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Rahn K, Abdallah AT, Gan L, Herbrich S, Sonntag R, Benitez O, Malaney P, Zhang X, Rodriguez AG, Brottem J, Marx G, Brümmendorf TH, Ostareck DH, Ostareck-Lederer A, Crysandt M, Post SM, Naarmann-de Vries IS. Insight into the mechanism of AML del(9q) progression: hnRNP K targets the myeloid master regulators CEBPA (C/EBPα) and SPI1 (PU.1). BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2024; 1867:195004. [PMID: 38008244 DOI: 10.1016/j.bbagrm.2023.195004] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 11/08/2023] [Accepted: 11/20/2023] [Indexed: 11/28/2023]
Abstract
Deletions on the long arm of chromosome 9 (del(9q)) are recurrent abnormalities in about 2 % of acute myeloid leukemia cases, which usually involve HNRNPK and are frequently associated with other known aberrations. Based on an Hnrnpk haploinsufficient mouse model, a recent study demonstrated a function of hnRNP K in pathogenesis of myeloid malignancies via the regulation of cellular proliferation and myeloid differentiation programs. Here, we provide evidence that reduced hnRNP K expression results in the dysregulated expression of C/EBPα and additional transcription factors. CyTOF analysis revealed monocytic skewing with increased levels of mature myeloid cells. To explore the role of hnRNP K during normal and pathological myeloid differentiation in humans, we characterized hnRNP K-interacting RNAs in human AML cell lines. Notably, RNA-sequencing revealed several mRNAs encoding key transcription factors involved in the regulation of myeloid differentiation as targets of hnRNP K. We showed that specific sequence motifs confer the interaction of SPI1 and CEBPA 5' and 3'UTRs with hnRNP K. The siRNA mediated reduction of hnRNP K in human AML cells resulted in an increase of PU.1 and C/EBPα that is most pronounced for the p30 isoform. The combinatorial treatment with the inducer of myeloid differentiation valproic acid resulted in increased C/EBPα expression and myeloid differentiation. Together, our results indicate that hnRNP K post-transcriptionally regulates the expression of myeloid master transcription factors. These novel findings can inaugurate novel options for targeted treatment of AML del(9q) by modulation of hnRNP K function.
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Affiliation(s)
- Kerstin Rahn
- Department of Intensive Care Medicine, University Hospital RWTH Aachen University, Aachen, Germany; Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ali T Abdallah
- Interdisciplinary Center for Clinical Research (IZKF) Aachen, RWTH Aachen University, Germany; Cluster of Excellence on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Lin Gan
- Interdisciplinary Center for Clinical Research (IZKF) Aachen, RWTH Aachen University, Germany
| | - Shelley Herbrich
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Roland Sonntag
- Department of Internal Medicine III, University Hospital RWTH Aachen University, Aachen, Germany
| | - Oscar Benitez
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Prerna Malaney
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Xiaorui Zhang
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ashely G Rodriguez
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jared Brottem
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Gernot Marx
- Department of Intensive Care Medicine, University Hospital RWTH Aachen University, Aachen, Germany
| | - Tim H Brümmendorf
- Department of Hematology, Oncology, Hemostaseology and Stem Cell Transplantation, University Hospital RWTH Aachen University, Aachen, Germany; Center for Integrated Oncology Aachen Bonn Cologne Duesseldorf (CIO ABCD), Aachen, Germany
| | - Dirk H Ostareck
- Department of Intensive Care Medicine, University Hospital RWTH Aachen University, Aachen, Germany
| | - Antje Ostareck-Lederer
- Department of Intensive Care Medicine, University Hospital RWTH Aachen University, Aachen, Germany
| | - Martina Crysandt
- Department of Hematology, Oncology, Hemostaseology and Stem Cell Transplantation, University Hospital RWTH Aachen University, Aachen, Germany; Center for Integrated Oncology Aachen Bonn Cologne Duesseldorf (CIO ABCD), Aachen, Germany
| | - Sean M Post
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
| | - Isabel S Naarmann-de Vries
- Department of Intensive Care Medicine, University Hospital RWTH Aachen University, Aachen, Germany; Section of Bioinformatics and Systems Cardiology, University Hospital Heidelberg, Heidelberg, Germany.
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Casado P, Cutillas PR. Proteomic Characterization of Acute Myeloid Leukemia for Precision Medicine. Mol Cell Proteomics 2023; 22:100517. [PMID: 36805445 PMCID: PMC10152134 DOI: 10.1016/j.mcpro.2023.100517] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2022] [Revised: 02/07/2023] [Accepted: 02/13/2023] [Indexed: 02/19/2023] Open
Abstract
Acute myeloid leukemia (AML) is a highly heterogeneous cancer of the hematopoietic system with no cure for most patients. In addition to chemotherapy, treatment options for AML include recently approved therapies that target proteins with roles in AML pathobiology, such as FLT3, BLC2, and IDH1/2. However, due to disease complexity, these therapies produce very diverse responses, and survival rates are still low. Thus, despite considerable advances, there remains a need for therapies that target different aspects of leukemic biology and for associated biomarkers that define patient populations likely to respond to each available therapy. To meet this need, drugs that target different AML vulnerabilities are currently in advanced stages of clinical development. Here, we review proteomics and phosphoproteomics studies that aimed to provide insights into AML biology and clinical disease heterogeneity not attainable with genomic approaches. To place the discussion in context, we first provide an overview of genetic and clinical aspects of the disease, followed by a summary of proteins targeted by compounds that have been approved or are under clinical trials for AML treatment and, if available, the biomarkers that predict responses. We then discuss proteomics and phosphoproteomics studies that provided insights into AML pathogenesis, from which potential biomarkers and drug targets were identified, and studies that aimed to rationalize the use of synergistic drug combinations. When considered as a whole, the evidence summarized here suggests that proteomics and phosphoproteomics approaches can play a crucial role in the development and implementation of precision medicine for AML patients.
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Affiliation(s)
- Pedro Casado
- Cell Signalling & Proteomics Group, Centre for Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, United Kingdom
| | - Pedro R Cutillas
- Cell Signalling & Proteomics Group, Centre for Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, United Kingdom; The Alan Turing Institute, The British Library, London, United Kingdom; Digital Environment Research Institute (DERI), Queen Mary University of London, London, United Kingdom.
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3
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Ren T, Wang J, Tang W, Chen D, Wang S, Zhang X, Yang D. ARID1A has prognostic value in acute myeloid leukemia and promotes cell proliferation via TGF-β1/SMAD3 signaling. Clin Exp Med 2022:10.1007/s10238-022-00863-8. [PMID: 35867200 DOI: 10.1007/s10238-022-00863-8] [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: 12/14/2021] [Accepted: 07/04/2022] [Indexed: 11/03/2022]
Abstract
Previous studies have shown that the gene AT-rich interactive domain-containing protein 1A (ARID1A) is a subunit of SWI/SNF chromatin remodeling complex that acts as a tumor suppressor gene in several cancers and plays a vital role in tumorigenesis. However, its biological functions in acute myeloid leukemia (AML) are still unclear. Here, we tried to elaborate the expression of ARID1A in patients with AML, in leukemia cells, as well as the molecular mechanisms. Our results indicated that the expression of ARID1A was significantly downregulated in the bone marrow of patients with AML and relapsed patients compared with healthy subjects and patients in complete remission. Meantime, receiver operating characteristic curve analysis showed that the expression of ARID1A could be used to discriminate between patients with AML and patients in complete remission. We further constructed a knockdown cell model to determine the regulatory mechanisms of ARID1A in AML cells. We found that the decreased expression of ARID1A promoted cell proliferation, suppressed cellular apoptosis, and impeded cell cycle arrest via TGF-β1/SMAD3 signaling pathway. These results revealed that the reduced expression of ARID1A promoted cell proliferation via the TGF-β1/SMAD3 cascade and served as a prognostic biomarker for AML and therapeutic targets.
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Affiliation(s)
- Tianying Ren
- Zhong Yuan Academy of Biological Medicine, Liaocheng People's Hospital, Liaocheng, 252000, Shandong, People's Republic of China
| | - Jing Wang
- Key Laboratory for Pediatrics of Integrated Traditional and Western Medicine, Liaocheng People's Hospital, Liaocheng, 252000, Shandong, People's Republic of China
| | - Wenqiang Tang
- Central Laboratory, Liaocheng People's Hospital, Liaocheng, 252000, Shandong, People's Republic of China
| | - Dongliang Chen
- Zhong Yuan Academy of Biological Medicine, Liaocheng People's Hospital, Liaocheng, 252000, Shandong, People's Republic of China
| | - Shuang Wang
- Zhong Yuan Academy of Biological Medicine, Liaocheng People's Hospital, Liaocheng, 252000, Shandong, People's Republic of China
| | - Xiaole Zhang
- Department of Hematology, Liaocheng People's Hospital, Liaocheng, 252000, Shandong, People's Republic of China.
| | - Dawei Yang
- Zhong Yuan Academy of Biological Medicine, Liaocheng People's Hospital, Liaocheng, 252000, Shandong, People's Republic of China.
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4
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Circular RNAs Activity in the Leukemic Bone Marrow Microenvironment. Noncoding RNA 2022; 8:ncrna8040050. [PMID: 35893233 PMCID: PMC9326527 DOI: 10.3390/ncrna8040050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 06/20/2022] [Accepted: 06/29/2022] [Indexed: 11/17/2022] Open
Abstract
Acute myeloid leukemia (AML) is a hematological malignancy originating from defective hematopoietic stem cells in the bone marrow. In spite of the recent approval of several molecular targeted therapies for AML treatment, disease recurrence remains an issue. Interestingly, increasing evidence has pointed out the relevance of bone marrow (BM) niche remodeling during leukemia onset and progression. Complex crosstalk between AML cells and microenvironment components shapes the leukemic BM niche, consequently affecting therapy responsiveness. Notably, circular RNAs are a new class of RNAs found to be relevant in AML progression and chemoresistance. In this review, we provided an overview of AML-driven niche remodeling. In particular, we analyzed the role of circRNAs and their possible contribution to cell–cell communication within the leukemic BM microenvironment. Understanding these mechanisms will help develop a more effective treatment for AML.
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5
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Okada Y, Nakasone H, Nakamura Y, Kawamura M, Kawamura S, Takeshita J, Yoshino N, Misaki Y, Yoshimura K, Matsumi S, Gomyo A, Kawamura T, Akahoshi Y, Kusuda M, Kameda K, Tanihara A, Tamaki M, Kimura SI, Kobayashi S, Kako S, Kimura F, Kanda Y. Prognostic impact of chromosomal changes at relapse after allogeneic hematopoietic cell transplantation for acute myeloid leukemia or myelodysplastic syndrome. Bone Marrow Transplant 2022; 57:810-816. [PMID: 35314792 DOI: 10.1038/s41409-022-01635-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 02/23/2022] [Accepted: 03/02/2022] [Indexed: 11/09/2022]
Abstract
Chromosome analysis is a powerful prognostic tool in myeloid malignancies. Recipients who experience relapse after allogeneic hematopoietic cell transplantation (allo-HCT) often show chromosomal changes between diagnosis and relapse. However, the clinical impact of chromosomal changes and the efficacy of post-relapse treatment according to chromosomal changes have not been fully investigated. We retrospectively analyzed 72 recipients who had experienced relapse after allo-HCT for acute myeloid leukemia or myelodysplastic syndrome. We categorized them into two groups: with or without clonal chromosomal changes at relapse after allo-HCT. Post-relapse survival was shorter in the clonal chromosomal change group (median 117 days vs 275 days, P = 0.019). Moreover, acquisition of chromosome 7 abnormality or complex changes tended to be associated with inferior survival in a univariate analysis (median 92 days vs median 173 days, P = 0.043), and this adverse impact was confirmed in a multivariate analysis (hazard ratio 2.07, P = 0.024). The patterns of chromosomal changes from diagnosis to relapse after allo-HCT were heterogenous, and further investigations are required to clarify the effect of individual chromosomal changes.
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Affiliation(s)
- Yosuke Okada
- Division of Hematology, Jichi Medical University Saitama Medical Center, Saitama, Japan.,Division of Hematology, Department of Internal Medicine, National Defense Medical College Hospital, Saitama, Japan
| | - Hideki Nakasone
- Division of Hematology, Jichi Medical University Saitama Medical Center, Saitama, Japan
| | - Yuhei Nakamura
- Division of Hematology, Jichi Medical University Saitama Medical Center, Saitama, Japan
| | - Masakatsu Kawamura
- Division of Hematology, Jichi Medical University Saitama Medical Center, Saitama, Japan
| | - Shunto Kawamura
- Division of Hematology, Jichi Medical University Saitama Medical Center, Saitama, Japan
| | - Junko Takeshita
- Division of Hematology, Jichi Medical University Saitama Medical Center, Saitama, Japan
| | - Nozomu Yoshino
- Division of Hematology, Jichi Medical University Saitama Medical Center, Saitama, Japan
| | - Yukiko Misaki
- Division of Hematology, Jichi Medical University Saitama Medical Center, Saitama, Japan
| | - Kazuki Yoshimura
- Division of Hematology, Jichi Medical University Saitama Medical Center, Saitama, Japan
| | - Shimpei Matsumi
- Division of Hematology, Jichi Medical University Saitama Medical Center, Saitama, Japan
| | - Ayumi Gomyo
- Division of Hematology, Jichi Medical University Saitama Medical Center, Saitama, Japan
| | - Toshikuni Kawamura
- Division of Hematology, Department of Internal Medicine, National Defense Medical College Hospital, Saitama, Japan
| | - Yu Akahoshi
- Division of Hematology, Jichi Medical University Saitama Medical Center, Saitama, Japan
| | - Machiko Kusuda
- Division of Hematology, Jichi Medical University Saitama Medical Center, Saitama, Japan
| | - Kazuaki Kameda
- Division of Hematology, Jichi Medical University Saitama Medical Center, Saitama, Japan
| | - Aki Tanihara
- Division of Hematology, Jichi Medical University Saitama Medical Center, Saitama, Japan
| | - Masaharu Tamaki
- Division of Hematology, Jichi Medical University Saitama Medical Center, Saitama, Japan
| | - Shun-Ichi Kimura
- Division of Hematology, Jichi Medical University Saitama Medical Center, Saitama, Japan
| | - Shinichi Kobayashi
- Division of Hematology, Department of Internal Medicine, National Defense Medical College Hospital, Saitama, Japan
| | - Shinichi Kako
- Division of Hematology, Jichi Medical University Saitama Medical Center, Saitama, Japan
| | - Fumihiko Kimura
- Division of Hematology, Department of Internal Medicine, National Defense Medical College Hospital, Saitama, Japan
| | - Yoshinobu Kanda
- Division of Hematology, Jichi Medical University Saitama Medical Center, Saitama, Japan.
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6
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Gleba JJ, Kłopotowska D, Banach J, Turlej E, Mielko KA, Gębura K, Bogunia-Kubik K, Kutner A, Wietrzyk J. Polymorphism of VDR Gene and the Sensitivity of Human Leukemia and Lymphoma Cells to Active Forms of Vitamin D. Cancers (Basel) 2022; 14:cancers14020387. [PMID: 35053549 PMCID: PMC8774213 DOI: 10.3390/cancers14020387] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 01/12/2022] [Accepted: 01/12/2022] [Indexed: 12/22/2022] Open
Abstract
Simple Summary Developing new therapeutic strategies is necessary for leukemias and lymphomas treatment. Therefore, the study aimed to determine the use of an active form of vitamin D3 calcitriol and its analog tacalcitol as an anticancer drug. Most of all, selecting the molecular factor responsible for the cell’s sensitivity to the tested agents. A biomarker that could be use in the future to select patients for therapy and improve survival outcomes. We examined nine cell lines and evaluated the proteins involved in the biological activity of calcitriol and tacalcitol: the classical vitamin D receptor and 1,25D3-MARRS, as well as polymorphism in the VDR gene receptor. Results showed that VDR polymorphism may predispose to response to calcitriol and tacalcitol anticancer therapy. Abstract The active forms of vitamin D3 (calcitriol and tacalcitol) coupled to the vitamin D receptor (VDR) are known to exhibit anti-cancer properties. However, not all cancer cells are sensitive to the active forms of vitamin D3 and its analogs. The study aimed to determine whether polymorphism of VDR is responsible for the sensitivity of human leukemia and lymphoma cells to calcitriol and tacalcitol. The impact of calcitriol and tacalcitol on the proliferation and morphology of nine different leukemia and lymphoma cell lines was determined. Only MV-4-11, Thp-1, and HL-60 cell lines sensitive to proliferation inhibition by calcitriol and tacalcitol showed morphology changes. Subsequently, the levels of the VDR and 1,25D3-MARRS proteins of calcitriol and tacalcitol binding receptors and the VDR receptor polymorphism in human leukemia and lymphoma cells were ascertained. Contrary to the current understanding, higher levels of VDR are not responsible for the greater sensitivity of cells to calcitriol and tacalcitol. Importantly, we first showed that sensitivity to calcitriol and tacalcitol in leukemias and lymphomas could be determined by the VDR polymorphism. The FokI polymorphism and the presence of the “bat” haplotype were observed only in the sensitive cells.
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Affiliation(s)
- Justyna Joanna Gleba
- Department of Experimental Oncology, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Weigla 12, 53–114 Wroclaw, Poland; (D.K.); (J.B.); (J.W.)
- Correspondence: ; Tel.: +1-904-207-2571
| | - Dagmara Kłopotowska
- Department of Experimental Oncology, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Weigla 12, 53–114 Wroclaw, Poland; (D.K.); (J.B.); (J.W.)
| | - Joanna Banach
- Department of Experimental Oncology, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Weigla 12, 53–114 Wroclaw, Poland; (D.K.); (J.B.); (J.W.)
| | - Eliza Turlej
- Department of Experimental Oncology, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Weigla 12, 53–114 Wroclaw, Poland; (D.K.); (J.B.); (J.W.)
- Department of Experimental Biology, Wroclaw University of Environmental and Life Sciences, Norwida 27 B, 50-375 Wroclaw, Poland;
| | - Karolina Anna Mielko
- Department of Experimental Oncology, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Weigla 12, 53–114 Wroclaw, Poland; (D.K.); (J.B.); (J.W.)
- Department of Biochemistry, Molecular Biology and Biotechnology, Faculty of Chemistry, Wroclaw University of Science and Technology, Norwida 4/6, 50-373 Wroclaw, Poland;
| | - Katarzyna Gębura
- Laboratory of Clinical Immunogenetics and Pharmacogenetics, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Weigla 12, 53–114 Wroclaw, Poland; (K.G.); (K.B.-K.)
| | - Katarzyna Bogunia-Kubik
- Laboratory of Clinical Immunogenetics and Pharmacogenetics, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Weigla 12, 53–114 Wroclaw, Poland; (K.G.); (K.B.-K.)
| | - Andrzej Kutner
- Department of Bioanalysis and Drug Analysis, Faculty of Pharmacy, Medical University of Warsaw, 1 Banacha, 02-097 Warsaw, Poland;
| | - Joanna Wietrzyk
- Department of Experimental Oncology, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Weigla 12, 53–114 Wroclaw, Poland; (D.K.); (J.B.); (J.W.)
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7
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Barabino SML, Citterio E, Ronchi AE. Transcription Factors, R-Loops and Deubiquitinating Enzymes: Emerging Targets in Myelodysplastic Syndromes and Acute Myeloid Leukemia. Cancers (Basel) 2021; 13:cancers13153753. [PMID: 34359655 PMCID: PMC8345071 DOI: 10.3390/cancers13153753] [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: 06/16/2021] [Revised: 07/21/2021] [Accepted: 07/23/2021] [Indexed: 12/19/2022] Open
Abstract
Simple Summary The advent of DNA massive sequencing technologies has allowed for the first time an extensive look into the heterogeneous spectrum of genes and mutations underpinning myelodysplastic syndromes (MDSs) and acute myeloid leukemia (AML). In this review, we wish to explore the most recent advances and the rationale for the potential therapeutic interest of three main actors in myelo-leukemic transformation: transcription factors that govern myeloid differentiation; RNA splicing factors, which ensure proper mRNA maturation and whose mutations increase R-loops formation; and deubiquitinating enzymes, which contribute to genome stability in hematopoietic stem cells (HSCs). Abstract Myeloid neoplasms encompass a very heterogeneous family of diseases characterized by the failure of the molecular mechanisms that ensure a balanced equilibrium between hematopoietic stem cells (HSCs) self-renewal and the proper production of differentiated cells. The origin of the driver mutations leading to preleukemia can be traced back to HSC/progenitor cells. Many properties typical to normal HSCs are exploited by leukemic stem cells (LSCs) to their advantage, leading to the emergence of a clonal population that can eventually progress to leukemia with variable latency and evolution. In fact, different subclones might in turn develop from the original malignant clone through accumulation of additional mutations, increasing their competitive fitness. This process ultimately leads to a complex cancer architecture where a mosaic of cellular clones—each carrying a unique set of mutations—coexists. The repertoire of genes whose mutations contribute to the progression toward leukemogenesis is broad. It encompasses genes involved in different cellular processes, including transcriptional regulation, epigenetics (DNA and histones modifications), DNA damage signaling and repair, chromosome segregation and replication (cohesin complex), RNA splicing, and signal transduction. Among these many players, transcription factors, RNA splicing proteins, and deubiquitinating enzymes are emerging as potential targets for therapeutic intervention.
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8
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de Oliveira Lisboa M, Brofman PRS, Schmid-Braz AT, Rangel-Pozzo A, Mai S. Chromosomal Instability in Acute Myeloid Leukemia. Cancers (Basel) 2021; 13:cancers13112655. [PMID: 34071283 PMCID: PMC8198625 DOI: 10.3390/cancers13112655] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 05/23/2021] [Accepted: 05/26/2021] [Indexed: 12/20/2022] Open
Abstract
Chromosomal instability (CIN), the increasing rate in which cells acquire new chromosomal alterations, is one of the hallmarks of cancer. Many studies highlighted CIN as an important mechanism in the origin, progression, and relapse of acute myeloid leukemia (AML). The ambivalent feature of CIN as a cancer-promoting or cancer-suppressing mechanism might explain the prognostic variability. The latter, however, is described in very few studies. This review highlights the important CIN mechanisms in AML, showing that CIN signatures can occur largely in all the three major AML types (de novo AML, secondary-AML, and therapy-related-AML). CIN features in AML could also be age-related and reflect the heterogeneity of the disease. Although most of these abnormalities show an adverse prognostic value, they also offer a strong new perspective on personalized therapy approaches, which goes beyond assessing CIN in vitro in patient tumor samples to predict prognosis. Current and emerging AML therapies are exploring CIN to improve AML treatment, which includes blocking CIN or increasing CIN beyond the limit threshold to induce cell death. We argue that the characterization of CIN features, not included yet in the routine diagnostic of AML patients, might provide a better stratification of patients and be extended to a more personalized therapeutic approach.
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Affiliation(s)
- Mateus de Oliveira Lisboa
- Core for Cell Technology, School of Medicine, Pontifícia Universidade Católica do Paraná—PUCPR, Curitiba 80215-901, Paraná, Brazil; (M.d.O.L.); (P.R.S.B.)
| | - Paulo Roberto Slud Brofman
- Core for Cell Technology, School of Medicine, Pontifícia Universidade Católica do Paraná—PUCPR, Curitiba 80215-901, Paraná, Brazil; (M.d.O.L.); (P.R.S.B.)
| | - Ana Teresa Schmid-Braz
- Hospital das Clínicas, Universidade Federal do Paraná, Curitiba 80060-240, Paraná, Brazil;
| | - Aline Rangel-Pozzo
- Department of Physiology and Pathophysiology, University of Manitoba, Cell Biology, CancerCare Manitoba Research Institute, Winnipeg, MB R3C 2B7, Canada
- Correspondence: (A.R.-P.); (S.M.); Tel.: +1-(204)787-4125 (S.M.)
| | - Sabine Mai
- Department of Physiology and Pathophysiology, University of Manitoba, Cell Biology, CancerCare Manitoba Research Institute, Winnipeg, MB R3C 2B7, Canada
- Correspondence: (A.R.-P.); (S.M.); Tel.: +1-(204)787-4125 (S.M.)
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9
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Pre-HCT mosaicism increases relapse risk and lowers survival in acute lymphoblastic leukemia patients post-unrelated HCT. Blood Adv 2021; 5:66-70. [PMID: 33570634 DOI: 10.1182/bloodadvances.2020003366] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Accepted: 11/13/2020] [Indexed: 12/11/2022] Open
Abstract
Key Points
Pre-HCT mosaicism is related to increased relapse risk and lower survival after unrelated HCT, independent of cytogenetics at diagnosis. Pre-HCT mosaicism could be a useful clinical tool to guide risk stratification in acute lymphoblastic leukemia patients.
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10
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Carter JL, Hege K, Yang J, Kalpage HA, Su Y, Edwards H, Hüttemann M, Taub JW, Ge Y. Targeting multiple signaling pathways: the new approach to acute myeloid leukemia therapy. Signal Transduct Target Ther 2020; 5:288. [PMID: 33335095 PMCID: PMC7746731 DOI: 10.1038/s41392-020-00361-x] [Citation(s) in RCA: 90] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 09/21/2020] [Accepted: 09/23/2020] [Indexed: 02/06/2023] Open
Abstract
Acute myeloid leukemia (AML) is the most common form of acute leukemia in adults and the second most common form of acute leukemia in children. Despite this, very little improvement in survival rates has been achieved over the past few decades. This is partially due to the heterogeneity of AML and the need for more targeted therapeutics than the traditional cytotoxic chemotherapies that have been a mainstay in therapy for the past 50 years. In the past 20 years, research has been diversifying the approach to treating AML by investigating molecular pathways uniquely relevant to AML cell proliferation and survival. Here we review the development of novel therapeutics in targeting apoptosis, receptor tyrosine kinase (RTK) signaling, hedgehog (HH) pathway, mitochondrial function, DNA repair, and c-Myc signaling. There has been an impressive effort into better understanding the diversity of AML cell characteristics and here we highlight important preclinical studies that have supported therapeutic development and continue to promote new ways to target AML cells. In addition, we describe clinical investigations that have led to FDA approval of new targeted AML therapies and ongoing clinical trials of novel therapies targeting AML survival pathways. We also describe the complexity of targeting leukemia stem cells (LSCs) as an approach to addressing relapse and remission in AML and targetable pathways that are unique to LSC survival. This comprehensive review details what we currently understand about the signaling pathways that support AML cell survival and the exceptional ways in which we disrupt them.
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Affiliation(s)
- Jenna L Carter
- Cancer Biology Graduate Program, Wayne State University School of Medicine, Detroit, MI, USA.,MD/PhD Program, Wayne State University School of Medicine, Detroit, MI, USA
| | - Katie Hege
- Cancer Biology Graduate Program, Wayne State University School of Medicine, Detroit, MI, USA
| | - Jay Yang
- Department of Oncology, Wayne State University School of Medicine, Detroit, MI, USA.,Molecular Therapeutics Program, Barbara Ann Karmanos Cancer Institute, Wayne State University School of Medicine, Detroit, MI, USA
| | - Hasini A Kalpage
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI, USA
| | - Yongwei Su
- Department of Oncology, Wayne State University School of Medicine, Detroit, MI, USA.,Molecular Therapeutics Program, Barbara Ann Karmanos Cancer Institute, Wayne State University School of Medicine, Detroit, MI, USA.,National Engineering Laboratory for AIDS Vaccine, Key Laboratory for Molecular Enzymology and Engineering, The Ministry of Education, School of Life Sciences, Jilin University, Changchun, China
| | - Holly Edwards
- Department of Oncology, Wayne State University School of Medicine, Detroit, MI, USA.,Molecular Therapeutics Program, Barbara Ann Karmanos Cancer Institute, Wayne State University School of Medicine, Detroit, MI, USA
| | - Maik Hüttemann
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI, USA
| | - Jeffrey W Taub
- Cancer Biology Graduate Program, Wayne State University School of Medicine, Detroit, MI, USA. .,Molecular Therapeutics Program, Barbara Ann Karmanos Cancer Institute, Wayne State University School of Medicine, Detroit, MI, USA. .,Division of Pediatric Hematology/Oncology, Children's Hospital of Michigan, Detroit, MI, USA. .,Department of Pediatrics, Wayne State University School of Medicine, Detroit, MI, USA.
| | - Yubin Ge
- Cancer Biology Graduate Program, Wayne State University School of Medicine, Detroit, MI, USA. .,Department of Oncology, Wayne State University School of Medicine, Detroit, MI, USA. .,Molecular Therapeutics Program, Barbara Ann Karmanos Cancer Institute, Wayne State University School of Medicine, Detroit, MI, USA.
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11
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Yuasa M, Yamamoto H, Mitsuki T, Kageyama K, Kaji D, Taya Y, Nishida A, Ishiwata K, Takagi S, Yamamoto G, Asano-Mori Y, Wake A, Koike Y, Makino S, Uchida N, Taniguchi S. Prognostic Impact of Cytogenetic Evolution on the Outcome of Allogeneic Stem Cell Transplantation in Patients with Acute Myeloid Leukemia in Nonremission: A Single-Institute Analysis of 212 Recipients. Biol Blood Marrow Transplant 2020; 26:2262-2270. [PMID: 32871257 DOI: 10.1016/j.bbmt.2020.08.026] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2020] [Revised: 08/16/2020] [Accepted: 08/22/2020] [Indexed: 12/16/2022]
Abstract
Recent progress in genetic analysis technology has helped researchers understand the pathogenesis of acute myeloid leukemia (AML). Considering this progress, AML karyotype is still one of the most significant prognostic factors that provides risk-adapted treatment approaches. Karyotype changes during treatment have been observed at times, but their prognostic impact is sparse, especially on allogeneic stem cell transplantation (allo-SCT). Here, we retrospectively investigated the effect of chromosomal changes between diagnosis and pretransplantation on the prognosis of allo-SCT by analyzing the outcomes of 212 consecutive patients who underwent allo-SCT for the first time at Toranomon Hospital, Tokyo, Japan, between 2008 and 2018. Cytogenetic abnormalities at diagnosis and pretransplantation were categorized based on the 2017 European Leukemia Net risk stratification. Genetic abnormalities such as FLT3-ITD and NPM1 were not considered in this study due to lack of genetic information in most patients. We defined cytogenetic evolution as chromosomal changes classified from lower category to higher category. Seventeen patients (8%) had cytogenetic evolution between diagnosis and pretransplantation, and they showed a significantly worse relapse rate than those who were categorized in the intermediate group based on the karyotype at diagnosis (3-year confidence interval [CI] of relapse, 57.4% versus 24.9%; P < .01). In multivariate analysis, cytogenetic evolution before allo-SCT had a significant impact on the CI of relapse (hazard ratio [HR], 3.89; CI, 1.75 to 8.67; P < .01), as well as the high score of the hematopoietic cell transplantation-specific comorbidity index (HR, 0.54; CI, 0.31 to 0.94; P = .03), but had no significant impact on overall survival or nonrelapse mortality. These results indicate that cytogenetic evolution has a significant impact after allo-SCT and should be considered during AML treatment.
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Affiliation(s)
| | | | - Takashi Mitsuki
- Department of Hematology, Toranomon Hospital Kajigaya, Kanagawa, Japan
| | - Kosei Kageyama
- Department of Hematology, Toranomon Hospital, Tokyo, Japan
| | - Daisuke Kaji
- Department of Hematology, Toranomon Hospital, Tokyo, Japan
| | - Yuki Taya
- Department of Hematology, Toranomon Hospital, Tokyo, Japan
| | - Aya Nishida
- Department of Hematology, Toranomon Hospital Kajigaya, Kanagawa, Japan
| | - Kazuya Ishiwata
- Department of Hematology, Toranomon Hospital Kajigaya, Kanagawa, Japan
| | | | - Go Yamamoto
- Department of Hematology, Toranomon Hospital, Tokyo, Japan
| | | | - Atsushi Wake
- Department of Hematology, Toranomon Hospital Kajigaya, Kanagawa, Japan
| | - Yukako Koike
- Department of Clinical Laboratory, Toranomon Hospital, Tokyo, Japan
| | - Shigeyoshi Makino
- Department of Transfusion Medicine, Toranomon Hospital, Tokyo, Japan
| | - Naoyuki Uchida
- Department of Hematology, Toranomon Hospital, Tokyo, Japan.
| | - Shuichi Taniguchi
- Department of Hematology, Toranomon Hospital, Tokyo, Japan; Okinaka Memorial Institute for Medical Research, Tokyo, Japan
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12
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Svobodova K, Lhotska H, Hodanova L, Pavlistova L, Vesela D, Belickova M, Vesela J, Brezinova J, Sarova I, Izakova S, Lizcova L, Siskova M, Jonasova A, Cermak J, Michalova K, Zemanova Z. Cryptic aberrations may allow more accurate prognostic classification of patients with myelodysplastic syndromes and clonal evolution. Genes Chromosomes Cancer 2020; 59:396-405. [PMID: 32170980 DOI: 10.1002/gcc.22841] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Revised: 01/03/2020] [Accepted: 02/29/2020] [Indexed: 11/05/2022] Open
Abstract
The karyotype of bone-marrow cells at the time of diagnosis is one of the most important prognostic factors in patients with myelodysplastic syndromes (MDS). In some cases, the acquisition of additional genetic aberrations (clonal evolution [CE]) associated with clinical progression may occur during the disease. We analyzed a cohort of 469 MDS patients using a combination of molecular cytogenomic methods to identify cryptic aberrations and to assess their potential role in CE. We confirmed CE in 36 (8%) patients. The analysis of bone-marrow samples with a combination of cytogenomic methods at diagnosis and after CE identified 214 chromosomal aberrations. The early genetic changes in the diagnostic samples were frequently MDS specific (17 MDS-specific/57 early changes). Most progression-related aberrations identified after CE were not MDS specific (131 non-MDS-specific/155 progression-related changes). Copy number neutral loss of heterozygosity (CN-LOH) was detected in 19% of patients. MDS-specific CN-LOH (4q, 17p) was identified in three patients, and probably pathogenic homozygous mutations were found in TET2 (4q24) and TP53 (17p13.1) genes. We observed a statistically significant difference in overall survival (OS) between the groups of patients divided according to their diagnostic cytogenomic findings, with worse OS in the group with complex karyotypes (P = .021). A combination of cytogenomic methods allowed us to detect many cryptic genomic changes and identify genes and genomic regions that may represent therapeutic targets in patients with progressive MDS.
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Affiliation(s)
- Karla Svobodova
- Center of Oncocytogenomics, Institute of Medical Biochemistry and Laboratory Diagnostics, General University Hospital and First Faculty of Medicine, Charles University in Prague, Prague, Czech Republic.,First Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
| | - Halka Lhotska
- Center of Oncocytogenomics, Institute of Medical Biochemistry and Laboratory Diagnostics, General University Hospital and First Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
| | - Lucie Hodanova
- Center of Oncocytogenomics, Institute of Medical Biochemistry and Laboratory Diagnostics, General University Hospital and First Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
| | - Lenka Pavlistova
- Center of Oncocytogenomics, Institute of Medical Biochemistry and Laboratory Diagnostics, General University Hospital and First Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
| | - Denisa Vesela
- Center of Oncocytogenomics, Institute of Medical Biochemistry and Laboratory Diagnostics, General University Hospital and First Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
| | - Monika Belickova
- Institute of Hematology and Blood Transfusion, Prague, Czech Republic
| | - Jitka Vesela
- Institute of Hematology and Blood Transfusion, Prague, Czech Republic
| | - Jana Brezinova
- Institute of Hematology and Blood Transfusion, Prague, Czech Republic
| | - Iveta Sarova
- Center of Oncocytogenomics, Institute of Medical Biochemistry and Laboratory Diagnostics, General University Hospital and First Faculty of Medicine, Charles University in Prague, Prague, Czech Republic.,Institute of Hematology and Blood Transfusion, Prague, Czech Republic
| | - Silvia Izakova
- Center of Oncocytogenomics, Institute of Medical Biochemistry and Laboratory Diagnostics, General University Hospital and First Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
| | - Libuse Lizcova
- Center of Oncocytogenomics, Institute of Medical Biochemistry and Laboratory Diagnostics, General University Hospital and First Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
| | - Magda Siskova
- First Medical Department, General University Hospital and First Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
| | - Anna Jonasova
- First Medical Department, General University Hospital and First Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
| | - Jaroslav Cermak
- Institute of Hematology and Blood Transfusion, Prague, Czech Republic
| | - Kyra Michalova
- Center of Oncocytogenomics, Institute of Medical Biochemistry and Laboratory Diagnostics, General University Hospital and First Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
| | - Zuzana Zemanova
- Center of Oncocytogenomics, Institute of Medical Biochemistry and Laboratory Diagnostics, General University Hospital and First Faculty of Medicine, Charles University in Prague, Prague, Czech Republic.,First Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
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13
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Knorr DA, Goldberg AD, Stein EM, Tallman MS. Immunotherapy for acute myeloid leukemia: from allogeneic stem cell transplant to novel therapeutics. Leuk Lymphoma 2019; 60:3350-3362. [PMID: 31335250 PMCID: PMC6928392 DOI: 10.1080/10428194.2019.1639167] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2019] [Revised: 06/20/2019] [Accepted: 06/23/2019] [Indexed: 12/18/2022]
Abstract
Immunotherapy in the form of allogeneic stem cell transplantation (SCT) plays an instrumental role in the treatment of acute myeloid leukemia (AML), with non-transplant modalities of immunotherapy including checkpoint blockade now being actively explored. Here, we provide an overview of the graft versus leukemia (GVL) effect in AML as a window into understanding the prospects of AML immunotherapy. We explore the roles of various cell types in orchestrating anti-leukemic immunity, as well as those contributing to the unique immune suppressive state of myeloid diseases. We discuss specific approaches to engage the immune system, while noting the challenges of the AML antigen landscape and the barriers to immune modulation. We review the potential for immunomodulatory agents in combination with cellular therapies, donor lymphocyte infusion, and following SCT. Finally, to address the challenge of minimal residual disease (MRD) following chemotherapy, we propose combination epigenetic and immunotherapy for the eradication of MRD.
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Affiliation(s)
- David A. Knorr
- Leukemia Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Laboratory of Molecular Genetics and Immunology, Rockefeller University, New York, NY, USA
| | - Aaron D. Goldberg
- Leukemia Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Eytan M. Stein
- Leukemia Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Martin S. Tallman
- Leukemia Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA
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14
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Nonclonal chromosomal alterations and poor survival in cytopenic patients without hematological malignancies. Mol Cytogenet 2019; 12:46. [PMID: 31754375 PMCID: PMC6852952 DOI: 10.1186/s13039-019-0458-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Accepted: 10/23/2019] [Indexed: 01/05/2023] Open
Abstract
Background Clonal chromosomal alterations (CCAs) reflect recurrent genetic changes derived from a single evolving clone, whereas nonclonal chromosomal alterations (NCCAs) comprise a single or nonrecurrent chromosomal abnormality. CCAs and NCCAs in hematopoietic cells have been partially investigated in cytopenic patients without hematological malignancies. Methods This single-center retrospective study included 253 consecutive patients who underwent bone marrow aspiration to determine the cause of cytopenia between 2012 and 2015. Patients with hematological malignancies were excluded. CCA was defined as a chromosomal aberration detected in more than two cells, and NCCA was defined as a chromosomal aberration detected in a single cell. Results The median age of the patients was 66 years. There were 135 patients without hematological malignancies (median age, 64 years; 69 females); of these, 27 patients (median age, 69 years; 8 females) harbored chromosomal abnormalities. CCAs were detected in 14 patients; the most common CCA was −Y in eight patients, followed by inv.(9) in three patients and mar1+, inv. (12), and t (19;21) in one patient each. NCCAs were detected in 13 patients; the most frequent NCCA was +Y in four patients, followed by del (20), + 8, inv. (2), − 8, and add (6) in one patient each. Moreover, nonclonal translocation abnormalities, including t (9;14), t (14;16), and t (13;21), were observed in three patients. One patient had a complex karyotype in a single cell. The remaining 106 patients with normal karyotypes comprised the control group (median age, 65 years; range, 1–92 years; 56 females). Further, follow-up analysis revealed that the overall survival of the NCCA group was worse than that of the CCA and the normal karyotype groups (P < 0.0001; log-rank test). The survival of the NCCA-harboring cytopenic patients was worse than that of the CCA-harboring cytopenic patients without hematological malignancies, suggesting that follow-up should be considered for both CCA- and NCCA-harboring cytopenic patients.
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15
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Bussel J, Kulasekararaj A, Cooper N, Verma A, Steidl U, Semple JW, Will B. Mechanisms and therapeutic prospects of thrombopoietin receptor agonists. Semin Hematol 2019; 56:262-278. [PMID: 31836033 DOI: 10.1053/j.seminhematol.2019.09.001] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Revised: 07/30/2019] [Accepted: 09/30/2019] [Indexed: 12/13/2022]
Abstract
The second-generation thrombopoietin (TPO) receptor agonists eltrombopag and romiplostim are potent activators of megakaryopoiesis and represent a growing treatment option for patients with thrombocytopenic hematological disorders. Both TPO receptor agonists have been approved worldwide for the treatment of children and adults with chronic immune thrombocytopenia. In the EU and USA, eltrombopag is approved for the treatment of patients with severe aplastic anemia who have had an insufficient response to immunosuppressive therapy and in the USA for the first-line treatment of severe aplastic anemia in combination with immunosuppressive therapy. Eltrombopag has also shown efficacy in several other disease settings, for example, chemotherapy-induced thrombocytopenia, selected inherited thrombocytopenias, and myelodysplastic syndromes. While both TPO receptor agonists stimulate TPO receptor signaling and enhance megakaryopoiesis, their vastly different biochemical structures bestow upon them markedly different molecular and functional properties. Here, we review and discuss results from preclinical and clinical studies on the functional and molecular mechanisms of action of this new class of drug.
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Affiliation(s)
- James Bussel
- Pediatric Hematology/Oncology, Weill Cornell Medicine, New York, NY.
| | | | | | - Amit Verma
- Albert Einstein College of Medicine, New York, NY
| | | | - John W Semple
- Division of Hematology and Transfusion Medicine, Lund University, Lund, Sweden
| | - Britta Will
- Albert Einstein College of Medicine, New York, NY.
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16
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Zhang H, Luo S, Zhang X, Liao J, Quan F, Zhao E, Zhou C, Yu F, Yin W, Zhang Y, Xiao Y, Li X. SEECancer: a resource for somatic events in evolution of cancer genome. Nucleic Acids Res 2019; 46:D1018-D1026. [PMID: 29069402 PMCID: PMC5753201 DOI: 10.1093/nar/gkx964] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Accepted: 10/09/2017] [Indexed: 01/08/2023] Open
Abstract
Cancer cells progressively evolve from a premalignant to a malignant state, which is driven by accumulating somatic alterations that confer normal cells a fitness advantage. Improvements in high-throughput sequencing techniques have led to an increase in construction of tumor phylogenetics and identification of somatic driver events that specifically occurred in different tumor progression stages. Here, we developed the SEECancer database (http://biocc.hrbmu.edu.cn/SEECancer), which aims to present the comprehensive cancer evolutionary stage-specific somatic events (including early-specific, late-specific, relapse-specific, metastasis-specific, drug-resistant and drug-induced genomic events) and their temporal orders. By manually curating over 10 000 published articles, 1231 evolutionary stage-specific genomic events and 5772 temporal orders involving 82 human cancers and 23 tissue origins were collected and deposited in the SEECancer database. Each entry contains the somatic event, evolutionary stage, cancer type, detection approach and relevant evidence. SEECancer provides a user-friendly interface for browsing, searching and downloading evolutionary stage-specific somatic events and temporal relationships in various cancers. With increasing attention on cancer genome evolution, the necessary information in SEECancer will facilitate understanding of cancer etiology and development of evolutionary therapeutics, and help clinicians to discover biomarkers for monitoring tumor progression.
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Affiliation(s)
- Hongyi Zhang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150081, China
| | - Shangyi Luo
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150081, China
| | - Xinxin Zhang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150081, China
| | - Jianlong Liao
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150081, China
| | - Fei Quan
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150081, China
| | - Erjie Zhao
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150081, China
| | - Chenfen Zhou
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150081, China
| | - Fulong Yu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150081, China
| | - Wenkang Yin
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150081, China
| | - Yunpeng Zhang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150081, China
| | - Yun Xiao
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150081, China
| | - Xia Li
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150081, China
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17
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Lee JK, Lee MS, Moon MH, Woo H, Hong YJ, Jang S, Oh S. Translocation Frequency in Patients with Repeated CT Exposure: Comparison with CT-Naive Patients. Radiat Res 2019; 192:23-27. [DOI: 10.1667/rr15286.1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
| | | | | | | | | | - Seongjae Jang
- Department of Laboratory of Biological Dosimetry, Korea Cancer Center Hospital, Korea Institute of Radiological and Medical Sciences, Seoul, South Korea
| | - Sohee Oh
- Department of Biostatistics, SMG-SNU Boramae Medical Center, Seoul National University College of Medicine, Seoul, South Korea
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18
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Datta A, Brosh RM. Holding All the Cards-How Fanconi Anemia Proteins Deal with Replication Stress and Preserve Genomic Stability. Genes (Basel) 2019; 10:genes10020170. [PMID: 30813363 PMCID: PMC6409899 DOI: 10.3390/genes10020170] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Revised: 02/14/2019] [Accepted: 02/15/2019] [Indexed: 12/18/2022] Open
Abstract
Fanconi anemia (FA) is a hereditary chromosomal instability disorder often displaying congenital abnormalities and characterized by a predisposition to progressive bone marrow failure (BMF) and cancer. Over the last 25 years since the discovery of the first linkage of genetic mutations to FA, its molecular genetic landscape has expanded tremendously as it became apparent that FA is a disease characterized by a defect in a specific DNA repair pathway responsible for the correction of covalent cross-links between the two complementary strands of the DNA double helix. This pathway has become increasingly complex, with the discovery of now over 20 FA-linked genes implicated in interstrand cross-link (ICL) repair. Moreover, gene products known to be involved in double-strand break (DSB) repair, mismatch repair (MMR), and nucleotide excision repair (NER) play roles in the ICL response and repair of associated DNA damage. While ICL repair is predominantly coupled with DNA replication, it also can occur in non-replicating cells. DNA damage accumulation and hematopoietic stem cell failure are thought to contribute to the increased inflammation and oxidative stress prevalent in FA. Adding to its confounding nature, certain FA gene products are also engaged in the response to replication stress, caused endogenously or by agents other than ICL-inducing drugs. In this review, we discuss the mechanistic aspects of the FA pathway and the molecular defects leading to elevated replication stress believed to underlie the cellular phenotypes and clinical features of FA.
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Affiliation(s)
- Arindam Datta
- Laboratory of Molecular Gerontology, National Institute on Aging, NIH, NIH Biomedical Research Center, Baltimore, MD 21224, USA.
| | - Robert M Brosh
- Laboratory of Molecular Gerontology, National Institute on Aging, NIH, NIH Biomedical Research Center, Baltimore, MD 21224, USA.
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19
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Yang C, Li D, Bai Y, Song S, Yan P, Wu R, Zhang Y, Hu G, Lin C, Li X, Huang L. DEAD-box helicase 27 plays a tumor-promoter role by regulating the stem cell-like activity of human colorectal cancer cells. Onco Targets Ther 2018; 12:233-241. [PMID: 30643421 PMCID: PMC6314319 DOI: 10.2147/ott.s190814] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Background Cancer stem cells (CSCs) are responsible for all important characteristics of tumors. DEAD-box helicase 27 (DDX27) is a member of the DEAD-box RNA helicase family, and there have been only a few studies on DDX27 function in cancer cells. This study is aimed at exploring whether DDX27 has any relation to tumorigenesis of colorectal cancer (CRC) and elucidating the potential mechanism. Methods Data from Catalog Of Somatic Mutations In Cancer, Gene Expression Omnibus, and The Cancer Genome Atlas databases reveal that DDX27 is overexpressed in CRC tissues. qRT-PCR and Western blots were used to evaluate the expression level of DDX27 in 40 paired clinical CRC samples. DDX27 was knockdown in HT29 and HCT116 cell line with shRNA. Then CCK-8, colony formation assay and flow cytometry assay were performed to examine proliferative ability, cell cycle and sensitivity to 5-fluorouracil. Sphere-formation assay and in vivo subcutaneous tumor-formation assay were used to assess self-renewal in vitro and vivo as well as the tumor-initiating potential. Results DDX27 is upregulated in CRC tissues and downregulation of DDX27 inhibits proliferation of colorectal cancer cell and promotes sensitivity to 5-fluorouracil. Downregulation of DDX27 can downregulate the gene expression of known CSC markers in CRC cells, inhibit sphere-formation ability, and promote colonosphere differentiation. Downregulation of DDX27 in CSCs can decrease the tumor-initiating ability of CRC cells in vivo. Conclusion DDX27 may play a tumorpromoter role of CRC by regulating the stem cell-like activity of CRC cells.
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Affiliation(s)
- Chunxing Yang
- Department of Gastrointestinal Surgery, The Third Xiangya Hospital of Central South University, Changsha, Hunan Province, China,
| | - Daojiang Li
- Department of Gastrointestinal Surgery, The Third Xiangya Hospital of Central South University, Changsha, Hunan Province, China,
| | - Yang Bai
- Department of Gastrointestinal Surgery, The Third Xiangya Hospital of Central South University, Changsha, Hunan Province, China,
| | - Shenglei Song
- Department of Gastrointestinal Surgery, The Third Xiangya Hospital of Central South University, Changsha, Hunan Province, China,
| | - Peicheng Yan
- Department of Gastrointestinal Surgery, The Third Xiangya Hospital of Central South University, Changsha, Hunan Province, China,
| | - Runliu Wu
- Department of Gastrointestinal Surgery, The Third Xiangya Hospital of Central South University, Changsha, Hunan Province, China,
| | - Yi Zhang
- Department of Gastrointestinal Surgery, The Third Xiangya Hospital of Central South University, Changsha, Hunan Province, China,
| | - Gui Hu
- Department of Gastrointestinal Surgery, The Third Xiangya Hospital of Central South University, Changsha, Hunan Province, China,
| | - Changwei Lin
- Department of Gastrointestinal Surgery, The Third Xiangya Hospital of Central South University, Changsha, Hunan Province, China,
| | - Xiaorong Li
- Department of Gastrointestinal Surgery, The Third Xiangya Hospital of Central South University, Changsha, Hunan Province, China,
| | - Lihuang Huang
- Department of Central laboratory, The Third Xiangya Hospital of Central South University, Changsha, Hunan Province, China
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20
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Kraft B, Lombard J, Kirsch M, Wuchter P, Bugert P, Hielscher T, Blank N, Krämer A. SMC3 protein levels impact on karyotype and outcome in acute myeloid leukemia. Leukemia 2018; 33:795-799. [PMID: 30323357 DOI: 10.1038/s41375-018-0287-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Accepted: 09/14/2018] [Indexed: 12/13/2022]
Affiliation(s)
- Bianca Kraft
- Clinical Cooperation Unit Molecular Hematology/Oncology, German Cancer Research Center (DKFZ) and Department of Internal Medicine V, University of Heidelberg, Heidelberg, Germany
| | - Jan Lombard
- Clinical Cooperation Unit Molecular Hematology/Oncology, German Cancer Research Center (DKFZ) and Department of Internal Medicine V, University of Heidelberg, Heidelberg, Germany
| | - Michael Kirsch
- Clinical Cooperation Unit Molecular Hematology/Oncology, German Cancer Research Center (DKFZ) and Department of Internal Medicine V, University of Heidelberg, Heidelberg, Germany
| | - Patrick Wuchter
- Institute of Transfusion Medicine and Immunology, Medical Faculty Mannheim, University of Heidelberg, German Red Cross Blood Service Baden-Wuerttemberg-Hessen, Mannheim, Germany
| | - Peter Bugert
- Institute of Transfusion Medicine and Immunology, Medical Faculty Mannheim, University of Heidelberg, German Red Cross Blood Service Baden-Wuerttemberg-Hessen, Mannheim, Germany
| | - Thomas Hielscher
- Division of Biostatistics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Norbert Blank
- Department of Internal Medicine V, University of Heidelberg, Heidelberg, Germany
| | - Alwin Krämer
- Clinical Cooperation Unit Molecular Hematology/Oncology, German Cancer Research Center (DKFZ) and Department of Internal Medicine V, University of Heidelberg, Heidelberg, Germany. .,Department of Internal Medicine V, University of Heidelberg, Heidelberg, Germany.
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21
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Valind A, Öra I, Mertens F, Gisselsson D. Neuroblastoma with flat genomic profile: a question of representativity? BMJ Case Rep 2018; 2018:bcr-2018-225568. [PMID: 30196258 DOI: 10.1136/bcr-2018-225568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
Neuroblastoma is one of the most common paediatric malignancies. Detection of somatic genetic alterations in this tumour is instrumental for its risk stratification and treatment. On the other hand, an absence of detected chromosomal imbalances in neuroblastoma biopsies is difficult to interpret because it is unclear whether this situation truly reflects the tumour genome or if it is due to suboptimal sampling. We here present a neuroblastoma in the left adrenal of a newborn. The tumour was subjected to single-nucleotide polymorphism array analysis of five tumour regions with >80% tumour cells in histological mirror sections. This revealed no aberrations compared with a normal reference sample from the patient. Whole exome sequencing identified two single-nucleotide variants present in most tumour regions, corroborating that the tumour resulted from monoclonal expansion. Our data provide proof-of-principle that rare cases of neuroblastoma can have a normal whole genome copy number and allelic profile.
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Affiliation(s)
- Anders Valind
- Division of Clinical Genetics, Lunds Universitet, Lund, Sweden
| | - Ingrid Öra
- Division of Clinical Genetics, Lunds Universitet, Lund, Sweden
| | - Fredrik Mertens
- Division of Clinical Genetics, Lunds Universitet, Lund, Sweden
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22
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Mizuno Y, Tsukamoto T, Kawata E, Uoshima N, Uchiyama H, Yokota I, Maegawa S, Takimoto T, Tanba K, Matsumura-Kimoto Y, Kuwahara-Ota S, Fujibayashi Y, Yamamoto-Sugitani M, Chinen Y, Shimura Y, Horiike S, Taniwaki M, Kobayashi T, Kuroda J. Chromosomal abnormality variation detected by G-banding is associated with prognosis of diffuse large B-cell lymphoma treated by R-CHOP-based therapy. Cancer Med 2018; 7:655-664. [PMID: 29473332 PMCID: PMC5852349 DOI: 10.1002/cam4.1342] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Revised: 12/02/2017] [Accepted: 12/21/2017] [Indexed: 12/13/2022] Open
Abstract
Diffuse large B-cell lymphoma (DLBCL), which is the most prevalent disease subtype of non-Hodgkin lymphoma, is highly heterogeneous in terms of cytogenetic and molecular features. This study retrospectively investigated the clinical impact of G-banding-defined chromosomal abnormality on treatment outcomes of DLBCL in the era of rituximab-containing immunochemotherapy. Of 181 patients who were diagnosed with DLBCL and treated with R-CHOP or an R-CHOP-like regimen between January 2006 and April 2014, metaphase spreads were evaluable for G-banding in 120. In these 120 patients, 40 were found to harbor a single chromosomal aberration type; 63 showed chromosomal abnormality variations (CAVs), which are defined by the presence of different types of chromosomal abnormalities in G-banding, including 19 with two CAVs and 44 with ≥3 CAVs; and 17 had normal karyotypes. No specific chromosomal break point or numerical abnormality was associated with overall survival (OS) or progression-free survival (PFS), but the presence of ≥3 CAVs was significantly associated with inferior OS rates (hazard ratio (HR): 2.222, 95% confidence interval (CI): 1.056-4.677, P = 0.031) and tended to be associated with shorter PFS (HR: 1.796, 95% CI: 0.965-3.344, P = 0.061). In addition, ≥3 CAVs more frequently accumulated in high-risk patients, as defined by several conventional prognostic indices, such as the revised International Prognostic Index. In conclusion, our results suggest that the emergence of more CAVs, especially ≥3, based on chromosomal instability underlies the development of high-risk disease features and a poor prognosis in DLBCL.
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Affiliation(s)
- Yoshimi Mizuno
- Division of Hematology and Oncology, Department of Medicine, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Taku Tsukamoto
- Division of Hematology and Oncology, Department of Medicine, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Eri Kawata
- Department of Hematology, Japanese Red Cross Kyoto Daini Hospital, Kyoto, Japan
| | - Nobuhiko Uoshima
- Department of Hematology, Japanese Red Cross Kyoto Daini Hospital, Kyoto, Japan
| | - Hitoji Uchiyama
- Department of Hematology, Japanese Red Cross Kyoto Daiichi Hospital, Kyoto, Japan
| | - Isao Yokota
- Department of Biostatistics, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Saori Maegawa
- Division of Hematology and Oncology, Department of Medicine, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Tomoko Takimoto
- Division of Hematology and Oncology, Department of Medicine, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Kazuna Tanba
- Division of Hematology and Oncology, Department of Medicine, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Yayoi Matsumura-Kimoto
- Division of Hematology and Oncology, Department of Medicine, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Saeko Kuwahara-Ota
- Division of Hematology and Oncology, Department of Medicine, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Yuto Fujibayashi
- Division of Hematology and Oncology, Department of Medicine, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Mio Yamamoto-Sugitani
- Division of Hematology and Oncology, Department of Medicine, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Yoshiaki Chinen
- Division of Hematology and Oncology, Department of Medicine, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Yuji Shimura
- Division of Hematology and Oncology, Department of Medicine, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Shigeo Horiike
- Division of Hematology and Oncology, Department of Medicine, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Masafumi Taniwaki
- Division of Hematology and Oncology, Department of Medicine, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Tsutomu Kobayashi
- Division of Hematology and Oncology, Department of Medicine, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Junya Kuroda
- Division of Hematology and Oncology, Department of Medicine, Kyoto Prefectural University of Medicine, Kyoto, Japan
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23
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Day TA, Layer JV, Cleary JP, Guha S, Stevenson KE, Tivey T, Kim S, Schinzel AC, Izzo F, Doench J, Root DE, Hahn WC, Price BD, Weinstock DM. PARP3 is a promoter of chromosomal rearrangements and limits G4 DNA. Nat Commun 2017; 8:15110. [PMID: 28447610 PMCID: PMC5414184 DOI: 10.1038/ncomms15110] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Accepted: 02/28/2017] [Indexed: 12/24/2022] Open
Abstract
Chromosomal rearrangements are essential events in the pathogenesis of both malignant and nonmalignant disorders, yet the factors affecting their formation are incompletely understood. Here we develop a zinc-finger nuclease translocation reporter and screen for factors that modulate rearrangements in human cells. We identify UBC9 and RAD50 as suppressors and 53BP1, DDB1 and poly(ADP)ribose polymerase 3 (PARP3) as promoters of chromosomal rearrangements across human cell types. We focus on PARP3 as it is dispensable for murine viability and has druggable catalytic activity. We find that PARP3 regulates G quadruplex (G4) DNA in response to DNA damage, which suppresses repair by nonhomologous end-joining and homologous recombination. Chemical stabilization of G4 DNA in PARP3-/- cells leads to widespread DNA double-strand breaks and synthetic lethality. We propose a model in which PARP3 suppresses G4 DNA and facilitates DNA repair by multiple pathways.
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Affiliation(s)
- Tovah A. Day
- Department of Medical Oncology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, Massachusetts 02215, USA
| | - Jacob V. Layer
- Department of Medical Oncology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, Massachusetts 02215, USA
| | - J. Patrick Cleary
- Department of Medical Oncology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, Massachusetts 02215, USA
| | - Srijoy Guha
- Department of Medical Oncology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, Massachusetts 02215, USA
| | - Kristen E. Stevenson
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, Massachusetts 02215, USA
| | - Trevor Tivey
- Department of Medical Oncology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, Massachusetts 02215, USA
| | - Sunhee Kim
- Department of Medical Oncology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, Massachusetts 02215, USA
| | - Anna C. Schinzel
- Genetic Perturbation Platform, Broad Institute of MIT and Harvard University, 415 Main Street, Cambridge, Massachusetts 02142, USA
| | - Francesca Izzo
- Department of Medical Oncology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, Massachusetts 02215, USA
- Genetic Perturbation Platform, Broad Institute of MIT and Harvard University, 415 Main Street, Cambridge, Massachusetts 02142, USA
| | - John Doench
- Genetic Perturbation Platform, Broad Institute of MIT and Harvard University, 415 Main Street, Cambridge, Massachusetts 02142, USA
| | - David E. Root
- Genetic Perturbation Platform, Broad Institute of MIT and Harvard University, 415 Main Street, Cambridge, Massachusetts 02142, USA
| | - William C. Hahn
- Department of Medical Oncology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, Massachusetts 02215, USA
- Genetic Perturbation Platform, Broad Institute of MIT and Harvard University, 415 Main Street, Cambridge, Massachusetts 02142, USA
| | - Brendan D. Price
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, 450 Brookline Avenue, Boston, Massachusetts 02215, USA
| | - David M. Weinstock
- Department of Medical Oncology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, Massachusetts 02215, USA
- Genetic Perturbation Platform, Broad Institute of MIT and Harvard University, 415 Main Street, Cambridge, Massachusetts 02142, USA
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24
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Marker chromosomes can arise from chromothripsis and predict adverse prognosis in acute myeloid leukemia. Blood 2017; 129:1333-1342. [PMID: 28119329 DOI: 10.1182/blood-2016-09-738161] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2016] [Accepted: 01/04/2017] [Indexed: 01/03/2023] Open
Abstract
Metaphase karyotyping is an established diagnostic standard in acute myeloid leukemia (AML) for risk stratification. One of the cytogenetic findings in AML is structurally highly abnormal marker chromosomes. In this study, we have assessed frequency, cytogenetic characteristics, prognostic impact, and underlying biological origin of marker chromosomes. Given their inherent gross structural chromosomal damage, we speculated that they may arise from chromothripsis, a recently described phenomenon of chromosome fragmentation in a single catastrophic event. In 2 large consecutive prospective, randomized, multicenter, intensive chemotherapy trials (AML96, AML2003) from the Study Alliance Leukemia, marker chromosomes were detectable in 165/1026 (16.1%) of aberrant non-core-binding-factor (CBF) karyotype patients. Adverse-risk karyotypes displayed a higher frequency of marker chromosomes (26.5% in adverse-risk, 40.3% in complex aberrant, and 41.2% in abnormality(17p) karyotypes, P < .0001 each). Marker chromosomes were associated with a poorer prognosis compared with other non-CBF aberrant karyotypes and led to lower remission rates (complete remission + complete remission with incomplete recovery), inferior event-free survival as well as overall survival in both trials. In multivariate analysis, marker chromosomes independently predicted poor prognosis in the AML96 trial ≤60 years. As detected by array comparative genomic hybridization, about one-third of marker chromosomes (18/49) had arisen from chromothripsis, whereas this phenomenon was virtually undetectable in a control group of marker chromosome-negative complex aberrant karyotypes (1/34). The chromothripsis-positive cases were characterized by a particularly high degree of karyotype complexity, TP53 mutations, and dismal prognosis. In conclusion, marker chromosomes are indicative of chromothripsis and associated with poor prognosis per se and not merely by association with other adverse cytogenetic features.
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25
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Sperling AS, Gibson CJ, Ebert BL. The genetics of myelodysplastic syndrome: from clonal haematopoiesis to secondary leukaemia. Nat Rev Cancer 2017; 17:5-19. [PMID: 27834397 PMCID: PMC5470392 DOI: 10.1038/nrc.2016.112] [Citation(s) in RCA: 373] [Impact Index Per Article: 53.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Myelodysplastic syndrome (MDS) is a clonal disease that arises from the expansion of mutated haematopoietic stem cells. In a spectrum of myeloid disorders ranging from clonal haematopoiesis of indeterminate potential (CHIP) to secondary acute myeloid leukaemia (sAML), MDS is distinguished by the presence of peripheral blood cytopenias, dysplastic haematopoietic differentiation and the absence of features that define acute leukaemia. More than 50 recurrently mutated genes are involved in the pathogenesis of MDS, including genes that encode proteins involved in pre-mRNA splicing, epigenetic regulation and transcription. In this Review we discuss the molecular processes that lead to CHIP and further clonal evolution to MDS and sAML. We also highlight the ways in which these insights are shaping the clinical management of MDS, including classification schemata, prognostic scoring systems and therapeutic approaches.
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Affiliation(s)
- Adam S Sperling
- Department of Medical Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Boston, Massachusetts 02115, USA
- Division of Hematology, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts 02115, USA
| | - Christopher J Gibson
- Department of Medical Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Boston, Massachusetts 02115, USA
- Division of Hematology, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts 02115, USA
| | - Benjamin L Ebert
- Department of Medical Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Boston, Massachusetts 02115, USA
- Division of Hematology, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts 02115, USA
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26
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Kadioglu O, Cao J, Kosyakova N, Mrasek K, Liehr T, Efferth T. Genomic and transcriptomic profiling of resistant CEM/ADR-5000 and sensitive CCRF-CEM leukaemia cells for unravelling the full complexity of multi-factorial multidrug resistance. Sci Rep 2016; 6:36754. [PMID: 27824156 PMCID: PMC5099876 DOI: 10.1038/srep36754] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Accepted: 10/17/2016] [Indexed: 12/18/2022] Open
Abstract
We systematically characterised multifactorial multidrug resistance (MDR) in CEM/ADR5000 cells, a doxorubicin-resistant sub-line derived from drug-sensitive, parental CCRF-CEM cells developed in vitro. RNA sequencing and network analyses (Ingenuity Pathway Analysis) were performed. Chromosomal aberrations were identified by array-comparative genomic hybridisation (aCGH) and multicolour fluorescence in situ hybridisation (mFISH). Fifteen ATP-binding cassette transporters and numerous new genes were overexpressed in CEM/ADR5000 cells. The basic karyotype in CCRF-CEM cells consisted of 47, XX, der(5)t(5;14) (q35.33;q32.3), del(9) (p14.1), +20. CEM/ADR5000 cells acquired additional aberrations, including X-chromosome loss, 4q and 14q deletion, chromosome 7 inversion, balanced and unbalanced two and three way translocations: t(3;10), der(3)t(3;13), der(5)t(18;5;14), t(10;16), der(18)t(7;18), der(18)t(21;18;5), der(21;21;18;5) and der(22)t(9;22). CCRF-CEM consisted of two and CEM/ADR5000 of five major sub-clones, indicating genetic tumor heterogeneity. Loss of 3q27.1 in CEM/ADR5000 caused down-regulation of ABCC5 and ABCF3 expression, Xq28 loss down-regulated ABCD1 expression. ABCB1, the most well-known MDR gene, was 448-fold up-regulated due to 7q21.12 amplification. In addition to well-known drug resistance genes, numerous novel genes and genomic aberrations were identified. Transcriptomics and genetics in CEM/AD5000 cells unravelled a range of MDR mechanisms, which is much more complex than estimated thus far. This may have important implications for future treatment strategies.
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Affiliation(s)
- Onat Kadioglu
- Department of Pharmaceutical Biology, Institute of Pharmacy and Biochemistry, Johannes Gutenberg University, Mainz, Germany
| | - Jingming Cao
- Department of Pharmaceutical Biology, Institute of Pharmacy and Biochemistry, Johannes Gutenberg University, Mainz, Germany
| | - Nadezda Kosyakova
- Jena University Hospital, Friedrich Schiller University, Institute of Human Genetics, Jena, Germany
| | - Kristin Mrasek
- Jena University Hospital, Friedrich Schiller University, Institute of Human Genetics, Jena, Germany
| | - Thomas Liehr
- Jena University Hospital, Friedrich Schiller University, Institute of Human Genetics, Jena, Germany
| | - Thomas Efferth
- Department of Pharmaceutical Biology, Institute of Pharmacy and Biochemistry, Johannes Gutenberg University, Mainz, Germany
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27
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[Clinical and biological prognostic factors in relapsed acute myeloid leukemia patients]. Med Clin (Barc) 2016; 147:185-191. [PMID: 27374030 DOI: 10.1016/j.medcli.2016.05.015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2015] [Revised: 05/17/2016] [Accepted: 05/19/2016] [Indexed: 11/20/2022]
Abstract
BACKGROUND AND OBJECTIVE Acute myeloid leukemia (AML) is the most frequent type of acute leukemia in adults. Despite recent advances in the characterization of pathogenesis of AML, the cure rates are under 40%, being leukemia relapse the most common cause of treatment failure. Leukaemia relapse occurs due to clonal evolution or clonal escape. In this study, we aimed to analyze the clinical and biological factors influencing outcomes in patients with AML relapse. PATIENTS AND METHODS We included a total of 75 AML patients who experienced leukaemia relapse after achieving complete remission. We performed complete immunophenotyping and conventional karyotyping in bone marrow aspirates obtained at diagnosis and at leukemia relapse. RESULTS Overall survival (OS) of the series was 3.7%±2.3, leukaemia progression being the most common cause of death. Patients relapsing before 12 months and those with adverse cytogenetic-molecular risk had statistically significant worse outcomes. A percentage of 52.5 of patients showed phenotypic changes and 50% cytogenetic changes at relapse. We did not find significant clinical factors predicting clonal evolution. The presence of clonal evolution at relapse did not have a significant impact on outcome. CONCLUSIONS Patients with relapsed AML have a dismal prognosis, especially those with early relapse and adverse cytogenetic-molecular risk. Clonal evolution with phenotypic and cytogenetic changes occurred in half of the patients without predictive clinical factors or impact on outcome.
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28
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Abe Y, Miura T, Yoshida MA, Ujiie R, Kurosu Y, Kato N, Katafuchi A, Tsuyama N, Kawamura F, Ohba T, Inamasu T, Shishido F, Noji H, Ogawa K, Yokouchi H, Kanazawa K, Ishida T, Muto S, Ohsugi J, Suzuki H, Ishikawa T, Kamiya K, Sakai A. Analysis of chromosome translocation frequency after a single CT scan in adults. JOURNAL OF RADIATION RESEARCH 2016; 57:220-6. [PMID: 26874116 PMCID: PMC4915535 DOI: 10.1093/jrr/rrv090] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2015] [Accepted: 11/03/2015] [Indexed: 05/04/2023]
Abstract
We recently reported an increase in dicentric chromosome (DIC) formation after a single computed tomography (CT) scan (5.78-60.27 mSv: mean 24.24 mSv) and we recommended analysis of 2000 metaphase cells stained with Giemsa and centromere-FISH for dicentric chromosome assay (DCA) in cases of low-dose radiation exposure. In the present study, we analyzed the frequency of chromosome translocations using stored Carnoy's-fixed lymphocyte specimens from the previous study; these specimens were from 12 patients who were subject to chromosome painting of Chromosomes 1, 2 and 4. Chromosomes 1, 2 and 4 were analyzed in ∼5000 cells, which is equivalent to the whole-genome analysis of almost 2000 cells. The frequency of chromosome translocation was higher than the number of DICs formed, both before and after CT scanning. The frequency of chromosome translocations tended to be higher, but not significantly higher, in patients with a treatment history compared with patients without such a history. However, in contrast to the results for DIC formation, the frequency of translocations detected before and after the CT scan did not differ significantly. Therefore, analysis of chromosome translocation may not be a suitable assay for detecting chromosome aberrations in cases of low-dose radiation exposure from a CT scan. A significant increase in the frequency of chromosome translocations was not likely to be detected due to the high baseline before the CT scan; the high and variable frequency of translocations was probably due to multiple confounding factors in adults.
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Affiliation(s)
- Yu Abe
- Department of Radiation Life Sciences, Fukushima Medical University School of Medicine, 1 Hikarigaoka, Fukushima, 960-1295, Japan
| | - Tomisato Miura
- Department of Pathologic Analysis, Hirosaki University Graduate School of Health Sciences, Hirosaki, 036-8564, Japan
| | - Mitsuaki A Yoshida
- Department of Radiation Biology, Institute of Radiation Emergency Medicine, Hirosaki University, Hirosaki, 036-8564, Japan
| | - Risa Ujiie
- Department of Radiation Life Sciences, Fukushima Medical University School of Medicine, 1 Hikarigaoka, Fukushima, 960-1295, Japan
| | - Yumiko Kurosu
- Department of Radiation Life Sciences, Fukushima Medical University School of Medicine, 1 Hikarigaoka, Fukushima, 960-1295, Japan
| | - Nagisa Kato
- Department of Radiation Life Sciences, Fukushima Medical University School of Medicine, 1 Hikarigaoka, Fukushima, 960-1295, Japan
| | - Atsushi Katafuchi
- Department of Radiation Life Sciences, Fukushima Medical University School of Medicine, 1 Hikarigaoka, Fukushima, 960-1295, Japan
| | - Naohiro Tsuyama
- Department of Radiation Life Sciences, Fukushima Medical University School of Medicine, 1 Hikarigaoka, Fukushima, 960-1295, Japan
| | - Fumihiko Kawamura
- Department of Radiation Life Sciences, Fukushima Medical University School of Medicine, 1 Hikarigaoka, Fukushima, 960-1295, Japan
| | - Takashi Ohba
- Department of Radiation Health Management, Fukushima Medical University School of Medicine, 1 Hikarigaoka, Fukushima, 960-1295, Japan
| | - Tomoko Inamasu
- Department of Radiation Health Management, Fukushima Medical University School of Medicine, 1 Hikarigaoka, Fukushima, 960-1295, Japan
| | - Fumio Shishido
- Department of Radiology, Fukushima Medical University School of Medicine, 1 Hikarigaoka, Fukushima, 960-1295, Japan
| | - Hideyoshi Noji
- Department of Cardiology and Hematology, Fukushima Medical University School of Medicine, 1 Hikarigaoka, Fukushima, 960-1295, Japan
| | - Kazuei Ogawa
- Department of Cardiology and Hematology, Fukushima Medical University School of Medicine, 1 Hikarigaoka, Fukushima, 960-1295, Japan
| | - Hiroshi Yokouchi
- Department of Pulmonary Medicine, Fukushima Medical University School of Medicine, 1 Hikarigaoka, Fukushima, 960-1295, Japan
| | - Kenya Kanazawa
- Department of Pulmonary Medicine, Fukushima Medical University School of Medicine, 1 Hikarigaoka, Fukushima, 960-1295, Japan
| | - Takashi Ishida
- Department of Pulmonary Medicine, Fukushima Medical University School of Medicine, 1 Hikarigaoka, Fukushima, 960-1295, Japan
| | - Satoshi Muto
- Department of Regenerative Surgery, Fukushima Medical University School of Medicine, 1 Hikarigaoka, Fukushima, 960-1295, Japan
| | - Jun Ohsugi
- Department of Regenerative Surgery, Fukushima Medical University School of Medicine, 1 Hikarigaoka, Fukushima, 960-1295, Japan
| | - Hiroyuki Suzuki
- Department of Regenerative Surgery, Fukushima Medical University School of Medicine, 1 Hikarigaoka, Fukushima, 960-1295, Japan
| | - Tetsuo Ishikawa
- Department of Radiation Physics and Chemistry, Fukushima Medical University School of Medicine, 1 Hikarigaoka, Fukushima, 960-1295, Japan Radiation Medical Science Center for the Fukushima Health Management Survey, Fukushima Medical University School of Medicine, 1 Hikarigaoka, Fukushima, 960-1295, Japan
| | - Kenji Kamiya
- Radiation Medical Science Center for the Fukushima Health Management Survey, Fukushima Medical University School of Medicine, 1 Hikarigaoka, Fukushima, 960-1295, Japan Department of Experimental Oncology, Research Institute for Radiation Biology and Medicine, Hiroshima University, Hiroshima, Japan
| | - Akira Sakai
- Department of Radiation Life Sciences, Fukushima Medical University School of Medicine, 1 Hikarigaoka, Fukushima, 960-1295, Japan Radiation Medical Science Center for the Fukushima Health Management Survey, Fukushima Medical University School of Medicine, 1 Hikarigaoka, Fukushima, 960-1295, Japan
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29
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Clonal dynamics in a single AML case tracked for 9 years reveals the complexity of leukemia progression. Leukemia 2015; 30:295-302. [PMID: 26424407 DOI: 10.1038/leu.2015.264] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2015] [Revised: 09/16/2015] [Accepted: 09/22/2015] [Indexed: 12/30/2022]
Abstract
Most types of cancers are made up of heterogeneous mixtures of genetically distinct subclones. In particular, acute myeloid leukemia (AML) has been shown to undergo substantial clonal evolution over the course of the disease. AML tends to harbor fewer mutations than solid tumors, making it challenging to infer clonal structure. Here, we present a 9-year, whole-exome sequencing study of a single case at 12 time points, from the initial diagnosis until a fourth relapse, including 6 remission samples in between. To the best of our knowledge, it covers the longest time span of any data set of its kind. We used these time series data to track the hierarchy and order of variant acquisition, and subsequently analyzed the evolution of somatic variants to infer clonal structure. From this, we postulate the development and extinction of subclones, as well as their anticorrelated expansion via varying drug responses. In particular, we show that new subclones started appearing after the first complete remission. The presence and absence of different subclones during remission and relapses implies differing drug responses among subclones. Our study shows that time series analysis contrasting remission and relapse periods provides a much more comprehensive view of clonal structure and evolution.
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30
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Abe Y, Miura T, Yoshida MA, Ujiie R, Kurosu Y, Kato N, Katafuchi A, Tsuyama N, Ohba T, Inamasu T, Shishido F, Noji H, Ogawa K, Yokouchi H, Kanazawa K, Ishida T, Muto S, Ohsugi J, Suzuki H, Ishikawa T, Kamiya K, Sakai A. Increase in dicentric chromosome formation after a single CT scan in adults. Sci Rep 2015; 5:13882. [PMID: 26349546 PMCID: PMC4563376 DOI: 10.1038/srep13882] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Accepted: 08/07/2015] [Indexed: 01/01/2023] Open
Abstract
Excess risk of leukemia and brain tumors after CT scans in children has been reported. We performed dicentric chromosome assay (DCAs) before and after CT scan to assess effects of low-dose ionizing radiation on chromosomes. Peripheral blood (PB) lymphocytes were collected from 10 patients before and after a CT scan. DCA was performed by analyzing either 1,000 or 2,000 metaphases using both Giemsa staining and centromere-fluorescence in situ hybridization (Centromere-FISH). The increment of DIC formation was compared with effective radiation dose calculated using the computational dosimetry system, WAZA-ARI and dose length product (DLP) in a CT scan. Dicentric chromosome (DIC) formation increased significantly after a single CT scan, and increased DIC formation was found in all patients. A good correlation between the increment of DIC formation determined by analysis of 2,000 metaphases using Giemsa staining and those by 2,000 metaphases using Centromere-FISH was observed. However, no correlation was observed between the increment of DIC formation and the effective radiation dose. Therefore, these results suggest that chromosome cleavage may be induced by one CT scan, and we recommend 2,000 or more metaphases be analyzed in Giemsa staining or Centromere-FISH for DCAs in cases of low-dose radiation exposure.
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Affiliation(s)
- Yu Abe
- Dept. of Radiation Life Sciences, Fukushima Medical University School of Medicine, Fukushima, Japan
| | - Tomisato Miura
- Dept. of Pathologic Analysis, Hirosaki University Graduate School of Health Sciences, Hirosaki, Japan
| | - Mitsuaki A Yoshida
- Dept. of Radiation Biology, Institute of Radiation Emergency Medicine, Hirosaki University, Hirosaki, Japan
| | - Risa Ujiie
- Dept. of Radiation Life Sciences, Fukushima Medical University School of Medicine, Fukushima, Japan
| | - Yumiko Kurosu
- Dept. of Radiation Life Sciences, Fukushima Medical University School of Medicine, Fukushima, Japan
| | - Nagisa Kato
- Dept. of Radiation Life Sciences, Fukushima Medical University School of Medicine, Fukushima, Japan
| | - Atsushi Katafuchi
- Dept. of Radiation Life Sciences, Fukushima Medical University School of Medicine, Fukushima, Japan
| | - Naohiro Tsuyama
- Dept. of Radiation Life Sciences, Fukushima Medical University School of Medicine, Fukushima, Japan
| | - Takashi Ohba
- Dept. of Radiation Health Management, Fukushima Medical University School of Medicine, Fukushima, Japan
| | - Tomoko Inamasu
- Dept. of Radiation Health Management, Fukushima Medical University School of Medicine, Fukushima, Japan
| | - Fumio Shishido
- Dept. of Radiology, Fukushima Medical University School of Medicine, Fukushima, Japan
| | - Hideyoshi Noji
- Dept. of Cardiology &Hematology, Fukushima Medical University School of Medicine, Fukushima, Japan
| | - Kazuei Ogawa
- Dept. of Cardiology &Hematology, Fukushima Medical University School of Medicine, Fukushima, Japan
| | - Hiroshi Yokouchi
- Dept. of Pulmonary Medicine, Fukushima Medical University School of Medicine, Fukushima, Japan
| | - Kenya Kanazawa
- Dept. of Pulmonary Medicine, Fukushima Medical University School of Medicine, Fukushima, Japan
| | - Takashi Ishida
- Dept. of Pulmonary Medicine, Fukushima Medical University School of Medicine, Fukushima, Japan
| | - Satoshi Muto
- Dept. of Regenerative Surgery, Fukushima Medical University School of Medicine, Fukushima, Japan
| | - Jun Ohsugi
- Dept. of Regenerative Surgery, Fukushima Medical University School of Medicine, Fukushima, Japan
| | - Hiroyuki Suzuki
- Dept. of Regenerative Surgery, Fukushima Medical University School of Medicine, Fukushima, Japan
| | - Tetsuo Ishikawa
- Dept. of Radiation Physics and Chemistry, Fukushima Medical University School of Medicine, Fukushima, Japan.,Radiation Medical Science Center for the Fukushima Health Management Survey, Fukushima Medical University School of Medicine, Fukushima, Japan
| | - Kenji Kamiya
- Dept. of Experimental Oncology, Research Institute for Radiation Biology and Medicine, Hiroshima University, Hiroshima, Japan.,Radiation Medical Science Center for the Fukushima Health Management Survey, Fukushima Medical University School of Medicine, Fukushima, Japan
| | - Akira Sakai
- Dept. of Radiation Life Sciences, Fukushima Medical University School of Medicine, Fukushima, Japan.,Radiation Medical Science Center for the Fukushima Health Management Survey, Fukushima Medical University School of Medicine, Fukushima, Japan
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