1
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Wang L, Xue Z, Wang J, Jian Y, Lu H, Ma H, Wang S, Zeng W, Zhang T. Targeted knockout of Mx in the DF-1 chicken fibroblast cell line impairs immune response against Newcastle disease virus. Poult Sci 2023; 102:102855. [PMID: 37390546 PMCID: PMC10331481 DOI: 10.1016/j.psj.2023.102855] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 06/04/2023] [Accepted: 06/05/2023] [Indexed: 07/02/2023] Open
Abstract
Newcastle disease virus (NDV) is an RNA virus taking poultry as the host, and the Newcastle disease (ND) caused by NDV is one of the diseases with serious damage to the health of poultry. Mx encoding by myxovirus resistance gene, induced by type I interferon (IFN), has a wide range of antiviral and GTPase activities in human, mice, and other species via inhibition virus replication. However, the antiviral ability of chicken Mx is still a controversial issue. To explore the effect of chicken Mx post-NDV infection, Mx-knockout DF-1 cells were constructed via CRISPR/Cas9 gene editing system. The number of copies of NDV was detected by RT-qPCR, and the mRNA expression levels of IRF-7, IFN-α, IFN-β, TNF-α, p21, p27, and Bak in DF-1 cells were analyzed after NDV infection. Compared with control cells, virus titers were much higher in Mx-knockout DF-1 cells post-NDV infection. The deficiency of Mx aggravated the cell pathological features post-NDV infection, and promoted the expression levels of IRF-7, IFN-α, IFN-β, and pro-inflammatory cytokine TNF-α in host cells. In addition, cells with Mx deficiency could alleviate the harm from virus by enhancing the expression of p21, p27, and Bak, which related to cell proliferation apoptosis. In conclusion, Mx played an important role in antivirus invasion. In the absence of Mx, cells could alleviate the harm from virus infection via retarding cell proliferation and enhancing cell apoptosis.
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Affiliation(s)
- Ling Wang
- School of Biological Science and Engineering, Shaanxi University of Technology, Hanzhong 723001, China; Engineering Research Center of quality improvement and safety control of Qinba special meat products, Universities of Shaanxi Province, Hanzhong 723001, China
| | - Zhen Xue
- School of Biological Science and Engineering, Shaanxi University of Technology, Hanzhong 723001, China
| | - Jinping Wang
- School of Biological Science and Engineering, Shaanxi University of Technology, Hanzhong 723001, China
| | - Yuwen Jian
- School of Biological Science and Engineering, Shaanxi University of Technology, Hanzhong 723001, China
| | - Hongzhao Lu
- School of Biological Science and Engineering, Shaanxi University of Technology, Hanzhong 723001, China; Engineering Research Center of quality improvement and safety control of Qinba special meat products, Universities of Shaanxi Province, Hanzhong 723001, China; Shaanxi Union Research Center of University and Enterprise for Zhenba Bacon, Hanzhong 723001, China
| | - Haidong Ma
- School of Biological Science and Engineering, Shaanxi University of Technology, Hanzhong 723001, China; Shaanxi Union Research Center of University and Enterprise for Zhenba Bacon, Hanzhong 723001, China; Qinba State Key Laboratory of Biological Resources and Ecological Environment, Hanzhong 723001, China
| | - Shanshan Wang
- School of Biological Science and Engineering, Shaanxi University of Technology, Hanzhong 723001, China; Engineering Research Center of quality improvement and safety control of Qinba special meat products, Universities of Shaanxi Province, Hanzhong 723001, China; QinLing-Bashan Mountains Bioresources Comprehensive Development C. I. C., Shaanxi University of Technology, Hanzhong 723001, China; Shaanxi Union Research Center of University and Enterprise for Zhenba Bacon, Hanzhong 723001, China
| | - Wenxian Zeng
- School of Biological Science and Engineering, Shaanxi University of Technology, Hanzhong 723001, China; Engineering Research Center of quality improvement and safety control of Qinba special meat products, Universities of Shaanxi Province, Hanzhong 723001, China; Qinba State Key Laboratory of Biological Resources and Ecological Environment, Hanzhong 723001, China
| | - Tao Zhang
- School of Biological Science and Engineering, Shaanxi University of Technology, Hanzhong 723001, China; Engineering Research Center of quality improvement and safety control of Qinba special meat products, Universities of Shaanxi Province, Hanzhong 723001, China; QinLing-Bashan Mountains Bioresources Comprehensive Development C. I. C., Shaanxi University of Technology, Hanzhong 723001, China; Shaanxi Union Research Center of University and Enterprise for Zhenba Bacon, Hanzhong 723001, China.
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2
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Kelesoglu N, Kori M, Turanli B, Arga KY, Yilmaz BK, Duru OA. Acute Myeloid Leukemia: New Multiomics Molecular Signatures and Implications for Systems Medicine Diagnostics and Therapeutics Innovation. OMICS : A JOURNAL OF INTEGRATIVE BIOLOGY 2022; 26:392-403. [PMID: 35763314 DOI: 10.1089/omi.2022.0051] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Acute myeloid leukemia (AML) is a common, complex, and multifactorial malignancy of the hematopoietic system. AML diagnosis and treatment outcomes display marked heterogeneity and patient-to-patient variations. To date, AML-related biomarker discovery research has employed single omics inquiries. Multiomics analyses that reconcile and integrate the data streams from multiple levels of the cellular hierarchy, from genes to proteins to metabolites, offer much promise for innovation in AML diagnostics and therapeutics. We report, in this study, a systems medicine and multiomics approach to integrate the AML transcriptome data and reporter biomolecules at the RNA, protein, and metabolite levels using genome-scale biological networks. We utilized two independent transcriptome datasets (GSE5122, GSE8970) in the Gene Expression Omnibus database. We identified new multiomics molecular signatures of relevance to AML: miRNAs (e.g., mir-484 and miR-519d-3p), receptors (ACVR1 and PTPRG), transcription factors (PRDM14 and GATA3), and metabolites (in particular, amino acid derivatives). The differential expression profiles of all reporter biomolecules were crossvalidated in independent RNA-Seq and miRNA-Seq datasets. Notably, we found that PTPRG holds important prognostication potential as evaluated by Kaplan-Meier survival analyses. The multiomics relationships unraveled in this analysis point toward the genomic pathogenesis of AML. These multiomics molecular leads warrant further research and development as potential diagnostic and therapeutic targets.
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Affiliation(s)
- Nurdan Kelesoglu
- Department of Bioengineering, Marmara University, Istanbul, Turkey
| | - Medi Kori
- Department of Bioengineering, Marmara University, Istanbul, Turkey
| | - Beste Turanli
- Department of Bioengineering, Marmara University, Istanbul, Turkey
| | - Kazim Yalcin Arga
- Department of Bioengineering, Marmara University, Istanbul, Turkey
- Genetic and Metabolic Diseases Research and Investigation Center, Marmara University, Istanbul, Turkey
| | - Betul Karademir Yilmaz
- Genetic and Metabolic Diseases Research and Investigation Center, Marmara University, Istanbul, Turkey
- Department of Biochemistry, Faculty of Medicine, Marmara University, Istanbul, Turkey
| | - Ozlem Ates Duru
- Department of Nutrition and Dietetics, School of Health Sciences, Nişantaşı University, Istanbul, Turkey
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3
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Erdogan F, Radu TB, Orlova A, Qadree AK, de Araujo ED, Israelian J, Valent P, Mustjoki SM, Herling M, Moriggl R, Gunning PT. JAK-STAT core cancer pathway: An integrative cancer interactome analysis. J Cell Mol Med 2022; 26:2049-2062. [PMID: 35229974 PMCID: PMC8980946 DOI: 10.1111/jcmm.17228] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 12/14/2021] [Accepted: 12/22/2021] [Indexed: 12/25/2022] Open
Abstract
Through a comprehensive review and in silico analysis of reported data on STAT-linked diseases, we analysed the communication pathways and interactome of the seven STATs in major cancer categories and proposed rational targeting approaches for therapeutic intervention to disrupt critical pathways and addictions to hyperactive JAK/STAT in neoplastic states. Although all STATs follow a similar molecular activation pathway, STAT1, STAT2, STAT4 and STAT6 exert specific biological profiles associated with a more restricted pattern of activation by cytokines. STAT3 and STAT5A as well as STAT5B have pleiotropic roles in the body and can act as critical oncogenes that promote many processes involved in cancer development. STAT1, STAT3 and STAT5 also possess tumour suppressive action in certain mutational and cancer type context. Here, we demonstrated member-specific STAT activity in major cancer types. Through systems biology approaches, we found surprising roles for EGFR family members, sex steroid hormone receptor ESR1 interplay with oncogenic STAT function and proposed new drug targeting approaches of oncogenic STAT pathway addiction.
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Affiliation(s)
- Fettah Erdogan
- Department of Chemical and Physical SciencesUniversity of Toronto MississaugaMississaugaOntarioCanada
- Department of ChemistryUniversity of TorontoTorontoOntarioCanada
| | - Tudor Bogdan Radu
- Department of Chemical and Physical SciencesUniversity of Toronto MississaugaMississaugaOntarioCanada
- Department of ChemistryUniversity of TorontoTorontoOntarioCanada
| | - Anna Orlova
- Institute of Animal Breeding and GeneticsUniversity of Veterinary MedicineViennaAustria
| | - Abdul Khawazak Qadree
- Department of Chemical and Physical SciencesUniversity of Toronto MississaugaMississaugaOntarioCanada
- Department of ChemistryUniversity of TorontoTorontoOntarioCanada
| | - Elvin Dominic de Araujo
- Department of Chemical and Physical SciencesUniversity of Toronto MississaugaMississaugaOntarioCanada
| | - Johan Israelian
- Department of Chemical and Physical SciencesUniversity of Toronto MississaugaMississaugaOntarioCanada
- Department of ChemistryUniversity of TorontoTorontoOntarioCanada
| | - Peter Valent
- Division of Hematology and HemostaseologyDepartment of Internal Medicine IMedical University of ViennaViennaAustria
- Ludwig Boltzmann Institute for Hematology and OncologyMedical University of ViennaViennaAustria
| | - Satu M. Mustjoki
- Translational Immunology Research Program and Department of Clinical Chemistry and HematologyUniversity of HelsinkiHelsinkiFinland
- Hematology Research UnitHelsinki University Hospital Comprehensive Cancer CenterHelsinkiFinland
- iCAN Digital Precision Cancer Medicine FlagshipHelsinkiFinland
| | - Marco Herling
- Department of Hematology, Cellular Therapy, and HemostaseologyUniversity of LeipzigLeipzigGermany
| | - Richard Moriggl
- Institute of Animal Breeding and GeneticsUniversity of Veterinary MedicineViennaAustria
| | - Patrick Thomas Gunning
- Department of Chemical and Physical SciencesUniversity of Toronto MississaugaMississaugaOntarioCanada
- Department of ChemistryUniversity of TorontoTorontoOntarioCanada
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4
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Estrogen Receptors Alpha and Beta in Acute Myeloid Leukemia. Cancers (Basel) 2020; 12:cancers12040907. [PMID: 32276421 PMCID: PMC7226505 DOI: 10.3390/cancers12040907] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Revised: 03/24/2020] [Accepted: 04/02/2020] [Indexed: 02/06/2023] Open
Abstract
Estrogen receptor (ER) signaling has been widely studied in a variety of solid tumors, where the differential expression of ERα and ERβ subtypes can impact prognosis. ER signaling has only recently emerged as a target of interest in acute myeloid leukemia (AML), an aggressive hematological malignancy with sub-optimal therapeutic options and poor clinical outcomes. In a variety of tumors, ERα activation has proliferative effects, while ERβ targeting results in cell senescence or death. Aberrant ER expression and hypermethylation have been characterized in AML, making ER targeting in this disease of great interest. This review describes the expression patterns of ERα and ERβ in AML and discusses the differing signaling pathways associated with each of these receptors. Furthermore, we assess how these signaling pathways can be targeted by various selective estrogen receptor modulators to induce AML cell death. We also provide insight into ER targeting in AML and discuss pending questions that require further study.
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5
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Kearns P, Zwaan CM, Reinhardt D, Gibson B, Moreno L, Nysom K, Nakahara S, Huang F, Zhou W, Parasrampuria DA, Nemat S. Phase 1-2 safety, efficacy and pharmacokinetic study of decitabine in sequential administration with cytarabine in children with relapsed or refractory acute myeloid leukaemia. Br J Haematol 2019; 186:e7-e11. [PMID: 30847896 DOI: 10.1111/bjh.15847] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Pamela Kearns
- NIHR Birmingham Biomedical Research Centre, University of Birmingham, Birmingham, UK
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6
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Ratajczak MZ. Why are hematopoietic stem cells so 'sexy'? on a search for developmental explanation. Leukemia 2017; 31:1671-1677. [PMID: 28502982 PMCID: PMC5540746 DOI: 10.1038/leu.2017.148] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Revised: 03/03/2017] [Accepted: 03/07/2017] [Indexed: 02/07/2023]
Abstract
Evidence has accumulated that normal human and murine hematopoietic stem cells express several functional pituitary and gonadal sex hormones, and that, in fact, some sex hormones, such as androgens, have been employed for many years to stimulate hematopoiesis in patients with bone marrow aplasia. Interestingly, sex hormone receptors are also expressed by leukemic cell lines and blasts. In this review, I will discuss the emerging question of why hematopoietic cells express these receptors. A tempting hypothetical explanation for this phenomenon is that hematopoietic stem cells are related to subpopulation of migrating primordial germ cells. To support of this notion, the anatomical sites of origin of primitive and definitive hematopoiesis during embryonic development are tightly connected with the migratory route of primordial germ cells: from the proximal epiblast to the extraembryonic endoderm at the bottom of the yolk sac and then back to the embryo proper via the primitive streak to the aorta-gonado-mesonephros (AGM) region on the way to the genital ridges. The migration of these cells overlaps with the emergence of primitive hematopoiesis in the blood islands at the bottom of the yolk sac, and definitive hematopoiesis that occurs in hemogenic endothelium in the embryonic dorsal aorta in AGM region.
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Affiliation(s)
- M Z Ratajczak
- Stem Cell Institute, James Graham Brown Cancer Center, University of Louisville, Louisville, KY, USA
- Department of Regenerative Medicine, Warsaw Medical University, Warsaw, Poland
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7
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Abdelbaset-Ismail A, Borkowska S, Janowska-Wieczorek A, Tonn T, Rodriguez C, Moniuszko M, Bolkun L, Koloczko J, Eljaszewicz A, Ratajczak J, Ratajczak MZ, Kucia M. Novel evidence that pituitary gonadotropins directly stimulate human leukemic cells-studies of myeloid cell lines and primary patient AML and CML cells. Oncotarget 2016; 7:3033-46. [PMID: 26701888 PMCID: PMC4823088 DOI: 10.18632/oncotarget.6698] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2015] [Accepted: 11/21/2015] [Indexed: 12/22/2022] Open
Abstract
We recently reported that normal hematopoietic stem cells express functional pituitary sex hormone (SexH) receptors. Here we report for the first time that pituitary-secreted gonadotrophins stimulate migration, adhesion, and proliferation of several human myeloid and lymphoid leukemia cell lines. Similar effects were observed after stimulation of human leukemic cell lines by gonadal SexHs. This effect seems to be direct, as the SexH receptors expressed by leukemic cells responded to stimulation by phosphorylation of MAPKp42/44 and AKTser473. Furthermore, in parallel studies we confirmed that human primary patient-derived AML and CML blasts also express several functional SexH receptors. These results shed more light on the potential role of SexHs in leukemogenesis and, in addition, provide further evidence suggesting a developmental link between hematopoiesis and the germline.
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Affiliation(s)
| | | | | | - Torsten Tonn
- Transfusion Medicine, Medical Faculty Carl Gustav Carus - Technische Universtität Dresden, German Red Cross Blood Donation Service North East, Dresden, Germany
| | - Cesar Rodriguez
- Stem Cell Institute at James Graham Brown Cancer Center, University of Louisville, KY, USA
| | - Marcin Moniuszko
- Department of Regenerative Medicine and Immune Regulation, Medical University of Bialystok, Bialystok, Poland
| | - Lukasz Bolkun
- Department of Hematology, Medical University of Bialystok, Bialystok, Poland
| | - Janusz Koloczko
- Department of Hematology, Medical University of Bialystok, Bialystok, Poland
| | - Andrzej Eljaszewicz
- Department of Regenerative Medicine and Immune Regulation, Medical University of Bialystok, Bialystok, Poland
| | - Janina Ratajczak
- Stem Cell Institute at James Graham Brown Cancer Center, University of Louisville, KY, USA
| | - Mariusz Z Ratajczak
- Stem Cell Institute at James Graham Brown Cancer Center, University of Louisville, KY, USA.,Department of Regenerative Medicine Medical University of Warsaw, Warsaw, Poland
| | - Magda Kucia
- Stem Cell Institute at James Graham Brown Cancer Center, University of Louisville, KY, USA.,Department of Regenerative Medicine Medical University of Warsaw, Warsaw, Poland
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8
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Affiliation(s)
| | - Eva Kassi
- Deparment of Biological Chemistry, Medical Scholl, National and Kapodistrian University of Athens, Athens, Greece
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9
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De Braekeleer M, Douet-Guilbert N, De Braekeleer E. Prognostic impact ofp15gene aberrations in acute leukemia. Leuk Lymphoma 2016; 58:257-265. [DOI: 10.1080/10428194.2016.1201574] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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10
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Differential network analysis reveals the genome-wide landscape of estrogen receptor modulation in hormonal cancers. Sci Rep 2016; 6:23035. [PMID: 26972162 PMCID: PMC4789788 DOI: 10.1038/srep23035] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Accepted: 02/23/2016] [Indexed: 12/14/2022] Open
Abstract
Several mutual information (MI)-based algorithms have been developed to identify dynamic gene-gene and function-function interactions governed by key modulators (genes, proteins, etc.). Due to intensive computation, however, these methods rely heavily on prior knowledge and are limited in genome-wide analysis. We present the modulated gene/gene set interaction (MAGIC) analysis to systematically identify genome-wide modulation of interaction networks. Based on a novel statistical test employing conjugate Fisher transformations of correlation coefficients, MAGIC features fast computation and adaption to variations of clinical cohorts. In simulated datasets MAGIC achieved greatly improved computation efficiency and overall superior performance than the MI-based method. We applied MAGIC to construct the estrogen receptor (ER) modulated gene and gene set (representing biological function) interaction networks in breast cancer. Several novel interaction hubs and functional interactions were discovered. ER+ dependent interaction between TGFβ and NFκB was further shown to be associated with patient survival. The findings were verified in independent datasets. Using MAGIC, we also assessed the essential roles of ER modulation in another hormonal cancer, ovarian cancer. Overall, MAGIC is a systematic framework for comprehensively identifying and constructing the modulated interaction networks in a whole-genome landscape. MATLAB implementation of MAGIC is available for academic uses at https://github.com/chiuyc/MAGIC.
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11
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Sánchez-Aguilera A, Arranz L, Martín-Pérez D, García-García A, Stavropoulou V, Kubovcakova L, Isern J, Martín-Salamanca S, Langa X, Skoda RC, Schwaller J, Méndez-Ferrer S. Estrogen signaling selectively induces apoptosis of hematopoietic progenitors and myeloid neoplasms without harming steady-state hematopoiesis. Cell Stem Cell 2015; 15:791-804. [PMID: 25479752 DOI: 10.1016/j.stem.2014.11.002] [Citation(s) in RCA: 85] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2014] [Revised: 10/08/2014] [Accepted: 11/05/2014] [Indexed: 12/31/2022]
Abstract
Estrogens are potent regulators of mature hematopoietic cells; however, their effects on primitive and malignant hematopoietic cells remain unclear. Using genetic and pharmacological approaches, we observed differential expression and function of estrogen receptors (ERs) in hematopoietic stem cell (HSC) and progenitor subsets. ERα activation with the selective ER modulator (SERM) tamoxifen induced apoptosis in short-term HSCs and multipotent progenitors. In contrast, tamoxifen induced proliferation of quiescent long-term HSCs, altered the expression of self-renewal genes, and compromised hematopoietic reconstitution after myelotoxic stress, which was reversible. In mice, tamoxifen treatment blocked development of JAK2(V617F)-induced myeloproliferative neoplasm in vivo, induced apoptosis of human JAK2(V617F+) HSPCs in a xenograft model, and sensitized MLL-AF9(+) leukemias to chemotherapy. Apoptosis was selectively observed in mutant cells, and tamoxifen treatment only had a minor impact on steady-state hematopoiesis in disease-free animals. Together, these results uncover specific regulation of hematopoietic progenitors by estrogens and potential antileukemic properties of SERMs.
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Affiliation(s)
- Abel Sánchez-Aguilera
- Stem Cell Niche Pathophysiology Group, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid 28029, Spain.
| | - Lorena Arranz
- Stem Cell Niche Pathophysiology Group, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid 28029, Spain
| | - Daniel Martín-Pérez
- Stem Cell Niche Pathophysiology Group, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid 28029, Spain
| | - Andrés García-García
- Stem Cell Niche Pathophysiology Group, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid 28029, Spain
| | - Vaia Stavropoulou
- Department of Biomedicine, University Hospital Basel, CH-4031 Basel, Switzerland
| | - Lucia Kubovcakova
- Department of Biomedicine, University Hospital Basel, CH-4031 Basel, Switzerland
| | - Joan Isern
- Stem Cell Niche Pathophysiology Group, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid 28029, Spain
| | - Sandra Martín-Salamanca
- Stem Cell Niche Pathophysiology Group, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid 28029, Spain
| | - Xavier Langa
- Stem Cell Niche Pathophysiology Group, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid 28029, Spain
| | - Radek C Skoda
- Department of Biomedicine, University Hospital Basel, CH-4031 Basel, Switzerland
| | - Jürg Schwaller
- Department of Biomedicine, University Hospital Basel, CH-4031 Basel, Switzerland
| | - Simón Méndez-Ferrer
- Stem Cell Niche Pathophysiology Group, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid 28029, Spain.
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12
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Fisser MC, Rommer A, Steinleitner K, Heller G, Herbst F, Wiese M, Glimm H, Sill H, Wieser R. Induction of the proapoptotic tumor suppressor gene Cell Adhesion Molecule 1 by chemotherapeutic agents is repressed in therapy resistant acute myeloid leukemia. Mol Carcinog 2014; 54:1815-9. [PMID: 25491945 DOI: 10.1002/mc.22252] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2014] [Accepted: 10/21/2014] [Indexed: 11/09/2022]
Abstract
Even though a large proportion of patients with acute myeloid leukemia (AML) achieve a complete remission upon initial therapy, the majority of them eventually relapse with resistant disease. Overexpression of the gene coding for the transcription factor Ecotropic Virus Integration site 1 (EVI1) is associated with rapid disease recurrence and shortened survival. We therefore sought to identify EVI1 target genes that may play a role in chemotherapy resistance using a previously established in vitro model system for EVI1 positive myeloid malignancies. Gene expression microarray analyses uncovered the Cell Adhesion Molecule 1 (CADM1) gene as a candidate whose deregulation by EVI1 may contribute to drug refractoriness. CADM1 is an apoptosis inducing tumor suppressor gene that is inactivated by methylation in a variety of tumor types. In the present study we provide evidence that it may play a role in chemotherapy induced cell death in AML: CADM1 was induced by drugs used in the treatment of AML in a human myeloid cell line and in primary diagnostic AML samples, and its experimental expression in a cell line model increased the proportion of apoptotic cells. CADM1 up-regulation was abolished by ectopic expression of EVI1, and EVI1 expression correlated with increased CADM1 promoter methylation both in a cell line model and in primary AML cells. Finally, CADM1 induction was repressed in primary samples from AML patients at relapse. In summary, these data suggest that failure to up-regulate CADM1 in response to chemotherapeutic drugs may contribute to therapy resistance in AML.
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Affiliation(s)
- Muriel C Fisser
- Department of Medicine I, Medical University of Vienna, Vienna, Austria.,Comprehensive Cancer Center of the Medical University of Vienna, Vienna, Austria
| | - Anna Rommer
- Department of Medicine I, Medical University of Vienna, Vienna, Austria.,Comprehensive Cancer Center of the Medical University of Vienna, Vienna, Austria
| | - Katarina Steinleitner
- Department of Medicine I, Medical University of Vienna, Vienna, Austria.,Comprehensive Cancer Center of the Medical University of Vienna, Vienna, Austria
| | - Gerwin Heller
- Department of Medicine I, Medical University of Vienna, Vienna, Austria.,Comprehensive Cancer Center of the Medical University of Vienna, Vienna, Austria
| | - Friederike Herbst
- Department of Translational Oncology, National Center for Tumor Diseases (NCT) and German Cancer Research Center (DKFZ), Heidelberg, Germany.,German Consortium for Translational Cancer Research (DKTK), Heidelberg, Germany
| | - Meike Wiese
- Department of Translational Oncology, National Center for Tumor Diseases (NCT) and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Hanno Glimm
- Department of Translational Oncology, National Center for Tumor Diseases (NCT) and German Cancer Research Center (DKFZ), Heidelberg, Germany.,German Consortium for Translational Cancer Research (DKTK), Heidelberg, Germany
| | - Heinz Sill
- Division of Hematology, Medical University of Graz, Graz, Austria
| | - Rotraud Wieser
- Department of Medicine I, Medical University of Vienna, Vienna, Austria.,Comprehensive Cancer Center of the Medical University of Vienna, Vienna, Austria
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13
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Karlic H, Herrmann H, Varga F, Thaler R, Reitermaier R, Spitzer S, Ghanim V, Blatt K, Sperr WR, Valent P, Pfeilstöcker M. The role of epigenetics in the regulation of apoptosis in myelodysplastic syndromes and acute myeloid leukemia. Crit Rev Oncol Hematol 2014; 90:1-16. [DOI: 10.1016/j.critrevonc.2013.10.003] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2013] [Revised: 09/03/2013] [Accepted: 10/02/2013] [Indexed: 01/17/2023] Open
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14
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Abáigar M, Ramos F, Benito R, Díez-Campelo M, Sánchez-del-Real J, Hermosín L, Rodríguez JN, Aguilar C, Recio I, Alonso JM, de las Heras N, Megido M, Fuertes M, del Cañizo MC, Hernández-Rivas JM. Prognostic impact of the number of methylated genes in myelodysplastic syndromes and acute myeloid leukemias treated with azacytidine. Ann Hematol 2013; 92:1543-52. [PMID: 23740492 DOI: 10.1007/s00277-013-1799-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2013] [Accepted: 05/16/2013] [Indexed: 10/26/2022]
Abstract
The prognostic impact of the aberrant hypermethylation in response to azacytidine (AZA) remains to be determined. Therefore, we have analyzed the influence of the methylation status prior to AZA treatment on the overall survival and clinical response of myeloid malignancies. DNA methylation status of 24 tumor suppressor genes was analyzed by methylation-specific multiplex ligation-dependent probe amplification in 63 patients with myelodysplastic syndromes and acute myeloid leukemia treated with azacytidine. Most patients (73 %) showed methylation of at least one gene, but only 12 % of patients displayed ≥3 methylated genes. The multivariate analysis demonstrated that the presence of a high number (≥2) of methylated genes (P = 0.022), a high WBC count (P = 0.033), or anemia (P = 0.029) were independent prognostic factors associated with shorter overall survival. The aberrant methylation status did not correlate with the response to AZA, although four of the five patients with ≥3 methylated genes did not respond. By contrast, favorable cytogenetics independently influenced the clinical response to AZA as 64.7 % of patients with good-risk cytogenetic abnormalities responded (P = 0.03). Aberrant methylation status influences the survival of patients treated with AZA, being shorter in those patients with a high number of methylated genes.
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Affiliation(s)
- María Abáigar
- Cancer Research Center-IBMCC (USAL-CSIC), Salamanca, Spain
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15
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Alpar D, de Jong D, Holczer-Nagy Z, Kajtar B, Savola S, Jakso P, David M, Kosztolanyi S, Kereskai L, Pajor L, Szuhai K. Multiplex ligation-dependent probe amplification and fluorescence in situ hybridization are complementary techniques to detect cytogenetic abnormalities in multiple myeloma. Genes Chromosomes Cancer 2013; 52:785-93. [PMID: 23720363 DOI: 10.1002/gcc.22074] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2013] [Accepted: 04/22/2013] [Indexed: 11/06/2022] Open
Abstract
Multiple myeloma (MM) is a genetically heterogeneous disease with diverse clinical outcomes. Interphase fluorescence in situ hybridization (i-FISH) is the most commonly used approach to detect recurrent cytogenetic abnormalities in this malignancy. We aimed to assess the performance of multiplex ligation-dependent probe amplification (MLPA) to reveal copy number abnormalities (CNAs) in MM. Diagnostic bone marrow samples from 81 patients were analyzed using 42 MLPA probes for the following regions: 1p32-31, 1p21, 1q21.3, 1q23.3, 5q31.3, 12p13.31, 13q14, 16q12, 16q23, and 17p13. All samples were also screened by i-FISH for the presence of hyperdiploidy, deletion/monosomy of chromosome 13, deletion of TP53, disruption of the immunoglobulin heavy-chain gene, t(4;14), t(11;14), t(14;16), t(8;14), gain of 5q and abnormalities of chromosome 1. A total of 245 alterations were detected in 79 cases (98%). Investigating the same aberrations, the two methods showed a congruency of higher than 90%. A low proportion of cells with the relevant abnormality, focal CNAs and unmatched probes were responsible for the discrepancies. MLPA revealed 95 CNAs not detected by i-FISH providing additional information in 53 cases (65%). Scrutiny of CNAs on chromosome 1, using more than 20 probes, revealed significant heterogeneity in size and location, and variable intra-chromosomal and intra-clonal rates of loss or gain. Our results suggest that MLPA is a reliable high-throughput technique to detect CNAs in MM. Since balanced aberrations are key to prognostic classification of this disease, MLPA and i-FISH should be applied as complementary techniques in diagnostic pathology.
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Affiliation(s)
- Donat Alpar
- Department of Pathology, Medical School, University of Pecs, Pecs, Hungary
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16
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Wertheim GBW, Hexner E, Bagg A. Molecular-based classification of acute myeloid leukemia and its role in directing rational therapy: personalized medicine for profoundly promiscuous proliferations. Mol Diagn Ther 2013. [PMID: 23184342 DOI: 10.1007/s40291-012-0009-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Acute myeloid leukemia (AML) is not a single pathologic entity but represents a heterogeneous group of malignancies. This heterogeneity is exemplified by the variable clinical outcomes that are observed in patients with AML, and it is largely the result of diverse mutations within the leukemic cells. These mutations range from relatively large genetic alterations, such as gains, losses, and translocations of chromosomes, to single nucleotide changes. Detection of many of these mutations is required for accurate diagnosis, prognosis, and treatment of patients with AML. As such, many testing modalities have been developed and are currently employed in clinical laboratories to ascertain mutational status at prognostically and therapeutically critical loci. The assays include those that specifically identify large chromosomal alterations, such as conventional metaphase analysis and fluorescence in situ hybridization, and methods that are geared more toward analysis of small mutations, such as PCR with allele-specific oligonucleotide primers. Furthermore, newer tests, including array analysis and next-generation sequencing, which can simultaneously probe numerous molecular aberrancies within tumor cells, are likely to become commonplace in AML diagnostics. Each testing method clearly has advantages and disadvantages, an understanding of which should influence the choice of test in various clinical circumstances. To aid such understanding, this review discusses both genetic mutations in AML and the clinical tests-including their pros and cons-that may be used to probe these abnormalities. Additionally, we highlight the significance of genetic testing by describing cases in which results of genetic testing significantly influence clinical management of patients with AML.
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Affiliation(s)
- Gerald B W Wertheim
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
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17
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Multiplex ligation-dependent probe amplification (MLPA) in tumor diagnostics and prognostics. ACTA ACUST UNITED AC 2013; 21:189-206. [PMID: 23111197 DOI: 10.1097/pdm.0b013e3182595516] [Citation(s) in RCA: 98] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The increasing knowledge about genetic alterations and molecular biomarkers in cancer initiation and progression opens new possibilities for the treatment of various types of cancer. This requires the inclusion of sensitive, and preferably multiplex, methods for the detection of molecular genetic alterations in the toolbox of classic pathology. Multiplex ligation-dependent probe amplification (MLPA) is a multiplex polymerase chain reaction-based method that can detect changes in the gene copy number status, DNA methylation, and point mutations simultaneously. MLPA probes recognize target sequences of only 50 to 100 nucleotides in length. This makes it possible to use MLPA even on highly fragmented DNA, and allows the detection of small deletions encompassing only a single exon. MLPA is a reliable, cost-effective, and robust method that can be performed using a standard thermocycler and capillary electrophoresis equipment, generating results within 24 hours with a short hands-on working time. Up to 50 different genomic locations can be tested in a single reaction, which can be sufficient to detect those genetic alterations that are of diagnostic and prognostic significance in a certain tumor entity. In the last years, MLPA has been used successfully in tumor diagnostics and in cancer research. This review gives an overview on the collected experience of MLPA applications on tumor DNA, about the advantages but also potential pitfalls and limitations of this technique.
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18
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MLPA is a powerful tool for detecting lymphoblastic transformation in chronic myeloid leukemia and revealing the clonal origin of relapse in pediatric acute lymphoblastic leukemia. Cancer Genet 2012; 205:465-9. [DOI: 10.1016/j.cancergen.2012.05.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2012] [Revised: 05/10/2012] [Accepted: 05/14/2012] [Indexed: 10/27/2022]
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19
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Qiu P, Zhang L. Identification of markers associated with global changes in DNA methylation regulation in cancers. BMC Bioinformatics 2012; 13 Suppl 13:S7. [PMID: 23320390 PMCID: PMC3426805 DOI: 10.1186/1471-2105-13-s13-s7] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
DNA methylation exhibits different patterns in different cancers. DNA methylation rates at different genomic loci appear to be highly correlated in some samples but not in others. We call such phenomena conditional concordant relationships (CCRs). In this study, we explored DNA methylation patterns in 12 common cancers using data of 2434 patient samples collected by The Cancer Genome Atlas project. We developed an exploratory method to characterize CCRs in the methylation data and identified the 200 gene markers whose on-and-off statuses in DNA methylation are most significantly associated with drastic changes in CCRs throughout the genome. Clustering analysis of the methylation data of the 200 markers showed that they are tightly associated with cancer subtypes. We also generated a library of the significant CCRs that may be of interest to future studies of the regulation network of DNA methylation in cancer.
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Affiliation(s)
- Peng Qiu
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
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20
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Alexandrova EM, Moll UM. Role of p53 family members p73 and p63 in human hematological malignancies. Leuk Lymphoma 2012; 53:2116-29. [PMID: 22497596 DOI: 10.3109/10428194.2012.684348] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
p53, mutated in over half of human cancers and about 13% of all hematological malignancies, maintains genomic integrity and triggers cellular senescence and apoptosis of damaged cells. In contrast to p53, the homologs p73 and p63 play critical roles in development of the central nervous system and skin/limbs, respectively. Moreover, dependent on the context they can exert tumor suppressor activities that cooperate with p53. Unlike p53, p73 and p63 are rarely mutated in cancers. Instead, up-regulation of the anti-apoptotic dominant-negative ΔNp73 and ΔNp63 isoforms is the most frequent abnormality in solid cancers. In hematological malignancies the most frequent p73 defect is promoter methylation and loss of expression, associated with unfavorable clinical outcomes. This suggests an essential tumor suppressor role of p73 in blood cells, also supported by genetic mouse models. Many therapeutic approaches aiming to restore p73 activity are currently being investigated. In contrast, the most frequent p63 abnormality is protein overexpression, associated with higher disease grade and poorer prognosis. Surprisingly, although available data are still scarce, the emerging picture is up-regulation of transactivation-competent TAp63 isoforms, suggesting a tumor-promoting role in this context.
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21
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Shaffer BC, Gillet JP, Patel C, Baer MR, Bates SE, Gottesman MM. Drug resistance: still a daunting challenge to the successful treatment of AML. Drug Resist Updat 2012; 15:62-9. [PMID: 22409994 DOI: 10.1016/j.drup.2012.02.001] [Citation(s) in RCA: 187] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Resistance to chemotherapy remains a challenging issue for patients and their physicians. P-glycoprotein (Pgp, MDR1, ABCB1), as well as a family of structurally and functionally related proteins, are plasma membrane transporters able to efflux a variety of substrates from the cell cytoplasm, including chemotherapeutic agents. The discovery of ABCB1 made available a potential target for pharmacologic down-regulation of efflux-mediated chemotherapy resistance. In patients with acute myeloid leukemia (AML), a neoplasm characterized by proliferation of poorly differentiated myeloid progenitor cells, leukemic cells often express ABCB1 at high levels, which may lead to the development of resistance to chemotherapy. Thus, AML seemed to be a likely cancer for which the addition of drug efflux inhibitors to the chemotherapeutic regimen would improve outcomes in patients. Despite this rational hypothesis, the majority of clinical trials evaluating this strategy have failed to reach a positive endpoint, most recently the Eastern Cooperative Oncology Group E3999 trial. Here we review data suggesting the importance of ABCB1 in AML, address the failure of clinical trials to support a therapeutic strategy aimed at modulating ABCB1-mediated resistance, and consider the type of research that should be conducted in this field going forward.
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Affiliation(s)
- Brian C Shaffer
- Medical Oncology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892-4255, USA
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22
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Stuppia L, Antonucci I, Palka G, Gatta V. Use of the MLPA assay in the molecular diagnosis of gene copy number alterations in human genetic diseases. Int J Mol Sci 2012; 13:3245-3276. [PMID: 22489151 PMCID: PMC3317712 DOI: 10.3390/ijms13033245] [Citation(s) in RCA: 149] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2011] [Revised: 02/28/2012] [Accepted: 02/29/2012] [Indexed: 11/16/2022] Open
Abstract
Multiplex Ligation-dependent Probe Amplification (MLPA) assay is a recently developed technique able to evidence variations in the copy number of several human genes. Due to this ability, MLPA can be used in the molecular diagnosis of several genetic diseases whose pathogenesis is related to the presence of deletions or duplications of specific genes. Moreover, MLPA assay can also be used in the molecular diagnosis of genetic diseases characterized by the presence of abnormal DNA methylation. Due to the large number of genes that can be analyzed by a single technique, MLPA assay represents the gold standard for molecular analysis of all pathologies derived from the presence of gene copy number variation. In this review, the main applications of the MLPA technique for the molecular diagnosis of human diseases are described.
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Affiliation(s)
- Liborio Stuppia
- Department of Oral Sciences, Nano and Biotechnologies, “G. d’Annunzio” University, Via dei Vestini 31, 66013 Chieti, Italy; E-Mails: (I.A.); (G.P.); (V.G.)
| | - Ivana Antonucci
- Department of Oral Sciences, Nano and Biotechnologies, “G. d’Annunzio” University, Via dei Vestini 31, 66013 Chieti, Italy; E-Mails: (I.A.); (G.P.); (V.G.)
| | - Giandomenico Palka
- Department of Oral Sciences, Nano and Biotechnologies, “G. d’Annunzio” University, Via dei Vestini 31, 66013 Chieti, Italy; E-Mails: (I.A.); (G.P.); (V.G.)
| | - Valentina Gatta
- Department of Oral Sciences, Nano and Biotechnologies, “G. d’Annunzio” University, Via dei Vestini 31, 66013 Chieti, Italy; E-Mails: (I.A.); (G.P.); (V.G.)
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23
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Abstract
Myeloid hematological malignancies are among the epigenetically best characterized neoplasms. The comparatively low number of recurring balanced and unbalanced chromosomal abnormalities as well as common genetic mutations has enabled scientists to relate epigenetic states to these. The ease of accessing malignant cells through bone marrow aspiration has certainly contributed to the fast expansion of knowledge. Even so, the clinical and pathogenetic relevance of epigenetic changes is still not known, and the field will certainly evolve very fast with the development of new analytic techniques. The first example of successful epigenetic therapy is seen in myeloid malignancies, in the high-risk myelodysplastic syndromes (MDS) which are routinely treated with the demethylating agent azacytidine.This chapter will concentrate on describing the epigenetic changes in acute myeloid leukemia (AML), chronic myeloid leukemia (CML) and MDS. An overview of clinical relevance and epigenetic therapeutic approaches is also made.
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Affiliation(s)
- Stefan Deneberg
- Center of Hematology, Karolinska University Hospital, Huddinge, Sweden.
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24
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Vigna E, Recchia AG, Madeo A, Gentile M, Bossio S, Mazzone C, Lucia E, Morabito L, Gigliotti V, Stefano LD, Caruso N, Servillo P, Franzese S, Fimognari F, Bisconte MG, Gentile C, Morabito F. Epigenetic regulation in myelodysplastic syndromes: implications for therapy. Expert Opin Investig Drugs 2011; 20:465-93. [DOI: 10.1517/13543784.2011.559164] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Ernesto Vigna
- Unità Operativa Complessa di Ematologia, Dipartimento Oncoematologico, Azienda Ospedaliera di Cosenza, Viale della Repubblica, 87100 Cosenza, Italy ;
| | - Anna Grazia Recchia
- Unità Operativa Complessa di Ematologia, Dipartimento Oncoematologico, Azienda Ospedaliera di Cosenza, Viale della Repubblica, 87100 Cosenza, Italy ;
| | - Antonio Madeo
- Unità Operativa Complessa di Ematologia, Dipartimento Oncoematologico, Azienda Ospedaliera di Cosenza, Viale della Repubblica, 87100 Cosenza, Italy ;
| | - Massimo Gentile
- Unità Operativa Complessa di Ematologia, Dipartimento Oncoematologico, Azienda Ospedaliera di Cosenza, Viale della Repubblica, 87100 Cosenza, Italy ;
| | - Sabrina Bossio
- Unità Operativa Complessa di Ematologia, Dipartimento Oncoematologico, Azienda Ospedaliera di Cosenza, Viale della Repubblica, 87100 Cosenza, Italy ;
| | - Carla Mazzone
- Unità Operativa Complessa di Ematologia, Dipartimento Oncoematologico, Azienda Ospedaliera di Cosenza, Viale della Repubblica, 87100 Cosenza, Italy ;
| | - Eugenio Lucia
- Unità Operativa Complessa di Ematologia, Dipartimento Oncoematologico, Azienda Ospedaliera di Cosenza, Viale della Repubblica, 87100 Cosenza, Italy ;
| | - Lucio Morabito
- Servicio de Hematología y Hemoterapia, Hospital Universitario de Canarias, La Laguna, Tenerife, Spain
| | - Vincenzo Gigliotti
- Unità Operativa Complessa di Ematologia, Dipartimento Oncoematologico, Azienda Ospedaliera di Cosenza, Viale della Repubblica, 87100 Cosenza, Italy ;
| | - Laura De Stefano
- Unità Operativa Complessa di Ematologia, Dipartimento Oncoematologico, Azienda Ospedaliera di Cosenza, Viale della Repubblica, 87100 Cosenza, Italy ;
| | - Nadia Caruso
- Unità Operativa Complessa di Ematologia, Dipartimento Oncoematologico, Azienda Ospedaliera di Cosenza, Viale della Repubblica, 87100 Cosenza, Italy ;
| | - Pasquale Servillo
- Unità Operativa Complessa di Ematologia, Dipartimento Oncoematologico, Azienda Ospedaliera di Cosenza, Viale della Repubblica, 87100 Cosenza, Italy ;
| | - Stefania Franzese
- Unità Operativa Complessa di Ematologia, Dipartimento Oncoematologico, Azienda Ospedaliera di Cosenza, Viale della Repubblica, 87100 Cosenza, Italy ;
| | | | - Maria Grazia Bisconte
- Unità Operativa Complessa di Ematologia, Dipartimento Oncoematologico, Azienda Ospedaliera di Cosenza, Viale della Repubblica, 87100 Cosenza, Italy ;
| | - Carlo Gentile
- Unità Operativa Complessa di Ematologia, Dipartimento Oncoematologico, Azienda Ospedaliera di Cosenza, Viale della Repubblica, 87100 Cosenza, Italy ;
| | - Fortunato Morabito
- Unità Operativa Complessa di Ematologia, Dipartimento Oncoematologico, Azienda Ospedaliera di Cosenza, Viale della Repubblica, 87100 Cosenza, Italy ;
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25
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Tran HTT, Kim HN, Lee IK, Kim YK, Ahn JS, Yang DH, Lee JJ, Kim HJ. DNA methylation changes following 5-azacitidine treatment in patients with myelodysplastic syndrome. J Korean Med Sci 2011; 26:207-13. [PMID: 21286011 PMCID: PMC3031004 DOI: 10.3346/jkms.2011.26.2.207] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/14/2010] [Accepted: 11/09/2010] [Indexed: 12/24/2022] Open
Abstract
DNA methyltransferase inhibitor, 5-azacitidine (AC) is effective in myelodysplastic syndromes (MDS) and can induce re-expression in cancer. We analyzed the methylation of 25 tumor suppressor genes in AC-treated MDS. Hypermethylation of CDKN2B, FHIT, ESR1, and IGSF4 gene was detected in 9/44 patients. In concordance with the clinical response, a lack of or decreased methylation in 4 patients with hematologic improvements and persistent methylation in 4 others with no response was observed. The mRNA expression of CDKN2B, IGSF4, and ESR1 was significantly reduced in MDS. Our results suggest that methylation changes contribute to disease pathogenesis and may serve as marker to monitor the efficacy of treatments.
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Affiliation(s)
- Huong Thi Thanh Tran
- Genome Research Center for Hematopoietic Diseases, Chonnam National University Hwasun Hospital, Hwasun, Korea
| | - Hee Nam Kim
- Genome Research Center for Hematopoietic Diseases, Chonnam National University Hwasun Hospital, Hwasun, Korea
| | - Il-Kwon Lee
- Genome Research Center for Hematopoietic Diseases, Chonnam National University Hwasun Hospital, Hwasun, Korea
| | - Yeo-Kyeoung Kim
- Department of Hematology-Oncology, Chonnam National University Medical School, Gwangju, Korea
| | - Jae-Sook Ahn
- Department of Hematology-Oncology, Chonnam National University Medical School, Gwangju, Korea
| | - Deok-Hwan Yang
- Department of Hematology-Oncology, Chonnam National University Medical School, Gwangju, Korea
| | - Je-Jung Lee
- Department of Hematology-Oncology, Chonnam National University Medical School, Gwangju, Korea
| | - Hyeoung-Joon Kim
- Genome Research Center for Hematopoietic Diseases, Chonnam National University Hwasun Hospital, Hwasun, Korea
- Department of Hematology-Oncology, Chonnam National University Medical School, Gwangju, Korea
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26
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Eijk-Van Os PGC, Schouten JP. Multiplex Ligation-dependent Probe Amplification (MLPA®) for the detection of copy number variation in genomic sequences. Methods Mol Biol 2011; 688:97-126. [PMID: 20938835 DOI: 10.1007/978-1-60761-947-5_8] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Multiplex Ligation-dependent Probe Amplification (MLPA®) is a high-throughput method developed to determine the copy number of up to 50 genomic DNA sequences in a single multiplex PCR-based reaction. MLPA is easy to perform, requires only 20 ng of sample DNA and can distinguish sequences differing in only a single nucleotide. The MLPA reaction results in a mixture of amplification fragments ranging between 100 and 500 nt in length which can be separated and quantified by capillary electrophoresis. The equipment necessary for MLPA is identical to that for performing standard sequencing reactions: a thermocycler and a fluorescent capillary electrophoresis system. Comparison of the peak pattern obtained on a DNA sample to that of a reference sample indicates which sequences show aberrant copy numbers.Fundamental for the MLPA technique is that it is not the sample DNA that is amplified during the PCR reaction, but MLPA probes that hybridise to the sample DNA. Each MLPA probe consists of two probe oligonucleotides, which should hybridise adjacent to the target DNA for a successful ligation. Only ligated probes can be exponentially amplified by PCR. In contrast to standard multiplex PCR, only one pair of PCR primers is used for the MLPA PCR reaction, resulting in a more robust system. This way, the relative number of fragments present after the PCR reaction depends on the relative amount of the target sequence present in a DNA sample.
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27
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Multiplexed methylation profiles of tumor suppressor genes in bladder cancer. J Mol Diagn 2010; 13:29-40. [PMID: 21227392 DOI: 10.1016/j.jmoldx.2010.11.008] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2010] [Revised: 07/19/2010] [Accepted: 07/20/2010] [Indexed: 12/18/2022] Open
Abstract
Changes in DNA methylation of tumor suppressors can occur early in carcinogenesis and are potentially important early indicators of cancer. The objective of this study was to assess the methylation of 25 tumor suppressor genes in bladder cancer using a methylation-specific (MS) multiplex ligation-dependent probe amplification assay (MLPA). Initial analyses in bladder cancer cell lines (n = 14) and fresh-frozen primary bladder tumor specimens (n = 31) supported the panel of genes selected being altered in bladder cancer. The process of MS-MLPA was optimized for its application in body fluids using two independent training and validation sets of urinary specimens (n = 146), including patients with bladder cancer (n = 96) and controls (n = 50). BRCA1 (71.0%), WT1 (38.7%), and RARB (38.7%) were the most frequently methylated genes in bladder tumors, with WT1 methylation being significantly associated with tumor stage (P = 0.011). WT1 and PAX5A were identified as methylated tumor suppressors. In addition, BRCA1, WT1, and RARB were the most frequently methylated genes in urinary specimens. Receiver operating characteristic curve analyses revealed significant diagnostic accuracies in both urinary sets for BRCA1, RARB, and WT1. The novelty of this report relates to applying MS-MLPA, a multiplexed methylation technique, for tumor suppressors in bladder cancer and body fluids. Methylation profiles of tumor suppressor genes were clinically relevant for histopathological stratification of bladder tumors and offered a noninvasive diagnostic strategy for the clinical management of patients affected with uroepithelial neoplasias.
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28
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Griffiths EA, Gore SD, Hooker CM, Mohammad HP, McDevitt MA, Smith BD, Karp JE, Herman JG, Carraway HE. Epigenetic differences in cytogenetically normal versus abnormal acute myeloid leukemia. Epigenetics 2010; 5:590-600. [PMID: 20671427 DOI: 10.4161/epi.5.7.12558] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Methylation of tumor suppression genes (TSGs) is common in myeloid malignancies. However, application of this as a molecular marker for risk stratification in patients with AML is limited. DESIGN AND METHODS To elucidate the impact of patterns of TSG methylation on outcome in cytogenetically normal patients, 106 samples from patients with having normal cytogenetic AML were evaluated for methylation of 12 genes by MSP. For sake of comparison, samples from patients with AML and abnormal cytogenetics (n = 63) were also evaluated. RESULTS Methylation frequencies in the whole group (n = 169) were similar to previous reports for CDH1 (31%), ER (31%), FHIT (9%), p15 (INK4b) (44%), p73 (25%), and SOCS1 (75%). Methylation of CTNNA1 was observed in 10%, CEBP-α in16%, CEBP-δ in 2%, MLH1 in 24%, MGMT in 11% and DAPK in 2% of AML samples. We find that DNA methylation was more prevalent in patients with normal compared to karyotypically abnormal AML for most genes; CEBPα (20% vs 9%), CTNNA1 (14% vs 4%), and ER (41% vs 19%) (p < 0.05 for all comparisons). In contrast, p73 was more frequently methylated in patients with karyotypic abnormalities (17% vs 38%; p < 0.05), perhaps due to specific silencing of the pro-apoptotic promoter shifting p73 gene expression to the anti-apoptotic transcript. In AML patients with normal cytogenetics, TSG methylation was not associated with event free or overall survival in a multivariate analysis. CONCLUSIONS In patients with AML, TSG methylation is more frequent in patients with normal karyotype than those with karyotypic abnormalities but does not confer independent prognostic information for patients with normal cytogenetics.
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Castro M, Grau L, Puerta P, Gimenez L, Venditti J, Quadrelli S, Sánchez-Carbayo M. Multiplexed methylation profiles of tumor suppressor genes and clinical outcome in lung cancer. J Transl Med 2010; 8:86. [PMID: 20849603 PMCID: PMC2955578 DOI: 10.1186/1479-5876-8-86] [Citation(s) in RCA: 99] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2010] [Accepted: 09/17/2010] [Indexed: 12/31/2022] Open
Abstract
Background Changes in DNA methylation of crucial cancer genes including tumor suppressors can occur early in carcinogenesis, being potentially important early indicators of cancer. The objective of this study was to examine a multiplexed approach to assess the methylation of tumor suppressor genes as tumor stratification and clinical outcome prognostic biomarkers for lung cancer. Methods A multicandidate probe panel interrogated DNA for aberrant methylation status in 18 tumor suppressor genes in lung cancer using a methylation-specific multiplex ligation-dependent probe amplification assay (MS-MLPA). Lung cancer cell lines (n = 7), and primary lung tumors (n = 54) were examined using MS-MLPA. Results Genes frequently methylated in lung cancer cell lines including SCGB3A1, ID4, CCND2 were found among the most commonly methylated in the lung tumors analyzed. HLTF, BNIP3, H2AFX, CACNA1G, TGIF, ID4 and CACNA1A were identified as novel tumor suppressor candidates methylated in lung tumors. The most frequently methylated genes in lung tumors were SCGB3A1 and DLC1 (both 50.0%). Methylation rates for ID4, DCL1, BNIP3, H2AFX, CACNA1G and TIMP3 were significantly different between squamous and adenocarcinomas. Methylation of RUNX3, SCGB3A1, SFRP4, and DLC1 was significantly associated with the extent of the disease when comparing localized versus metastatic tumors. Moreover, methylation of HTLF, SFRP5 and TIMP3 were significantly associated with overall survival. Conclusions MS-MLPA can be used for classification of certain types of lung tumors and clinical outcome prediction. This latter is clinically relevant by offering an adjunct strategy for the clinical management of lung cancer patients.
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Affiliation(s)
- Mónica Castro
- Oncology Department, Instituto Angel H. Roffo, Buenos Aires, Argentina
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30
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DNA methylation profiles and their relationship with cytogenetic status in adult acute myeloid leukemia. PLoS One 2010; 5:e12197. [PMID: 20808941 PMCID: PMC2922373 DOI: 10.1371/journal.pone.0012197] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2010] [Accepted: 07/14/2010] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Aberrant promoter DNA methylation has been shown to play a role in acute myeloid leukemia (AML) pathophysiology. However, further studies to discuss the prognostic value and the relationship of the epigenetic signatures with defined genomic rearrangements in acute myeloid leukemia are required. METHODOLOGY/PRINCIPAL FINDINGS We carried out high-throughput methylation profiling on 116 de novo AML cases and we validated the significant biomarkers in an independent cohort of 244 AML cases. Methylation signatures were associated with the presence of a specific cytogenetic status. In normal karyotype cases, aberrant methylation of the promoter of DBC1 was validated as a predictor of the disease-free and overall survival. Furthermore, DBC1 expression was significantly silenced in the aberrantly methylated samples. Patients with chromosome rearrangements showed distinct methylation signatures. To establish the role of fusion proteins in the epigenetic profiles, 20 additional samples of human hematopoietic stem/progenitor cells (HSPC) transduced with common fusion genes were studied and compared with patient samples carrying the same rearrangements. The presence of MLL rearrangements in HSPC induced the methylation profile observed in the MLL-positive primary samples. In contrast, fusion genes such as AML1/ETO or CBFB/MYH11 failed to reproduce the epigenetic signature observed in the patients. CONCLUSIONS/SIGNIFICANCE Our study provides a comprehensive epigenetic profiling of AML, identifies new clinical markers for cases with a normal karyotype, and reveals relevant biological information related to the role of fusion proteins on the methylation signature.
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Benetatos L, Hatzimichael E, Dasoula A, Dranitsaris G, Tsiara S, Syrrou M, Georgiou I, Bourantas KL. CpG methylation analysis of the MEG3 and SNRPN imprinted genes in acute myeloid leukemia and myelodysplastic syndromes. Leuk Res 2010; 34:148-53. [PMID: 19595458 DOI: 10.1016/j.leukres.2009.06.019] [Citation(s) in RCA: 117] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2009] [Revised: 06/12/2009] [Accepted: 06/15/2009] [Indexed: 11/25/2022]
Abstract
Methylation is now established as a fundamental regulator of gene transcription. To investigate this in haematologic malignancies, we evaluated the aberrant promoter methylation of two imprinted genes (MEG3 and SNRPN) in 43 MDS and 42 AML patients. MEG3 hypermethylation occurred in 15 MDS patients (34.9%), and in 20 AML patients (47.6%). SNRPN hypermethylation was observed in 15 MDS patients (34.9%), and in 21 AML patients (50%). There were no significant correlations between WHO subtype, WPSS score, karyotype, haemoglobin levels, white blood cell count, platelet count and CpG methylation of any gene. MEG3 hypermethylation was associated with significantly reduced overall survival in individuals with AML (HR=1.98, p=0.04), while SNRPN CpG methylation was not associated with survival (HR=0.94, p=0.87). In addition, no association between survival and aberrant MEG3 (HR=2.15, p=0.072) or SNRPN methylation (HR=1.08, p=0.85) was observed in patients MDS. Our findings suggest that these genes are abnormally methylated in AML and MDS patients, and methylation of MEG3 confers worse overall prognosis. The MEG3 methylation status may serve as a useful biomarker in leukemia.
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Affiliation(s)
- Leonidas Benetatos
- Department of Hematology, University Hospital of Ioannina, Niarchos Avenue, 45500 Ioannina, Greece.
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Epigenetic mechanisms regulating normal and malignant haematopoiesis: new therapeutic targets for clinical medicine. Expert Rev Mol Med 2010; 12:e6. [PMID: 20152067 DOI: 10.1017/s1462399410001377] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
It is now well established that epigenetic phenomena and aberrant gene regulation play a major role in carcinogenesis. These include aberrant gene silencing by imposing inactive histone marks on promoters, aberrant methylation of DNA at CpG islands, and the active repression of promoters by oncoproteins. In addition, many malignant cells also show aberrant gene activation due to constitutively active signalling. The next frontier in cancer research will be to examine how, at the molecular level, small mutations that alter the regulatory phenotype of a cell give rise after a number of cell divisions to the vast deregulation phenomena seen in malignant cells. This review outlines recent insights into how normal cell differentiation in the haematopoietic system is subverted in leukaemia and it introduces the molecular players involved in this process. It also summarises the results of recent clinical trials trying to reverse aberrant epigenetic regulation by employing agents influencing global epigenetic regulators.
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Hypomethylation and expression of BEX2, IGSF4 and TIMP3 indicative of MLL translocations in acute myeloid leukemia. Mol Cancer 2009; 8:86. [PMID: 19835597 PMCID: PMC2770485 DOI: 10.1186/1476-4598-8-86] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2009] [Accepted: 10/16/2009] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Translocations of the Mixed Lineage Leukemia (MLL) gene occur in a subset (5%) of acute myeloid leukemias (AML), and in mixed phenotype acute leukemias in infancy - a disease with extremely poor prognosis. Animal model systems show that MLL gain of function mutations may contribute to leukemogenesis. Wild-type (wt) MLL possesses histone methyltransferase activity and functions at the level of chromatin organization by affecting the expression of specific target genes. While numerous MLL fusion proteins exert a diverse array of functions, they ultimately serve to induce transcription of specific genes. Hence, acute lymphoblastic leukemias (ALL) with MLL mutations (MLLmu) exhibit characteristic gene expression profiles including high-level expression of HOXA cluster genes. Here, we aimed to relate MLL mutational status and tumor suppressor gene (TSG) methylation/expression in acute leukemia cell lines. RESULTS Using MS-MLPA (methylation-specific multiplex ligation-dependent probe amplification assay), methylation of 24 different TSG was analyzed in 28 MLLmu and MLLwt acute leukemia cell lines. On average, 1.8/24 TSG were methylated in MLLmu AML cells, while 6.2/24 TSG were methylated in MLLwt AML cells. Hypomethylation and expression of the TSG BEX2, IGSF4 and TIMP3 turned out to be characteristic of MLLmu AML cell lines. MLLwt AML cell lines displayed hypermethylated TSG promoters resulting in transcriptional silencing. Demethylating agents and inhibitors of histone deacetylases restored expression of BEX2, IGSF4 and TIMP3, confirming epigenetic silencing of these genes in MLLwt cells. The positive correlation between MLL translocation, TSG hypomethylation and expression suggested that MLL fusion proteins were responsible for dysregulation of TSG expression in MLLmu cells. This concept was supported by our observation that Bex2 mRNA levels in MLL-ENL transgenic mouse cell lines required expression of the MLL fusion gene. CONCLUSION These results suggest that the conspicuous expression of the TSG BEX2, IGSF4 and TIMP3 in MLLmu AML cell lines is the consequence of altered epigenetic properties of MLL fusion proteins.
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Affiliation(s)
- Carla Kurkjian
- Advanced Developmental Therapeutics Training Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, Bethesda, Maryland, USA
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