammad Akram
- Department of Zoology, Division of Science and Technology, University of Education, Township, Lahore, Pakistan
| | - Asma Chaudhary
- Department of Zoology, Division of Science and Technology, University of Education, Township, Lahore, Pakistan
| | - Humera Kausar
- Department of Biotechnology, Kinnaird College for Women, Lahore, Pakistan
| | - Fayez Althobaiti
- Department of Biotechnology, College of Science, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia
| | - Afshan Syed Abbas
- Department of Zoology, University of Education, Lower Mall Campus, Lahore, Pakistan
| | - Zawar Hussain
- Department of Zoology, Division of Science and Technology, University of Education, Township, Lahore, Pakistan
| | - Naz Fatima
- Molecular Biology Laboratory, Department of Zoology, University of the Punjab, Lahore, Pakistan
| | - Erum Zafar
- Department of Zoology, Division of Science and Technology, University of Education, Township, Lahore, Pakistan
| | - Wajiha Asif
- Department of Zoology, Division of Science and Technology, University of Education, Township, Lahore, Pakistan
| | - Umair Afzal
- Department of Zoology, Division of Science and Technology, University of Education, Township, Lahore, Pakistan
| | - Zoufishan Yousaf
- Department of Zoology, Division of Science and Technology, University of Education, Township, Lahore, Pakistan
| | - Amjad Zafar
- Department of Oncology, Mayo Hospital, Anarkali Bazar, Lahore, Pakistan
| | - Steve M Harakeh
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Samina Qamer
- Department of Zoology, Government College University, Faisalabad, Pakistan
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11
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13q12.2 deletions in acute lymphoblastic leukemia lead to upregulation of FLT3 through enhancer hijacking. Blood 2021; 136:946-956. [PMID: 32384149 DOI: 10.1182/blood.2019004684] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Accepted: 04/20/2020] [Indexed: 12/14/2022] Open
Abstract
Mutations in the FMS-like tyrosine kinase 3 (FLT3) gene in 13q12.2 are among the most common driver events in acute leukemia, leading to increased cell proliferation and survival through activation of the phosphatidylinositol 3-kinase/AKT-, RAS/MAPK-, and STAT5-signaling pathways. In this study, we examine the pathogenetic impact of somatic hemizygous 13q12.2 microdeletions in B-cell precursor (BCP) acute lymphoblastic leukemia (ALL) using 5 different patient cohorts (in total including 1418 cases). The 13q12.2 deletions occur immediately 5' of FLT3 and involve the PAN3 locus. By detailed analysis of the 13q12.2 segment, we show that the deletions lead to loss of a topologically associating domain border and an enhancer of FLT3. This results in increased cis interactions between the FLT3 promoter and another enhancer located distally to the deletion breakpoints, with subsequent allele-specific upregulation of FLT3 expression, expected to lead to ligand-independent activation of the receptor and downstream signaling. The 13q12.2 deletions are highly enriched in the high-hyperdiploid BCP ALL subtype (frequency 3.9% vs 0.5% in other BCP ALL) and in cases that subsequently relapsed. Taken together, our study describes a novel mechanism of FLT3 involvement in leukemogenesis by upregulation via chromatin remodeling and enhancer hijacking. These data further emphasize the role of FLT3 as a driver gene in BCP ALL.
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12
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Li J, Galbo PM, Gong W, Storey AJ, Tsai YH, Yu X, Ahn JH, Guo Y, Mackintosh SG, Edmondson RD, Byrum SD, Farrar JE, He S, Cai L, Jin J, Tackett AJ, Zheng D, Wang GG. ZMYND11-MBTD1 induces leukemogenesis through hijacking NuA4/TIP60 acetyltransferase complex and a PWWP-mediated chromatin association mechanism. Nat Commun 2021; 12:1045. [PMID: 33594072 PMCID: PMC7886901 DOI: 10.1038/s41467-021-21357-3] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Accepted: 01/22/2021] [Indexed: 12/26/2022] Open
Abstract
Recurring chromosomal translocation t(10;17)(p15;q21) present in a subset of human acute myeloid leukemia (AML) patients creates an aberrant fusion gene termed ZMYND11-MBTD1 (ZM); however, its function remains undetermined. Here, we show that ZM confers primary murine hematopoietic stem/progenitor cells indefinite self-renewal capability ex vivo and causes AML in vivo. Genomics profilings reveal that ZM directly binds to and maintains high expression of pro-leukemic genes including Hoxa, Meis1, Myb, Myc and Sox4. Mechanistically, ZM recruits the NuA4/Tip60 histone acetyltransferase complex to cis-regulatory elements, sustaining an active chromatin state enriched in histone acetylation and devoid of repressive histone marks. Systematic mutagenesis of ZM demonstrates essential requirements of Tip60 interaction and an H3K36me3-binding PWWP (Pro-Trp-Trp-Pro) domain for oncogenesis. Inhibitor of histone acetylation-'reading' bromodomain proteins, which act downstream of ZM, is efficacious in treating ZM-induced AML. Collectively, this study demonstrates AML-causing effects of ZM, examines its gene-regulatory roles, and reports an attractive mechanism-guided therapeutic strategy.
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MESH Headings
- Acetylation
- Animals
- Carcinogenesis
- Cell Cycle Proteins/chemistry
- Cell Cycle Proteins/metabolism
- Cell Differentiation
- Cell Proliferation
- Cell Transformation, Neoplastic
- Chromatin/metabolism
- Chromosomal Proteins, Non-Histone/chemistry
- Chromosomal Proteins, Non-Histone/metabolism
- Co-Repressor Proteins/chemistry
- Co-Repressor Proteins/metabolism
- DNA-Binding Proteins/chemistry
- DNA-Binding Proteins/metabolism
- Disease Models, Animal
- Enhancer Elements, Genetic/genetics
- Gene Expression Regulation, Leukemic
- Genome, Human
- HEK293 Cells
- Hematopoietic Stem Cells/metabolism
- Histones/metabolism
- Humans
- Leukemia, Myeloid, Acute/genetics
- Leukemia, Myeloid, Acute/pathology
- Lysine Acetyltransferase 5/metabolism
- Mice, Inbred BALB C
- Neoplastic Stem Cells/metabolism
- Neoplastic Stem Cells/pathology
- Oncogene Proteins, Fusion/metabolism
- Protein Binding
- Protein Domains
- Transcription Factors/metabolism
- Mice
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Affiliation(s)
- Jie Li
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Phillip M Galbo
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Weida Gong
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
| | - Aaron J Storey
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Yi-Hsuan Tsai
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
| | - Xufen Yu
- Mount Sinai Center for Therapeutics Discovery, Departments of Pharmacological Sciences and Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jeong Hyun Ahn
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
| | - Yiran Guo
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Samuel G Mackintosh
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Ricky D Edmondson
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Stephanie D Byrum
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Jason E Farrar
- Winthrop P. Rockefeller Cancer Institute, University of Arkansas for Medical Sciences and Arkansas Children's Research Institute, Little Rock, AR, USA
| | - Shenghui He
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
- Department of Genetics, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
| | - Ling Cai
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
- Department of Genetics, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
| | - Jian Jin
- Mount Sinai Center for Therapeutics Discovery, Departments of Pharmacological Sciences and Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Alan J Tackett
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR, USA
- Winthrop P. Rockefeller Cancer Institute, University of Arkansas for Medical Sciences and Arkansas Children's Research Institute, Little Rock, AR, USA
| | - Deyou Zheng
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
- Department of Neurology and Department of Neuroscience, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Gang Greg Wang
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA.
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA.
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
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13
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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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14
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RAS-protein activation but not mutation status is an outcome predictor and unifying therapeutic target for high-risk acute lymphoblastic leukemia. Oncogene 2020; 40:746-762. [PMID: 33247204 PMCID: PMC7843419 DOI: 10.1038/s41388-020-01567-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 10/30/2020] [Accepted: 11/11/2020] [Indexed: 02/07/2023]
Abstract
Leukemias are routinely sub-typed for risk/outcome prediction and therapy choice using acquired mutations and chromosomal rearrangements. Down syndrome acute lymphoblastic leukemia (DS-ALL) is characterized by high frequency of CRLF2-rearrangements, JAK2-mutations, or RAS-pathway mutations. Intriguingly, JAK2 and RAS-mutations are mutually exclusive in leukemic sub-clones, causing dichotomy in therapeutic target choices. We prove in a cell model that elevated CRLF2 in combination with constitutionally active JAK2 is sufficient to activate wtRAS. On primary clinical DS-ALL samples, we show that wtRAS-activation is an obligatory consequence of mutated/hyperphosphorylated JAK2. We further prove that CRLF2-ligand TSLP boosts the direct binding of active PTPN11 to wtRAS, providing the molecular mechanism for the wtRAS activation. Pre-inhibition of RAS or PTPN11, but not of PI3K or JAK-signaling, prevented TSLP-induced RAS-GTP boost. Cytotoxicity assays on primary clinical DS-ALL samples demonstrated that, regardless of mutation status, high-risk leukemic cells could only be killed using RAS-inhibitor or PTPN11-inhibitor, but not PI3K/JAK-inhibitors, suggesting a unified treatment target for up to 80% of DS-ALL. Importantly, protein activities-based principal-component-analysis multivariate clusters analyzed for independent outcome prediction using Cox proportional-hazards model showed that protein-activity (but not mutation-status) was independently predictive of outcome, demanding a paradigm-shift in patient-stratification strategy for precision therapy in high-risk ALL.
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15
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Zarubina KI, Parovichnikova EN, Surin VL, Pshenichnikova OS, Gavrilina OA, Isinova GA, Troitskaia VV, Sokolov AN, Gal'tseva IV, Kapranov NM, Davydova IO, Obukhova TN, Sudarikov AB, Savchenko VG. [Detection of activating mutations in RAS/RAF/MEK/ERK and JAK/STAT signaling pathways]. TERAPEVT ARKH 2020; 92:31-42. [PMID: 33346443 DOI: 10.26442/00403660.2020.07.000772] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Indexed: 11/22/2022]
Abstract
ISSUE The study of activating mutations (NRAS,KRAS,FLT3,JAK2,CRLF2genes) of RAS/RAF/MEK/ERK and JAK/STAT signaling pathways in B-cell acute lymphoblastic leukemia (B-ALL) in adult patients which are included in Russian multicenter clinical trials. MATERIALS AND METHODS Within the multicenter study there were 119 adult patients included withde novoB-ALL. The study was considered as prospective and retrospective. The group withBCR-ABL1-negative B-ALL consisted of up to 93 patients (45 male and 48 female, at the age of 17 to 59, the median age 31), they were treated according to the protocols ALL-2009, ALL-2016. The median follow-up lasted for 19 months (1119). The group withBCR-ABL1-positive B-ALL with up to 26 patients (10 male and 16 female, at the age of 23 to 78, the median age 34 years) was included in the study as well. The treatment was carried out according to the protocols ALL-2009 and ALL-2012 in combination with tyrosine kinase inhibitors. The median follow-up lasted for 23 months (4120). The molecular analysis of activating mutations inNRAS,KRASgenes (RAS/RAF/MEK/ERK signaling pathway) andJAK2,CRLF2genes (JAK/STAT signaling cascade) was performed via Sanger sequencing. The internal tandem duplications (ITDs) inFLT3gene were studied by fragment analysis. The evaluation of CRLF2 expression was fulfilled via flow cytometry. RESULTS Activating mutations inNRAS,KRAS,FLT3genes were found in 22 (23.6%) patients withBCR-ABL1-negative B-ALL. In total, 23 mutations were revealed in theNRAS(n=9),KRAS(n=12), andFLT3(n=2) genes, according to statistics that was significantly more frequent than withBCR-ABL1-positive B-ALL, these genes mutations were not identified in patients (p=0.007). The frequency of mutations detection inKRASandNRASgenes in patients withBCR-ABL1-negative B-ALL was comparable as 12.9% (12 of 93) to 9.7% (9 of 93), respectively (p=0.488). One patient was simultaneously revealed 2 mutations in theKRASgene (in codons 13 and 61).FLT3-ITD mutations were detected in 3.5% (2 of 57) cases ofBCR-ABL1-negative B-ALL. In patients withBCR-ABL1-positive B-ALLFLT3-ITD mutations were not assessed. Violations in the JAK/STAT signaling cascade were detected in 4 (4.3%) patients withBCR-ABL1-negative B-ALL. They were represented by the missense mutations ofJAK2gene (n=3) and the overexpression of CRLF2 (n=2); in one patient were detected the overexpression of CRLF2 and a mutation inJAK2gene simultaneously. No mutations were found inCRLF2gene. In patients withBCR-ABL1-positive B-ALL noJAK2mutations were detected. As long as analyzing demographic and clinical laboratory parameters between groups of patients with and without mutations, there were no statistically significant differences obtained. In the analyzed groups of patients, long-term therapy results did not differentiate according to the mutations presence inNRAS,KRAS,FLT3,JAK2genes. Also, substantive differences were not shown in the rate of the negative status achievement of the minimum residual disease between patients with and without activating mutations in the control points of the protocol (on the 70th, 133rd and 190th days). CONCLUSION NRAS,KRAS,FLT3,JAK2activating mutations do not affect the long-term results of the therapy and the rate of the negative status achievement of the minimum residual disease in patients withBCR-ABL1-negative B-ALL treated by the Russian multicenter clinical trials.
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Affiliation(s)
| | | | - V L Surin
- National Research Center for Hematology
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16
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Goyal H, Chachoua I, Pecquet C, Vainchenker W, Constantinescu SN. A p53-JAK-STAT connection involved in myeloproliferative neoplasm pathogenesis and progression to secondary acute myeloid leukemia. Blood Rev 2020; 42:100712. [PMID: 32660739 DOI: 10.1016/j.blre.2020.100712] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Revised: 02/25/2020] [Accepted: 05/27/2020] [Indexed: 01/14/2023]
Abstract
Since the discovery of JAK2 V617F as a highly prevalent somatic acquired mutation in the majority of myeloproliferative neoplasms (MPNs), it has become clear that these diseases are driven by pathologic activation of JAK2 and eventually of STAT5 and other members of the STAT family. The concept was strengthened by the discovery of the other activating driver mutations in MPL (thrombopoietin receptor, TpoR) and in calreticulin gene, which all lead to persistent activation of wild type JAK2. Although with a rare frequency, MPNs can evolve to secondary acute myeloid leukemia (sAML), a condition that is resistant to treatment. Here we focus on the role of p53 in this transition. In sAML mutations in TP53 or amplification in genes coding for negative regulators of p53 are much more frequent than in de novo AML. We review studies that explore a signaling and biochemical interaction between activated STATs and p53 in MPNs and other cancers. With the development of advanced sequencing efforts, strong evidence has been presented for dominant negative effects of mutated p53 in leukemia. In other studies, gain of function effects have been described that might be cell type specific. A more profound understanding of the potential interaction between p53 and activated STATs is necessary in order to take full advantage of novel p53-targeted therapies.
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Affiliation(s)
- Harsh Goyal
- Ludwig Institute for Cancer Research Brussels, Brussels, Belgium; Université catholique de Louvain and de Duve Institute, Brussels, Belgium; WELBIO (Walloon Excellence in Life Sciences and Biotechnology), Brussels, Belgium
| | - Ilyas Chachoua
- Ludwig Institute for Cancer Research Brussels, Brussels, Belgium; Université catholique de Louvain and de Duve Institute, Brussels, Belgium; Karolinska Institutet, Department of Oncology-Pathology, Stockholm, Sweden
| | - Christian Pecquet
- Ludwig Institute for Cancer Research Brussels, Brussels, Belgium; Université catholique de Louvain and de Duve Institute, Brussels, Belgium; WELBIO (Walloon Excellence in Life Sciences and Biotechnology), Brussels, Belgium
| | - William Vainchenker
- INSERM, Unité Mixte de Recherche 1170, Institut Gustave Roussy, Villejuif, France; Paris-Saclay, Unité Mixte de Recherche 1170, Institut Gustave Roussy, Villejuif, France; Gustave Roussy, Unité Mixte de Recherche 1170, Villejuif, France
| | - Stefan N Constantinescu
- Ludwig Institute for Cancer Research Brussels, Brussels, Belgium; Université catholique de Louvain and de Duve Institute, Brussels, Belgium; WELBIO (Walloon Excellence in Life Sciences and Biotechnology), Brussels, Belgium.
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17
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Jin A, Feng J, Wei G, Wu W, Yang L, Xu H, Zhang Y, Cui J, Chang AH, Hu Y, Huang H. CD19/CD22 chimeric antigen receptor T-cell therapy for refractory acute B-cell lymphoblastic leukemia with FLT3-ITD mutations. Bone Marrow Transplant 2020; 55:717-721. [DOI: 10.1038/s41409-020-0807-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Revised: 01/14/2020] [Accepted: 01/21/2020] [Indexed: 11/09/2022]
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18
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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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19
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Frisch A, Ofran Y. How I diagnose and manage Philadelphia chromosome-like acute lymphoblastic leukemia. Haematologica 2019; 104:2135-2143. [PMID: 31582548 PMCID: PMC6821607 DOI: 10.3324/haematol.2018.207506] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Accepted: 09/03/2019] [Indexed: 01/31/2023] Open
Abstract
Advances in our understanding of mechanisms of leukemogenesis and driver mutations in acute lymphoblastic leukemia (ALL) lead to a more precise and informative sub-classification, mainly of B-cell ALL. In parallel, in recent years, novel agents have been approved for the therapy of B-cell ALL, and many others are in active clinical research. Among the newly recognized disease subtypes, Philadelphia-chromosome-like ALL is the most heterogeneous and thus, diagnostically challenging. Given that this subtype of B-cell ALL is associated with a poorer prognosis, improvement of available therapeutic approaches and protocols is a burning issue. Herein, we summarize, in a clinically relevant manner, up-to-date information regarding diagnostic strategies developed for the identification of patients with Philadelphia-chromosome-like ALL. Common therapeutic dilemmas, presented as several case scenarios, are also discussed. It is currently acceptable that patients with B-cell ALL, treated with an aim of cure, irrespective of their age, be evaluated for a Philadelphia-chromosome-like signature as early as possible. Following Philadelphia-chromosome-like recognition, a higher risk of resistance or relapse must be realized and treatment should be modified based on the patient’s specific genetic driver and clinical features. However, while active targeted therapeutic options are limited, there is much more to do than just prescribe a matched inhibitor to the identified mutated driver genes. In this review, we present a comprehensive evidence-based approach to the diagnosis and management of Philadelphia-chromosome-like ALL at different time-points during the disease course.
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Affiliation(s)
- Avraham Frisch
- Department of Hematology and Bone Marrow Transplantation, Rambam Health Care Campus, Haifa
| | - Yishai Ofran
- Department of Hematology and Bone Marrow Transplantation, Rambam Health Care Campus, Haifa .,Bruce Rappaport Faculty of Medicine, Technion, Israel Institute of Technology, Haifa, Israel
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20
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Kubota Y, Uryu K, Ito T, Seki M, Kawai T, Isobe T, Kumagai T, Toki T, Yoshida K, Suzuki H, Kataoka K, Shiraishi Y, Chiba K, Tanaka H, Ohki K, Kiyokawa N, Kagawa J, Miyano S, Oka A, Hayashi Y, Ogawa S, Terui K, Sato A, Hata K, Ito E, Takita J. Integrated genetic and epigenetic analysis revealed heterogeneity of acute lymphoblastic leukemia in Down syndrome. Cancer Sci 2019; 110:3358-3367. [PMID: 31385395 PMCID: PMC6778645 DOI: 10.1111/cas.14160] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Revised: 07/19/2019] [Accepted: 08/03/2019] [Indexed: 12/28/2022] Open
Abstract
Children with Down syndrome (DS) are at a 20‐fold increased risk for acute lymphoblastic leukemia (ALL). Compared to children with ALL and no DS (non‐DS‐ALL), those with DS and ALL (DS‐ALL) harbor uncommon genetic alterations, suggesting DS‐ALL could have distinct biological features. Recent studies have implicated several genes on chromosome 21 in DS‐ALL, but the precise mechanisms predisposing children with DS to ALL remain unknown. Our integrated genetic/epigenetic analysis revealed that DS‐ALL was highly heterogeneous with many subtypes. Although each subtype had genetic/epigenetic profiles similar to those found in non‐DS‐ALL, the subtype distribution differed significantly between groups. The Philadelphia chromosome‐like subtype, a high‐risk B‐cell lineage variant relatively rare among the entire pediatric ALL population, was the most common form in DS‐ALL. Hypermethylation of RUNX1 on chromosome 21 was also found in DS‐ALL, but not non‐DS‐ALL. RUNX1 is essential for differentiation of blood cells, especially B cells; thus, hypermethylation of the RUNX1 promoter in B‐cell precursors might be associated with increased incidence of B‐cell precursor ALL in DS patients.
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Affiliation(s)
- Yasuo Kubota
- Department of Pediatrics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Kumiko Uryu
- Department of Pediatrics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Tatsuya Ito
- Department of Pediatrics, Hirosaki University Graduate School of Medicine, Hirosaki, Japan
| | - Masafumi Seki
- Department of Pediatrics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Tomoko Kawai
- Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Tomoya Isobe
- Department of Pediatrics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Tadayuki Kumagai
- Department of Pediatrics, Fujieda Municipal General Hospital, Fujieda, Japan
| | - Tsutomu Toki
- Department of Pediatrics, Hirosaki University Graduate School of Medicine, Hirosaki, Japan
| | - Kenichi Yoshida
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Hiromichi Suzuki
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Keisuke Kataoka
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Yuichi Shiraishi
- Section of Genome Analysis Platform, Center for Cancer Genomic and Advanced Therapeutics, National Cancer Center, Tokyo, Japan
| | - Kenichi Chiba
- Section of Genome Analysis Platform, Center for Cancer Genomic and Advanced Therapeutics, National Cancer Center, Tokyo, Japan
| | - Hiroko Tanaka
- Laboratory of DNA Information Analysis, Human Genome Center, Institute of Medical Science, University of Tokyo, Tokyo, Japan
| | - Kentaro Ohki
- Department of Pediatric Hematology and Oncology Research, National Research Institute for Child Health and Development, Setagaya-ku, Japan
| | - Nobutaka Kiyokawa
- Department of Pediatric Hematology and Oncology Research, National Research Institute for Child Health and Development, Setagaya-ku, Japan
| | - Jiro Kagawa
- Department of Pediatrics, Fujieda Municipal General Hospital, Fujieda, Japan
| | - Satoru Miyano
- Laboratory of DNA Information Analysis, Human Genome Center, Institute of Medical Science, University of Tokyo, Tokyo, Japan
| | - Akira Oka
- Department of Pediatrics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Yasuhide Hayashi
- Institute of Physiology and Medicine, Jobu University, Takasaki, Japan
| | - Seishi Ogawa
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Kiminori Terui
- Department of Pediatrics, Hirosaki University Graduate School of Medicine, Hirosaki, Japan
| | - Atsushi Sato
- Department of Hematology and Oncology, Miyagi Children's Hospital, Sendai, Japan
| | - Kenichiro Hata
- Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Etsuro Ito
- Department of Pediatrics, Hirosaki University Graduate School of Medicine, Hirosaki, Japan
| | - Junko Takita
- Department of Pediatrics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
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21
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Groeneveld‐Krentz S, Schroeder MP, Reiter M, Pogodzinski MJ, Pimentel‐Gutiérrez HJ, Vagkopoulou R, Hof J, Chen‐Santel C, Nebral K, Bradtke J, Türkmen S, Baldus CD, Gattenlöhner S, Haas OA, Stackelberg A, Karawajew L, Eckert C, Kirschner‐Schwabe R. Aneuploidy in children with relapsed B‐cell precursor acute lymphoblastic leukaemia: clinical importance of detecting a hypodiploid origin of relapse. Br J Haematol 2019; 185:266-283. [DOI: 10.1111/bjh.15770] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Accepted: 11/05/2018] [Indexed: 12/17/2022]
Affiliation(s)
| | - Michael P. Schroeder
- Department of Haematology/Oncology Charité Universitätsmedizin Berlin Berlin Germany
| | - Michael Reiter
- Institute of Visual Computing & Human‐Centered Technology Vienna University of Technology Vienna Austria
| | - Malwine J. Pogodzinski
- Department of Paediatric Oncology/Haematology Charité Universitätsmedizin Berlin Berlin Germany
| | | | - Renia Vagkopoulou
- Department of Paediatric Oncology/Haematology Charité Universitätsmedizin Berlin Berlin Germany
| | - Jana Hof
- Department of Paediatric Oncology/Haematology Charité Universitätsmedizin Berlin Berlin Germany
| | - Christiane Chen‐Santel
- Department of Paediatric Oncology/Haematology Charité Universitätsmedizin Berlin Berlin Germany
| | - Karin Nebral
- Children's Cancer Research Institute St. Anna Kinderkrebsforschung Vienna Austria
| | - Jutta Bradtke
- Department of Pathology University of Gießen Gießen Germany
| | - Seval Türkmen
- Labor Berlin Charité Vivantes Berlin Germany
- Institute of Medical Genetics and Human Genetics Charité Universitätsmedizin Berlin Berlin Germany
| | - Claudia D. Baldus
- Department of Haematology/Oncology Charité Universitätsmedizin Berlin Berlin Germany
| | | | - Oskar A. Haas
- Children's Cancer Research Institute St. Anna Kinderkrebsforschung Vienna Austria
- St. Anna Children's Hospital Medical University of Vienna Austria
| | - Arend Stackelberg
- Department of Paediatric Oncology/Haematology Charité Universitätsmedizin Berlin Berlin Germany
| | - Leonid Karawajew
- Department of Paediatric Oncology/Haematology Charité Universitätsmedizin Berlin Berlin Germany
| | - Cornelia Eckert
- Department of Paediatric Oncology/Haematology Charité Universitätsmedizin Berlin Berlin Germany
- German Cancer Consortium (DKTK), and German Research Center (DKFZ) Heidelberg Germany
| | - Renate Kirschner‐Schwabe
- Department of Paediatric Oncology/Haematology Charité Universitätsmedizin Berlin Berlin Germany
- German Cancer Consortium (DKTK), and German Research Center (DKFZ) Heidelberg Germany
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22
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Lindqvist CM, Lundmark A, Nordlund J, Freyhult E, Ekman D, Carlsson Almlöf J, Raine A, Övernäs E, Abrahamsson J, Frost BM, Grandér D, Heyman M, Palle J, Forestier E, Lönnerholm G, Berglund EC, Syvänen AC. Deep targeted sequencing in pediatric acute lymphoblastic leukemia unveils distinct mutational patterns between genetic subtypes and novel relapse-associated genes. Oncotarget 2018; 7:64071-64088. [PMID: 27590521 PMCID: PMC5325426 DOI: 10.18632/oncotarget.11773] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2016] [Accepted: 08/25/2016] [Indexed: 12/29/2022] Open
Abstract
To characterize the mutational patterns of acute lymphoblastic leukemia (ALL) we performed deep next generation sequencing of 872 cancer genes in 172 diagnostic and 24 relapse samples from 172 pediatric ALL patients. We found an overall greater mutational burden and more driver mutations in T-cell ALL (T-ALL) patients compared to B-cell precursor ALL (BCP-ALL) patients. In addition, the majority of the mutations in T-ALL had occurred in the original leukemic clone, while most of the mutations in BCP-ALL were subclonal. BCP-ALL patients carrying any of the recurrent translocations ETV6-RUNX1, BCR-ABL or TCF3-PBX1 harbored few mutations in driver genes compared to other BCP-ALL patients. Specifically in BCP-ALL, we identified ATRX as a novel putative driver gene and uncovered an association between somatic mutations in the Notch signaling pathway at ALL diagnosis and increased risk of relapse. Furthermore, we identified EP300, ARID1A and SH2B3 as relapse-associated genes. The genes highlighted in our study were frequently involved in epigenetic regulation, associated with germline susceptibility to ALL, and present in minor subclones at diagnosis that became dominant at relapse. We observed a high degree of clonal heterogeneity and evolution between diagnosis and relapse in both BCP-ALL and T-ALL, which could have implications for the treatment efficiency.
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Affiliation(s)
- C Mårten Lindqvist
- Department of Medical Sciences, Molecular Medicine and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Anders Lundmark
- Department of Medical Sciences, Molecular Medicine and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Jessica Nordlund
- Department of Medical Sciences, Molecular Medicine and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Eva Freyhult
- Cancer Pharmacology and Computational Medicine, Department of Medical Sciences, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Diana Ekman
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Jonas Carlsson Almlöf
- Department of Medical Sciences, Molecular Medicine and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Amanda Raine
- Department of Medical Sciences, Molecular Medicine and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Elin Övernäs
- Department of Medical Sciences, Molecular Medicine and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Jonas Abrahamsson
- Department of Pediatrics, Queen Silvia Children's Hospital, Gothenburg, Sweden.,Nordic Society of Pediatric Hematology and Oncology
| | - Britt-Marie Frost
- Department of Women's and Children's Health, University Children's Hospital, Uppsala, Sweden.,Nordic Society of Pediatric Hematology and Oncology
| | - Dan Grandér
- Department of Oncology-Pathology, Karolinska Institute, Stockholm, Sweden
| | - Mats Heyman
- Childhood Cancer Research Unit, Department of Women and Child Health, Astrid Lindgren Children's Hospital, Karolinska University Hospital, Stockholm, Sweden.,Nordic Society of Pediatric Hematology and Oncology
| | - Josefine Palle
- Department of Medical Sciences, Molecular Medicine and Science for Life Laboratory, Uppsala University, Uppsala, Sweden.,Department of Women's and Children's Health, University Children's Hospital, Uppsala, Sweden.,Nordic Society of Pediatric Hematology and Oncology
| | - Erik Forestier
- Department of Medical Biosciences, University of Umeå, Umeå, Sweden.,Nordic Society of Pediatric Hematology and Oncology
| | - Gudmar Lönnerholm
- Department of Women's and Children's Health, University Children's Hospital, Uppsala, Sweden.,Nordic Society of Pediatric Hematology and Oncology
| | - Eva C Berglund
- Department of Medical Sciences, Molecular Medicine and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Ann-Christine Syvänen
- Department of Medical Sciences, Molecular Medicine and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
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23
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de Smith AJ, Ojha J, Francis SS, Sanders E, Endicott AA, Hansen HM, Smirnov I, Termuhlen AM, Walsh KM, Metayer C, Wiemels JL. Clonal and microclonal mutational heterogeneity in high hyperdiploid acute lymphoblastic leukemia. Oncotarget 2018; 7:72733-72745. [PMID: 27683039 PMCID: PMC5341940 DOI: 10.18632/oncotarget.12238] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Accepted: 09/17/2016] [Indexed: 12/31/2022] Open
Abstract
High hyperdiploidy (HD), the most common cytogenetic subtype of B-cell acute lymphoblastic leukemia (B-ALL), is largely curable but significant treatment-related morbidity warrants investigating the biology and identifying novel drug targets. Targeted deep-sequencing of 538 cancer-relevant genes was performed in 57 HD-ALL patients lacking overt KRAS and NRAS hotspot mutations and lacking common B-ALL deletions to enrich for discovery of novel driver genes. One-third of patients harbored damaging mutations in epigenetic regulatory genes, including the putative novel driver DOT1L (n=4). Receptor tyrosine kinase (RTK)/Ras/MAPK signaling pathway mutations were found in two-thirds of patients, including novel mutations in ROS1, which mediates phosphorylation of the PTPN11-encoded protein SHP2. Mutations in FLT3 significantly co-occurred with DOT1L (p=0.04), suggesting functional cooperation in leukemogenesis. We detected an extraordinary level of tumor heterogeneity, with microclonal (mutant allele fraction <0.10) KRAS, NRAS, FLT3, and/or PTPN11 hotspot mutations evident in 31/57 (54.4%) patients. Multiple KRAS and NRAS codon 12 and 13 microclonal mutations significantly co-occurred within tumor samples (p=4.8x10-4), suggesting ongoing formation of and selection for Ras-activating mutations. Future work is required to investigate whether tumor microheterogeneity impacts clinical outcome and to elucidate the functional consequences of epigenetic dysregulation in HD-ALL, potentially leading to novel therapeutic approaches.
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Affiliation(s)
- Adam J de Smith
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, California, United States of America
| | - Juhi Ojha
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, California, United States of America
| | - Stephen S Francis
- Division of Neuroepidemiology, Department of Neurological Surgery, University of California San Francisco, San Francisco, California, United States of America
| | - Erica Sanders
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, California, United States of America
| | - Alyson A Endicott
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, California, United States of America
| | - Helen M Hansen
- Division of Neuroepidemiology, Department of Neurological Surgery, University of California San Francisco, San Francisco, California, United States of America
| | - Ivan Smirnov
- Division of Neuroepidemiology, Department of Neurological Surgery, University of California San Francisco, San Francisco, California, United States of America
| | - Amanda M Termuhlen
- Children's Hospital Los Angeles, Department of Pediatrics, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
| | - Kyle M Walsh
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, California, United States of America.,Division of Neuroepidemiology, Department of Neurological Surgery, University of California San Francisco, San Francisco, California, United States of America
| | - Catherine Metayer
- School of Public Health, University of California Berkeley, Berkeley, California, United States of America
| | - Joseph L Wiemels
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, California, United States of America.,Division of Neuroepidemiology, Department of Neurological Surgery, University of California San Francisco, San Francisco, California, United States of America
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24
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Malouf C, Ottersbach K. Molecular processes involved in B cell acute lymphoblastic leukaemia. Cell Mol Life Sci 2018; 75:417-446. [PMID: 28819864 PMCID: PMC5765206 DOI: 10.1007/s00018-017-2620-z] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Revised: 08/01/2017] [Accepted: 08/04/2017] [Indexed: 12/19/2022]
Abstract
B cell leukaemia is one of the most frequent malignancies in the paediatric population, but also affects a significant proportion of adults in developed countries. The majority of infant and paediatric cases initiate the process of leukaemogenesis during foetal development (in utero) through the formation of a chromosomal translocation or the acquisition/deletion of genetic material (hyperdiploidy or hypodiploidy, respectively). This first genetic insult is the major determinant for the prognosis and therapeutic outcome of patients. B cell leukaemia in adults displays similar molecular features as its paediatric counterpart. However, since this disease is highly represented in the infant and paediatric population, this review will focus on this demographic group and summarise the biological, clinical and epidemiological knowledge on B cell acute lymphoblastic leukaemia of four well characterised subtypes: t(4;11) MLL-AF4, t(12;21) ETV6-RUNX1, t(1;19) E2A-PBX1 and t(9;22) BCR-ABL1.
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Affiliation(s)
- Camille Malouf
- MRC Centre for Regenerative Medicine, The University of Edinburgh, 5 Little France Drive, Edinburgh, EH16 4UU, UK
| | - Katrin Ottersbach
- MRC Centre for Regenerative Medicine, The University of Edinburgh, 5 Little France Drive, Edinburgh, EH16 4UU, UK.
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25
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Liang DC, Chen SH, Liu HC, Yang CP, Yeh TC, Jaing TH, Hung IJ, Hou JY, Lin TH, Lin CH, Shih LY. Mutational status of NRAS, KRAS, and PTPN11 genes is associated with genetic/cytogenetic features in children with B-precursor acute lymphoblastic leukemia. Pediatr Blood Cancer 2018; 65. [PMID: 28853218 DOI: 10.1002/pbc.26786] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Revised: 08/06/2017] [Accepted: 08/07/2017] [Indexed: 12/15/2022]
Abstract
BACKGROUND We aimed to investigate the frequencies and the association with genetic/cytogenetic abnormalities as well as prognostic relevance of RAS pathway mutations in Taiwanese children with B-precursor acute lymphoblastic leukemia (ALL), the largest cohort in Asians. PROCEDURE Between 1995 and 2012, marrow samples at diagnosis from 535 children were studied for NRAS, KRAS, and PTPN11 mutations. The mutational status of each gene was correlated with the clinico-hematological features, recurrent genetic abnormalities, and outcomes for those treated with TPOG-ALL-2002 protocol (n = 346). RESULTS The frequencies of NRAS, KRAS, and PTPN11 mutations were 10.8% (57/530), 10.2% (54/530), and 3.0% (16/526), respectively. NRAS mutations were associated with a higher frequency of hyperdiploidy (P = 0.01) and lower frequency of ETV6-RUNX1 (P < 0.01), whereas KRAS mutations were associated with younger age (P < 0.01), a higher frequency of KMT2A rearranged (P < 0.01) but no significant difference if infants with ALL were excluded, and inferior event-free survival (66.6% vs. 80.5%, P = 0.04). None of patients with TCF3-PBX1 had KRAS mutation (P = 0.02). CONCLUSIONS Our study showed that the frequency of KRAS mutations in Taiwan was significantly higher than that reported in Caucasians. The occurrence of RAS pathway mutations was associated with recurrent genetic/cytogenetic abnormalities in pediatric B-precursor ALL.
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Affiliation(s)
- Der-Cherng Liang
- Division of Pediatric Hematology-Oncology, Mackay Memorial Hospital and Mackay Medical College, Taipei, Taiwan
| | - Shih-Hsiang Chen
- Division of Hematology-Oncology, Department of Pediatrics, Chang Gung Memorial Hospital, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Hsi-Che Liu
- Division of Pediatric Hematology-Oncology, Mackay Memorial Hospital and Mackay Medical College, Taipei, Taiwan
| | - Chao-Ping Yang
- Division of Hematology-Oncology, Department of Pediatrics, Chang Gung Memorial Hospital, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Ting-Chi Yeh
- Division of Pediatric Hematology-Oncology, Mackay Memorial Hospital and Mackay Medical College, Taipei, Taiwan
| | - Tang-Her Jaing
- Division of Hematology-Oncology, Department of Pediatrics, Chang Gung Memorial Hospital, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Iou-Jih Hung
- Division of Hematology-Oncology, Department of Pediatrics, Chang Gung Memorial Hospital, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Jen-Yin Hou
- Division of Pediatric Hematology-Oncology, Mackay Memorial Hospital and Mackay Medical College, Taipei, Taiwan
| | - Tung-Huei Lin
- Division of Hematology-Oncology, Department of Internal Medicine, Chang Gung Memorial Hospital, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Chun-Hui Lin
- Division of Pediatric Hematology-Oncology, Mackay Memorial Hospital and Mackay Medical College, Taipei, Taiwan
| | - Lee-Yung Shih
- Division of Hematology-Oncology, Department of Internal Medicine, Chang Gung Memorial Hospital, College of Medicine, Chang Gung University, Taoyuan, Taiwan
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26
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Messina M, Chiaretti S, Wang J, Fedullo AL, Peragine N, Gianfelici V, Piciocchi A, Brugnoletti F, Di Giacomo F, Pauselli S, Holmes AB, Puzzolo MC, Ceglie G, Apicella V, Mancini M, Te Kronnie G, Testi AM, Vitale A, Vignetti M, Guarini A, Rabadan R, Foà R. Prognostic and therapeutic role of targetable lesions in B-lineage acute lymphoblastic leukemia without recurrent fusion genes. Oncotarget 2017; 7:13886-901. [PMID: 26883104 PMCID: PMC4924686 DOI: 10.18632/oncotarget.7356] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2015] [Accepted: 01/28/2016] [Indexed: 12/03/2022] Open
Abstract
To shed light into the molecular bases of B-lineage acute lymphoblastic leukemia lacking known fusion transcripts, i.e. BCR-ABL1, ETV6-RUNX1, E2A-PBX1, and MLL rearrangements (B-NEG ALL) and the differences between children, adolescents/young adults (AYA) and adults, we analyzed 168 B-NEG ALLs by genome-wide technologies. This approach showed that B-NEG cases carry 10.5 mutations and 9.1 copy-number aberrations/sample. The most frequently mutated druggable pathways were those pertaining to RAS/RTK (26.8%) and JAK/STAT (12.5%) signaling. In particular, FLT3 and JAK/STAT mutations were detected mainly in AYA and adults, while KRAS and NRAS mutations were more frequent in children. RAS/RTK mutations negatively affected the outcome of AYA and adults, but not that of children. Furthermore, adult B-NEG ALL carrying JAK/STAT mutations had a shorter survival. In vitro experiments showed that FLT3 inhibitors reduced significantly the proliferation of FLT3-mutated primary B-NEG ALL cells. Likewise, PI3K/mTOR inhibitors reduced the proliferation of primary cells harboring RAS and IL7R mutations. These results refine the genetic landscape of B-NEG ALL and suggest that the different distribution of lesions and their prognostic impact might sustain the diverse outcome between children, adults and partly AYA - whose genomic scenario is similar to adults - and open the way to targeted therapeutic strategies.
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Affiliation(s)
- Monica Messina
- Hematology, Department of Cellular Biotechnologies and Hematology, Sapienza University, Rome, Italy
| | - Sabina Chiaretti
- Hematology, Department of Cellular Biotechnologies and Hematology, Sapienza University, Rome, Italy
| | - Jiguang Wang
- Department of Systems Biology, Biomedical Informatics and Center for Computational Biology and Bioinformatics, Columbia University, New York, NY, USA
| | - Anna Lucia Fedullo
- Hematology, Department of Cellular Biotechnologies and Hematology, Sapienza University, Rome, Italy
| | - Nadia Peragine
- Hematology, Department of Cellular Biotechnologies and Hematology, Sapienza University, Rome, Italy
| | - Valentina Gianfelici
- Hematology, Department of Cellular Biotechnologies and Hematology, Sapienza University, Rome, Italy
| | | | - Fulvia Brugnoletti
- Hematology, Department of Cellular Biotechnologies and Hematology, Sapienza University, Rome, Italy
| | - Filomena Di Giacomo
- Department of Molecular Biotechnology and Health Science, and Center for Experimental Research and Medical Studies (CeRMS), University of Torino, Torino, Italy
| | - Simona Pauselli
- Hematology, Department of Cellular Biotechnologies and Hematology, Sapienza University, Rome, Italy
| | - Antony B Holmes
- Institute for Cancer Genetics and The Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY, USA
| | - Maria Cristina Puzzolo
- Hematology, Department of Cellular Biotechnologies and Hematology, Sapienza University, Rome, Italy
| | - Giulia Ceglie
- Hematology, Department of Cellular Biotechnologies and Hematology, Sapienza University, Rome, Italy
| | - Valerio Apicella
- Hematology, Department of Cellular Biotechnologies and Hematology, Sapienza University, Rome, Italy
| | - Marco Mancini
- Hematology, Department of Cellular Biotechnologies and Hematology, Sapienza University, Rome, Italy
| | - Geertruy Te Kronnie
- Department of Women's and Children's Health, University of Padova, Padova, Italy
| | - Anna Maria Testi
- Hematology, Department of Cellular Biotechnologies and Hematology, Sapienza University, Rome, Italy
| | - Antonella Vitale
- Hematology, Department of Cellular Biotechnologies and Hematology, Sapienza University, Rome, Italy
| | | | - Anna Guarini
- Hematology, Department of Cellular Biotechnologies and Hematology, Sapienza University, Rome, Italy
| | - Raul Rabadan
- Department of Systems Biology, Biomedical Informatics and Center for Computational Biology and Bioinformatics, Columbia University, New York, NY, USA
| | - Robin Foà
- Hematology, Department of Cellular Biotechnologies and Hematology, Sapienza University, Rome, Italy
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27
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Marincevic-Zuniga Y, Dahlberg J, Nilsson S, Raine A, Nystedt S, Lindqvist CM, Berglund EC, Abrahamsson J, Cavelier L, Forestier E, Heyman M, Lönnerholm G, Nordlund J, Syvänen AC. Transcriptome sequencing in pediatric acute lymphoblastic leukemia identifies fusion genes associated with distinct DNA methylation profiles. J Hematol Oncol 2017; 10:148. [PMID: 28806978 PMCID: PMC5557398 DOI: 10.1186/s13045-017-0515-y] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Accepted: 08/03/2017] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Structural chromosomal rearrangements that lead to expressed fusion genes are a hallmark of acute lymphoblastic leukemia (ALL). In this study, we performed transcriptome sequencing of 134 primary ALL patient samples to comprehensively detect fusion transcripts. METHODS We combined fusion gene detection with genome-wide DNA methylation analysis, gene expression profiling, and targeted sequencing to determine molecular signatures of emerging ALL subtypes. RESULTS We identified 64 unique fusion events distributed among 80 individual patients, of which over 50% have not previously been reported in ALL. Although the majority of the fusion genes were found only in a single patient, we identified several recurrent fusion gene families defined by promiscuous fusion gene partners, such as ETV6, RUNX1, PAX5, and ZNF384, or recurrent fusion genes, such as DUX4-IGH. Our data show that patients harboring these fusion genes displayed characteristic genome-wide DNA methylation and gene expression signatures in addition to distinct patterns in single nucleotide variants and recurrent copy number alterations. CONCLUSION Our study delineates the fusion gene landscape in pediatric ALL, including both known and novel fusion genes, and highlights fusion gene families with shared molecular etiologies, which may provide additional information for prognosis and therapeutic options in the future.
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Affiliation(s)
- Yanara Marincevic-Zuniga
- Department of Medical Sciences, Molecular Medicine and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Johan Dahlberg
- Department of Medical Sciences, Molecular Medicine and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Sara Nilsson
- Department of Medical Sciences, Molecular Medicine and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Amanda Raine
- Department of Medical Sciences, Molecular Medicine and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Sara Nystedt
- Department of Medical Sciences, Molecular Medicine and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Carl Mårten Lindqvist
- Department of Medical Sciences, Molecular Medicine and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Eva C Berglund
- Department of Medical Sciences, Molecular Medicine and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Jonas Abrahamsson
- Department of Pediatrics, Institution for Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Lucia Cavelier
- Clinical Genetics, Uppsala University Hospital, Uppsala, Sweden
| | - Erik Forestier
- Department of Medical Biosciences, University of Umeå, Umeå, Sweden
| | - Mats Heyman
- Karolinska Institutet, Childhood Cancer Research Unit, Astrid Lindgren Children's Hospital, Karolinska University Hospital, Stockholm, Sweden
| | - Gudmar Lönnerholm
- Department of Women's and Children's Health, Pediatric Oncology, Uppsala University, Uppsala, Sweden
| | - Jessica Nordlund
- Department of Medical Sciences, Molecular Medicine and Science for Life Laboratory, Uppsala University, Uppsala, Sweden.
| | - Ann-Christine Syvänen
- Department of Medical Sciences, Molecular Medicine and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
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28
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Advances in B-lymphoblastic leukemia: cytogenetic and genomic lesions. Ann Diagn Pathol 2016; 23:43-50. [DOI: 10.1016/j.anndiagpath.2016.02.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Accepted: 02/08/2016] [Indexed: 12/11/2022]
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29
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Lilljebjörn H, Henningsson R, Hyrenius-Wittsten A, Olsson L, Orsmark-Pietras C, von Palffy S, Askmyr M, Rissler M, Schrappe M, Cario G, Castor A, Pronk CJH, Behrendtz M, Mitelman F, Johansson B, Paulsson K, Andersson AK, Fontes M, Fioretos T. Identification of ETV6-RUNX1-like and DUX4-rearranged subtypes in paediatric B-cell precursor acute lymphoblastic leukaemia. Nat Commun 2016; 7:11790. [PMID: 27265895 PMCID: PMC4897744 DOI: 10.1038/ncomms11790] [Citation(s) in RCA: 209] [Impact Index Per Article: 26.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Revised: 04/11/2016] [Accepted: 04/28/2016] [Indexed: 12/16/2022] Open
Abstract
Fusion genes are potent driver mutations in cancer. In this study, we delineate the fusion gene landscape in a consecutive series of 195 paediatric B-cell precursor acute lymphoblastic leukaemia (BCP ALL). Using RNA sequencing, we find in-frame fusion genes in 127 (65%) cases, including 27 novel fusions. We describe a subtype characterized by recurrent IGH-DUX4 or ERG-DUX4 fusions, representing 4% of cases, leading to overexpression of DUX4 and frequently co-occurring with intragenic ERG deletions. Furthermore, we identify a subtype characterized by an ETV6-RUNX1-like gene-expression profile and coexisting ETV6 and IKZF1 alterations. Thus, this study provides a detailed overview of fusion genes in paediatric BCP ALL and adds new pathogenetic insights, which may improve risk stratification and provide therapeutic options for this disease.
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Affiliation(s)
- Henrik Lilljebjörn
- Department of Laboratory Medicine, Division of Clinical Genetics, Lund University, Lund 22184, Sweden
| | | | - Axel Hyrenius-Wittsten
- Department of Laboratory Medicine, Division of Clinical Genetics, Lund University, Lund 22184, Sweden
| | - Linda Olsson
- Department of Laboratory Medicine, Division of Clinical Genetics, Lund University, Lund 22184, Sweden
| | - Christina Orsmark-Pietras
- Department of Laboratory Medicine, Division of Clinical Genetics, Lund University, Lund 22184, Sweden
| | - Sofia von Palffy
- Department of Laboratory Medicine, Division of Clinical Genetics, Lund University, Lund 22184, Sweden
| | - Maria Askmyr
- Department of Laboratory Medicine, Division of Clinical Genetics, Lund University, Lund 22184, Sweden
| | - Marianne Rissler
- Department of Laboratory Medicine, Division of Clinical Genetics, Lund University, Lund 22184, Sweden
| | - Martin Schrappe
- Department of Pediatrics, University Hospital Schleswig-Holstein, Kiel 24105, Germany
| | - Gunnar Cario
- Department of Pediatrics, University Hospital Schleswig-Holstein, Kiel 24105, Germany
| | - Anders Castor
- Department of Pediatrics, Skåne University Hospital, Lund University, Lund 22185, Sweden
| | - Cornelis J. H. Pronk
- Department of Pediatrics, Skåne University Hospital, Lund University, Lund 22185, Sweden
| | - Mikael Behrendtz
- Department of Pediatrics, Linköping University Hospital, Linköping 58185, Sweden
| | - Felix Mitelman
- Department of Laboratory Medicine, Division of Clinical Genetics, Lund University, Lund 22184, Sweden
| | - Bertil Johansson
- Department of Laboratory Medicine, Division of Clinical Genetics, Lund University, Lund 22184, Sweden
- Department of Clinical Genetics, University and Regional Laboratories Region Skåne, Lund 22185, Sweden
| | - Kajsa Paulsson
- Department of Laboratory Medicine, Division of Clinical Genetics, Lund University, Lund 22184, Sweden
| | - Anna K. Andersson
- Department of Laboratory Medicine, Division of Clinical Genetics, Lund University, Lund 22184, Sweden
| | - Magnus Fontes
- Centre for Mathematical Sciences, Lund University, Lund 22362, Sweden
| | - Thoas Fioretos
- Department of Laboratory Medicine, Division of Clinical Genetics, Lund University, Lund 22184, Sweden
- Department of Clinical Genetics, University and Regional Laboratories Region Skåne, Lund 22185, Sweden
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30
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The role of the RAS pathway in iAMP21-ALL. Leukemia 2016; 30:1824-31. [PMID: 27168466 PMCID: PMC5017527 DOI: 10.1038/leu.2016.80] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Revised: 02/10/2016] [Accepted: 03/22/2016] [Indexed: 01/20/2023]
Abstract
Intrachromosomal amplification of chromosome 21 (iAMP21) identifies a high-risk subtype of acute lymphoblastic leukaemia (ALL), requiring intensive treatment to reduce their relapse risk. Improved understanding of the genomic landscape of iAMP21-ALL will ascertain whether these patients may benefit from targeted therapy. We performed whole-exome sequencing of eight iAMP21-ALL samples. The mutation rate was dramatically disparate between cases (average 24.9, range 5-51) and a large number of novel variants were identified, including frequent mutation of the RAS/MEK/ERK pathway. Targeted sequencing of a larger cohort revealed that 60% (25/42) of diagnostic iAMP21-ALL samples harboured 42 distinct RAS pathway mutations. High sequencing coverage demonstrated heterogeneity in the form of multiple RAS pathway mutations within the same sample and diverse variant allele frequencies (VAFs) (2-52%), similar to other subtypes of ALL. Constitutive RAS pathway activation was observed in iAMP21 samples that harboured mutations in the predominant clone (⩾35% VAF). Viable iAMP21 cells from primary xenografts showed reduced viability in response to the MEK1/2 inhibitor, selumetinib, in vitro. As clonal (⩾35% VAF) mutations were detected in 26% (11/42) of iAMP21-ALL, this evidence of response to RAS pathway inhibitors may offer the possibility to introduce targeted therapy to improve therapeutic efficacy in these high-risk patients.
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31
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Liu X, Zheng H, Li X, Wang S, Meyerson HJ, Yang W, Neel BG, Qu CK. Gain-of-function mutations of Ptpn11 (Shp2) cause aberrant mitosis and increase susceptibility to DNA damage-induced malignancies. Proc Natl Acad Sci U S A 2016; 113:984-9. [PMID: 26755576 PMCID: PMC4743778 DOI: 10.1073/pnas.1508535113] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Gain-of-function (GOF) mutations of protein tyrosine phosphatase nonreceptor type 11 Ptpn11 (Shp2), a protein tyrosine phosphatase implicated in multiple cell signaling pathways, are associated with childhood leukemias and solid tumors. The underlying mechanisms are not fully understood. Here, we report that Ptpn11 GOF mutations disturb mitosis and cytokinesis, causing chromosomal instability and greatly increased susceptibility to DNA damage-induced malignancies. We find that Shp2 is distributed to the kinetochore, centrosome, spindle midzone, and midbody, all of which are known to play critical roles in chromosome segregation and cytokinesis. Mouse embryonic fibroblasts with Ptpn11 GOF mutations show a compromised mitotic checkpoint. Centrosome amplification and aberrant mitosis with misaligned or lagging chromosomes are significantly increased in Ptpn11-mutated mouse and patient cells. Abnormal cytokinesis is also markedly increased in these cells. Further mechanistic analyses reveal that GOF mutant Shp2 hyperactivates the Polo-like kinase 1 (Plk1) kinase by enhancing c-Src kinase-mediated tyrosine phosphorylation of Plk1. This study provides novel insights into the tumorigenesis associated with Ptpn11 GOF mutations and cautions that DNA-damaging treatments in Noonan syndrome patients with germ-line Ptpn11 GOF mutations could increase the risk of therapy-induced malignancies.
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Affiliation(s)
- Xia Liu
- Division of Hematology/Oncology, Department of Medicine, Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH 44106
| | - Hong Zheng
- Division of Hematology/Oncology, Department of Medicine, Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH 44106; Division of Hematology/Oncology, Department of Pediatrics, Aflac Cancer and Blood Disorders Center, Children's Healthcare of Atlanta, Emory University, Atlanta, GA 30322
| | - Xiaobo Li
- Division of Hematology/Oncology, Department of Medicine, Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH 44106; Division of Hematology/Oncology, Department of Pediatrics, Aflac Cancer and Blood Disorders Center, Children's Healthcare of Atlanta, Emory University, Atlanta, GA 30322
| | - Siying Wang
- Division of Hematology/Oncology, Department of Medicine, Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH 44106
| | - Howard J Meyerson
- Department of Pathology, Case Western Reserve University, Cleveland, OH 44106
| | - Wentian Yang
- Department of Orthopaedics, Brown University Alpert Medical School, Providence, RI 02912
| | - Benjamin G Neel
- Princess Margaret Cancer Center, Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 2M9, Canada
| | - Cheng-Kui Qu
- Division of Hematology/Oncology, Department of Medicine, Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH 44106; Division of Hematology/Oncology, Department of Pediatrics, Aflac Cancer and Blood Disorders Center, Children's Healthcare of Atlanta, Emory University, Atlanta, GA 30322;
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32
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Al-Kzayer LFY, Sakashita K, Al-Jadiry MF, Al-Hadad SA, Ghali HH, Uyen LTN, Liu T, Matsuda K, Abdulkadhim JMH, Al-Shujairi TA, Matti ZIIK, Sughayer MA, Rihani R, Madanat FF, Inoshita T, Kamata M, Koike K. Analysis of KRAS and NRAS Gene Mutations in Arab Asian Children With Acute Leukemia: High Frequency of RAS Mutations in Acute Lymphoblastic Leukemia. Pediatr Blood Cancer 2015. [PMID: 26222068 DOI: 10.1002/pbc.25683] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
BACKGROUND KRAS and NRAS gene mutations are frequently observed in childhood leukemia. The objective of this study was to determine the frequency of RAS mutations and the association between RAS mutations and other genetic aberrations in Arab Asian children with acute lymphoblastic leukemia (ALL) or acute myeloid leukemia (AML). METHODS Diagnostic samples of 485 patients (<18 years) with acute leukemia from Iraq and Jordan were obtained, using Flinders Technology Associates filter papers. Polymerase chain reaction and direct sequencing were performed in Japan. RESULTS RAS mutations were detected in 86/318 (27%) of ALL cases and 35/167 (21%) of AML cases. The frequency of NRAS mutation was similar to that of KRAS mutation in ALL. Two RAS mutations were detected in nine patients. Among 264 Iraqi patients with ALL, RAS mutation was significantly associated with lower initial white blood cell count. Of 57 patients with chimeric transcripts, only two patients with either TEL-AML1 or E2A-PBX1 had KRAS mutation. The frequency of NRAS mutation was four times higher than that of KRAS mutation in AML. FAB-M4 and M5 subsets were associated with RAS mutation. Among 134 Iraqi patients with AML, 18 patients had RAS mutations and other genetic aberrations. In particular, 9 of 25 (36%) with MLL-rearrangement had RAS mutations. CONCLUSION The prevalence of oncogenic RAS mutations was higher among Arab Asian children than in other countries. RAS mutations in AML were found to coexist with other genetic aberrations, particularly MLL rearrangement.
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Affiliation(s)
| | - Kazuo Sakashita
- Department of Pediatrics, Shinshu University School of Medicine, Matsumoto, Nagano, Japan
| | - Mazin Faisal Al-Jadiry
- Department of Pediatrics, College of Medicine, Baghdad University, Baghdad Medical City, Baghdad, Iraq.,Department of Pediatric Oncology, Children's Welfare Teaching Hospital, Baghdad Medical City, Baghdad, Iraq
| | - Salma Abbas Al-Hadad
- Department of Pediatrics, College of Medicine, Baghdad University, Baghdad Medical City, Baghdad, Iraq.,Department of Pediatric Oncology, Children's Welfare Teaching Hospital, Baghdad Medical City, Baghdad, Iraq
| | - Hasanein Habeeb Ghali
- Department of Pediatrics, College of Medicine, Baghdad University, Baghdad Medical City, Baghdad, Iraq.,Department of Pediatric Oncology, Children's Welfare Teaching Hospital, Baghdad Medical City, Baghdad, Iraq
| | - Le T N Uyen
- Department of Pediatrics, Shinshu University School of Medicine, Matsumoto, Nagano, Japan
| | - Tingting Liu
- Department of Pediatrics, Shinshu University School of Medicine, Matsumoto, Nagano, Japan
| | - Kazuyuki Matsuda
- Department of Laboratory Medicine, Shinshu University Hospital, Matsumoto, Nagano, Japan
| | | | | | - Zead Ismael I K Matti
- Department of Pediatric Oncology, Central Teaching Hospital for Children, Baghdad, Iraq
| | - Maher A Sughayer
- Department of Pathology, King Hussein Cancer Center, Amman, Jordan
| | - Rawad Rihani
- Department of Pediatrics, King Hussein Cancer Center, Amman, Jordan
| | - Faris F Madanat
- Department of Pediatrics, King Hussein Cancer Center, Amman, Jordan
| | | | - Minoru Kamata
- Japan Chernobyl Foundation, Matsumoto, Nagano, Japan
| | - Kenichi Koike
- Department of Pediatrics, Shinshu University School of Medicine, Matsumoto, Nagano, Japan
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33
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Chen C, Bartenhagen C, Gombert M, Okpanyi V, Binder V, Röttgers S, Bradtke J, Teigler-Schlegel A, Harbott J, Ginzel S, Thiele R, Husemann P, Krell PF, Borkhardt A, Dugas M, Hu J, Fischer U. Next-generation-sequencing of recurrent childhood high hyperdiploid acute lymphoblastic leukemia reveals mutations typically associated with high risk patients. Leuk Res 2015; 39:990-1001. [DOI: 10.1016/j.leukres.2015.06.005] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2015] [Revised: 06/08/2015] [Accepted: 06/10/2015] [Indexed: 01/07/2023]
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34
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MLL leukemia induction by genome editing of human CD34+ hematopoietic cells. Blood 2015; 126:1683-94. [PMID: 26311362 DOI: 10.1182/blood-2015-05-646398] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2015] [Accepted: 08/23/2015] [Indexed: 01/01/2023] Open
Abstract
Chromosomal rearrangements involving the mixed-lineage leukemia (MLL) gene occur in primary and treatment-related leukemias and confer a poor prognosis. Studies based primarily on mouse models have substantially advanced our understanding of MLL leukemia pathogenesis, but often use supraphysiological oncogene expression with uncertain implications for human leukemia. Genome editing using site-specific nucleases provides a powerful new technology for gene modification to potentially model human disease, however, this approach has not been used to re-create acute leukemia in human cells of origin comparable to disease observed in patients. We applied transcription activator-like effector nuclease-mediated genome editing to generate endogenous MLL-AF9 and MLL-ENL oncogenes through insertional mutagenesis in primary human hematopoietic stem and progenitor cells (HSPCs) derived from human umbilical cord blood. Engineered HSPCs displayed altered in vitro growth potentials and induced acute leukemias following transplantation in immunocompromised mice at a mean latency of 16 weeks. The leukemias displayed phenotypic and morphologic similarities with patient leukemia blasts including a subset with mixed phenotype, a distinctive feature seen in clinical disease. The leukemic blasts expressed an MLL-associated transcriptional program with elevated levels of crucial MLL target genes, displayed heightened sensitivity to DOT1L inhibition, and demonstrated increased oncogenic potential ex vivo and in secondary transplant assays. Thus, genome editing to create endogenous MLL oncogenes in primary human HSPCs faithfully models acute MLL-rearranged leukemia and provides an experimental platform for prospective studies of leukemia initiation and stem cell biology in a genetic subtype of poor prognosis leukemia.
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35
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Ghazavi F, Lammens T, Van Roy N, Poppe B, Speleman F, Benoit Y, Van Vlierberghe P, De Moerloose B. Molecular basis and clinical significance of genetic aberrations in B-cell precursor acute lymphoblastic leukemia. Exp Hematol 2015; 43:640-53. [DOI: 10.1016/j.exphem.2015.05.015] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2015] [Revised: 05/26/2015] [Accepted: 05/28/2015] [Indexed: 12/25/2022]
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36
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Paulsson K. High hyperdiploid childhood acute lymphoblastic leukemia: Chromosomal gains as the main driver event. Mol Cell Oncol 2015; 3:e1064555. [PMID: 27308574 DOI: 10.1080/23723556.2015.1064555] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Revised: 06/17/2015] [Accepted: 06/17/2015] [Indexed: 10/23/2022]
Abstract
High hyperdiploid childhood acute lymphoblastic leukemia is characterized by multiple chromosomal gains. Recent results show that this subtype harbors relatively few genetic abnormalities besides the extra chromosomes, which appear to arise early and are likely the main driver event. Secondary hits primarily target genes in the rat sarcoma (RAS) signaling pathway and histone modifiers.
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Affiliation(s)
- Kajsa Paulsson
- Division of Clinical Genetics, Lund University , Lund, Sweden
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37
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The genomic landscape of high hyperdiploid childhood acute lymphoblastic leukemia. Nat Genet 2015; 47:672-6. [PMID: 25961940 DOI: 10.1038/ng.3301] [Citation(s) in RCA: 125] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2014] [Accepted: 04/16/2015] [Indexed: 12/16/2022]
Abstract
High hyperdiploid (51-67 chromosomes) acute lymphoblastic leukemia (ALL) is one of the most common childhood malignancies, comprising 30% of all pediatric B cell-precursor ALL. Its characteristic genetic feature is the nonrandom gain of chromosomes X, 4, 6, 10, 14, 17, 18 and 21, with individual trisomies or tetrasomies being seen in over 75% of cases, but the pathogenesis remains poorly understood. We performed whole-genome sequencing (WGS) (n = 16) and/or whole-exome sequencing (WES) (n = 39) of diagnostic and remission samples from 51 cases of high hyperdiploid ALL to further define the genomic landscape of this malignancy. The majority of cases showed involvement of the RTK-RAS pathway and of histone modifiers. No recurrent fusion gene-forming rearrangement was found, and an analysis of mutations on trisomic chromosomes indicated that the chromosomal gains were early events, strengthening the notion that the high hyperdiploid pattern is the main driver event in this common pediatric malignancy.
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38
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KRAS and CREBBP mutations: a relapse-linked malicious liaison in childhood high hyperdiploid acute lymphoblastic leukemia. Leukemia 2015; 29:1656-67. [PMID: 25917266 PMCID: PMC4530204 DOI: 10.1038/leu.2015.107] [Citation(s) in RCA: 79] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2015] [Accepted: 04/16/2015] [Indexed: 12/24/2022]
Abstract
High hyperdiploidy defines the largest genetic entity of childhood acute lymphoblastic leukemia (ALL). Despite its relatively low recurrence risk, this subgroup generates a high proportion of relapses. The cause and origin of these relapses remains obscure. We therefore explored the mutational landscape in high hyperdiploid (HD) ALL with whole-exome (n=19) and subsequent targeted deep sequencing of 60 genes in 100 relapsing and 51 non-relapsing cases. We identified multiple clones at diagnosis that were primarily defined by a variety of mutations in receptor tyrosine kinase (RTK)/Ras pathway and chromatin-modifying genes. The relapse clones consisted of reappearing as well as new mutations, and overall contained more mutations. Although RTK/Ras pathway mutations were similarly frequent between diagnosis and relapse, both intergenic and intragenic heterogeneity was essentially lost at relapse. CREBBP mutations, however, increased from initially 18–30% at relapse, then commonly co-occurred with KRAS mutations (P<0.001) and these relapses appeared primarily early (P=0.012). Our results confirm the exceptional susceptibility of HD ALL to RTK/Ras pathway and CREBBP mutations, but, more importantly, suggest that mutant KRAS and CREBBP might cooperate and equip cells with the necessary capacity to evolve into a relapse-generating clone.
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39
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Roberts KG, Mullighan CG. Genomics in acute lymphoblastic leukaemia: insights and treatment implications. Nat Rev Clin Oncol 2015; 12:344-57. [PMID: 25781572 DOI: 10.1038/nrclinonc.2015.38] [Citation(s) in RCA: 195] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Acute lymphoblastic leukaemia (ALL) is the commonest childhood cancer and an important cause of morbidity from haematological malignancies in adults. In the past several years, we have witnessed major advances in the understanding of the genetic basis of ALL. Genome-wide profiling studies, including microarray analysis and genome sequencing, have helped identify multiple key cellular pathways that are frequently mutated in ALL such as lymphoid development, tumour suppression, cytokine receptors, kinase and Ras signalling, and chromatin remodeling. These studies have characterized new subtypes of ALL, notably Philadelphia chromosome-like ALL, which is a high-risk subtype characterized by a diverse range of alterations that activate cytokine receptors or tyrosine kinases amenable to inhibition with approved tyrosine kinase inhibitors. Genomic profiling has also enabled the identification of inherited genetic variants of ALL that influence the risk of leukaemia development, and characterization of the relationship between genetic variants, clonal heterogeneity and the risk of relapse. Many of these findings are of direct clinical relevance and ongoing studies implementing clinical sequencing in leukaemia diagnosis and management have great potential to improve the outcome of patients with high-risk ALL.
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Affiliation(s)
- Kathryn G Roberts
- Department of Pathology, St Jude Children's Research Hospital, 262 Danny Thomas Place, Mail Stop 342, Memphis, TN 38105, USA
| | - Charles G Mullighan
- Department of Pathology, St Jude Children's Research Hospital, 262 Danny Thomas Place, Mail Stop 342, Memphis, TN 38105, USA
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40
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Chen L, Chen W, Mysliwski M, Serio J, Ropa J, Abulwerdi FA, Chan RJ, Patel JP, Tallman MS, Paietta E, Melnick A, Levine RL, Abdel-Wahab O, Nikolovska-Coleska Z, Muntean AG. Mutated Ptpn11 alters leukemic stem cell frequency and reduces the sensitivity of acute myeloid leukemia cells to Mcl1 inhibition. Leukemia 2015; 29:1290-300. [PMID: 25650089 PMCID: PMC4456293 DOI: 10.1038/leu.2015.18] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2014] [Revised: 01/05/2015] [Accepted: 01/29/2015] [Indexed: 02/07/2023]
Abstract
PTPN11 encodes the Shp2 non-receptor protein-tyrosine phosphatase implicated in several signaling pathways. Activating mutations in Shp2 are commonly associated with juvenile myelomonocytic leukemia (JMML) but are not as well defined in other neoplasms. Here we report that Shp2 mutations occur in human acute myeloid leukemia (AML) at a rate of 6.6% (6/91) in the ECOG E1900 dataset. We examined the role of mutated Shp2 in leukemias harboring MLL translocations which co-occur in human AML. The hyperactive Shp2E76K mutant, commonly observed in leukemia patients, significantly accelerated MLL-AF9 mediated leukemogenesis in vivo. Shp2E76K increased leukemic stem cell frequency and affords MLL-AF9 leukemic cells IL3 cytokine hypersensitivity. As Shp2 is reported to regulate anti-apoptotic genes, we investigated Bcl2, Bcl-xL and Mcl1 expression in MLL-AF9 leukemic cells with and without Shp2E76K. While the Bcl2 family of genes was upregulated in Shp2E76K cells, Mcl1 showed the highest upregulation in MLL-AF9 cells in response to Shp2E76K. Indeed, expression of Mcl1 in MLL-AF9 cells phenocopies expression of Shp2E76K suggesting Shp2 mutations cooperate through activation of anti-apoptotic genes. Finally, we show Shp2E76K mutations reduce sensitivity of AML cells to small molecule mediated Mcl1 inhibition suggesting reduced efficacy of drugs targeting MCL1 in patients with hyperactive Shp2.
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Affiliation(s)
- L Chen
- 1] Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA [2] Department of Medicine, University of Michigan Medical School, Ann Arbor, MI, USA
| | - W Chen
- 1] Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA [2] Department of Medicine, University of Michigan Medical School, Ann Arbor, MI, USA
| | - M Mysliwski
- 1] Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA [2] Department of Medicine, University of Michigan Medical School, Ann Arbor, MI, USA
| | - J Serio
- 1] Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA [2] Department of Medicine, University of Michigan Medical School, Ann Arbor, MI, USA
| | - J Ropa
- 1] Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA [2] Department of Medicine, University of Michigan Medical School, Ann Arbor, MI, USA
| | - F A Abulwerdi
- 1] Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA [2] Interdepartmental Program in Medicinal Chemistry, College of Pharmacy, University of Michigan, Ann Arbor, MI, USA
| | - R J Chan
- 1] Herman B Wells Center for Pediatric Research, Department of Medical and Molecular Genetics, University School of Medicine, Indianapolis, IN, USA [2] Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - J P Patel
- Human Oncology and Pathogenesis Program and Leukemia Service, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - M S Tallman
- Human Oncology and Pathogenesis Program and Leukemia Service, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - E Paietta
- Montefiore Medical Center-North Division, Immunology Laboratory, Cancer Center, Bronx, NY, USA
| | - A Melnick
- 1] Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medical College, New York, NY, USA [2] Department of Pharmacology, Weill Cornell Medical College, New York, NY, USA
| | - R L Levine
- Human Oncology and Pathogenesis Program and Leukemia Service, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - O Abdel-Wahab
- Human Oncology and Pathogenesis Program and Leukemia Service, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - Z Nikolovska-Coleska
- 1] Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA [2] Department of Medicine, University of Michigan Medical School, Ann Arbor, MI, USA
| | - A G Muntean
- 1] Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA [2] Department of Medicine, University of Michigan Medical School, Ann Arbor, MI, USA
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41
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Ariës IM, van den Dungen RE, Koudijs MJ, Cuppen E, Voest E, Molenaar JJ, Caron HN, Pieters R, den Boer ML. Towards personalized therapy in pediatric acute lymphoblastic leukemia: RAS mutations and prednisolone resistance. Haematologica 2014; 100:e132-6. [PMID: 25480501 DOI: 10.3324/haematol.2014.112995] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Affiliation(s)
- Ingrid M Ariës
- Department of Pediatric Oncology/Hematology, Erasmus Medical Center-Sophia Children's Hospital, Rotterdam
| | - Rosanna E van den Dungen
- Department of Pediatric Oncology/Hematology, Erasmus Medical Center-Sophia Children's Hospital, Rotterdam
| | - Marco J Koudijs
- Department of Medical Genetics, University Medical Center Utrecht Center for Personalized Cancer Treatment
| | - Edwin Cuppen
- Department of Medical Genetics, University Medical Center Utrecht Center for Personalized Cancer Treatment
| | - Emile Voest
- Department of Medical Genetics, University Medical Center Utrecht Center for Personalized Cancer Treatment
| | - Jan J Molenaar
- Department of Human Genetics, Academic Medical Centre, University of Amsterdam Individualized Therapies for Children with Cancer Study Group
| | - Huib N Caron
- Department of Human Genetics, Academic Medical Centre, University of Amsterdam Individualized Therapies for Children with Cancer Study Group
| | - Rob Pieters
- Department of Pediatric Oncology/Hematology, Erasmus Medical Center-Sophia Children's Hospital, Rotterdam Individualized Therapies for Children with Cancer Study Group Dutch Childhood Oncology Group, The Hague, The Netherlands
| | - Monique L den Boer
- Department of Pediatric Oncology/Hematology, Erasmus Medical Center-Sophia Children's Hospital, Rotterdam Individualized Therapies for Children with Cancer Study Group Dutch Childhood Oncology Group, The Hague, The Netherlands
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42
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Ras pathway mutations are prevalent in relapsed childhood acute lymphoblastic leukemia and confer sensitivity to MEK inhibition. Blood 2014; 124:3420-30. [PMID: 25253770 DOI: 10.1182/blood-2014-04-531871] [Citation(s) in RCA: 181] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
For most children who relapse with acute lymphoblastic leukemia (ALL), the prognosis is poor, and there is a need for novel therapies to improve outcome. We screened samples from children with B-lineage ALL entered into the ALL-REZ BFM 2002 clinical trial (www.clinicaltrials.gov, #NCT00114348) for somatic mutations activating the Ras pathway (KRAS, NRAS, FLT3, and PTPN11) and showed mutation to be highly prevalent (76 from 206). Clinically, they were associated with high-risk features including early relapse, central nervous system (CNS) involvement, and specifically for NRAS/KRAS mutations, chemoresistance. KRAS mutations were associated with a reduced overall survival. Mutation screening of the matched diagnostic samples found many to be wild type (WT); however, by using more sensitive allelic-specific assays, low-level mutated subpopulations were found in many cases, suggesting that they survived up-front therapy and subsequently emerged at relapse. Preclinical evaluation of the mitogen-activated protein kinase kinase 1/2 inhibitor selumetinib (AZD6244, ARRY-142886) showed significant differential sensitivity in Ras pathway-mutated ALL compared with WT cells both in vitro and in an orthotopic xenograft model engrafted with primary ALL; in the latter, reduced RAS-mutated CNS leukemia. Given these data, clinical evaluation of selumetinib may be warranted for Ras pathway-mutated relapsed ALL.
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Knight T, Irving JAE. Ras/Raf/MEK/ERK Pathway Activation in Childhood Acute Lymphoblastic Leukemia and Its Therapeutic Targeting. Front Oncol 2014; 4:160. [PMID: 25009801 PMCID: PMC4067595 DOI: 10.3389/fonc.2014.00160] [Citation(s) in RCA: 99] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2014] [Accepted: 06/06/2014] [Indexed: 01/11/2023] Open
Abstract
Deregulation of the Ras/Raf/MEK/extracellular signal-regulated kinase pathway is a common event in childhood acute lymphoblastic leukemia and is caused by point mutation, gene deletion, and chromosomal translocation of a vast array of gene types, highlighting its importance in leukemia biology. Pathway activation can be therapeutically exploited and may guide new therapies needed for relapsed acute lymphoblastic leukemia and other high risk subgroups.
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Affiliation(s)
- Thomas Knight
- Newcastle Cancer Centre at the Northern Institute for Cancer Research, Newcastle University, Newcastle upon Tyne, UK
| | - Julie Anne Elizabeth Irving
- Newcastle Cancer Centre at the Northern Institute for Cancer Research, Newcastle University, Newcastle upon Tyne, UK
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Evolutionary trajectories of hyperdiploid ALL in monozygotic twins. Leukemia 2014; 29:58-65. [PMID: 24897505 DOI: 10.1038/leu.2014.177] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2014] [Revised: 05/08/2014] [Accepted: 05/20/2014] [Indexed: 02/08/2023]
Abstract
Identical twins have provided unique insights on timing or sequence of genetic events in acute lymphoblastic leukaemia (ALL). To date, this has mainly focused on ALL with MLL or ETV6-RUNX1 fusions, with hyperdiploid ALL remaining less well characterised. We examined three pairs of monozygotic twins, two concordant and one discordant for hyperdiploid ALL, for single-nucleotide polymorphism (SNP)-defined copy number alterations (CNAs), IGH/L plus TCR gene rearrangements and mutations in NRAS, KRAS, FLT3 and PTPN11 genes. We performed whole exome sequencing in one concordant twin pair. Potential 'driver' CNAs were low, 0-3 per case, and all were different within a pair. One patient had an NRAS mutation that was lacking from leukaemic cells of the twin sibling. By exome sequencing, there were 12 nonsynonymous mutations found in one twin and 5 in the other, one of which in SCL44A2 was shared or identical. Concordant pairs had some identical IGH/L and TCR rearrangements. In the twin pair with discordant hyperdiploid ALL, the healthy co-twin had persistent low level hyperdiploid CD19+ cells that lacked a CNA present in the ALL cells of her sibling. From these data, we propose that hyperdiploid ALL arises in a pre-B cell in utero and mutational changes necessary for clinical ALL accumulate subclonally and postnatally.
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FLT3 Internal Tandem Duplication and D835 Mutations in Patients with Acute Lymphoblastic Leukemia and its Clinical Significance. Mediterr J Hematol Infect Dis 2014; 6:e2014038. [PMID: 24959335 PMCID: PMC4063605 DOI: 10.4084/mjhid.2014.038] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2014] [Accepted: 05/09/2014] [Indexed: 12/26/2022] Open
Abstract
The fms-like tyrosine kinase 3 (FLT3) gene is a member of the class III receptor tyrosine kinase family. Mutations of FLT3 were first described in 1997 and account for the most frequent molecular mutations in acute myeloid leukemia. Currently, there is no published data on FLT3 mutations in Saudi acute lymphoblastic leukemia (ALL) patients. In this retrospective study, we have examined a cohort of 77 ALL patients to determine the prevalence of FLT3 mutations and the possible prognostic relevance of these mutations in ALL patients. Correlations to other biologic factors such as karyotype, molecular mutations, and leukocyte count were also considered. FLT3 internal tandem duplication (ITD) mutations and point mutation in tyrosine kinase domain (D835) were analyzed in ALL patients, at diagnosis, by polymerase chain reaction (PCR). Two cases (2.6%, 2/77) were positive for FLT3 mutations; one was found to have FLT3/ITD and the other FLT3/D835. Our findings suggest that FLT3 mutations are not common in Saudi ALL and do not affect clinical outcome.
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Barbosa TC, Andrade FG, Lopes BA, de Andrade CFG, Mansur MB, Emerenciano M, Pombo-de-Oliveira MS. Impact of mutations in FLT3, PTPN11 and RAS genes on the overall survival of pediatric B cell precursor acute lymphoblastic leukemia in Brazil. Leuk Lymphoma 2014; 55:1501-9. [PMID: 24067137 DOI: 10.3109/10428194.2013.847934] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
We analyzed mutations in four genes (FLT3, KRAS/NRAS and PTPN11) that might disrupt the RAS/mitogen activated protein kinase (MAPKinase) signaling pathway, to evaluate their prognostic value in children younger than 16 years old with B-cell precursor acute lymphoblastic leukemia (Bcp-ALL). The overall survival (OS) was determined with the Kaplan-Meier method. MAPKinase genes were mutated in 25.4% and 20.1% of childhood and infant Bcp-ALL, respectively. Children with hyperdiploidy were more prone to harboring a MAPKinase gene mutation (odds ratio [OR] 3.18; 95% confidence interval [CI] 1.07-9.49). The mean OS of all cases was 54.0 months. FLT3 and PTPN11 mutations had no impact on OS. K/NRAS mutations were strongly associated with MLL-AFF1 (OR 5.78; 95% CI 1.00-33.24), and conferred poorer OS (p = 0.034) in univariate analysis.
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Affiliation(s)
- Thayana Conceição Barbosa
- Pediatric Hematology and Oncology Program, Research Center, Instituto Nacional de Câncer , Rio de Janeiro , Brazil
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Polyploidy in myelofibrosis: analysis by cytogenetic and SNP array indicates association with advancing disease. Mol Cytogenet 2013; 6:59. [PMID: 24341401 PMCID: PMC3906908 DOI: 10.1186/1755-8166-6-59] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2013] [Accepted: 11/25/2013] [Indexed: 11/10/2022] Open
Abstract
Background Myelofibrosis occurs as primary myelofibrosis or as a late occurrence in the evolution of essential thrombocythaemia and polycythaemia vera. It is the rarest of the three classic myeloproliferative neoplasms (MPN). Polyploidy has only rarely been reported in MPN despite the prominent involvement of abnormal megakaryocytes. The use of peripheral blood samples containing increased numbers of haematopoietic progenitors has improved the output from cytogenetic studies in myelofibrosis and together with the use of single nucleotide polymorphism arrays (SNPa) has contributed to an improved knowledge regarding the diverse genetic landscape of this rare disease. Results Cytogenetic studies performed on a consecutive cohort of 42 patients with primary or post ET/PV myelofibrosis showed an abnormal karyotype in 24 cases and of these, nine showed a polyploid clone. Six of the nine cases showed a tetraploid (4n) subclone, whereas three showed mixed polyploid subclones with both tetraploid and octoploid (4n/8n) cell lines. The abnormal clone evolved from a near diploid karyotype at the initial investigation to a tetraploid karyotype in follow-up cytogenetic analysis in four cases. In total, six of the nine polyploid cases showed gain of 1q material. The remaining three cases showed polyploid metaphases, but with no detectable structural karyotypic rearrangements. Three of the nine cases showed chromosome abnormalities of 6p, either at diagnosis or later acquired. SNPa analysis on eight polyploid cases showed additional changes not previously recognised by karyotype analysis alone, including recurring changes involving 9p, 14q, 17q and 22q. Except for gain of 1q, SNPa findings from the polyploid group compared to eight non-polyploid cases with myelofibrosis found no significant differences in the type of abnormality detected. Conclusions The study showed the use of peripheral blood samples to be suitable for standard karyotyping evaluation and DNA based studies. The overall profile of abnormalities found were comparable with that of post-MPN acute myeloid leukaemia or secondary myelodysplastic syndrome and cases in the polyploidy group were associated with features of high risk disease. The above represents the first documented series of polyploid karyotypes in myelofibrosis and shows a high representation of gain of 1q.
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Mutation of NRAS but not KRAS significantly reduces myeloma sensitivity to single-agent bortezomib therapy. Blood 2013; 123:632-9. [PMID: 24335104 DOI: 10.1182/blood-2013-05-504340] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Various translocations and mutations have been identified in myeloma, and certain aberrations, such as t(4;14) and del17, are linked with disease prognosis. To investigate mutational prevalence in myeloma and associations between mutations and patient outcomes, we tested a panel of 41 known oncogenes and tumor suppressor genes in tumor samples from 133 relapsed myeloma patients participating in phase 2 or 3 clinical trials of bortezomib. DNA mutations were identified in 14 genes. BRAF as well as RAS genes were mutated in a large proportion of cases (45.9%) and these mutations were mutually exclusive. New recurrent mutations were also identified, including in the PDGFRA and JAK3 genes. NRAS mutations were associated with a significantly lower response rate to single-agent bortezomib (7% vs 53% in patients with mutant vs wild-type NRAS, P = .00116, Bonferroni-corrected P = .016), as well as shorter time to progression in bortezomib-treated patients (P = .0058, Bonferroni-corrected P = .012). However, NRAS mutation did not impact outcome in patients treated with high-dose dexamethasone. KRAS mutation did not reduce sensitivity to bortezomib or dexamethasone. These findings identify a significant clinical impact of NRAS mutation in myeloma and demonstrate a clear example of functional differences between the KRAS and NRAS oncogenes.
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Targeted cancer exome sequencing reveals recurrent mutations in myeloproliferative neoplasms. Leukemia 2013; 28:1052-9. [PMID: 24150215 PMCID: PMC4017260 DOI: 10.1038/leu.2013.302] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2013] [Revised: 09/28/2013] [Accepted: 10/07/2013] [Indexed: 02/08/2023]
Abstract
With the intent of dissecting the molecular complexity of Philadelphia-negative myeloproliferative neoplasms (MPN), we designed a target enrichment panel to explore, using next-generation sequencing (NGS), the mutational status of an extensive list of 2000 cancer-associated genes and microRNAs. The genomic DNA of granulocytes and in vitro-expanded CD3+T-lymphocytes, as a germline control, was target-enriched and sequenced in a learning cohort of 20 MPN patients using Roche 454 technology. We identified 141 genuine somatic mutations, most of which were not previously described. To test the frequency of the identified variants, a larger validation cohort of 189 MPN patients was additionally screened for these mutations using Ion Torrent AmpliSeq NGS. Excluding the genes already described in MPN, for 8 genes (SCRIB, MIR662, BARD1, TCF12, FAT4, DAP3, POLG and NRAS), we demonstrated a mutation frequency between 3 and 8%. We also found that mutations at codon 12 of NRAS (NRASG12V and NRASG12D) were significantly associated, for primary myelofibrosis (PMF), with highest dynamic international prognostic scoring system (DIPSS)-plus score categories. This association was then confirmed in 66 additional PMF patients composing a final dataset of 168 PMF showing a NRAS mutation frequency of 4.7%, which was associated with a worse outcome, as defined by the DIPSS plus score.
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Harrison CJ. Targeting signaling pathways in acute lymphoblastic leukemia: new insights. HEMATOLOGY. AMERICAN SOCIETY OF HEMATOLOGY. EDUCATION PROGRAM 2013; 2013:118-125. [PMID: 24319172 DOI: 10.1182/asheducation-2013.1.118] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
The genetics of acute lymphoblastic leukemia are becoming well understood and the incidence of individual chromosomal abnormalities varies considerably with age. Cytogenetics provide reliable risk stratification for treatment: high hyperdiploidy and ETV6-RUNX1 are good risk, whereas BCR-ABL1, MLL rearrangements, and hypodiploidy are poor risk. Nevertheless, some patients within the good- and intermediate-risk groups will unpredictably relapse. With advancing technologies in array-based approaches (single nucleotide polymorphism arrays) and next-generation sequencing to study the genome, increasing numbers of new genetic changes are being discovered. These include deletions of B-cell differentiation and cell cycle control genes, as well as mutations of genes in key signaling pathways. Their associations and interactions with established cytogenetic subgroups and with each other are becoming elucidated. Whether they have a link to outcome is the most important factor for refinement of risk factors in relation to clinical trials. For several newly identified abnormalities, including intrachromosomal amplification of chromosome 21 (iAMP21), that are associated with a poor prognosis with standard therapy, appropriately modified treatment has significantly improved outcome. After the successful use of tyrosine kinase inhibitors in the treatment of BCR-ABL1-positive acute lymphoblastic leukemia, patients with alternative ABL1 translocations and rearrangements involving PDGFRB may benefit from treatment with tyrosine kinase inhibitors. Other aberrations, for example, CRLF2 overexpression and JAK2 mutations, are also providing potential novel therapeutic targets with the prospect of reduced toxicity.
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MESH Headings
- Chromosome Aberrations
- Chromosomes, Human, Pair 21/genetics
- Chromosomes, Human, Pair 21/metabolism
- Core Binding Factor Alpha 2 Subunit/genetics
- Core Binding Factor Alpha 2 Subunit/metabolism
- Drug Delivery Systems/methods
- Fusion Proteins, bcr-abl/genetics
- Fusion Proteins, bcr-abl/metabolism
- Gene Rearrangement
- Histone-Lysine N-Methyltransferase
- Humans
- Janus Kinase 2/genetics
- Janus Kinase 2/metabolism
- Myeloid-Lymphoid Leukemia Protein/genetics
- Myeloid-Lymphoid Leukemia Protein/metabolism
- Oncogene Proteins, Fusion/genetics
- Oncogene Proteins, Fusion/metabolism
- Precursor Cell Lymphoblastic Leukemia-Lymphoma/drug therapy
- Precursor Cell Lymphoblastic Leukemia-Lymphoma/genetics
- Precursor Cell Lymphoblastic Leukemia-Lymphoma/metabolism
- Receptor, Platelet-Derived Growth Factor beta/genetics
- Receptor, Platelet-Derived Growth Factor beta/metabolism
- Receptors, Cytokine/genetics
- Receptors, Cytokine/metabolism
- Signal Transduction
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Affiliation(s)
- Christine J Harrison
- 1Northern Institute for Cancer Research, Newcastle University, Newcastle-upon-Tyne, United Kingdom
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