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Zhu J, Zhu X, Shi C, Li Q, Jiang Y, Chen X, Sun P, Jin Y, Wang T, Chen J. Integrative analysis of aging-related genes reveals CEBPA as a novel therapeutic target in non-small cell lung cancer. Cancer Cell Int 2024; 24:267. [PMID: 39068458 PMCID: PMC11282817 DOI: 10.1186/s12935-024-03457-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Accepted: 07/20/2024] [Indexed: 07/30/2024] Open
Abstract
BACKGROUND To explore the impact of ARGs on the prognosis of NSCLC, and its correlation with clinicopathological parameters and immune microenvironment. Preliminary research on the biological functions of CEBPA in NSCLC. METHODS Using consensus clustering analysis to identify molecular subtypes of ARGs in NSCLC patients; employing LASSO regression and multivariate Cox analysis to select 7 prognostic risk genes and construct a prognostic risk model; validating independent prognostic factors of NSCLC using forest plot analysis; analyzing immune microenvironment correlations using ESTIMATE and ssGSEA; assessing correlations between prognostic risk genes via qPCR and Western blot in NSCLC; measuring mRNA and protein expression levels of knocked down and overexpressed CEBPA in NSCLC using CCK-8 and EdU assays; evaluating the effects of knocked down and overexpressed CEBPA on cell proliferation using Transwell experiments; examining the correlation of CEBPA with T cells and B cells using mIHC analysis. RESULTS Consensus clustering analysis identified three molecular subtypes, suggesting significant differential expression of these ARGs in NSCLC prognosis and clinical pathological parameters. There was significant differential expression between the two risk groups in the prognostic risk model, with P < 0.001. The risk score of the prognostic risk model was also P < 0.001. CEBPA exhibited higher mRNA and protein expression levels in NSCLC cell lines. Knockdown of CEBPA significantly reduced mRNA and protein expression levels of CEBPB, YWHAZ, ABL1, and CDK1 in H1650 and A549 cells. siRNA-mediated knockdown of CEBPA markedly inhibited proliferation, migration, and invasion of NSCLC cells, whereas overexpression of CEBPA showed the opposite trend. mIHC results indicated a significant increase in CD3 + CD4+, CD3 + CD8+, and CD20 + cell counts in the high CEBPA expression group. CONCLUSIONS The risk score of the prognostic risk model can serve as an independent prognostic factor, guiding the diagnosis and treatment of NSCLC. CEBPA may serve as a potential tumor biomarker and immune target, facilitating further exploration of the biological functions and immunological relevance in NSCLC.
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Affiliation(s)
- Jiaqi Zhu
- Department of Thoracic Surgery, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong, China
| | - Xiaoren Zhu
- Department of Radiotherapy and Oncology, Affiliated Kunshan Hospital of Jiangsu University, Kunshan, China
| | - Conglin Shi
- Cancer Immunotherapy Center, Cancer Research Institute, Xuzhou Medical University, Xuzhou, China
| | - Qixuan Li
- Department of Thoracic Surgery, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong, China
| | - Yun Jiang
- Department of Burn and Plastic Surgery, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong, China
| | - Xingyou Chen
- School of Medicine, Nantong University, Nantong, China
| | - Pingping Sun
- Department of Clinical Biobank, The Institute of Oncology, Affiliated Hospital of Nantong University, Nantong, China
| | - Yi Jin
- Department of Rheumatology, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong, China.
| | - Tianyi Wang
- Department of Thoracic Surgery, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong, China.
| | - Jianle Chen
- Department of Thoracic Surgery, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong, China.
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Stefańczyk SA, Hayn C, Heitmann J, Jung S, Zekri L, Märklin M. Expression and Prognostic Value of a Novel B7-H3 (CD276) Antibody in Acute Myeloid Leukemia. Cancers (Basel) 2024; 16:2455. [PMID: 39001517 PMCID: PMC11240323 DOI: 10.3390/cancers16132455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2024] [Revised: 06/27/2024] [Accepted: 07/02/2024] [Indexed: 07/16/2024] Open
Abstract
Despite recent advances in immunophenotyping, the prognosis of acute myeloid leukemia (AML) is still mainly estimated using age and genetic markers. As the genetic heterogeneity of AML patients is high, flow cytometry-based classification with appropriate biomarkers can efficiently complement risk stratification and treatment selection. An increased expression of B7-H3 (CD276), an immune checkpoint protein, has been reported and associated with poor prognosis. However, the available data are limited and heterogeneous. Here, we used a novel, proprietary murine anti-B7-H3 8H8 antibody for the flow cytometric analysis of B7-H3 expression in AML blasts from 77 patients. Our antibody reliably detected substantial B7-H3 expression in 62.3% of AML patients. B7-H3 expression was higher in the monocytic French-American-British (FAB) M5 group and in intermediate and poor risk patients according to the European Leukemia Network. Using receiver operating characteristics (ROCs), we identified a specific fluorescence intensity cut-off of 4.45 to discriminate between B7-H3high and B7-H3low expression. High B7-H3 expression was associated with shorter overall survival (OS) and progression-free survival (PFS). In conclusion, we have developed a novel B7-H3 antibody that serves as a new tool for the detection of B7-H3 expression in AML and may help to facilitate risk stratification and treatment selection in AML patients.
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Affiliation(s)
- Sylwia A. Stefańczyk
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tuebingen, 72076 Tuebingen, Germany; (S.A.S.); (C.H.); (J.H.); (S.J.)
- Cluster of Excellence iFIT (EXC 2180) ‘Image-Guided and Functionally Instructed Tumor Therapies’, Eberhard Karls University Tuebingen, 72076 Tuebingen, Germany
| | - Clara Hayn
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tuebingen, 72076 Tuebingen, Germany; (S.A.S.); (C.H.); (J.H.); (S.J.)
- Cluster of Excellence iFIT (EXC 2180) ‘Image-Guided and Functionally Instructed Tumor Therapies’, Eberhard Karls University Tuebingen, 72076 Tuebingen, Germany
| | - Jonas Heitmann
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tuebingen, 72076 Tuebingen, Germany; (S.A.S.); (C.H.); (J.H.); (S.J.)
- Cluster of Excellence iFIT (EXC 2180) ‘Image-Guided and Functionally Instructed Tumor Therapies’, Eberhard Karls University Tuebingen, 72076 Tuebingen, Germany
| | - Susanne Jung
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tuebingen, 72076 Tuebingen, Germany; (S.A.S.); (C.H.); (J.H.); (S.J.)
- Cluster of Excellence iFIT (EXC 2180) ‘Image-Guided and Functionally Instructed Tumor Therapies’, Eberhard Karls University Tuebingen, 72076 Tuebingen, Germany
- Department of Peptide−based Immunotherapy, Institute of Immunology, University and University Hospital Tuebingen, 72076 Tuebingen, Germany
| | - Latifa Zekri
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tuebingen, 72076 Tuebingen, Germany; (S.A.S.); (C.H.); (J.H.); (S.J.)
- Cluster of Excellence iFIT (EXC 2180) ‘Image-Guided and Functionally Instructed Tumor Therapies’, Eberhard Karls University Tuebingen, 72076 Tuebingen, Germany
| | - Melanie Märklin
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tuebingen, 72076 Tuebingen, Germany; (S.A.S.); (C.H.); (J.H.); (S.J.)
- Cluster of Excellence iFIT (EXC 2180) ‘Image-Guided and Functionally Instructed Tumor Therapies’, Eberhard Karls University Tuebingen, 72076 Tuebingen, Germany
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Tien FM, Hou HA. CEBPA mutations in acute myeloid leukemia: implications in risk stratification and treatment. Int J Hematol 2024:10.1007/s12185-024-03773-5. [PMID: 38671183 DOI: 10.1007/s12185-024-03773-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Revised: 04/02/2024] [Accepted: 04/08/2024] [Indexed: 04/28/2024]
Abstract
Mutations in CCAAT enhancer binding protein α (CEBPA) occur in approximately 10% of patients with de novo acute myeloid leukemia (AML). Emerging evidence supports that in-frame mutations in the basic leucine zipper domain of CEBPA (CEBPAbZIP-inf) confer a survival benefit, and CEBPAbZIP-inf replaced CEBPA double mutations (CEBPAdm) as a unique entity in the 2022 World Health Organization (WHO-2022) classification and International Consensus Classification (ICC). However, challenges remain in daily clinical practice since more than 30% patients with CEBPAbZIP-inf die of AML despite intensive treatment. This review aims to provide a comprehensive summary of the heterogeneities observed in AML with CEBPAdm and CEBPAbZIP-inf, and will discuss the prognostic implications of concurrent mutations and novel mechanistic targets that may inform future drug development. The ultimate goal is to optimize clinical management and to provide precision medicine for this category of patients.
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Affiliation(s)
- Feng-Ming Tien
- Division of Hematology, Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
- Graduate Institute of Clinical Medicine, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Hsin-An Hou
- Division of Hematology, Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan.
- Division of General Medicine, Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan.
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Georgi JA, Stasik S, Kramer M, Meggendorfer M, Röllig C, Haferlach T, Valk P, Linch D, Herold T, Duployez N, Taube F, Middeke JM, Platzbecker U, Serve H, Baldus CD, Muller-Tidow C, Haferlach C, Koch S, Berdel WE, Woermann BJ, Krug U, Braess J, Hiddemann W, Spiekermann K, Boertjes EL, Hills RK, Burnett A, Ehninger G, Metzeler K, Rothenberg-Thurley M, Dufour A, Dombret H, Pautas C, Preudhomme C, Fenwarth L, Bornhäuser M, Gale R, Thiede C. Prognostic impact of CEBPA mutational subgroups in adult AML. Leukemia 2024; 38:281-290. [PMID: 38228680 PMCID: PMC10844079 DOI: 10.1038/s41375-024-02140-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 12/28/2023] [Accepted: 01/05/2024] [Indexed: 01/18/2024]
Abstract
Despite recent refinements in the diagnostic and prognostic assessment of CEBPA mutations in AML, several questions remain open, i.e. implications of different types of basic region leucin zipper (bZIP) mutations, the role of co-mutations and the allelic state. Using pooled primary data analysis on 1010 CEBPA-mutant adult AML patients, a comparison was performed taking into account the type of mutation (bZIP: either typical in-frame insertion/deletion (InDel) mutations (bZIPInDel), frameshift InDel or nonsense mutations inducing translational stop (bZIPSTOP) or single base-pair missense alterations (bZIPms), and transcription activation domain (TAD) mutations) and the allelic state (single (smCEBPA) vs. double mutant (dmCEBPA)). Only bZIPInDel patients had significantly higher rates of complete remission and longer relapse free and overall survival (OS) compared with all other CEBPA-mutant subgroups. Moreover, co-mutations in bZIPInDel patients (e.g. GATA2, FLT3, WT1 as well as ELN2022 adverse risk aberrations) had no independent impact on OS, whereas in non-bZIPInDel patients, grouping according to ELN2022 recommendations added significant prognostic information. In conclusion, these results demonstrate bZIPInDel mutations to be the major independent determinant of outcome in CEBPA-mutant AML, thereby refining current classifications according to WHO (including all dmCEBPA and smCEBPA bZIP) as well as ELN2022 and ICC recommendations (including CEBPA bZIPms).
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Affiliation(s)
- Julia-Annabell Georgi
- Medizinische Klinik und Poliklinik 1, Medizinische Fakultät und Universitätsklinikum Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Sebastian Stasik
- Medizinische Klinik und Poliklinik 1, Medizinische Fakultät und Universitätsklinikum Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | | | | | - Christoph Röllig
- Medizinische Klinik und Poliklinik 1, Medizinische Fakultät und Universitätsklinikum Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | | | - Peter Valk
- Erasmus University Medical Center, Rotterdam, Netherlands
| | - David Linch
- Department of Haematology, UCL Cancer Institute, London, UK
| | - Tobias Herold
- Laboratory for Leukemia Diagnostics, Department of Medicine III, University Hospital, LMU Munich, Munich, Germany
| | - Nicolas Duployez
- Institut de Recherche contre le Cancer de Lille, Centre Hospitalier Universitaire de Lille, Lille, France
| | - Franziska Taube
- Medizinische Klinik und Poliklinik 1, Medizinische Fakultät und Universitätsklinikum Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Jan Moritz Middeke
- Medizinische Klinik und Poliklinik 1, Medizinische Fakultät und Universitätsklinikum Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Uwe Platzbecker
- Klinik und Poliklinik fur Hämatologie, Zelltherapie und Hämostaseologie, Universitätsklinikum Leipzig, Leipzig, Germany
| | - Hubert Serve
- Medizinische Klinik 2, Universitätsklinikum Frankfurt, Frankfurt am Main, Germany
| | - Claudia D Baldus
- Klinik für Innere Medizin II, Universitätsklinikum Schleswig-Holstein, Kiel, Germany
| | - Carsten Muller-Tidow
- Klinik für Hämatologie, Onkologie und Rheumatologie, Universitätsklinikum Heidelberg, Heidelberg, Germany
| | | | - Sarah Koch
- MLL Münchner Leukämielabor GmbH, Munich, Germany
| | - Wolfgang E Berdel
- Department of Medicine A, University Hospital Münster, Münster, Germany
| | | | - Utz Krug
- Department of Medicine 3, Klinikum Leverkusen, Leverkusen, Germany
| | - Jan Braess
- Department of Oncology and Hematology, Hospital Barmherzige Brüder, Regensburg, Germany
| | - Wolfgang Hiddemann
- Department of Medicine III, University Hospital LMU Munich, Munich, Germany
| | | | | | - Robert K Hills
- Nuffield Department of Population Health, Oxford University, Oxford, UK
| | - Alan Burnett
- Department of Haematology, Cardiff University, University Hospital of Wales, Cardiff, UK
| | | | - Klaus Metzeler
- Klinik und Poliklinik fur Hämatologie, Zelltherapie und Hämostaseologie, Universitätsklinikum Leipzig, Leipzig, Germany
| | | | - Annika Dufour
- Department of Medicine III, University Hospital LMU Munich, Munich, Germany
| | - Hervé Dombret
- Hôpital Saint-Louis (AP-HP), EA 3518, Université de Paris, Paris, France
| | - Cecile Pautas
- Service d'Hématologie et de thérapie cellulaire, Hôpital Henri Mondor, Créteil, France
| | - Claude Preudhomme
- Institut de Recherche contre le Cancer de Lille, Centre Hospitalier Universitaire de Lille, Lille, France
| | - Laurene Fenwarth
- Institut de Recherche contre le Cancer de Lille, Centre Hospitalier Universitaire de Lille, Lille, France
| | - Martin Bornhäuser
- Medizinische Klinik und Poliklinik 1, Medizinische Fakultät und Universitätsklinikum Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
- Nationales Zentrum für Tumorerkrankungen (NCT), Dresden, Germany
| | - Rosemary Gale
- Department of Haematology, UCL Cancer Institute, London, UK
| | - Christian Thiede
- Medizinische Klinik und Poliklinik 1, Medizinische Fakultät und Universitätsklinikum Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany.
- AgenDix GmbH, Dresden, Germany.
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Rivera JC, Nuñez D, Millar E, Ramirez K, Chandía M, Aguayo C. Mutations in the bZip region of the CEBPA gene: A novel prognostic factor in patients with acute myeloid leukemia. Int J Lab Hematol 2023; 45:833-838. [PMID: 37621152 DOI: 10.1111/ijlh.14157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 08/02/2023] [Indexed: 08/26/2023]
Abstract
BACKGROUND Hematopoiesis, the process of blood cell formation involves on a complex network of transcription factors. Among them, the CCAAT-enhancer-binding protein alpha (CEBPA) plays a crucial role in maintaining the balance between myeloid proliferation and differentiation. Imbalances in this network can lead to disrupted differentiation and contribute to the development of malignant diseases. AIM Understanding of disease development and explore potential therapeutic strategies for hematological disorders associated CEPBA gen. MATERIALS AND METHODS The research involved a comprehensive analysis of CEBPA gene mutations in the context of acute myeloid leukemia (AML). This encompassed a thorough exploration of point mutations and double mutations in AML patients. RESULTS In the context of acute myeloid leukemia (AML), mutations in the CEBPA gene, especially point mutations, are frequently observed. A significant number of AML patients present with double mutations in CEBPA, which have been linked to a more favorable prognosis in terms of overall survival and event-free survival. These patients also tend to exhibit enhanced responsiveness to treatment. DISCUSSION Unraveling the intricate interplay of transcription factors, particularly CEBPA, holds significant implications for decoding the mechanisms governing hematopoiesis. This understanding offers a potential avenue for deciphering disease development and devising novel therapeutic strategies for hematological disorders. CONCLUSION The findings underscore that CEBPA mutations correlate with enhanced overall survival and event-free survival, with relevance to those presenting within the bZip framework. This knowledge may contribute to advancing personalized treatments for hematological conditions.
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Affiliation(s)
- Juan Carlos Rivera
- Department Medical Technology, Faculty of Medicine, University of Concepción, Concepción, Chile
| | - Daniel Nuñez
- Department Medical Technology, Faculty of Medicine, University of Concepción, Concepción, Chile
| | - Elizabet Millar
- Department Medical Technology, Faculty of Medicine, University of Concepción, Concepción, Chile
| | - Kimberly Ramirez
- Department Medical Technology, Faculty of Medicine, University of Concepción, Concepción, Chile
| | - Mauricio Chandía
- Flow Cytometry Laboratory, Pathological Anatomy Unit, Hospital Regional Clinical Dr. Guillermo Grant Benavente, Concepción, Chile
| | - Claudio Aguayo
- Department of Clinical Biochemistry and Immunology, Faculty of Pharmacy, University of Concepción, Concepción, Chile
- Group of Research and Innovation in Vascular Health (GRIVAS Health), Chillan, Chile
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Liu Q, Qi L, Yang M, Zhang X, Li F, Wei H, Wang J. Immunophenotype distinctions of CEBPA mutation subtypes in acute myeloid leukemia. Int J Lab Hematol 2023; 45:743-750. [PMID: 37334560 DOI: 10.1111/ijlh.14124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 06/07/2023] [Indexed: 06/20/2023]
Abstract
INTRODUCTION Acute myeloid leukemia (AML) patients with CEBPA double mutation (CEBPAdm ) were associated with distinct immunophenotypes and prognosis. Recently, both International Consensus Classification (ICC) and World Health Organization (WHO) classifications incorporated BZIP single mutations (CEBPAsmBZIP ) into the favorable risk group. However, the immunophenotypes of CEBPAsmBZIP mutations have not been characterized, especially when compared with the immunophenotypes of CEBPAdm . METHODS Retrospectively, we investigated and compared the immunophenotypes of AML with CEBPA mutations. Randomforest model and XGBoost algorithm were used to set up a scoring system based on the immunophenotypes of those patients. RESULTS In a total of 967 AML patients: 218 were CEBPAdm (198 consisted of mutations in the BZIP region [CEBPAdmBZIP ], 20 were double mutations outside BZIP region [CEBPAdm-woBZIP ]), 117 were CEBPAsm (54 CEBPAsmBZIP and 63 were single mutations outside BZIP region [CEBPAsm-woBZIP ]) and the others were wildtype CEBPA (CEBPAwt ). Patients with CEBPAdmBZIP , CEBPAdm-woBZIP and CEBPAsmBZIP shared the distinct immunophenotype of CD7+ CD34+ MPO+ HLA-DR+ CD19- , in contrast to patients with CEBPAsm-woBZIP and CEBPAwt who showed reduced expression of CD7, HLA-DR, MPO, CD34 and a higher expression of CD19. Based on these immunophenotypes, we developed a scoring system to preemptively identify AML with CEBPAsmBZIP and CEBPAdm and validated it internally and externally. CONCLUSIONS AML with CEBPAdmBZIP , CEBPAdm-woBZIP , and CEBPAsmBZIP shared similar immunophenotypic profiles, whereas profoundly differed from the CEBPAsm-woBZIP and CEBPAwt AML.
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Affiliation(s)
- Qiaoxue Liu
- State Key Laboratory of Experimental Hematology, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
| | - Ling Qi
- The Center of Hematology, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Miao Yang
- State Key Laboratory of Experimental Hematology, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
| | - Xue Zhang
- State Key Laboratory of Experimental Hematology, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
| | - Fei Li
- The Center of Hematology, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Hui Wei
- State Key Laboratory of Experimental Hematology, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
- National Clinical Research Center for Blood Disease, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
- Haihe Laboratory of Cell Ecosystem, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
- Leukemia Center, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
| | - Jianxiang Wang
- State Key Laboratory of Experimental Hematology, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
- National Clinical Research Center for Blood Disease, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
- Haihe Laboratory of Cell Ecosystem, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
- Leukemia Center, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
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Deng C, Zeng T, Zhu P, Zhao S, Huang Z, Huang W, Zhang W, Huang X, Fu L. A novel 5-gene prognostic signature to improve risk stratification of cytogenetically normal acute myeloid leukemia. J Cancer Res Clin Oncol 2023; 149:10015-10025. [PMID: 37258721 DOI: 10.1007/s00432-023-04884-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Accepted: 05/19/2023] [Indexed: 06/02/2023]
Abstract
PURPOSE Prognostic prediction is a challenging task in cytogenetically normal acute myeloid leukemia (CN-AML) patients. In this study, we aimed at developing a novel prognostic signature to predict and stratify the survival of CN-AML patients. METHODS Using a training dataset (GSE12417), 5-gene prognostic signature was established to predict survival of CN-AML patients. The prognostic performance of this prognostic signature was further validated in testing dataset (TCGA CN-AML cohort) and validation dataset (GSE6891 CN-AML cohort). RESULTS In training, testing and validation datasets, the increased 5-gene risk score was significantly related with inferior overall survival (OS) of patients, and the area under the receiver operating characteristic curve (AUC) demonstrated that our prognostic signature had overall prediction accuracy. The excellent prognostic value of the 5-gene prognostic signature was also supported by the comparison with three previously proposed prognostic models. For the intermediate-risk CN-AML patients and the CN-AML patients with FLT3 or NPM1 mutation, our model could also well dichotomize them into two subgroups with distinct prognosis. Multivariate analysis demonstrated that 5-gene risk score was the only independent risk factor in TCGA CN-AML cohort. Nomogram including the 5-gene risk score performed well in predicting 1-year, 2-year and 3-year OS. CONCLUSION In summary, our novel 5-gene prognostic signature facilitated the improvement in risk stratification of CN-AML patients.
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Affiliation(s)
- Cong Deng
- Department of Hematology, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510260, China
- Department of Clinical Laboratory, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510260, China
- Central Laboratory, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510260, China
| | - Tiansheng Zeng
- Department of Hematology, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510260, China
- Central Laboratory, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510260, China
| | - Pei Zhu
- Department of Hematology, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510260, China
- Central Laboratory, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510260, China
| | - Sijie Zhao
- The Second Clinical School of Guangzhou Medical University, Guangzhou, 511436, China
| | - Zeyong Huang
- Department of Hematology, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510260, China
- Central Laboratory, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510260, China
| | - Wenhui Huang
- Department of Hematology, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510260, China
- Central Laboratory, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510260, China
| | - Wenjuan Zhang
- Department of Hematology, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510260, China
- Central Laboratory, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510260, China
| | - Xiaojuan Huang
- Department of Hematology, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510260, China
- Central Laboratory, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510260, China
| | - Lin Fu
- Department of Hematology, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510260, China.
- Central Laboratory, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510260, China.
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8
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Genomic Alterations, Gene Expression Profiles and Functional Enrichment of Normal-Karyotype Acute Myeloid Leukaemia Based on Targeted Next-Generation Sequencing. Cancers (Basel) 2023; 15:cancers15051386. [PMID: 36900179 PMCID: PMC10000176 DOI: 10.3390/cancers15051386] [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: 01/10/2023] [Revised: 02/08/2023] [Accepted: 02/16/2023] [Indexed: 02/24/2023] Open
Abstract
Characterising genomic variants is paramount in understanding the pathogenesis and heterogeneity of normal-karyotype acute myeloid leukaemia (AML-NK). In this study, clinically significant genomic biomarkers were ascertained using targeted DNA sequencing and RNA sequencing on eight AML-NK patients' samples collected at disease presentation and after complete remission. In silico and Sanger sequencing validations were performed to validate variants of interest, and they were followed by the performance of functional and pathway enrichment analyses for overrepresentation analysis of genes with somatic variants. Somatic variants involving 26 genes were identified and classified as follows: 18/42 (42.9%) as pathogenic, 4/42 (9.5%) as likely pathogenic, 4/42 (9.5%) as variants of unknown significance, 7/42 (16.7%) as likely benign and 9/42 (21.4%) as benign. Nine novel somatic variants were discovered, of which three were likely pathogenic, in the CEBPA gene with significant association with its upregulation. Transcription misregulation in cancer tops the affected pathways involving upstream genes (CEBPA and RUNX1) that were deregulated in most patients during disease presentation and were closely related to the most enriched molecular function gene ontology category, DNA-binding transcription activator activity RNA polymerase II-specific (GO:0001228). In summary, this study elucidated putative variants and their gene expression profiles along with functional and pathway enrichment in AML-NK patients.
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Bąk A, Skonieczka K, Jaśkowiec A, Junkiert-Czarnecka A, Heise M, Pilarska-Deltow M, Potoczek S, Czyżewska M, Haus O. Germline mutations among Polish patients with acute myeloid leukemia. Hered Cancer Clin Pract 2021; 19:42. [PMID: 34641967 PMCID: PMC8507332 DOI: 10.1186/s13053-021-00200-2] [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: 05/11/2021] [Accepted: 09/21/2021] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND A small but important proportion of patients (4-10 %) with AML have germline mutations. They can cause the development of AML at an earlier age, confer a higher risk of relapse or predispose to secondary leukemias, including therapy-related leukemias. The analysis of germline mutations in a patient and his/her family is also critical for the selection of suitable family donors if the patient is a candidate for hematopoietic stem cell transplantation (HSCT). METHODS 103 unrelated consecutive patients with de novo AML were enrolled in the study. Control group consisted of 103 persons from the general population. We performed NGS sequencing of bone marrow cells and buccal swabs DNA of six genes: CEBPA, DDX41, ETV6, TERT, GATA2, and IDH2 to detect germline pathogenic mutations. RESULTS In the investigated group, 49 variants were detected in six genes. 26 of them were somatic and 23 germline. Germline variants were detected in all six tested genes. Eight pathogenic germline mutations were detected in 7 AML patients, in three genes: CEBPA, ETV6, and IDH2. One patient had two pathogenic germinal mutations, one in ETV6 and one in CEBPA gene. We identified one novel pathogenic germline mutation in CEBPA gene. The difference in frequency of all pathogenic germline mutations between the tested (7.77 %) and control groups (0.97 %) was statistically significant (p = 0.046). In the tested group, the median age at AML diagnosis was 11 years lower in patients with pathogenic germline mutations than in patients without them (p = 0.028). CONCLUSIONS We showed higher frequency of CEBPA, ETV6, and IDH2 germline mutations in AML patients than in control group, which confirms the role of these mutations in the development of AML. We also showed that the median age at the onset of AML in patients with pathogenic germline mutations is significantly lower than in patients without them.
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Affiliation(s)
- Aneta Bąk
- Department of Clinical Genetics, Collegium Medicum, Nicolaus Copernicus University, Bydgoszcz, Toruń, Poland.
| | - Katarzyna Skonieczka
- Department of Clinical Genetics, Collegium Medicum, Nicolaus Copernicus University, Bydgoszcz, Toruń, Poland
| | - Anna Jaśkowiec
- Department of Hematology, Blood Neoplasms and Bone Marrow Transplantation, Medical University, Wrocław, Poland
| | - Anna Junkiert-Czarnecka
- Department of Clinical Genetics, Collegium Medicum, Nicolaus Copernicus University, Bydgoszcz, Toruń, Poland
| | - Marta Heise
- Department of Clinical Genetics, Collegium Medicum, Nicolaus Copernicus University, Bydgoszcz, Toruń, Poland
| | - Maria Pilarska-Deltow
- Department of Clinical Genetics, Collegium Medicum, Nicolaus Copernicus University, Bydgoszcz, Toruń, Poland
| | - Stanisław Potoczek
- Department of Hematology, Blood Neoplasms and Bone Marrow Transplantation, Medical University, Wrocław, Poland
| | | | - Olga Haus
- Department of Clinical Genetics, Collegium Medicum, Nicolaus Copernicus University, Bydgoszcz, Toruń, Poland
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Hindley A, Catherwood MA, McMullin MF, Mills KI. Significance of NPM1 Gene Mutations in AML. Int J Mol Sci 2021; 22:ijms221810040. [PMID: 34576201 PMCID: PMC8467861 DOI: 10.3390/ijms221810040] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 09/03/2021] [Accepted: 09/14/2021] [Indexed: 12/16/2022] Open
Abstract
The aim of this literature review is to examine the significance of the nucleophosmin 1 (NPM1) gene in acute myeloid leukaemia (AML). This will include analysis of the structure and normal cellular function of NPM1, the type of mutations commonly witnessed in NPM1, and the mechanism by which this influences the development and progression of AML. The importance of NPM1 mutation on prognosis and the treatment options available to patients will also be reviewed along with current guidelines recommending the rapid return of NPM1 mutational screening results and the importance of employing a suitable laboratory assay to achieve this. Finally, future developments in the field including research into new therapies targeting NPM1 mutated AML are considered.
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Affiliation(s)
- Andrew Hindley
- Clinical Haematology, Belfast City Hospital, Belfast BT9 7AB, UK;
- Correspondence:
| | | | - Mary Frances McMullin
- Centre for Medical Education, Queen’s University Belfast, Belfast BT7 1NN, UK;
- Northern Ireland and Belfast Health and Social Care Trust, Belfast BT9 7AB, UK
| | - Ken I. Mills
- Patrick G Johnston Center for Cancer Research, Queens University Belfast, Belfast BT9 7AE, UK;
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11
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CEBPA Mutations in 4708 Patients with Acute Myeloid Leukemia - Differential Impact of bZIP and TAD Mutations on Outcome. Blood 2021; 139:87-103. [PMID: 34320176 DOI: 10.1182/blood.2020009680] [Citation(s) in RCA: 73] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Accepted: 07/18/2021] [Indexed: 11/20/2022] Open
Abstract
Biallelic mutations of the CEBPA gene (CEBPAbi) define a distinct entity associated with favorable prognosis, however the role of monoallelic mutations (CEBPAsm) is poorly understood. We retrospectively analyzed 4708 adult AML patients recruited into Study Alliance Leukemia trials to investigate the prognostic impact of CEBPAsm. CEBPA mutations were identified in 240 patients (5.1%), 131 CEBPAbi and 109 CEBPAsm (60 affecting the amino-terminal transactivation domains (CEBPAsmTAD) and 49 the carboxy-terminal DNA-binding or basic leucine zipper region (CEBPAsmbZIP)). Interestingly, CEBPAbi and CEBPAsmbZIP patients shared several clinical factors, i.e. were significantly younger (median 46 years and 50 years) and had higher WBC counts at diagnosis (median 23.7 and 35.7 109/l) compared to CEBPAsmTAD patients (median age 63 yrs., median WBC 13.1 109/l; p<.001). Co-mutations were also similar in both groups, e.g. GATA2 mutations (35.1% CEBPAbi; 36.7% CEBPAsmbZIP vs. 6.7% CEBPAsmTAD; p<.001) or NPM1 mutations (3.1% CEBPAbi; 8.2% CEBPAsmbZIP vs. 38.3% CEBPAsmTAD; p<.001). CEBPAbi and CEBPAsmbZIP, but not CEBPAsmTAD were associated with significantly improved overall (median OS: 103 and 63 vs. 13 months) and event-free survival (median EFS: 20.7 and 17.1 vs. 5.7 months), in univariate and multivariable analyses. More detailed analysis revealed that the clinical and molecular features as well as the favorable survival were confined to patients showing in-frame mutations in bZIP (CEBPAbZIP-inf). When grouping patients into CEBPAbZIP-inf and CEBPAother (including CEBPAsmTAD and other non-CEBPAbZIP-inf patients), only CEBPAbZIP-inf patients showed superior CR rates and the longest median OS and EFS, arguing for a previously undefined prognostic role of this type of mutations.
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12
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Nie Y, Su L, Li W, Gao S. Novel insights of acute myeloid leukemia with CEBPA deregulation: Heterogeneity dissection and re-stratification. Crit Rev Oncol Hematol 2021; 163:103379. [PMID: 34087345 DOI: 10.1016/j.critrevonc.2021.103379] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Revised: 03/21/2021] [Accepted: 05/29/2021] [Indexed: 12/17/2022] Open
Abstract
Acute myeloid leukemia with bi-allelic CEBPA mutation was categorized as an independent disease entity with favorable prognosis, however, recent researches have revealed huge heterogeneity within this disease group, and for some patients, relapse remained a major cause of treatment failure. Further risk stratification is essentially needed. Here by reviewing the latest literature, we summarized the characteristics of CEBPA mutation profiles and clinical features, with a special intention of dissecting the heterogeneity within the seemingly homogeneous AML with bi-allelic CEBPA mutations. Specifically, non-classical CEBPA mutation, miscellaneous companion genetic aberrations and the presence of germline CEBPA mutation are three major sources of heterogeneity. Identifying these factors can help us predict patients at a higher risk of relapse, for whom aggressive treatment may be recommended. Novel therapeutic approaches regarding manipulating potentially druggable targets as well as the debate over post remission consolidation regimens has also been discussed.
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Affiliation(s)
- Yuanyuan Nie
- Department of Hematology, The First Hospital of Jilin University, Changchun, 130012, China
| | - Long Su
- Department of Hematology, The First Hospital of Jilin University, Changchun, 130012, China
| | - Wei Li
- Department of Hematology, The First Hospital of Jilin University, Changchun, 130012, China; Stem Cell and Cancer Center, The First Hospital of Jilin University, Changchun, 130012, China
| | - Sujun Gao
- Department of Hematology, The First Hospital of Jilin University, Changchun, 130012, China.
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Hassan NM, Said F, Shafik RE, Abdellateif MS. Dysregulation of CCAAT/enhancer binding protein-alpha (CEBPA) expression in the bone marrow of acute myeloid leukemia patients. EGYPTIAN JOURNAL OF MEDICAL HUMAN GENETICS 2021. [DOI: 10.1186/s43042-021-00154-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
Acute myeloid leukemia (AML) is a heterogeneous malignant disease characterized by accumulation of different types of mutations commonly the CCAAT/enhancer binding protein-alpha (CEBPA). However, the dysregulations of CEBPA expression in AML is still a debatable issue. The aim of the current study was to assess CEBPA gene expression in bone marrow (BM) aspiration specimens of 91 AML patients, compared to 20 control donors of bone marrow transplantation (BMT), using RT-PCR. Data were correlated with patients’ clinico-pathological features, response to treatment, progression-free survival (PFS), and overall survival (OS) rates.
Results
There was overexpression of CEBPA gene in AML patients compared to normal control [1.7 (0.04–25.6) versus 0.17 (0–4.78), respectively, P < 0.001]. Upregulation of CEBPA expression associated significantly with increased BM hypercellularity, total leucocyte counts, peripheral blood blast cell count, and poor PFS (P < 0.001, 0.002, 0.001, and 0.013, respectively). There was no significant association between CEBPA expression and any other relevant clinico-pathological features or OS rates (P = 0.610) of the patients. ROC analysis for biological relevance of CEBPA expression with AML showed that sensitivity and specificity of CEBPA expression at a cut-off value of 0.28 are 92.3% and 78.6%, respectively (P < 0.001). All patients who had CEBPA overexpression and mutant FLT3 showed BM hypercellularity, adverse cytogenetic risk, increased TLC, and PB blast cells count (P = 0.007, P < 0.001, 0.016, and 0.002, respectively).
Conclusion
CEBPA overexpression could be used as a genetic biological marker for AML diagnosis, as well as a poor prognostic factor for disease progression. It has no impact on OS rates of the patients.
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Krygier A, Szmajda-Krygier D, Sałagacka-Kubiak A, Jamroziak K, Żebrowska-Nawrocka M, Balcerczak E. Association between the CEBPA and c-MYC genes expression levels and acute myeloid leukemia pathogenesis and development. Med Oncol 2020; 37:109. [PMID: 33170359 PMCID: PMC7655568 DOI: 10.1007/s12032-020-01436-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2020] [Accepted: 10/27/2020] [Indexed: 11/30/2022]
Abstract
CEBPA and c-MYC genes belong to TF and play an essential role in hematologic malignancies development. Furthermore, these genes also co-regulate with RUNX1 and lead to bone marrow differentiation and may contribute to the leukemic transformation. Understanding the function and full characteristics of selected genes in the group of patients with AML can be helpful in assessing prognosis, and their usefulness as prognostic factors can be revealed. The aim of the study was to evaluate CEBPA and c-MYC mRNA expression level and to seek their association with demographical and clinical features of AML patients such as: age, gender, FAB classification, mortality or leukemia cell karyotype. Obtained results were also correlated with the expression level of the RUNX gene family. To assess of relative gene expression level the qPCR method was used. The expression levels of CEBPA and c-MYC gene varied among patients. Neither CEBPA nor c-MYC expression levels differed significantly between women and men (p=0.8325 and p=0.1698, respectively). No statistically significant correlation between age at the time of diagnosis and expression of CEBPA (p=0.4314) or c-MYC (p=0.9524) was stated. There were no significant associations between relative CEBPA (p=0.4247) or c-MYC (p=0.4655) expression level and FAB subtype and mortality among the enrolled patients (p=0.5858 and p=0.8437, respectively). However, it was observed that c-MYC and RUNX1 expression levels were significantly positively correlated (rS=0.328, p=0.0411). Overall, AML pathogenesis involves a complex interaction among CEBPA, c-MYC and RUNX family genes.
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Affiliation(s)
- Adrian Krygier
- Laboratory of Molecular Diagnostics and Pharmacogenomics, Department of Pharmaceutical Biochemistry and Molecular Diagnostics, Medical University of Lodz, Muszynskiego 1 Street, 90-151 Lodz, Poland
| | - Dagmara Szmajda-Krygier
- Laboratory of Molecular Diagnostics and Pharmacogenomics, Department of Pharmaceutical Biochemistry and Molecular Diagnostics, Medical University of Lodz, Muszynskiego 1 Street, 90-151 Lodz, Poland
| | - Aleksandra Sałagacka-Kubiak
- Laboratory of Molecular Diagnostics and Pharmacogenomics, Department of Pharmaceutical Biochemistry and Molecular Diagnostics, Medical University of Lodz, Muszynskiego 1 Street, 90-151 Lodz, Poland
| | - Krzysztof Jamroziak
- Department of Hematology, Institute of Hematology and Transfusion Medicine, Chocimska 5 Street, 00-791 Warsaw, Poland
| | - Marta Żebrowska-Nawrocka
- Laboratory of Molecular Diagnostics and Pharmacogenomics, Department of Pharmaceutical Biochemistry and Molecular Diagnostics, Medical University of Lodz, Muszynskiego 1 Street, 90-151 Lodz, Poland
| | - Ewa Balcerczak
- Laboratory of Molecular Diagnostics and Pharmacogenomics, Department of Pharmaceutical Biochemistry and Molecular Diagnostics, Medical University of Lodz, Muszynskiego 1 Street, 90-151 Lodz, Poland
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15
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Nagdy B, Kassem HA, Abdel-Ghaffar ARB, Seoudi DM, Kassem NM. The Clinicopathological Impact of Granulocyte-Macrophage Colony-Stimulating Factor Gene Expression and Different Molecular Prognostic Biomarkers in Egyptian Acute Myeloid Leukemia Patients. Asian Pac J Cancer Prev 2020; 21:1993-2001. [PMID: 32711425 PMCID: PMC7573395 DOI: 10.31557/apjcp.2020.21.7.1993] [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: 02/07/2020] [Indexed: 11/29/2022] Open
Abstract
Background: Acute myeloid leukemia (AML) is characterized by clonal expansion of myeloid precursors with diminished capacity for differentiation. It develops as the consequence of a series of genetic changes in a hematopoietic precursor cell. Purpose This study aimed to investigate the correlation between GM-CSF gene expression and different molecular prognostic markers such as FLT3-ITD, NPM1 mutation A and CEBPA gene expression in 100 Egyptian AML patients. As well as, correlation with the response to induction therapy, DFS andOS in these patients. Methodology: Quantitative assessment of GM-CSF gene expression was performed by qRT-PCR. Additional prognostic molecular markers were determined as FLT3-ITD and NPM1 mutation A together with quantitative assessment of CEBPA gene expression by qRT-PCR. Results: Patients with high GM-CSF expression levels had better OS and DFS with p value 0.004 and 0.02, respectively. However, no statistically significant difference between low andhigh GM-CSF gene expression was found regarding the response to therapy (p value= 0.08). Most patients with low CEBPA expression had resistant disease together with poor OS and DFS (P value = <0.001 for each). Our results showed that patients with high CEBPA gene expression whether GM-CSF gene expression was high or low had significant higher complete remission rates (p value = 0.1 for each). However, low GM-CSF gene expression andlow CEBPA gene expression showed poor response to treatment. Conclusion: Our findings suggest that molecular diagnostic biomarkers for AML are an essential tool that improves prognostication andhence better patients’ management.
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Affiliation(s)
- Bassant Nagdy
- Molecular Oncology Unit, Kasr Al-Aiby Centre of Clinical Oncology; Nuclear Medicine, School of Medicine, Cairo University, Egypt
| | - Hebatallah A Kassem
- Department of Clinical and Chemical Pathology, Kasr Al Ainy Centre of Clinical Oncology, Nuclear Medicine, School of Medicine, Cairo University, Cairo, Egypt
| | | | - Dina M Seoudi
- Department of Biochemistry, Faculty of Science, Ain Shams University, Cairo, Egypt
| | - Neemat M Kassem
- Department of Clinical and Chemical Pathology, Kasr Al Ainy Centre of Clinical Oncology, Nuclear Medicine, School of Medicine, Cairo University, Cairo, Egypt
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16
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Churpek JE, Bresnick EH. Transcription factor mutations as a cause of familial myeloid neoplasms. J Clin Invest 2019; 129:476-488. [PMID: 30707109 DOI: 10.1172/jci120854] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The initiation and evolution of myelodysplastic syndrome (MDS) and acute myeloid leukemia (AML) are driven by genomic events that disrupt multiple genes controlling hematopoiesis. Human genetic studies have discovered germline mutations in single genes that instigate familial MDS/AML. The best understood of these genes encode transcription factors, such as GATA-2, RUNX1, ETV6, and C/EBPα, which establish and maintain genetic networks governing the genesis and function of blood stem and progenitor cells. Many questions remain unanswered regarding how genes and circuits within these networks function in physiology and disease and whether network integrity is exquisitely sensitive to or efficiently buffered from perturbations. In familial MDS/AML, mutations change the coding sequence of a gene to generate a mutant protein with altered activity or introduce frameshifts or stop codons or disrupt regulatory elements to alter protein expression. Each mutation has the potential to exert quantitatively and qualitatively distinct influences on networks. Consistent with this mechanistic diversity, disease onset is unpredictable and phenotypic variability can be considerable. Efforts to elucidate mechanisms and forge prognostic and therapeutic strategies must therefore contend with a spectrum of patient-specific leukemogenic scenarios. Here we illustrate mechanistic advances in our understanding of familial MDS/AML syndromes caused by germline mutations of hematopoietic transcription factors.
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Affiliation(s)
- Jane E Churpek
- Section of Hematology/Oncology and Center for Clinical Cancer Genetics, The University of Chicago, Chicago, Illinois, USA
| | - Emery H Bresnick
- UW-Madison Blood Research Program, Department of Cell and Regenerative Biology, Wisconsin Institutes for Medical Research, UW Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, USA
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17
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Gebhard C, Glatz D, Schwarzfischer L, Wimmer J, Stasik S, Nuetzel M, Heudobler D, Andreesen R, Ehninger G, Thiede C, Rehli M. Profiling of aberrant DNA methylation in acute myeloid leukemia reveals subclasses of CG-rich regions with epigenetic or genetic association. Leukemia 2018; 33:26-36. [PMID: 29925905 DOI: 10.1038/s41375-018-0165-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2017] [Revised: 03/19/2018] [Accepted: 04/24/2018] [Indexed: 12/31/2022]
Abstract
Malignant transformation is frequently associated with disease-specific epigenetic alterations, but the underlying mechanisms and pathophysiological consequences remain poorly understood. Here, we used global comparative DNA methylation profiling at CG-rich regions of 27 acute myeloid leukemia (AML) samples to select a subset of aberrantly methylated CG-rich regions (~400 regions, ~15,000 CpGs) for quantitative DNA methylation profiling in a large cohort of AML patients (n = 196) using MALDI-TOF analysis of bisulfite-treated DNA. Meta-analysis separated a subgroup of CG-rich regions showing highly correlated DNA methylation changes that were marked by histone H3 lysine 27 trimethylation in normal hematopoietic progenitor cells. While the group of non-polycomb group (PcG) target regions displayed methylation patterns that correlated well with molecular and cytogenetic markers, PcG target regions displayed a much weaker association with genetic features. However, the degree of methylation gain across the latter panel showed significant correlation with active DNMT3A levels and with overall survival. Our study suggests that both epigenetic as well as genetic aberrations underlay AML-related changes in DNA methylation at CG-rich regions and that the former may provide a marker to improve classification and prognostication of adult AML patients.
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Affiliation(s)
- Claudia Gebhard
- Department of Internal Medicine III, University Hospital Regensburg, 93042, Regensburg, Germany.,RCI Regensburg Centre for Interventional Immunology, University Hospital Regensburg, 93042, Regensburg, Germany
| | - Dagmar Glatz
- Department of Internal Medicine III, University Hospital Regensburg, 93042, Regensburg, Germany.,RCI Regensburg Centre for Interventional Immunology, University Hospital Regensburg, 93042, Regensburg, Germany
| | - Lucia Schwarzfischer
- Department of Internal Medicine III, University Hospital Regensburg, 93042, Regensburg, Germany
| | - Julia Wimmer
- Department of Internal Medicine III, University Hospital Regensburg, 93042, Regensburg, Germany
| | - Sebastian Stasik
- Department of Internal Medicine I, University Hospital Carl Gustav Carus, 01307, Dresden, Germany
| | - Margit Nuetzel
- Department of Internal Medicine III, University Hospital Regensburg, 93042, Regensburg, Germany
| | - Daniel Heudobler
- Department of Internal Medicine III, University Hospital Regensburg, 93042, Regensburg, Germany
| | - Reinhard Andreesen
- Department of Internal Medicine III, University Hospital Regensburg, 93042, Regensburg, Germany.,RCI Regensburg Centre for Interventional Immunology, University Hospital Regensburg, 93042, Regensburg, Germany
| | - Gerhard Ehninger
- Department of Internal Medicine I, University Hospital Carl Gustav Carus, 01307, Dresden, Germany
| | - Christian Thiede
- Department of Internal Medicine I, University Hospital Carl Gustav Carus, 01307, Dresden, Germany
| | - Michael Rehli
- Department of Internal Medicine III, University Hospital Regensburg, 93042, Regensburg, Germany. .,RCI Regensburg Centre for Interventional Immunology, University Hospital Regensburg, 93042, Regensburg, Germany.
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Obulkasim A, Katsman-Kuipers JE, Verboon L, Sanders M, Touw I, Jongen-Lavrencic M, Pieters R, Klusmann JH, Michel Zwaan C, van den Heuvel-Eibrink MM, Fornerod M. Classification of pediatric acute myeloid leukemia based on miRNA expression profiles. Oncotarget 2018; 8:33078-33085. [PMID: 28380436 PMCID: PMC5464851 DOI: 10.18632/oncotarget.16525] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Accepted: 03/01/2017] [Indexed: 12/28/2022] Open
Abstract
Pediatric acute myeloid leukemia (AML) is a heterogeneous disease with respect to biology as well as outcome. In this study, we investigated whether known biological subgroups of pediatric AML are reflected by a common microRNA (miRNA) expression pattern. We assayed 665 miRNAs on 165 pediatric AML samples. First, unsupervised clustering was performed to identify patient clusters with common miRNA expression profiles. Our analysis unraveled 14 clusters, seven of which had a known (cyto-)genetic denominator. Finally, a robust classifier was constructed to discriminate six molecular aberration groups: 11q23-rearrangements, t(8;21)(q22;q22), inv(16)(p13q22), t(15;17) (q21;q22), NPM1 and CEBPA mutations. The classifier achieved accuracies of 89%, 95%, 95%, 98%, 91% and 96%, respectively. Although lower sensitivities were obtained for the NPM1 and CEBPA (32% and 66%), relatively high sensitivities (84%−94%) were attained for the rest. Specificity was high in all groups (87%−100%). Due to a robust double-loop cross validation procedure employed, the classifier only employed 47 miRNAs to achieve the aforementioned accuracies. To validate the 47 miRNA signatures, we applied them to a publicly available adult AML dataset. Albeit partial overlap of the array platforms and molecular differences between pediatric and adult AML, the signatures performed reasonably well. This corroborates our claim that the identified miRNA signatures are not dominated by sample size bias in the pediatric AML dataset. In conclusion, cytogenetic subtypes of pediatric AML have distinct miRNA expression patterns. Reproducibility of the miRNA signatures in adult dataset suggests that the respective aberrations have a similar biology both in pediatric and adult AML.
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Affiliation(s)
- Askar Obulkasim
- Pediatric Oncology-Hematology, Erasmus MC, Sophia Children's Hospital, The Netherlands
| | | | - Lonneke Verboon
- Pediatric Oncology-Hematology, Erasmus MC, Sophia Children's Hospital, The Netherlands
| | - Mathijs Sanders
- Department of Hematology, ErasmusMC, Rotterdam, The Netherlands
| | - Ivo Touw
- Department of Hematology, ErasmusMC, Rotterdam, The Netherlands
| | | | - Rob Pieters
- Pediatric Oncology-Hematology, Erasmus MC, Sophia Children's Hospital, The Netherlands.,Prinses Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - Jan-Henning Klusmann
- Department of Pediatric Hematology and Oncology, Hannover Medical School, Hannover, German
| | - C Michel Zwaan
- Pediatric Oncology-Hematology, Erasmus MC, Sophia Children's Hospital, The Netherlands
| | - Marry M van den Heuvel-Eibrink
- Pediatric Oncology-Hematology, Erasmus MC, Sophia Children's Hospital, The Netherlands.,Prinses Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - Maarten Fornerod
- Pediatric Oncology-Hematology, Erasmus MC, Sophia Children's Hospital, The Netherlands
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Application of the AMLprofiler Diagnostic Microarray in the South African Setting. Stem Cells Int 2017; 2017:2560191. [PMID: 29238371 PMCID: PMC5697127 DOI: 10.1155/2017/2560191] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2017] [Revised: 08/09/2017] [Accepted: 10/12/2017] [Indexed: 11/17/2022] Open
Abstract
Acute myeloid leukemia (AML) is characterized by proliferation of the myeloid lineage and accumulation of immature hematopoietic cells in the bone marrow and is typified by marked heterogeneity both in response to treatment and survival. AMLprofiler is a qualitative in vitro diagnostic microarray incorporating seven molecular biomarkers used to diagnose and predict posttherapy survival rates. In this study, we compared AMLprofiler to routine AML diagnostic methodologies employed in South Africa, focusing on consistency of the results, cost, and time to result. RNA was isolated from bone marrow and peripheral blood samples from patients with de novo AML and was processed using Affymetrix Gene Profiling Reagent kits. The results from AMLprofiler and standard methodologies were highly comparable. In addition, many samples were determined to be positive for biomarkers not routinely investigated in South Africa, namely, CEBPA double mutants, NPM1 variants, and altered expression levels of BAALC and EVI1. 38% of samples presented with no positive biomarker; AMLprofiler nonetheless enabled 26% of AML patients to be classified into either favorable or poor prognostic categories. This study highlights the comprehensive nature of the microarray. Decreased time to result and refinement of risk stratification are notable benefits.
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20
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Ng CWS, Kosmo B, Lee PL, Lee CK, Guo J, Chen Z, Chiu L, Lee HK, Ho S, Zhou J, Lin M, Tan KML, Ban KHK, Tan TW, Chng WJ, Yan B. CEBPA mutational analysis in acute myeloid leukaemia by a laboratory-developed next-generation sequencing assay. J Clin Pathol 2017; 71:522-531. [PMID: 29180507 DOI: 10.1136/jclinpath-2017-204825] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Revised: 11/10/2017] [Accepted: 11/10/2017] [Indexed: 11/03/2022]
Abstract
AIM The presence of biallelic CEBPA mutations is a favourable prognostic feature in acute myeloid leukaemia (AML). CEBPA mutations are currently identified through conventional capillary sequencing (CCS). With the increasing adoption of next-generation sequencing (NGS) platforms, challenges with regard to amplification efficiency of CEBPA due to the high GC content may be encountered, potentially resulting in suboptimal coverage. Here, the performance of an amplicon-based NGS method using a laboratory-developed CEBPA-specific Nextera XT (CEBNX) was evaluated. METHODS Mutational analyses of the CEBPA gene of 137 AML bone marrow or peripheral blood retrospective specimens were performed by the amplification of the CEBPA gene using the Expand Long Range dNTPack and the amplicons processed by CCS and NGS. CEBPA-specific libraries were then constructed using the Nextera XT V.2 kit. All FASTQ files were then processed with the MiSeq Reporter V.2.6.2.3 using the PCR Amplicon workflow via the customised CEBPA-specific manifest file. The variant calling format files were analysed using the Illumina Variant Studio V.2.2. RESULTS A coverage per base of 3631X to 28184X was achieved. 22 samples (16.1%) were found to contain CEBPA mutations, with variant allele frequencies (VAF) ranging from 3.8% to 58.2%. Taking CCS as the 'gold standard', sensitivity and specificity of 97% and 97% was achieved. For the transactivation domain 2 polymorphism (c.584_589dupACCCGC/p.His195_Pro196dup), the CEBNX achieved 100% sensitivity and 100% specificity relative to CCS. CONCLUSIONS Our laboratory-developed CEBNX workflow shows high coverage and thus overcomes the challenges associated with amplification efficiency and low coverage of CEBPA. Therefore, our assay is suitable for deployment in the clinical laboratory.
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Affiliation(s)
- Christopher Wai Siong Ng
- Department of Laboratory Medicine, Molecular Diagnosis Centre, National University Health System, Singapore, Singapore
| | - Bustamin Kosmo
- Department of Laboratory Medicine, Molecular Diagnosis Centre, National University Health System, Singapore, Singapore
| | - Peak-Ling Lee
- Department of Laboratory Medicine, Molecular Diagnosis Centre, National University Health System, Singapore, Singapore
| | - Chun Kiat Lee
- Department of Laboratory Medicine, Molecular Diagnosis Centre, National University Health System, Singapore, Singapore
| | - Jingxue Guo
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Zhaojin Chen
- Investigational Medicine Unit, National University Health System, Singapore, Singapore
| | - Lily Chiu
- Department of Laboratory Medicine, Molecular Diagnosis Centre, National University Health System, Singapore, Singapore
| | - Hong Kai Lee
- Department of Laboratory Medicine, Molecular Diagnosis Centre, National University Health System, Singapore, Singapore
| | - Sherry Ho
- Department of Laboratory Medicine, Molecular Diagnosis Centre, National University Health System, Singapore, Singapore
| | - Jianbiao Zhou
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.,Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Mingxuan Lin
- Department of Laboratory Medicine, Molecular Diagnosis Centre, National University Health System, Singapore, Singapore
| | - Karen M L Tan
- Department of Laboratory Medicine, Molecular Diagnosis Centre, National University Health System, Singapore, Singapore
| | - Kenneth H K Ban
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Tin Wee Tan
- National Supercomputing Centre Singapore, Singapore, Singapore
| | - Wee Joo Chng
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.,Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore.,Department of Haematology-Oncology, National University Cancer Institute, National University Health System, Singapore, Singapore
| | - Benedict Yan
- Department of Laboratory Medicine, Molecular Diagnosis Centre, National University Health System, Singapore, Singapore.,Translational Centre for Development and Research, National University Health System, Singapore, Singapore
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21
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22
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McCurdy SR, Levis MJ. Emerging molecular predictive and prognostic factors in acute myeloid leukemia. Leuk Lymphoma 2017; 59:2021-2039. [DOI: 10.1080/10428194.2017.1393669] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Shannon R. McCurdy
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Mark J. Levis
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
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23
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Salarpour F, Goudarzipour K, Mohammadi MH, Ahmadzadeh A, Faraahi S, Farsani MA. Evaluation of CCAAT/Enhancer Binding Protein (C/EBP) Alpha (CEBPA) and Runt-Related Transcription Factor 1 (RUNX1) Expression in Patients with De Novo Acute Myeloid Leukemia. Ann Hum Genet 2017; 81:276-283. [DOI: 10.1111/ahg.12210] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Accepted: 07/20/2017] [Indexed: 12/19/2022]
Affiliation(s)
- Fatemeh Salarpour
- Laboratory Hematology and blood Banking Department; School of Allied Medical Sciences; Shahid Beheshti University of Medical Science; Tehran Iran
| | - Kourosh Goudarzipour
- Pediatric Congenital Hematologic Disorders Research Center; Shahid Beheshti University of Medical Science; Tehran Iran
| | - Mohammad Hossein Mohammadi
- Laboratory Hematology and Blood Bank Department; Faculty of Paramedical; Shahid Beheshti University of Medical Sciences
- HSCT Research Center; Shahid Beheshti University of Medical Sciences; Tehran
| | - Ahmad Ahmadzadeh
- Health Research Institute; Research Center of Thalassemia & Hemoglobinopathy; Ahvaz jundishapur University of Medical Science; Ahvaz Iran
| | - Sara Faraahi
- Laboratory Hematology and blood Banking Department; School of Allied Medical Sciences; Shahid Beheshti University of Medical Science; Tehran Iran
| | - Mehdi Allahbakhshian Farsani
- Laboratory Hematology and Blood Bank Department; Faculty of Paramedical; Shahid Beheshti University of Medical Sciences
- HSCT Research Center; Shahid Beheshti University of Medical Sciences; Tehran
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24
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Glass JL, Hassane D, Wouters BJ, Kunimoto H, Avellino R, Garrett-Bakelman FE, Guryanova OA, Bowman R, Redlich S, Intlekofer AM, Meydan C, Qin T, Fall M, Alonso A, Guzman ML, Valk PJM, Thompson CB, Levine R, Elemento O, Delwel R, Melnick A, Figueroa ME. Epigenetic Identity in AML Depends on Disruption of Nonpromoter Regulatory Elements and Is Affected by Antagonistic Effects of Mutations in Epigenetic Modifiers. Cancer Discov 2017; 7:868-883. [PMID: 28408400 DOI: 10.1158/2159-8290.cd-16-1032] [Citation(s) in RCA: 88] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Revised: 10/20/2016] [Accepted: 04/07/2017] [Indexed: 11/16/2022]
Abstract
We performed cytosine methylation sequencing on genetically diverse patients with acute myeloid leukemia (AML) and found leukemic DNA methylation patterning is primarily driven by nonpromoter regulatory elements and CpG shores. Enhancers displayed stronger differential methylation than promoters, consisting predominantly of hypomethylation. AMLs with dominant hypermethylation featured greater epigenetic disruption of promoters, whereas those with dominant hypomethylation displayed greater disruption of distal and intronic regions. Mutations in IDH and DNMT3A had opposing and mutually exclusive effects on the epigenome. Notably, co-occurrence of both mutations resulted in epigenetic antagonism, with most CpGs affected by either mutation alone no longer affected in double-mutant AMLs. Importantly, this epigenetic antagonism precedes malignant transformation and can be observed in preleukemic LSK cells from Idh2R140Q or Dnmt3aR882H single-mutant and Idh2R140Q/Dnmt3aR882H double-mutant mice. Notably, IDH/DNMT3A double-mutant AMLs manifested upregulation of a RAS signaling signature and displayed unique sensitivity to MEK inhibition ex vivo as compared with AMLs with either single mutation.Significance: AML is biologically heterogeneous with subtypes characterized by specific genetic and epigenetic abnormalities. Comprehensive DNA methylation profiling revealed that differential methylation of nonpromoter regulatory elements is a driver of epigenetic identity, that gene mutations can be context-dependent, and that co-occurrence of mutations in epigenetic modifiers can result in epigenetic antagonism. Cancer Discov; 7(8); 868-83. ©2017 AACR.This article is highlighted in the In This Issue feature, p. 783.
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Affiliation(s)
- Jacob L Glass
- Leukemia Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York.,Department of Medicine, Hematology/Oncology Division, Weill Medical College of Cornell University, New York, New York
| | - Duane Hassane
- Institute of Computational Biomedicine, Weill Medical College of Cornell University, New York, New York
| | - Bas J Wouters
- Department of Medicine, Hematology/Oncology Division, Weill Medical College of Cornell University, New York, New York.,Department of Hematology, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Hiroyoshi Kunimoto
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Roberto Avellino
- Department of Hematology, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Francine E Garrett-Bakelman
- Department of Medicine, Hematology/Oncology Division, Weill Medical College of Cornell University, New York, New York.,Department of Medicine, University of Virginia, Charlottesville, Virginia.,Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, Virginia
| | - Olga A Guryanova
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Robert Bowman
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Shira Redlich
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Andrew M Intlekofer
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Cem Meydan
- Department of Medicine, University of Virginia, Charlottesville, Virginia
| | - Tingting Qin
- Department of Pathology, University of Michigan Medical School, Ann Arbor, Michigan
| | - Mame Fall
- Epigenomics Core Facility, Weill Medical College of Cornell University, New York, New York
| | - Alicia Alonso
- Epigenomics Core Facility, Weill Medical College of Cornell University, New York, New York
| | - Monica L Guzman
- Department of Medicine, Hematology/Oncology Division, Weill Medical College of Cornell University, New York, New York
| | - Peter J M Valk
- Department of Hematology, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Craig B Thompson
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Ross Levine
- Leukemia Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York.,Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York.,Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Olivier Elemento
- Institute of Computational Biomedicine, Weill Medical College of Cornell University, New York, New York
| | - Ruud Delwel
- Department of Hematology, Erasmus University Medical Center, Rotterdam, the Netherlands.
| | - Ari Melnick
- Department of Medicine, Hematology/Oncology Division, Weill Medical College of Cornell University, New York, New York.
| | - Maria E Figueroa
- Department of Human Genetics and Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, Florida.
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25
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Expression and regulation of C/EBPα in normal myelopoiesis and in malignant transformation. Blood 2017; 129:2083-2091. [PMID: 28179278 DOI: 10.1182/blood-2016-09-687822] [Citation(s) in RCA: 102] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Accepted: 10/14/2016] [Indexed: 12/13/2022] Open
Abstract
One of the most studied transcription factors in hematopoiesis is the leucine zipper CCAAT-enhancer binding protein α (C/EBPα), which is mainly involved in cell fate decisions for myeloid differentiation. Its involvement in acute myeloid leukemia (AML) is diverse, with patients frequently exhibiting mutations, deregulation of gene expression, or alterations in the function of C/EBPα. In this review, we emphasize the importance of C/EBPα for neutrophil maturation, its role in myeloid priming of hematopoietic stem and progenitor cells, and its indispensable requirement for AML development. We discuss that mutations in the open reading frame of CEBPA lead to an altered C/EBPα function, affecting the expression of downstream genes and consequently deregulating myelopoiesis. The emerging transcriptional mechanisms of CEBPA are discussed based on recent studies. Novel insights on how these mechanisms may be deregulated by oncoproteins or mutations/variants in CEBPA enhancers are suggested in principal to reveal novel mechanisms of how CEBPA is deregulated at the transcriptional level.
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26
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Prada-Arismendy J, Arroyave JC, Röthlisberger S. Molecular biomarkers in acute myeloid leukemia. Blood Rev 2016; 31:63-76. [PMID: 27639498 DOI: 10.1016/j.blre.2016.08.005] [Citation(s) in RCA: 181] [Impact Index Per Article: 22.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Revised: 08/24/2016] [Accepted: 08/26/2016] [Indexed: 12/11/2022]
Abstract
Acute myeloid leukemia (AML) is the most common acute leukemia in adults. The pathophysiology of this disease is just beginning to be understood at the cellular and molecular level, and currently cytogenetic markers are the most important for risk stratification and treatment of AML patients. However, with the advent of new technologies, the detection of other molecular markers such as point mutations and characterization of epigenetic and proteomic profiles, have begun to play an important role in how the disease is approached. Recent evidence shows that the identification of new AML biomarkers contributes to a better understanding of the molecular basis of the disease, is significantly useful in screening, diagnosis, prognosis and monitoring of AML, as well as the possibility of predicting each individual's response to treatment. This review summarizes the most relevant molecular (genetic, epigenetic, and protein) biomarkers associated with acute myeloid leukemia and discusses their clinical importance in terms of risk prediction, diagnosis and prognosis.
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MESH Headings
- Biomarkers, Tumor
- DNA Methylation
- Disease Susceptibility
- Epigenesis, Genetic
- Genetic Variation
- Humans
- Leukemia, Myeloid, Acute/diagnosis
- Leukemia, Myeloid, Acute/genetics
- Leukemia, Myeloid, Acute/metabolism
- Leukemia, Myeloid, Acute/mortality
- Mutation
- Prognosis
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Affiliation(s)
- Jeanette Prada-Arismendy
- Grupo de Investigación e Innovación Biomédica, Instituto Tecnológico Metropolitano, Medellín, Colombia.
| | - Johanna C Arroyave
- Grupo de Investigación e Innovación Biomédica, Instituto Tecnológico Metropolitano, Medellín, Colombia
| | - Sarah Röthlisberger
- Grupo de Investigación e Innovación Biomédica, Instituto Tecnológico Metropolitano, Medellín, Colombia
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27
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Zhao X, Huang X, Wang X, Wu Y, Eisfeld AK, Schwind S, Gallego-Perez D, Boukany PE, Marcucci GI, Lee LJ. Nanochannel Electroporation as a Platform for Living Cell Interrogation in Acute Myeloid Leukemia. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2015; 2:1500111. [PMID: 27980918 PMCID: PMC5115302 DOI: 10.1002/advs.201500111] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2015] [Revised: 06/03/2015] [Indexed: 05/29/2023]
Abstract
A living cell interrogation platform based on nanochannel electroporation is demonstrated with analysis of RNAs in single cells. This minimally invasive process is based on individual cells and allows both multi-target analysis and stimulus-response analysis by sequential deliveries. The unique platform possesses a great potential to the comprehensive and lysis-free nucleic acid analysis on rare or hard-to-transfect cells.
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Affiliation(s)
- Xi Zhao
- Center for Affordable Nanoengineering of Polymeric Biomedical Devices The Ohio State University Columbus OH 43212 USA; William G. Lowrie, Department of Chemical and Biomolecular Engineering The Ohio State University Columbus OH 43210 USA
| | - Xiaomeng Huang
- Center for Affordable Nanoengineering of Polymeric Biomedical Devices The Ohio State University Columbus OH 43212 USA
| | - Xinmei Wang
- Center for Affordable Nanoengineering of Polymeric Biomedical Devices The Ohio State University Columbus OH 43212 USA
| | - Yun Wu
- Center for Affordable Nanoengineering of Polymeric Biomedical Devices The Ohio State University Columbus OH 43212 USA
| | - Ann-Kathrin Eisfeld
- Department of Internal Medicine Comprehensive Cancer Center The Ohio State University Columbus OH 43210 USA
| | - Sebastian Schwind
- Department of Internal Medicine Comprehensive Cancer Center The Ohio State University Columbus OH 43210 USA
| | - Daniel Gallego-Perez
- Center for Affordable Nanoengineering of Polymeric Biomedical Devices The Ohio State University Columbus OH 43212 USA
| | - Pouyan E Boukany
- Center for Affordable Nanoengineering of Polymeric Biomedical Devices The Ohio State University Columbus OH 43212 USA
| | - Guido I Marcucci
- Department of Internal Medicine Comprehensive Cancer Center The Ohio State University Columbus OH 43210 USA
| | - Ly James Lee
- Center for Affordable Nanoengineering of Polymeric Biomedical Devices The Ohio State University Columbus OH 43212 USA; William G. Lowrie, Department of Chemical and Biomolecular Engineering The Ohio State University Columbus OH 43210 USA
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28
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Said SB, El-Masry SA, Salem DA, Taalab MM, Al-Posttany AS. Prevalence and Prognostic Impact of CEBPA Gene Mutation (Simplified Assay Technique) in Egyptian Acute Myeloid Leukemia Patients with Normal Cytogenetics. Indian J Hematol Blood Transfus 2015; 32:405-411. [PMID: 27812248 DOI: 10.1007/s12288-015-0623-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2015] [Accepted: 11/26/2015] [Indexed: 11/29/2022] Open
Abstract
Mutations of the CCAAT/enhancer binding protein alpha (CEBPA) gene have been associated with a favorable outcome in patients with acute myeloid leukemia (AML), especially in those with a normal cytogenetics. However, few studies were done on Egyptian AML patients and none of them look for easier and less expensive method for CEBPA mutation screening. This study is aimed to investigate the prevalence of CEBPA mutations and its clinical and prognostic impact in Egyptian patients with cytogenetically normal AML (CN-AML). This was done using fragment analysis to assess this method as a cheaper and less laborious screening method compared to sequencing. Fluorescent PCR was done to amplify CEBPA gene in DNA extracted from 40 CN-AML patients. This was followed by fragment analysis of post-PCR products using GeneMapper software for detection of CEBPA mutations. CEBPA gene mutations were found in 7/40 CN-AML patients (17.5 %) and it was significantly associated with lower LDH levels (p = 0.039). All patients with CEBPA mutations achieved clinical remission and none of them showed refractoriness, relapsed, or died by the end of the 2 years study period. Furthermore, those patients demonstrate significantly longer overall and disease free survival than those with wild type CEBPA gene (p = 0.001 and 0.004 respectively). CEBPA mutation has a favorable prognostic impact in CN-AML. Fragment analysis is a good, lees laborious and cheaper method that can be used for CEBPA mutation screening in patients with CN-AML.
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Affiliation(s)
- Samy B Said
- Department of Chemistry, Faculty of Science, Damietta University, El Roda, Damietta City, Egypt
| | - Samir A El-Masry
- Institute of Genetic Engineering and Biotechnology, Sadat City University, Sadat City, Egypt
| | - Dalia A Salem
- Faculty of Medicine, Mansoura University, Mansoura, Egypt
| | - Mona M Taalab
- Hematology Unit, Internal Medicine Department, Faculty of Medicine, Mansoura University, Mansoura, Egypt
| | - Amr S Al-Posttany
- Department of Chemistry, Faculty of Science, Damietta University, El Roda, Damietta City, Egypt
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29
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Libura M, Pawełczyk M, Florek I, Matiakowska K, Jaźwiec B, Borg K, Solarska I, Zawada M, Czekalska S, Libura J, Salamanczuk Z, Jakóbczyk M, Mucha B, Duszeńko E, Soszyńska K, Karabin K, Piątkowska-Jakubas B, Całbecka M, Gajkowska-Kulig J, Gadomska G, Kiełbiński M, Ejduk A, Kata D, Grosicki S, Kyrcz-Krzemień S, Warzocha K, Kuliczkowski K, Skotnicki A, Jęrzejczak WW, Haus O. CEBPA copy number variations in normal karyotype acute myeloid leukemia: Possible role of breakpoint-associated microhomology and chromatin status in CEBPA mutagenesis. Blood Cells Mol Dis 2015; 55:284-92. [PMID: 26460249 DOI: 10.1016/j.bcmd.2015.07.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2015] [Revised: 07/03/2015] [Accepted: 07/04/2015] [Indexed: 10/23/2022]
Abstract
Copy number variations (CNV) in CEBPA locus represent heterogeneous group of mutations accompanying acute myeloid leukemia (AML). The aim of this study was to characterize different CEBPA mutation categories in regard to biological data like age, cytology, CD7, and molecular markers, and identify possible factors affecting their etiology. We report here the incidence of 12.6% of CEBPA mutants in the population of 262 normal karyotype AML (NK-AML) patients. We confirmed that double mutant AMLs presented uniform biological features when compared to single CEBPA mutations and accompanied mostly younger patients. We hypothesized that pathogenesis of distinct CEBPA mutation categories might be influenced by different factors. The detailed sequence analysis revealed frequent breakpoint-associated microhomologies of 2 to 12bp. The analysis of distribution of microhomology motifs along CEBPA gene showed that longer stretches of microhomology at the mutational junctions were relatively rare by chance which suggests their functional role in the CEBPA mutagenesis. Additionally, accurate quantification of CEBPA transcript levels showed that double CEBPA mutations correlated with high-level CEBPA expression, whereas single N-terminal CEBPA mutations were associated with low-level CEBPA expression. This might suggest that high-level CEBPA expression and/or accessibility of CEBPA locus contribute to B-ZIP in-frame duplications.
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Affiliation(s)
- Marta Libura
- Department of Haematology, Oncology and Internal Diseases, Medical University and University Hospital, 1A Banacha Str., 02-097 Warsaw, Poland.
| | - Marta Pawełczyk
- Department of Haematology, Oncology and Internal Diseases, Medical University and University Hospital, 1A Banacha Str., 02-097 Warsaw, Poland.
| | - Izabella Florek
- Department of Haematology, Faculty of Medicine Jagiellonian University, 19 Kopernika Str., 31-501 Cracow, Poland.
| | - Karolina Matiakowska
- Department of Clinical Genetics, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, 9 Skłodowska-Curie Str., 85-094 Bydgoszcz, Poland.
| | - Bożena Jaźwiec
- Department of Haematology, Blood Neoplasms, and Bone Marrow Transplantation, Medical University, 4 Pasteura Str., 50-367 Wrocław, Poland.
| | - Katarzyna Borg
- Institute of Haematology and Transfusion Medicine, 14 Gandhi Str., 02-776 Warsaw, Poland.
| | - Iwona Solarska
- Institute of Haematology and Transfusion Medicine, 14 Gandhi Str., 02-776 Warsaw, Poland.
| | - Magdalena Zawada
- Department of Haematology, Faculty of Medicine Jagiellonian University, 19 Kopernika Str., 31-501 Cracow, Poland.
| | - Sylwia Czekalska
- Department of Haematology, Faculty of Medicine Jagiellonian University, 19 Kopernika Str., 31-501 Cracow, Poland.
| | - Jolanta Libura
- Department of Haematology, Oncology and Internal Diseases, Medical University and University Hospital, 1A Banacha Str., 02-097 Warsaw, Poland.
| | - Zoriana Salamanczuk
- Department of Haematology, Faculty of Medicine Jagiellonian University, 19 Kopernika Str., 31-501 Cracow, Poland.
| | - Małgorzata Jakóbczyk
- Department of Haematology, Faculty of Medicine Jagiellonian University, 19 Kopernika Str., 31-501 Cracow, Poland.
| | - Barbara Mucha
- Department of Clinical Genetics, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, 9 Skłodowska-Curie Str., 85-094 Bydgoszcz, Poland.
| | - Ewa Duszeńko
- Department of Haematology, Blood Neoplasms, and Bone Marrow Transplantation, Medical University, 4 Pasteura Str., 50-367 Wrocław, Poland.
| | - Krystyna Soszyńska
- Department of Haematology, Blood Neoplasms, and Bone Marrow Transplantation, Medical University, 4 Pasteura Str., 50-367 Wrocław, Poland.
| | - Karolina Karabin
- Department of Haematology, Oncology and Internal Diseases, Medical University and University Hospital, 1A Banacha Str., 02-097 Warsaw, Poland.
| | - Beata Piątkowska-Jakubas
- Department of Haematology, Faculty of Medicine Jagiellonian University, 19 Kopernika Str., 31-501 Cracow, Poland.
| | - Małgorzata Całbecka
- Department of Haematology, Copernicus Hospital, 17/19 Batory Str., 87-100 Toruń, Poland.
| | | | - Grażyna Gadomska
- Department of Haematology, Dr Biziel University Hospital, 75 Ujejskiego Str., 85-168 Bydgoszcz, Poland.
| | - Marek Kiełbiński
- Department of Haematology, Blood Neoplasms, and Bone Marrow Transplantation, Medical University, 4 Pasteura Str., 50-367 Wrocław, Poland.
| | - Anna Ejduk
- Institute of Haematology and Transfusion Medicine, 14 Gandhi Str., 02-776 Warsaw, Poland.
| | - Dariusz Kata
- Department of Hematology and Bone Marrow Transplantation, Medical University of Silesia, 20/24 Francuska str., 40-027 Katowice, Poland.
| | - Sebastian Grosicki
- Department of Hematology, SPZOZ ZSM Chorzów, 11 Strzelców Bytomskich Str., 41-500 Chorzów, Poland.
| | - Sławomira Kyrcz-Krzemień
- Department of Hematology and Bone Marrow Transplantation, Medical University of Silesia, 20/24 Francuska str., 40-027 Katowice, Poland.
| | - Krzysztof Warzocha
- Institute of Haematology and Transfusion Medicine, 14 Gandhi Str., 02-776 Warsaw, Poland.
| | - Kazimierz Kuliczkowski
- Department of Haematology, Blood Neoplasms, and Bone Marrow Transplantation, Medical University, 4 Pasteura Str., 50-367 Wrocław, Poland.
| | - Aleksander Skotnicki
- Department of Haematology, Faculty of Medicine Jagiellonian University, 19 Kopernika Str., 31-501 Cracow, Poland.
| | - Wiesław Wiktor Jęrzejczak
- Department of Haematology, Oncology and Internal Diseases, Medical University and University Hospital, 1A Banacha Str., 02-097 Warsaw, Poland.
| | - Olga Haus
- Department of Clinical Genetics, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, 9 Skłodowska-Curie Str., 85-094 Bydgoszcz, Poland; Department of Haematology, Blood Neoplasms, and Bone Marrow Transplantation, Medical University, 4 Pasteura Str., 50-367 Wrocław, Poland.
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Vinhas R, Tolmatcheva A, Canto R, Ribeiro P, Lourenço A, Sousa ABD, Baptista PV, Fernandes AR. A novel mutation in CEBPA gene in a patient with acute myeloid leukemia. Leuk Lymphoma 2015; 57:711-3. [PMID: 26419342 DOI: 10.3109/10428194.2015.1065979] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Raquel Vinhas
- a UCIBIO, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa , Caparica
| | - Anna Tolmatcheva
- a UCIBIO, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa , Caparica
| | - Rafaela Canto
- a UCIBIO, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa , Caparica
| | - Patrícia Ribeiro
- b Serviço de Hematologia, Hospital dos Capuchos (CHLC) , Lisboa , Portugal
| | - Alexandra Lourenço
- b Serviço de Hematologia, Hospital dos Capuchos (CHLC) , Lisboa , Portugal
| | | | - Pedro V Baptista
- a UCIBIO, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa , Caparica
| | - Alexandra R Fernandes
- a UCIBIO, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa , Caparica
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Ziai JM, Siddon AJ. Pathology Consultation on Gene Mutations in Acute Myeloid Leukemia. Am J Clin Pathol 2015; 144:539-54. [PMID: 26386075 DOI: 10.1309/ajcp77zfpuqgygwy] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
OBJECTIVES Acute myeloid leukemia (AML) is a rapidly fatal disease without the use of aggressive chemotherapy regimens. Cytogenetic and molecular studies are commonly used to classify types of AML based on prognosis, as well as to determine therapeutic regimens. METHODS Although there are several AML classifications determined by particular translocations, cytogenetically normal AML represents a molecularly, as well as clinically, heterogeneous group of diseases. Laboratory evaluation of AML will become increasingly important as new mutations with both prognostic and therapeutic implications are being recognized. Moreover, because many patients with AML are being treated more effectively, these mutations may become increasingly useful as markers of minimal residual disease, which can be interpreted in an individualized approach. RESULTS Current laboratory studies of gene mutations in AML include analysis of NPM1, FLT3, CEBPA, and KIT. In addition to these genes, many other genes are emerging as potentially useful in determining patients' prognosis, therapy, and disease course. CONCLUSIONS This article briefly reviews the current most clinically relevant gene mutations and their clinical and immunophenotypic features, prognostic information, and methods used for detection.
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Affiliation(s)
| | - Alexa J. Siddon
- Departments of Pathology, Yale School of Medicine, New Haven, CT
- Laboratory Medicine, Yale School of Medicine, New Haven, CT
- VA Connecticut Healthcare, West Haven, CT
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CEBPA methylation and mutation in myelodysplastic syndrome. Med Oncol 2015; 32:192. [DOI: 10.1007/s12032-015-0605-z] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2015] [Accepted: 03/26/2015] [Indexed: 12/30/2022]
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Li HY, Deng DH, Huang Y, Ye FH, Huang LL, Xiao Q, Zhang B, Ye BB, Lai YR, Mo ZN, Liu ZF. Favorable prognosis of biallelic CEBPA gene mutations in acute myeloid leukemia patients: a meta-analysis. Eur J Haematol 2015; 94:439-48. [PMID: 25227715 DOI: 10.1111/ejh.12450] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/10/2014] [Indexed: 01/21/2023]
Abstract
OBJECTIVES Increasing number of studies suggested that biallelic CEBPA (bi CEBPA) mutations were associated with favorable prognosis in patients with acute myeloid leukemia (AML), but the results remain inconclusive. We therefore present a meta-analysis to evaluate the prognostic value of bi CEBPA mutations in patients with AML. METHODS A comprehensive literature search was undertaken through August 2014 looking for eligible studies. Pooled hazard ratios (HRs) estimates and 95% confidence intervals (95% CIs) in overall survival (OS) and event-free survival (EFS) were used to calculate estimated effect. RESULTS Ten studies covering a total of 6219 subjects were included in this analysis. Overall, bi CEBPA mutations were associated with favorable clinical outcome in patients with AML (HR for EFS: 0.41, 95% CI: 0.32-0.52; for OS: 0.37, 95% CI: 0.27-0.50), in cytogenetically normal (CN)-AML (HR for EFS: 0.38, 95% CI: 0.29-0.49; for OS: 0.32, 95% CI: 0.23-0.43). When took the cohort of monoallelic CEBPA (mo CEBPA) mutated and wild-type CEBPA (wt CEBPA) AML as a reference group, bi CEBPA mutated AML also shown beneficial outcomes (HR for OS: 0.52, 95% CI: 0.37-0.72). No significant difference was found between mo CEBPA mutation and wt CEBPA in patients with AML or CN-AML (P > 0.05). CONCLUSION Bi CEBPA mutations in patients with AML are strongly associated with a favorable prognosis, which suggested that bi CEBPA mutations would potentially serve as a novel prognostic marker in AML.
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Affiliation(s)
- Hong-Ying Li
- Hematology Department, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
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Association of ABCB1 polymorphisms with prognostic outcomes of anthracycline and cytarabine in Chinese patients with acute myeloid leukemia. Eur J Clin Pharmacol 2015; 71:293-302. [PMID: 25567217 DOI: 10.1007/s00228-014-1795-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2014] [Accepted: 12/10/2014] [Indexed: 02/02/2023]
Abstract
PURPOSE To investigate the influence of ABCB1 polymorphisms on prognostic outcomes in Chinese patients with de novo intermediate-risk acute myeloid leukemia (AML) and to examine the gene expression level in relation to the genetic variation. METHODS In total, 263 Chinese intermediate-risk AML patients treated with anthracycline and cytarabine were enrolled. G2677T, C1236T, and C3435T of the ABCB1 gene were analyzed by the allele-specific matrix-assisted laser desorption. Expression of ABCB1 messenger RNA (mRNA) was tested in 101 patients of known genotype and haplotype for ABCB1 polymorphisms. Basic clinical characteristics of these patients were collected from medical records. RESULTS Survival analysis showed that patients with AML (TTT haplotype) had a longer overall survival (OS) (p < 0.001, 29.2 months, 95 % confidence interval [CI], 26.9-31.5 months) and relapse-free survival (RFS) (p = 0.005, 21.8 months, 95 % CI, 19.5-24.0 months) compared with those without TTT haplotype (21.9 months, 95 % CI, 19.6-24.2 months; 16.5 months, 95 % CI, 14.6-18.5 months). After adjusting for age; gender; leukocyte count; hemoglobin level; platelet levels; French, American, and British classification; lactate dehydrogenase levels; Eastern Cooperative Oncology Group performance status; nucleophosmin gene; and fms-related tyrosine kinase 3 gene, the multivariate survival analysis showed that the TTT haplotype appeared to be a predicting factor for OS (p = 0.001, hazard ratio = 1.854, 95 % CI, 1.301-2.641) and RFS (p = 0.009, hazard ratio = 1.755, 95 % CI, 1.153-2.671). Moreover, a significant association between the TTT haplotype and relapse in AML patients was observed in this study (p = 0.002, odds ratio = 0.410, 95 % CI, 0.235-0.715). Gene expression level was significantly lower in patients with the TTT haplotype than in the patients with the other haplotypes (p = 0.004). CONCLUSIONS The findings suggested the TTT haplotype was possibly related to the OS, RFS, and relapse in Chinese patients with AML.
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A Clinical Grade Sequencing-Based Assay for CEBPA Mutation Testing. J Mol Diagn 2015; 17:76-84. [DOI: 10.1016/j.jmoldx.2014.09.007] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2014] [Revised: 09/19/2014] [Accepted: 09/29/2014] [Indexed: 11/21/2022] Open
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Pastore F, Kling D, Hoster E, Dufour A, Konstandin NP, Schneider S, Sauerland MC, Berdel WE, Buechner T, Woermann B, Braess J, Hiddemann W, Spiekermann K. Long-term follow-up of cytogenetically normal CEBPA-mutated AML. J Hematol Oncol 2014; 7:55. [PMID: 25214041 PMCID: PMC4172831 DOI: 10.1186/s13045-014-0055-7] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2014] [Accepted: 07/24/2014] [Indexed: 12/18/2022] Open
Abstract
Background The aim of this study was to analyze the long-term survival of AML patients with CEBPA mutations. Patients and methods We investigated 88 AML patients with a median age of 61 years and (1) cytogenetically normal AML (CN-AML), (2) monoallelic (moCEBPA) or biallelic (biCEBPA) CEBPA mutation, and (3) intensive induction treatment. 60/88 patients have been described previously with a shorter follow-up. Results Median follow-up time was 9.8 years (95% CI: 9.4-10.1 years) compared to 3.2 and 5.2 years in our former analyses. Patients with biCEBPA mutations survived significantly longer compared to those with moCEBPA (median overall survival (OS) 9.6 years vs. 1.7 years, p = 0.008). Patients ≤ 60 years and biCEBPA mutations showed a favorable prognosis with a 10-year OS rate of 81%. Both, bi- and moCEBPA-mutated groups had a low early death (d60) rate of 7% and 9%, respectively. Complete remission (CR) rates for biCEBPA- and moCEBPA-mutated patients were 82% vs. 70% (p = 0.17). biCEBPA-mutated patients showed a longer relapse free survival (RFS) (median RFS 9.4 years vs. 1.5 years, p = 0.021) and a lower cumulative incidence of relapse (CIR) compared to moCEBPA-mutated patients. These differences in OS and RFS were confirmed after adjustment for known clinical and molecular prognostic factors. Conclusions In this long-term observation we confirmed the favorable prognostic outcome of patients with biCEBPA mutations compared to moCEBPA-mutated CN-AML. The high probability of OS (81%) in younger patients is helpful to guide intensity of postremission therapy. Electronic supplementary material The online version of this article (doi:10.1186/s13045-014-0055-7) contains supplementary material, which is available to authorized users.
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Musialik E, Bujko M, Kober P, Grygorowicz MA, Libura M, Przestrzelska M, Juszczyński P, Borg K, Florek I, Jakóbczyk M, Baranowska A, Siedlecki JA. Comparison of promoter DNA methylation and expression levels of genes encoding CCAAT/enhancer binding proteins in AML patients. Leuk Res 2014; 38:850-6. [DOI: 10.1016/j.leukres.2014.04.013] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2013] [Revised: 04/22/2014] [Accepted: 04/27/2014] [Indexed: 11/28/2022]
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Nieto MJ, Scalise A, Najfeld V. Cytogenetically normal acute myeloid leukemia with a novel KIT mutation in exon 11 G565V developing a sole trisomy 13 at relapse: a clinical dilemma. Acta Haematol 2014; 133:1-5. [PMID: 24968822 DOI: 10.1159/000360389] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2013] [Accepted: 01/27/2014] [Indexed: 11/19/2022]
Abstract
We describe a patient with acute myeloid leukemia (AML) who had a normal karyotype at diagnosis and was negative for NPM1 and FLT3 mutations, but had a KIT G565V mutation in exon 11. This has not been described previously in AML. The patient received induction and consolidation chemotherapy and was in hematologic remission for 351 days when deletion 7q was cytogenetically detected in 8% of the bone marrow cells. After an initial treatment of azacitidine followed by decitabine, an unrelated trisomy 13 clone was identified, followed by subclonal rearrangement of ETV6. The patient underwent reinduction with high-dose cytarabine and mitoxantrone followed by voluntary-unrelated-donor allogeneic stem cell transplantation with a reduced-intensity conditioning. As of writing, the patient is in complete hematologic and cytogenetic remission with 100% donor cell engraftment.
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MESH Headings
- Chromosomes, Human, Pair 13
- Cytogenetic Analysis
- Disease Progression
- Exons
- Female
- Hematopoietic Stem Cell Transplantation
- Humans
- Leukemia, Myeloid, Acute/diagnosis
- Leukemia, Myeloid, Acute/genetics
- Leukemia, Myeloid, Acute/pathology
- Leukemia, Myeloid, Acute/therapy
- Middle Aged
- Mutation
- Nucleophosmin
- Proto-Oncogene Proteins c-kit/genetics
- Recurrence
- Remission Induction
- Transplantation, Homologous
- Treatment Outcome
- Trisomy
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Affiliation(s)
- Maria Jacqueline Nieto
- Department of Medicine, Tisch Cancer Institute, Ichan School of Medicine at The Mount Sinai, New York, N.Y., USA
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Two splice-factor mutant leukemia subgroups uncovered at the boundaries of MDS and AML using combined gene expression and DNA-methylation profiling. Blood 2014; 123:3327-35. [DOI: 10.1182/blood-2013-07-512855] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Key Points
SF-mutant myeloid malignancies transcend the boundaries between AML and MDS. Integrated analysis of gene expression and DNA-methylation profiles in leukemia uncovers novel subtypes.
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Thomas R, Hubbard AE, McHale CM, Zhang L, Rappaport SM, Lan Q, Rothman N, Vermeulen R, Guyton KZ, Jinot J, Sonawane BR, Smith MT. Characterization of changes in gene expression and biochemical pathways at low levels of benzene exposure. PLoS One 2014; 9:e91828. [PMID: 24786086 PMCID: PMC4006721 DOI: 10.1371/journal.pone.0091828] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2013] [Accepted: 02/14/2014] [Indexed: 11/19/2022] Open
Abstract
Benzene, a ubiquitous environmental pollutant, causes acute myeloid leukemia (AML). Recently, through transcriptome profiling of peripheral blood mononuclear cells (PBMC), we reported dose-dependent effects of benzene exposure on gene expression and biochemical pathways in 83 workers exposed across four airborne concentration ranges (from <1 ppm to >10 ppm) compared with 42 subjects with non-workplace ambient exposure levels. Here, we further characterize these dose-dependent effects with continuous benzene exposure in all 125 study subjects. We estimated air benzene exposure levels in the 42 environmentally-exposed subjects from their unmetabolized urinary benzene levels. We used a novel non-parametric, data-adaptive model selection method to estimate the change with dose in the expression of each gene. We describe non-parametric approaches to model pathway responses and used these to estimate the dose responses of the AML pathway and 4 other pathways of interest. The response patterns of majority of genes as captured by mean estimates of the first and second principal components of the dose-response for the five pathways and the profiles of 6 AML pathway response-representative genes (identified by clustering) exhibited similar apparent supra-linear responses. Responses at or below 0.1 ppm benzene were observed for altered expression of AML pathway genes and CYP2E1. Together, these data show that benzene alters disease-relevant pathways and genes in a dose-dependent manner, with effects apparent at doses as low as 100 ppb in air. Studies with extensive exposure assessment of subjects exposed in the low-dose range between 10 ppb and 1 ppm are needed to confirm these findings.
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Affiliation(s)
- Reuben Thomas
- Superfund Research Program, School of Public Health, University of California, Berkeley, California, United States of America
| | - Alan E. Hubbard
- Superfund Research Program, School of Public Health, University of California, Berkeley, California, United States of America
| | - Cliona M. McHale
- Superfund Research Program, School of Public Health, University of California, Berkeley, California, United States of America
| | - Luoping Zhang
- Superfund Research Program, School of Public Health, University of California, Berkeley, California, United States of America
| | - Stephen M. Rappaport
- Superfund Research Program, School of Public Health, University of California, Berkeley, California, United States of America
| | - Qing Lan
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Nathaniel Rothman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Roel Vermeulen
- Institute of Risk assessment Sciences, Utrecht University, Utrecht, The Netherlands
| | - Kathryn Z. Guyton
- National Center for Environmental Assessment, Office of Research and Development, US EPA, Washington, DC, United States of America
| | - Jennifer Jinot
- National Center for Environmental Assessment, Office of Research and Development, US EPA, Washington, DC, United States of America
| | - Babasaheb R. Sonawane
- National Center for Environmental Assessment, Office of Research and Development, US EPA, Washington, DC, United States of America
| | - Martyn T. Smith
- Superfund Research Program, School of Public Health, University of California, Berkeley, California, United States of America
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He H, Xu YJ, Yin JY, Li X, Qu J, Xu XJ, Liu ZG, Zhou F, Zhai M, Li Y, Zhou HH, Liu ZQ. Association of nitric oxide synthase 3 (NOS3) 894 G>T polymorphism with prognostic outcomes of anthracycline in Chinese patients with acute myeloid leukaemia. Clin Exp Pharmacol Physiol 2014; 41:400-7. [PMID: 24684492 DOI: 10.1111/1440-1681.12235] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2013] [Revised: 03/13/2014] [Accepted: 03/16/2014] [Indexed: 11/29/2022]
Abstract
The aim of the present study was to investigate the influence of the nitric oxide synthase 3 (NOS3) 894 G>T polymorphism on prognostic outcomes of anthracycline in Chinese patients with de novo intermediate-risk acute myeloid leukaemia (AML) and to examine the gene expression level in relation to genetic variation. In all, 225 Chinese patients with intermediate-risk AML (at the complete remission stage) treated with anthracycline were enrolled in the study. The 894 G>T polymorphism of the NOS3 gene was analysed by allele-specific matrix-assisted laser desorption ionization time-of-flight. Expression of NOS3 mRNA was tested in 72 patients of known genotype for NOS3 894 G>T. The clinical characteristics of these patients were obtained from medical records. Survival analysis showed that patients with AML (GG genotype) had a longer overall survival (OS; P = 0.006). After adjusting for age, gender, leucocyte count, haemoglobin level, platelet level, French, American and Britain (FAB) classification, lactate dehydrogenase levels, Eastern Cooperative Oncology Group Performance Status, nucleophosmin gene and fms-related tyrosine kinase 3 gene, multivariate survival analysis showed that the NOS3 894 G>T polymorphism appeared to be a predicting factor for OS (P = 0.014; hazard ratio = 1.856). However, no significant associations between the NOS3 894 G>T polymorphism and relapse-free survival and relapse in patients with AML were observed. Gene expression levels were significantly higher in patients with the GG genotype than in patients with the GT and TT genotypes (P = 0.033). The findings suggest that the NOS3 894 G>T variant may be a biomarker for the prediction of OS in Chinese patients with AML.
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Affiliation(s)
- Hui He
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, China; Institute of Clinical Pharmacology, Central South University, Benxi, China; Hunan Key Laboratory of Pharmacogenetics, Changsha, China; Department of Hematology, Benxi Central Hospital of China Medical University, Benxi, China
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Pten regulates homeostasis and inflammation-induced migration of myelocytes in zebrafish. J Hematol Oncol 2014; 7:17. [PMID: 24598081 PMCID: PMC4015859 DOI: 10.1186/1756-8722-7-17] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2014] [Accepted: 02/27/2014] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND Loss of the tumor suppressor phosphatase and tensin homolog (PTEN) is frequently observed in hematopoietic malignancies. Although PTEN has been implicated in maintaining the quiescence of hematopoietic stem cells (HSCs), its role in hematopoiesis during ontogeny remains largely unexplored. METHODS The expression of hematopoietic marker genes was analyzed via whole mount in situ hybridization assay in ptena and ptenb double mutant zebrafish. The embryonic myelopoiesis was characterized by living imaging and whole mount in situ immunofluorescence with confocal microscopy, as well as cell-specific chemical staining for neutrophils and macrophages. Analyses of the involved signaling pathway were carried out by inhibitor treatment and mRNA injection. RESULTS Pten-deficient zebrafish embryos exhibited a strikingly increased number of myeloid cells, which were further characterized as being immune deficient. In accordance with this finding, the inhibition of phosphoinositide 3-kinase (PI3K) or the mechanistic target of rapamycin (mTOR) corrected the expansive myelopoiesis in the pten-deficient embryos. Further mechanistic studies revealed that the expression of cebpa, a critical transcription factor in myeloid precursor cells, was downregulated in the pten-deficient myeloid cells, whereas the injection of cebpa mRNA markedly ameliorated the dysmyelopoiesis induced by the loss of pten. CONCLUSIONS Our data provide in vivo evidence that definitive myelopoiesis in zebrafish is critically regulated by pten via the elevation of cebpa expression.
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Fasan A, Haferlach C, Alpermann T, Jeromin S, Grossmann V, Eder C, Weissmann S, Dicker F, Kohlmann A, Schindela S, Kern W, Haferlach T, Schnittger S. The role of different genetic subtypes of CEBPA mutated AML. Leukemia 2013; 28:794-803. [PMID: 24056881 DOI: 10.1038/leu.2013.273] [Citation(s) in RCA: 113] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2013] [Accepted: 09/06/2013] [Indexed: 11/09/2022]
Abstract
The prognostic impact of mutations in the CCAAT/enhancer binding protein α (CEBPA) gene was evaluated in the context of concomitant molecular mutations and cytogenetic aberrations in acute myeloid leukemia (AML). CEBPA was screened in a cohort of 2296 adult AML cases. Of 244 patients (10.6%) with CEBPA mutations, 140 cases (6.1%) were single-mutated (CEBPAsm) and 104 cases (4.5%) were double-mutated (CEBPAdm). Cytogenetic analysis revealed normal karyotype in 172/244 (70.5%) of CEBPAmut cases, whereas in 72/244 cases (29.5%) at least one cytogenetic aberration was detected. Concurrent molecular mutations were seen less frequently in CEBPAdm than in CEBPAsm AML cases (69.2% vs 88.6% P<0.001). In detail, the spectrum of concurrent mutations was different in both groups with the frequent occurrence of GATA1 and WT1 mutations in CEBPAdm patients. In contrast, FLT3-ITD, NPM1, ASXL1 and RUNX1 mutations were detected more frequently in CEBPAsm cases. Favorable outcome was restricted to CEBPAdm cases and remained an independent prognostic factor for a favorable outcome in multivariate analysis (hazard ratio: 0.438, P=0.020). Outcome in CEBPAsm cases strongly depended on concurrent FLT3-ITD. In conclusion, we propose that only CEBPAdm should be considered as an entity in the WHO classification of AML and should be clearly distinguished from CEBPAsm AML.
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Affiliation(s)
- A Fasan
- MLL Munich Leukemia Laboratory, Munich, Germany
| | - C Haferlach
- MLL Munich Leukemia Laboratory, Munich, Germany
| | - T Alpermann
- MLL Munich Leukemia Laboratory, Munich, Germany
| | - S Jeromin
- MLL Munich Leukemia Laboratory, Munich, Germany
| | - V Grossmann
- MLL Munich Leukemia Laboratory, Munich, Germany
| | - C Eder
- MLL Munich Leukemia Laboratory, Munich, Germany
| | - S Weissmann
- MLL Munich Leukemia Laboratory, Munich, Germany
| | - F Dicker
- MLL Munich Leukemia Laboratory, Munich, Germany
| | - A Kohlmann
- MLL Munich Leukemia Laboratory, Munich, Germany
| | - S Schindela
- MLL Munich Leukemia Laboratory, Munich, Germany
| | - W Kern
- MLL Munich Leukemia Laboratory, Munich, Germany
| | - T Haferlach
- MLL Munich Leukemia Laboratory, Munich, Germany
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Kassem N, Fahmy AEG, Desoky M, Medhat N, Zawam HM. CCAAT/enhancer binding protein α gene expression in Egyptian patients with acute myeloid leukemia. J Egypt Natl Canc Inst 2013; 25:115-20. [DOI: 10.1016/j.jnci.2013.02.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2012] [Revised: 02/04/2013] [Accepted: 02/08/2013] [Indexed: 11/17/2022] Open
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Peloquin GL, Chen YB, Fathi AT. The evolving landscape in the therapy of acute myeloid leukemia. Protein Cell 2013; 4:735-46. [PMID: 23982740 DOI: 10.1007/s13238-013-3057-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2013] [Accepted: 07/25/2013] [Indexed: 11/26/2022] Open
Abstract
Acute myeloid leukemia (AML) is a heterogeneous clonal disorder of myeloid precursors arrested in their maturation, creating a diverse disease entity with a wide range of responses to historically standard treatment approaches. While significant progress has been made in characterizing and individualizing the disease at diagnosis to optimally inform those affected, progress in treatment to reduce relapse and induce remission has been limited thus far. In addition to a brief summary of the factors that shape prognostication at diagnosis, this review attempts to expand on the current therapies under investigation that have shown promise in treating AML, including hypomethylating agents, gemtuzumab ozogamicin, FLT3 tyrosine kinase inhibitors, antisense oligonucleotides, and other novel therapies, including aurora kinases, mTOR and PI3 kinase inhibitors, PIM kinase inhibitors, HDAC inhibitors, and IDH targeted therapies. With these, and undoubtedly many others in the future, it is the hope that by combining more accurate prognostication with more effective therapies, patients will begin to have a different, and more complete, outlook on their disease that allows for safer and more successful treatment strategies.
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Affiliation(s)
- Grace L Peloquin
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, 02114, USA
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Awad MM, Aladle DA, Abousamra NK, Elghannam DM, Fawzy IM. CEBPA gene mutations in Egyptian acute myeloid leukemia patients: impact on prognosis. Hematology 2013; 18:61-8. [DOI: 10.1179/1607845412y.0000000032] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Affiliation(s)
- Mohamed M. Awad
- Hematology UnitDepartment of Clinical Pathology, Faculty of Medicine, Mansoura University, Mansoura, Egypt
| | - Doaa A. Aladle
- Hematology UnitDepartment of Clinical Pathology, Faculty of Medicine, Mansoura University, Mansoura, Egypt
| | - Nashwa K. Abousamra
- Hematology UnitDepartment of Clinical Pathology, Faculty of Medicine, Mansoura University, Mansoura, Egypt
| | - Doaa M. Elghannam
- Hematology UnitDepartment of Clinical Pathology, Faculty of Medicine, Mansoura University, Mansoura, Egypt
| | - Iman M. Fawzy
- Hematology UnitDepartment of Clinical Pathology, Faculty of Medicine, Mansoura University, Mansoura, Egypt
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van Vliet MH, Burgmer P, de Quartel L, Brand JPL, de Best LCM, Viëtor H, Löwenberg B, Valk PJM, van Beers EH. Detection of CEBPA double mutants in acute myeloid leukemia using a custom gene expression array. Genet Test Mol Biomarkers 2013; 17:395-400. [PMID: 23485358 DOI: 10.1089/gtmb.2012.0437] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Double (bi-allelic) mutations in the gene encoding the CCAAT/enhancer-binding protein-alpha (CEBPA) transcription factor have a favorable prognostic impact in acute myeloid leukemia (AML). Double mutations in CEBPA can be detected using various techniques, but it is a notoriously difficult gene to sequence due to its high GC-content. Here we developed a two-step gene expression classifier for accurate and standardized detection of CEBPA double mutations. The key feature of the two-step classifier is that it explicitly removes cases with low CEBPA expression, thereby excluding CEBPA hypermethylated cases that have similar gene expression profiles as a CEBPA double mutant, which would result in false-positive predictions. In the second step, we have developed a 55 gene signature to identity the true CEBPA double-mutation cases. This two-step classifier was tested on a cohort of 505 unselected AML cases, including 26 CEBPA double mutants, 12 CEBPA single mutants, and seven CEBPA promoter hypermethylated cases, on which its performance was estimated by a double-loop cross-validation protocol. The two-step classifier achieves a sensitivity of 96.2% (95% confidence interval [CI] 81.1 to 99.3) and specificity of 100.0% (95% CI 99.2 to 100.0). There are no false-positive detections. This two-step CEBPA double-mutation classifier has been incorporated on a microarray platform that can simultaneously detect other relevant molecular biomarkers, which allows for a standardized comprehensive diagnostic assay. In conclusion, gene expression profiling provides a reliable method for CEBPA double-mutation detection in patients with AML for clinical use.
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Fasan A, Alpermann T, Haferlach C, Grossmann V, Roller A, Kohlmann A, Eder C, Kern W, Haferlach T, Schnittger S. Frequency and prognostic impact of CEBPA proximal, distal and core promoter methylation in normal karyotype AML: a study on 623 cases. PLoS One 2013; 8:e54365. [PMID: 23383300 PMCID: PMC3562230 DOI: 10.1371/journal.pone.0054365] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2012] [Accepted: 12/11/2012] [Indexed: 11/26/2022] Open
Abstract
The clinical impact of aberrant CEBPA promoter methylation (PM) in AML is controversially discussed. The aim of this study was to clarify the significance of aberrant CEBPA PM with regard to clinical features in a cohort of 623 cytogenetically normal (CN) de novo AML. 555 cases had wild-type CEBPA, 68 cases harbored CEBPA mutations. The distal promoter was methylated in 238/623 cases (38.2%), the core promoter in 8 of 326 cases (2.5%), whereas proximal PM was never detected. CEBPA PM and CEBPA mutations were mutually exclusive. CEBPA distal PM positive cases were characterized by reduced CEBPA mRNA expression levels and elevated white blood cell counts. CEBPA distal PM was less frequent in patients with mutations in FLT3, NPM1 and TET2 and more frequent in cases with RUNX1 and IDH2R140 mutations. Overall, no association of methylation to prognosis was seen. However CEBPA distal PM was associated with inferior outcome in cases with low FLT3-ITD ratio or TET2 mutations. A distinct gene expression profile of CEBPA distal PM positive cases compared to CEBPA mutated and CEBPA distal PM negative cases was observed. In conclusion, the presence of aberrant CEBPA PM is associated with distinct biological features but impact on outcome is weak.
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50
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Taskesen E, Wouters B, Delwel R. HAT: a novel statistical approach to discover functional regions in the genome. Methods Mol Biol 2013; 1067:125-141. [PMID: 23975790 DOI: 10.1007/978-1-62703-607-8_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Tiling arrays are useful for exploring local functions of regions of the genome in an unbiased fashion. The exact determination of those genomic regions based on tiling-array data, e.g., generated by means of hybridization with immunopreciptated DNA-fragments to the arrays is a challenge. Many different statistical methodologies have been developed to find biological relevant regions-of-interest (ROI) by using the quantitative signal intensity of each probe. We previously developed a method called Hypergeometric Analysis of Tiling arrays (HAT) for the analysis of tiling-array data, but it is developed such that it can also be used to study data derived by genome-wide deep sequencing approaches. Here we applied HAT to analyze two publicly available tiling-array data sets. After the detection of statistically significant ROI, these are often used in additional analysis for hypothesis testing. We therefore discuss, by using the results of the tiling-array experiment, pathway and motif analyses.
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Affiliation(s)
- Erdogan Taskesen
- Department of Hematology, Erasmus University Medical Center, Rotterdam, The Netherlands
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