1
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Kirkiz E, Meers O, Grebien F, Buschbeck M. Histone Variants and Their Chaperones in Hematological Malignancies. Hemasphere 2023; 7:e927. [PMID: 37449197 PMCID: PMC10337764 DOI: 10.1097/hs9.0000000000000927] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Accepted: 06/13/2023] [Indexed: 07/18/2023] Open
Abstract
Epigenetic regulation occurs on the level of compacting DNA into chromatin. The functional unit of chromatin is the nucleosome, which consists of DNA wrapped around a core of histone proteins. While canonical histone proteins are incorporated into chromatin through a replication-coupled process, structural variants of histones, commonly named histone variants, are deposited into chromatin in a replication-independent manner. Specific chaperones and chromatin remodelers mediate the locus-specific deposition of histone variants. Although histone variants comprise one of the least understood layers of epigenetic regulation, it has been proposed that they play an essential role in directly regulating gene expression in health and disease. Here, we review the emerging evidence suggesting that histone variants have a role at different stages of hematopoiesis, with a particular focus on the histone variants H2A, H3, and H1. Moreover, we discuss the current knowledge on how the dysregulation of histone variants can contribute to hematopoietic malignancies.
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Affiliation(s)
- Ecem Kirkiz
- Institute for Medical Biochemistry, University of Veterinary Medicine, Vienna, Austria
| | - Oliver Meers
- Cancer and Leukaemia Epigenetics and Biology Program, Josep Carreras Leukaemia Research Institute (IJC), Campus Can Ruti, Badalona, Spain
- PhD Programme in Biomedicine, University of Barcelona, Spain
| | - Florian Grebien
- Institute for Medical Biochemistry, University of Veterinary Medicine, Vienna, Austria
- St. Anna Children’s Cancer Research Institute (CCRI), Vienna, Austria
| | - Marcus Buschbeck
- Cancer and Leukaemia Epigenetics and Biology Program, Josep Carreras Leukaemia Research Institute (IJC), Campus Can Ruti, Badalona, Spain
- Germans Trias i Pujol Research Institute (IGTP), Badalona, Spain
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2
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Liu S, Zhou J, Ye X, Chen D, Chen W, Lin Y, Chen Z, Chen B, Shang J. A novel lncRNA SNHG29 regulates EP300- related histone acetylation modification and inhibits FLT3-ITD AML development. Leukemia 2023; 37:1421-1434. [PMID: 37157016 DOI: 10.1038/s41375-023-01923-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Revised: 04/26/2023] [Accepted: 04/26/2023] [Indexed: 05/10/2023]
Abstract
Internal tandem duplication (ITD) mutations within the FMS-like tyrosine kinase-3 (FLT3) occur in up to 25% of acute myeloid leukemia (AML) patients and indicate a very poor prognosis. The role of long noncoding RNAs (lncRNAs) in FLT3-ITD AML progression remains unexplored. We identified a novel lncRNA, SNHG29, whose expression is specifically regulated by the FLT3-STAT5 signaling pathway and is abnormally down-regulated in FLT3-ITD AML cell lines. SNHG29 functions as a tumor suppressor, significantly inhibiting FLT3-ITD AML cell proliferation and decreasing sensitivity to cytarabine in vitro and in vivo models. Mechanistically, we demonstrated that SNHG29's molecular mechanism is EP300-binding dependent and identified the EP300-interacting region of SNHG29. SNHG29 modulates genome-wide EP300 genomic binding, affecting EP300-mediated histone modification and consequently influencing the expression of varies downstream AML-associated genes. Our study uncovers a novel molecular mechanism for SNHG29 in mediating FLT3-ITD AML biological behaviors through epigenetic modification, suggesting that SNHG29 could be a potential therapeutic target for FLT3-ITD AML.
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Affiliation(s)
- Shan Liu
- Department of Hematology-Oncology, Fujian Children's Hospital; College of Clinical Medicine for Obstetrics and Gynecology and Pediatrics, Fujian Medical University, Fuzhou, Fujian, China
| | - Jie Zhou
- Shengli Clinical Medical College of Fujian Medical University; Department of Hematology, Fujian Provincial Hospital, Fuzhou, Fujian, China
| | - Xiangling Ye
- Shengli Clinical Medical College of Fujian Medical University; Department of Hematology, Fujian Provincial Hospital, Fuzhou, Fujian, China
| | - Danni Chen
- Shengli Clinical Medical College of Fujian Medical University; Department of Hematology, Fujian Provincial Hospital, Fuzhou, Fujian, China
| | - Weimin Chen
- Shengli Clinical Medical College of Fujian Medical University; Department of Hematology, Fujian Provincial Hospital, Fuzhou, Fujian, China
| | - Yaobin Lin
- Clinical Oncology School of Fujian Medical University, Fujian Cancer Hospital, Fuzhou, Fujian, China
| | - Zhizhong Chen
- Shengli Clinical Medical College of Fujian Medical University; Department of Pathology, Fujian Provincial Hospital, Fuzhou, Fujian, China
| | - Biyun Chen
- Shengli Clinical Medical College of Fujian Medical University; Department of Hematology, Fujian Provincial Hospital, Fuzhou, Fujian, China
| | - Jin Shang
- Shengli Clinical Medical College of Fujian Medical University; Department of Hematology, Fujian Provincial Hospital, Fuzhou, Fujian, China.
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3
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Mas G, Santoro F, Blanco E, Gamarra Figueroa GP, Le Dily F, Frigè G, Vidal E, Mugianesi F, Ballaré C, Gutierrez A, Sparavier A, Marti-Renom MA, Minucci S, Di Croce L. In vivo temporal resolution of acute promyelocytic leukemia progression reveals a role of Klf4 in suppressing early leukemic transformation. Genes Dev 2022; 36:451-467. [PMID: 35450883 PMCID: PMC9067408 DOI: 10.1101/gad.349115.121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Accepted: 03/25/2022] [Indexed: 11/25/2022]
Abstract
In this study, Mas et al. used primary hematopoietic stem and progenitor cells (HSPCs) and leukemic blasts that express the fusion protein PML-RARα as a paradigm to temporally dissect the dynamic changes in the epigenome, transcriptome, and genome architecture induced during oncogenic transformation. Their multiomics-integrated analysis identified Klf4 as an early down-regulated gene in PML-RARα-driven leukemogenesis, and they characterized the dynamic alterations in the Klf4 cis-regulatory network during APL progression and demonstrated that ectopic Klf4 overexpression can suppress self-renewal and reverse the differentiation block induced by PML-RARα. Genome organization plays a pivotal role in transcription, but how transcription factors (TFs) rewire the structure of the genome to initiate and maintain the programs that lead to oncogenic transformation remains poorly understood. Acute promyelocytic leukemia (APL) is a fatal subtype of leukemia driven by a chromosomal translocation between the promyelocytic leukemia (PML) and retinoic acid receptor α (RARα) genes. We used primary hematopoietic stem and progenitor cells (HSPCs) and leukemic blasts that express the fusion protein PML-RARα as a paradigm to temporally dissect the dynamic changes in the epigenome, transcriptome, and genome architecture induced during oncogenic transformation. We found that PML-RARα initiates a continuum of topologic alterations, including switches from A to B compartments, transcriptional repression, loss of active histone marks, and gain of repressive histone marks. Our multiomics-integrated analysis identifies Klf4 as an early down-regulated gene in PML-RARα-driven leukemogenesis. Furthermore, we characterized the dynamic alterations in the Klf4 cis-regulatory network during APL progression and demonstrated that ectopic Klf4 overexpression can suppress self-renewal and reverse the differentiation block induced by PML-RARα. Our study provides a comprehensive in vivo temporal dissection of the epigenomic and topological reprogramming induced by an oncogenic TF and illustrates how topological architecture can be used to identify new drivers of malignant transformation.
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Affiliation(s)
- Glòria Mas
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona 08003, Spain
| | - Fabio Santoro
- Department of Experimental Oncology, European Institute of Oncology (IEO), Milan 20139, Italy.,Department of Oncology and Hemato-oncology, University of Milan, Milan 20139, Italy
| | - Enrique Blanco
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona 08003, Spain
| | | | - François Le Dily
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona 08003, Spain
| | - Gianmaria Frigè
- Department of Experimental Oncology, European Institute of Oncology (IEO), Milan 20139, Italy.,Department of Oncology and Hemato-oncology, University of Milan, Milan 20139, Italy
| | - Enrique Vidal
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona 08003, Spain
| | - Francesca Mugianesi
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona 08003, Spain.,Centro Nacional de Análisis Genómico (CNAG), Centre for Genomic Regulation (CRG), the Barcelona Institute of Science and Technology, Barcelona 08028, Spain
| | - Cecilia Ballaré
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona 08003, Spain
| | - Arantxa Gutierrez
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona 08003, Spain
| | - Aleksandra Sparavier
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona 08003, Spain.,Centro Nacional de Análisis Genómico (CNAG), Centre for Genomic Regulation (CRG), the Barcelona Institute of Science and Technology, Barcelona 08028, Spain
| | - Marc A Marti-Renom
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona 08003, Spain.,Centro Nacional de Análisis Genómico (CNAG), Centre for Genomic Regulation (CRG), the Barcelona Institute of Science and Technology, Barcelona 08028, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona 08010, Spain
| | - Saverio Minucci
- Department of Experimental Oncology, European Institute of Oncology (IEO), Milan 20139, Italy.,Department of Oncology and Hemato-oncology, University of Milan, Milan 20139, Italy
| | - Luciano Di Croce
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona 08003, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona 08010, Spain
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4
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Vervoort SJ, Devlin JR, Kwiatkowski N, Teng M, Gray NS, Johnstone RW. Targeting transcription cycles in cancer. Nat Rev Cancer 2022; 22:5-24. [PMID: 34675395 DOI: 10.1038/s41568-021-00411-8] [Citation(s) in RCA: 57] [Impact Index Per Article: 28.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 09/09/2021] [Indexed: 12/15/2022]
Abstract
Accurate control of gene expression is essential for normal development and dysregulation of transcription underpins cancer onset and progression. Similar to cell cycle regulation, RNA polymerase II-driven transcription can be considered as a unidirectional multistep cycle, with thousands of unique transcription cycles occurring in concert within each cell. Each transcription cycle comprises recruitment, initiation, pausing, elongation, termination and recycling stages that are tightly controlled by the coordinated action of transcriptional cyclin-dependent kinases and their cognate cyclins as well as the opposing activity of transcriptional phosphatases. Oncogenic dysregulation of transcription can entail defective control of gene expression, either at select loci or more globally, impacting a large proportion of the genome. The resultant dependency on the core-transcriptional machinery is believed to render 'transcriptionally addicted' cancers sensitive to perturbation of transcription. Based on these findings, small molecules targeting transcriptional cyclin-dependent kinases and associated proteins hold promise for the treatment of cancer. Here, we utilize the transcription cycles concept to explain how dysregulation of these finely tuned gene expression processes may drive tumorigenesis and how therapeutically beneficial responses may arise from global or selective transcriptional perturbation. This conceptual framework helps to explain tumour-selective transcriptional dependencies and facilitates the rational design of combination therapies.
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Affiliation(s)
- Stephin J Vervoort
- Gene Regulation Laboratory, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
- The Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC, Australia
| | - Jennifer R Devlin
- Gene Regulation Laboratory, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
- The Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC, Australia
| | - Nicholas Kwiatkowski
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Mingxing Teng
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Nathanael S Gray
- Department of Chemical and Systems Biology, CHEM-H and SCI, Stanford Medical School, Stanford University, Stanford, CA, USA.
| | - Ricky W Johnstone
- Gene Regulation Laboratory, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia.
- The Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC, Australia.
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5
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KDM5A suppresses PML-RARα target gene expression and APL differentiation through repressing H3K4me2. Blood Adv 2021; 5:3241-3253. [PMID: 34448811 DOI: 10.1182/bloodadvances.2020002819] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 03/29/2021] [Indexed: 11/20/2022] Open
Abstract
Epigenetic abnormalities are frequently involved in the initiation and progression of cancers, including acute myeloid leukemia (AML). A subtype of AML, acute promyelocytic leukemia (APL), is mainly driven by a specific oncogenic fusion event of promyelocytic leukemia-RA receptor fusion oncoprotein (PML-RARα). PML-RARα was reported as a transcription repressor through the interaction with nuclear receptor corepressor and histone deacetylase complexes leading to the mis-suppression of its target genes and differentiation blockage. Although previous studies were mainly focused on the connection of histone acetylation, it is still largely unknown whether alternative epigenetics mechanisms are involved in APL progression. KDM5A is a demethylase of histone H3 lysine 4 di- and tri-methylations (H3K4me2/3) and a transcription corepressor. Here, we found that the loss of KDM5A led to APL NB4 cell differentiation and retarded growth. Mechanistically, through epigenomics and transcriptomics analyses, KDM5A binding was detected in 1889 genes, with the majority of the binding events at promoter regions. KDM5A suppressed the expression of 621 genes, including 42 PML-RARα target genes, primarily by controlling the H3K4me2 in the promoters and 5' end intragenic regions. In addition, a recently reported pan-KDM5 inhibitor, CPI-455, on its own could phenocopy the differentiation effects as KDM5A loss in NB4 cells. CPI-455 treatment or KDM5A knockout could greatly sensitize NB4 cells to all-trans retinoic acid-induced differentiation. Our findings indicate that KDM5A contributed to the differentiation blockage in the APL cell line NB4, and inhibition of KDM5A could greatly potentiate NB4 differentiation.
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6
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Beta-Genus Human Papillomavirus 8 E6 Destabilizes the Host Genome by Promoting p300 Degradation. Viruses 2021; 13:v13081662. [PMID: 34452526 PMCID: PMC8402844 DOI: 10.3390/v13081662] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 08/16/2021] [Accepted: 08/18/2021] [Indexed: 01/10/2023] Open
Abstract
The beta genus of human papillomaviruses infects cutaneous keratinocytes. Their replication depends on actively proliferating cells and, thus, they conflict with the cellular response to the DNA damage frequently encountered by these cells. This review focus on one of these viruses (HPV8) that counters the cellular response to damaged DNA and mitotic errors by expressing a protein (HPV8 E6) that destabilizes a histone acetyltransferase, p300. The loss of p300 results in broad dysregulation of cell signaling that decreases genome stability. In addition to discussing phenotypes caused by p300 destabilization, the review contains a discussion of the extent to which E6 from other β-HPVs destabilizes p300, and provides a discussion on dissecting HPV8 E6 biology using mutants.
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7
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Rejeski K, Duque-Afonso J, Lübbert M. AML1/ETO and its function as a regulator of gene transcription via epigenetic mechanisms. Oncogene 2021; 40:5665-5676. [PMID: 34331016 PMCID: PMC8460439 DOI: 10.1038/s41388-021-01952-w] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 06/11/2021] [Accepted: 07/07/2021] [Indexed: 01/10/2023]
Abstract
The chromosomal translocation t(8;21) and the resulting oncofusion gene AML1/ETO have long served as a prototypical genetic lesion to model and understand leukemogenesis. In this review, we describe the wide-ranging role of AML1/ETO in AML leukemogenesis, with a particular focus on the aberrant epigenetic regulation of gene transcription driven by this AML-defining mutation. We begin by analyzing how structural changes secondary to distinct genomic breakpoints and splice changes, as well as posttranscriptional modifications, influence AML1/ETO protein function. Next, we characterize how AML1/ETO recruits chromatin-modifying enzymes to target genes and how the oncofusion protein alters chromatin marks, transcription factor binding, and gene expression. We explore the specific impact of these global changes in the epigenetic network facilitated by the AML1/ETO oncofusion on cellular processes and leukemic growth. Furthermore, we define the genetic landscape of AML1/ETO-positive AML, presenting the current literature concerning the incidence of cooperating mutations in genes such as KIT, FLT3, and NRAS. Finally, we outline how alterations in transcriptional regulation patterns create potential vulnerabilities that may be exploited by epigenetically active agents and other therapeutics.
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Affiliation(s)
- Kai Rejeski
- Department of Hematology, Oncology and Stem Cell Transplantation, University of Freiburg Medical Center, Freiburg, Germany.,Department of Hematology and Oncology, University Hospital of the LMU Munich, Munich, Germany.,German Cancer Consortium (DKTK) Freiburg Partner Site, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Jesús Duque-Afonso
- Department of Hematology, Oncology and Stem Cell Transplantation, University of Freiburg Medical Center, Freiburg, Germany.,Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Michael Lübbert
- Department of Hematology, Oncology and Stem Cell Transplantation, University of Freiburg Medical Center, Freiburg, Germany. .,German Cancer Consortium (DKTK) Freiburg Partner Site, German Cancer Research Center (DKFZ), Heidelberg, Germany. .,Faculty of Medicine, University of Freiburg, Freiburg, Germany.
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8
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Tan Y, Wang X, Song H, Zhang Y, Zhang R, Li S, Jin W, Chen S, Fang H, Chen Z, Wang K. A PML/RARα direct target atlas redefines transcriptional deregulation in acute promyelocytic leukemia. Blood 2021; 137:1503-1516. [PMID: 32854112 PMCID: PMC7976511 DOI: 10.1182/blood.2020005698] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Accepted: 08/20/2020] [Indexed: 12/12/2022] Open
Abstract
Transcriptional deregulation initiated by oncogenic fusion proteins plays a vital role in leukemia. The prevailing view is that the oncogenic fusion protein promyelocytic leukemia/retinoic acid receptor-α (PML/RARα), generated by the chromosome translocation t(15;17), functions as a transcriptional repressor in acute promyelocytic leukemia (APL). Here, we provide rich evidence of how PML/RARα drives oncogenesis through both repressive and activating functions, particularly the importance of the newly identified activation role for the leukemogenesis of APL. The activating function of PML/RARα is achieved by recruiting both abundant P300 and HDAC1 and by the formation of super-enhancers. All-trans retinoic acid and arsenic trioxide, 2 widely used drugs in APL therapy, exert synergistic effects on controlling super-enhancer-associated PML/RARα-regulated targets in APL cells. We use a series of in vitro and in vivo experiments to demonstrate that PML/RARα-activated target gene GFI1 is necessary for the maintenance of APL cells and that PML/RARα, likely oligomerized, transactivates GFI1 through chromatin conformation at the super-enhancer region. Finally, we profile GFI1 targets and reveal the interplay between GFI1 and PML/RARα on chromatin in coregulating target genes. Our study provides genomic insight into the dual role of fusion transcription factors in transcriptional deregulation to drive leukemia development, highlighting the importance of globally dissecting regulatory circuits.
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Affiliation(s)
- Yun Tan
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xiaoling Wang
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China; and
| | - Huan Song
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yi Zhang
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Rongsheng Zhang
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China; and
| | - Shufen Li
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Wen Jin
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Saijuan Chen
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Hai Fang
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zhu Chen
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Sino-French Research Center for Life Sciences and Genomics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Kankan Wang
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China; and
- Sino-French Research Center for Life Sciences and Genomics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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9
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Dirks RAM, Thomas PC, Wu H, Jones RC, Stunnenberg HG, Marks H. A plug and play microfluidic platform for standardized sensitive low-input chromatin immunoprecipitation. Genome Res 2021; 31:919-933. [PMID: 33707229 PMCID: PMC8092002 DOI: 10.1101/gr.260745.120] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Accepted: 02/22/2021] [Indexed: 11/24/2022]
Abstract
Epigenetic profiling by chromatin immunoprecipitation followed by sequencing (ChIP-seq) has become a powerful tool for genome-wide identification of regulatory elements, for defining transcriptional regulatory networks, and for screening for biomarkers. However, the ChIP-seq protocol for low-input samples is laborious and time-consuming and suffers from experimental variation, resulting in poor reproducibility and low throughput. Although prototypic microfluidic ChIP-seq platforms have been developed, these are poorly transferable as they require sophisticated custom-made equipment and in-depth microfluidic and ChIP expertise, while lacking parallelization. To enable standardized, automated ChIP-seq profiling of low-input samples, we constructed microfluidic PDMS-based plates capable of performing 24 sensitive ChIP reactions within 30 min of hands-on time and 4.5 h of machine-running time. These disposable plates can be conveniently loaded into a widely available controller for pneumatics and thermocycling. In light of the plug and play (PnP) ChIP plates and workflow, we named our procedure PnP-ChIP-seq. We show high-quality ChIP-seq on hundreds to a few thousand of cells for all six post-translational histone modifications that are included in the International Human Epigenome Consortium set of reference epigenomes. PnP-ChIP-seq robustly detects epigenetic differences on promoters and enhancers between naive and more primed mouse embryonic stem cells (mESCs). Furthermore, we used our platform to generate epigenetic profiles of rare subpopulations of mESCs that resemble the two-cell stage of embryonic development. PnP-ChIP-seq allows nonexpert laboratories worldwide to conveniently run robust, standardized ChIP-seq, whereas its high throughput, consistency, and sensitivity pave the way toward large-scale profiling of precious sample types such as rare subpopulations of cells or biopsies.
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Affiliation(s)
- René A M Dirks
- Department of Molecular Biology, Faculty of Science, Radboud University, Radboud Institute for Molecular Life Sciences (RIMLS), 6525GA Nijmegen, the Netherlands
| | - Peter C Thomas
- Fluidigm Corporation, South San Francisco, California 94080, USA
| | - Haoyu Wu
- Department of Molecular Biology, Faculty of Science, Radboud University, Radboud Institute for Molecular Life Sciences (RIMLS), 6525GA Nijmegen, the Netherlands
| | - Robert C Jones
- Fluidigm Corporation, South San Francisco, California 94080, USA
| | - Hendrik G Stunnenberg
- Department of Molecular Biology, Faculty of Science, Radboud University, Radboud Institute for Molecular Life Sciences (RIMLS), 6525GA Nijmegen, the Netherlands
| | - Hendrik Marks
- Department of Molecular Biology, Faculty of Science, Radboud University, Radboud Institute for Molecular Life Sciences (RIMLS), 6525GA Nijmegen, the Netherlands
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10
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Wang Z, Wang P, Li Y, Peng H, Zhu Y, Mohandas N, Liu J. Interplay between cofactors and transcription factors in hematopoiesis and hematological malignancies. Signal Transduct Target Ther 2021; 6:24. [PMID: 33468999 PMCID: PMC7815747 DOI: 10.1038/s41392-020-00422-1] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Revised: 10/16/2020] [Accepted: 10/26/2020] [Indexed: 02/07/2023] Open
Abstract
Hematopoiesis requires finely tuned regulation of gene expression at each stage of development. The regulation of gene transcription involves not only individual transcription factors (TFs) but also transcription complexes (TCs) composed of transcription factor(s) and multisubunit cofactors. In their normal compositions, TCs orchestrate lineage-specific patterns of gene expression and ensure the production of the correct proportions of individual cell lineages during hematopoiesis. The integration of posttranslational and conformational modifications in the chromatin landscape, nucleosomes, histones and interacting components via the cofactor–TF interplay is critical to optimal TF activity. Mutations or translocations of cofactor genes are expected to alter cofactor–TF interactions, which may be causative for the pathogenesis of various hematologic disorders. Blocking TF oncogenic activity in hematologic disorders through targeting cofactors in aberrant complexes has been an exciting therapeutic strategy. In this review, we summarize the current knowledge regarding the models and functions of cofactor–TF interplay in physiological hematopoiesis and highlight their implications in the etiology of hematological malignancies. This review presents a deep insight into the physiological and pathological implications of transcription machinery in the blood system.
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Affiliation(s)
- Zi Wang
- Department of Hematology, Institute of Molecular Hematology, The Second Xiangya Hospital, Central South University, 410011, ChangSha, Hunan, China. .,Molecular Biology Research Center and Hunan Province Key Laboratory of Basic and Applied Hematology, School of Life Sciences, Central South University, 410078, Changsha, Hunan, China.
| | - Pan Wang
- Molecular Biology Research Center and Hunan Province Key Laboratory of Basic and Applied Hematology, School of Life Sciences, Central South University, 410078, Changsha, Hunan, China
| | - Yanan Li
- Molecular Biology Research Center and Hunan Province Key Laboratory of Basic and Applied Hematology, School of Life Sciences, Central South University, 410078, Changsha, Hunan, China
| | - Hongling Peng
- Department of Hematology, Institute of Molecular Hematology, The Second Xiangya Hospital, Central South University, 410011, ChangSha, Hunan, China
| | - Yu Zhu
- Molecular Biology Research Center and Hunan Province Key Laboratory of Basic and Applied Hematology, School of Life Sciences, Central South University, 410078, Changsha, Hunan, China
| | - Narla Mohandas
- Red Cell Physiology Laboratory, New York Blood Center, New York, NY, USA
| | - Jing Liu
- Molecular Biology Research Center and Hunan Province Key Laboratory of Basic and Applied Hematology, School of Life Sciences, Central South University, 410078, Changsha, Hunan, China.
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11
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Kellaway S, Chin PS, Barneh F, Bonifer C, Heidenreich O. t(8;21) Acute Myeloid Leukemia as a Paradigm for the Understanding of Leukemogenesis at the Level of Gene Regulation and Chromatin Programming. Cells 2020; 9:E2681. [PMID: 33322186 PMCID: PMC7763303 DOI: 10.3390/cells9122681] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 12/09/2020] [Indexed: 12/15/2022] Open
Abstract
Acute myeloid leukemia (AML) is a heterogenous disease with multiple sub-types which are defined by different somatic mutations that cause blood cell differentiation to go astray. Mutations occur in genes encoding members of the cellular machinery controlling transcription and chromatin structure, including transcription factors, chromatin modifiers, DNA-methyltransferases, but also signaling molecules that activate inducible transcription factors controlling gene expression and cell growth. Mutant cells in AML patients are unable to differentiate and adopt new identities that are shaped by the original driver mutation and by rewiring their gene regulatory networks into regulatory phenotypes with enhanced fitness. One of the best-studied AML-subtypes is the t(8;21) AML which carries a translocation fusing the DNA-binding domain of the hematopoietic master regulator RUNX1 to the ETO gene. The resulting oncoprotein, RUNX1/ETO has been studied for decades, both at the biochemical but also at the systems biology level. It functions as a dominant-negative version of RUNX1 and interferes with multiple cellular processes associated with myeloid differentiation, growth regulation and genome stability. In this review, we summarize our current knowledge of how this protein reprograms normal into malignant cells and how our current knowledge could be harnessed to treat the disease.
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Affiliation(s)
- Sophie Kellaway
- Institute of Cancer and Genomica Sciences, College of Medicine and Dentistry, University of Birmingham, Birmingham B152TT, UK; (S.K.); (P.S.C.)
| | - Paulynn S. Chin
- Institute of Cancer and Genomica Sciences, College of Medicine and Dentistry, University of Birmingham, Birmingham B152TT, UK; (S.K.); (P.S.C.)
| | - Farnaz Barneh
- Princess Máxima Centrum for Pediatric Oncology, Heidelberglaan 25, 3584CS Utrecht, The Netherlands;
| | - Constanze Bonifer
- Institute of Cancer and Genomica Sciences, College of Medicine and Dentistry, University of Birmingham, Birmingham B152TT, UK; (S.K.); (P.S.C.)
| | - Olaf Heidenreich
- Princess Máxima Centrum for Pediatric Oncology, Heidelberglaan 25, 3584CS Utrecht, The Netherlands;
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12
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Liquori A, Ibañez M, Sargas C, Sanz MÁ, Barragán E, Cervera J. Acute Promyelocytic Leukemia: A Constellation of Molecular Events around a Single PML-RARA Fusion Gene. Cancers (Basel) 2020; 12:cancers12030624. [PMID: 32182684 PMCID: PMC7139833 DOI: 10.3390/cancers12030624] [Citation(s) in RCA: 68] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 02/27/2020] [Accepted: 03/05/2020] [Indexed: 12/11/2022] Open
Abstract
Although acute promyelocytic leukemia (APL) is one of the most characterized forms of acute myeloid leukemia (AML), the molecular mechanisms involved in the development and progression of this disease are still a matter of study. APL is defined by the PML-RARA rearrangement as a consequence of the translocation t(15;17)(q24;q21). However, this abnormality alone is not able to trigger the whole leukemic phenotype and secondary cooperating events might contribute to APL pathogenesis. Additional somatic mutations are known to occur recurrently in several genes, such as FLT3, WT1, NRAS and KRAS, whereas mutations in other common AML genes are rarely detected, resulting in a different molecular profile compared to other AML subtypes. How this mutational spectrum, including point mutations in the PML-RARA fusion gene, could contribute to the 10%–15% of relapsed or resistant APL patients is still unknown. Moreover, due to the uncertain impact of additional mutations on prognosis, the identification of the APL-specific genetic lesion is still the only method recommended in the routine evaluation/screening at diagnosis and for minimal residual disease (MRD) assessment. However, the gene expression profile of genes, such as ID1, BAALC, ERG, and KMT2E, once combined with the molecular events, might improve future prognostic models, allowing us to predict clinical outcomes and to categorize APL patients in different risk subsets, as recently reported. In this review, we will focus on the molecular characterization of APL patients at diagnosis, relapse and resistance, in both children and adults. We will also describe different standardized molecular approaches to study MRD, including those recently developed. Finally, we will discuss how novel molecular findings can improve the management of this disease.
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Affiliation(s)
- Alessandro Liquori
- Accredited Research Group in Hematology and Hemotherapy, Instituto de Investigación Sanitaria La Fe, 46026 Valencia, Spain; (A.L.); (C.S.)
| | - Mariam Ibañez
- Department of Hematology, Hospital Universitario y Politécnico La Fe, 46026 Valencia, Spain; (M.I.); (M.Á.S.); (E.B.)
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), 28029 Madrid, Spain
| | - Claudia Sargas
- Accredited Research Group in Hematology and Hemotherapy, Instituto de Investigación Sanitaria La Fe, 46026 Valencia, Spain; (A.L.); (C.S.)
| | - Miguel Ángel Sanz
- Department of Hematology, Hospital Universitario y Politécnico La Fe, 46026 Valencia, Spain; (M.I.); (M.Á.S.); (E.B.)
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), 28029 Madrid, Spain
| | - Eva Barragán
- Department of Hematology, Hospital Universitario y Politécnico La Fe, 46026 Valencia, Spain; (M.I.); (M.Á.S.); (E.B.)
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), 28029 Madrid, Spain
| | - José Cervera
- Department of Hematology, Hospital Universitario y Politécnico La Fe, 46026 Valencia, Spain; (M.I.); (M.Á.S.); (E.B.)
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), 28029 Madrid, Spain
- Correspondence:
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13
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RUNX1 mutations enhance self-renewal and block granulocytic differentiation in human in vitro models and primary AMLs. Blood Adv 2020; 3:320-332. [PMID: 30709863 DOI: 10.1182/bloodadvances.2018024422] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Accepted: 12/24/2018] [Indexed: 12/21/2022] Open
Abstract
To unravel molecular mechanisms by which Runt-related transcription factor 1 (RUNX1) mutations contribute to leukemic transformation, we introduced the RUNX1-S291fs300X mutation in human CD34+ stem/progenitor cells and in human induced pluripotent stem cells (iPSCs). In both models, RUNX1mut overexpression strongly impaired myeloid commitment. Instead, self-renewal was enhanced, as shown, by increased long-term culture-initiating cell frequencies and enhanced colony-forming cell replating capacity. Long-term suspension cultures with RUNX1mut-transduced cord blood (CB) CD34+ cells continued for more than 100 days, during which the cells displayed an immature granulocyte-macrophage progenitor-like CD34+/CD123+/CD45RA+ phenotype. The CD34+/CD38- hematopoietic stem cell (HSC) population most likely acted as cell of origin, as HSCs provided the best long-term proliferative potential on overexpression of RUNX1mut. CEBPA expression was reduced in RUNX1mut cells, and reexpression of CEBPA partly restored differentiation. RNA-seq analysis on CB/iPSC systems and on primary patient samples confirmed that RUNX1 mutations induce a myeloid differentiation block, and that a common set of RUNX1mut-upregulated target genes was strongly enriched for gene ontology terms associated with nucleosome assembly and chromatin structure. Interestingly, in comparison with AML1-ETO binding in acute myeloid leukemias (AMLs), we found significantly distinct genomic distribution and differential expression for RUNX1mut of genes such as TCF4, MEIS1, and HMGA2 that may potentially contribute to the underlying difference in clinical outcomes between RUNX1mut and AML1-ETO patients. In conclusion, RUNX1mut appears to induce a specific transcriptional program that contributes to leukemic transformation.
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14
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Benedetti R, Dell’Aversana C, De Marchi T, Rotili D, Liu NQ, Novakovic B, Boccella S, Di Maro S, Cosconati S, Baldi A, Niméus E, Schultz J, Höglund U, Maione S, Papulino C, Chianese U, Iovino F, Federico A, Mai A, Stunnenberg HG, Nebbioso A, Altucci L. Inhibition of Histone Demethylases LSD1 and UTX Regulates ERα Signaling in Breast Cancer. Cancers (Basel) 2019; 11:cancers11122027. [PMID: 31888209 PMCID: PMC6966629 DOI: 10.3390/cancers11122027] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Revised: 12/09/2019] [Accepted: 12/11/2019] [Indexed: 02/06/2023] Open
Abstract
In breast cancer, Lysine-specific demethylase-1 (LSD1) and other lysine demethylases (KDMs), such as Lysine-specific demethylase 6A also known as Ubiquitously transcribed tetratricopeptide repeat, X chromosome (UTX), are co-expressed and co-localize with estrogen receptors (ERs), suggesting the potential use of hybrid (epi)molecules to target histone methylation and therefore regulate/redirect hormone receptor signaling. Here, we report on the biological activity of a dual-KDM inhibitor (MC3324), obtained by coupling the chemical properties of tranylcypromine, a known LSD1 inhibitor, with the 2OG competitive moiety developed for JmjC inhibition. MC3324 displays unique features not exhibited by the single moieties and well-characterized mono-pharmacological inhibitors. Inhibiting LSD1 and UTX, MC3324 induces significant growth arrest and apoptosis in hormone-responsive breast cancer model accompanied by a robust increase in H3K4me2 and H3K27me3. MC3324 down-regulates ERα in breast cancer at both transcriptional and non-transcriptional levels, mimicking the action of a selective endocrine receptor disruptor. MC3324 alters the histone methylation of ERα-regulated promoters, thereby affecting the transcription of genes involved in cell surveillance, hormone response, and death. MC3324 reduces cell proliferation in ex vivo breast cancers, as well as in breast models with acquired resistance to endocrine therapies. Similarly, MC3324 displays tumor-selective potential in vivo, in both xenograft mice and chicken embryo models, with no toxicity and good oral efficacy. This epigenetic multi-target approach is effective and may overcome potential mechanism(s) of resistance in breast cancer.
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Affiliation(s)
- Rosaria Benedetti
- Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, 80138 Naples, Italy; (C.D.); (C.P.); (U.C.); (A.N.)
- Correspondence: (R.B.); (L.A.); Tel.: +39-081-5667564 (R.B.); +39-081-5667569 (L.A.)
| | - Carmela Dell’Aversana
- Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, 80138 Naples, Italy; (C.D.); (C.P.); (U.C.); (A.N.)
- Institute Experimental Endocrinology and Oncology “Gaetano Salvatore” (IEOS)-National Research Council (CNR) Via Sergio Pansini, 5-80131 Napoli, Italy
| | - Tommaso De Marchi
- Department of Oncology and Pathology, Lund University, SE-221 00 Lund, Sweden; (T.D.M.); (E.N.)
| | - Dante Rotili
- Department of Drug Chemistry and Technologies, Sapienza University of Rome, 00185 Rome, Italy; (D.R.); (A.M.)
| | - Ning Qing Liu
- Department of Molecular Biology, Radboud University, 6500 HB Nijmegen, The Netherlands; (N.Q.L.); (H.G.S.)
| | - Boris Novakovic
- Murdoch Children’s Research Institute and Department of Paediatrics, University of Melbourne, Melbourne, Parkville Victoria 3052, Australia;
| | - Serena Boccella
- Department of Experimental Medicine, Section of Pharmacology “L. Donatelli”, University of Campania “Luigi Vanvitelli”, 80138 Naples, Italy; (S.B.); (S.M.)
| | - Salvatore Di Maro
- Dipartimento di Scienze e Tecnologie Ambientali Biologiche e Farmaceutiche, University of Campania ’Luigi Vanvitelli’, 81100 Caserta, Italy; (S.D.M.); (S.C.); (A.B.)
| | - Sandro Cosconati
- Dipartimento di Scienze e Tecnologie Ambientali Biologiche e Farmaceutiche, University of Campania ’Luigi Vanvitelli’, 81100 Caserta, Italy; (S.D.M.); (S.C.); (A.B.)
| | - Alfonso Baldi
- Dipartimento di Scienze e Tecnologie Ambientali Biologiche e Farmaceutiche, University of Campania ’Luigi Vanvitelli’, 81100 Caserta, Italy; (S.D.M.); (S.C.); (A.B.)
| | - Emma Niméus
- Department of Oncology and Pathology, Lund University, SE-221 00 Lund, Sweden; (T.D.M.); (E.N.)
- Department of Surgery, Skånes University Hospital, 222 29 Lund, Sweden
| | - Johan Schultz
- Kancera AB, Banvaktsvagen 22, SE-17148 Solna, Sweden;
| | - Urban Höglund
- Adlego Biomedical AB, P.O. Box 42, SE-751 03 Uppsala, Sweden;
| | - Sabatino Maione
- Department of Experimental Medicine, Section of Pharmacology “L. Donatelli”, University of Campania “Luigi Vanvitelli”, 80138 Naples, Italy; (S.B.); (S.M.)
| | - Chiara Papulino
- Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, 80138 Naples, Italy; (C.D.); (C.P.); (U.C.); (A.N.)
| | - Ugo Chianese
- Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, 80138 Naples, Italy; (C.D.); (C.P.); (U.C.); (A.N.)
| | - Francesco Iovino
- Department of Translational Medical Sciences, University of Campania “Luigi Vanvitelli”, Via L. De Crecchio 7, 80138 Naples, Italy;
| | - Antonio Federico
- Faculty of Medicine and Health Technology, Tampere University, 33100 Tampere, Finland;
| | - Antonello Mai
- Department of Drug Chemistry and Technologies, Sapienza University of Rome, 00185 Rome, Italy; (D.R.); (A.M.)
| | - Hendrik G. Stunnenberg
- Department of Molecular Biology, Radboud University, 6500 HB Nijmegen, The Netherlands; (N.Q.L.); (H.G.S.)
- Prinses Maxima Centrum, Heidelberglaan 25, 3584CS Utrecht, The Netherlands
| | - Angela Nebbioso
- Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, 80138 Naples, Italy; (C.D.); (C.P.); (U.C.); (A.N.)
| | - Lucia Altucci
- Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, 80138 Naples, Italy; (C.D.); (C.P.); (U.C.); (A.N.)
- Correspondence: (R.B.); (L.A.); Tel.: +39-081-5667564 (R.B.); +39-081-5667569 (L.A.)
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15
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Du Y, Li K, Wang X, Kaushik AC, Junaid M, Wei D. Identification of chlorprothixene as a potential drug that induces apoptosis and autophagic cell death in acute myeloid leukemia cells. FEBS J 2019; 287:1645-1665. [PMID: 31625692 DOI: 10.1111/febs.15102] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Revised: 07/16/2019] [Accepted: 10/16/2019] [Indexed: 01/07/2023]
Abstract
Although acute myeloid leukemia (AML) is a highly heterogeneous malignance, the common molecular mechanisms shared by different AML subtypes play critical roles in AML development. It is possible to identify new drugs that are effective for various AML subtypes based on the common molecular mechanisms. Therefore, we developed a hypothesis-driven bioinformatic drug screening framework by integrating multiple omics data. In this study, we identified that chlorprothixene, a dopamine receptor antagonist, could effectively inhibit growth of AML cells from different subtypes. RNA-seq analysis suggested that chlorprothixene perturbed a series of crucial biological processes such as cell cycle, apoptosis, and autophagy in AML cells. Further investigations indicated that chlorprothixene could induce both apoptosis and autophagy in AML cells, and apoptosis and autophagy could act as partners to induce cell death cooperatively. Remarkably, chlorprothixene was found to inhibit tumor growth and induce in situ leukemic cell apoptosis in the murine xenograft model. Furthermore, chlorprothixene treatment could reduce the level of oncofusion proteins PML-RARα and AML1-ETO, thus elevate the expression of apoptosis-related genes, and lead to AML cell death. Our results provided new insights for drug repositioning of AML therapy and confirmed that chlorprothixene might be a potential candidate for treatment of different subtypes of AML by reducing expression of oncofusion proteins. DATABASE: RNA-seq data are available in GEO database under the accession number GSE124316.
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Affiliation(s)
- Yuxin Du
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, China.,State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology, Rui-Jin Hospital, Shanghai Jiao Tong University, China
| | - Kening Li
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, China.,State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology, Rui-Jin Hospital, Shanghai Jiao Tong University, China
| | - Xiangeng Wang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, China
| | - Aman Chandra Kaushik
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, China
| | - Muhammad Junaid
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, China
| | - Dongqing Wei
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, China
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16
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Wang X, Fan H, Xu C, Jiang G, Wang H, Zhang J. KDM3B suppresses APL progression by restricting chromatin accessibility and facilitating the ATRA-mediated degradation of PML/RARα. Cancer Cell Int 2019; 19:256. [PMID: 31592194 PMCID: PMC6778369 DOI: 10.1186/s12935-019-0979-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Accepted: 09/26/2019] [Indexed: 12/01/2022] Open
Abstract
Background A hallmark of acute promyelocytic leukemia (APL) is the expression of PML/RARα fusion protein. Treatment with all-trans retinoic acid (ATRA) results in the terminal differentiation of neutrophil granulocytes. However, the underlying mechanisms remain largely unknown. Here, we identify and elucidate a novel differentiation-suppressive model of APL involving the histone demethylase KDM3B, which has been identified as a suppressor of the tumor genes involved in hematopoietic malignancies. Methods First, we established a KDM3B knockdown NB4 cell model to determine the functional characteristics of KDM3B by cell proliferation assay and flow cytometry. Then, we performed ChIP-seq and ATAC-seq to search for potential relationships among KDM3B, histone modification (H3K9me1/me2) and the chromatin state. Finally, molecular biological techniques and a multi-omics analysis were used to explore the role of KDM3B in differentiation of the leukemia cells after ATRA treatment. Results We found that knocking down KDM3B contributed to the growth of NB4 APL cells via the promotion of cell-cycle progression and blocked granulocytic differentiation. Through global and molecular approaches, we provided futher evidence that knocking down KDM3B altered the global distribution of H3K9me1/me2 and increased the chromatin accessibility. Moreover, knocking down KDM3B inhibited the ATRA-induced degradation of the PML/RARα oncoprotein. Conclusion Our study suggested that KDM3B was able to inhibit APL progression by maintaining chromatin in a compact state and facilitating the ATRA-mediated degradation of PML/RARα. Taken together, the results show that KDM3B may be an alternative target for the treatment regimens and the targeted therapy for APL by sustaining the function of PML/RARα fusion protein.
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Affiliation(s)
- Xinrui Wang
- 1State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology, Rui-Jin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025 China
| | - Huiyong Fan
- 1State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology, Rui-Jin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025 China
| | - Congling Xu
- 1State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology, Rui-Jin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025 China
| | - Guojuan Jiang
- 1State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology, Rui-Jin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025 China
| | - Haiwei Wang
- 2Institute of Health Sciences, Shanghai Institutes for Biological Sciences and Graduate School, Chinese Academy of Sciences, Shanghai, 200025 China
| | - Ji Zhang
- 1State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology, Rui-Jin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025 China
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17
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Aberrant DNA Methylation in Acute Myeloid Leukemia and Its Clinical Implications. Int J Mol Sci 2019; 20:ijms20184576. [PMID: 31527484 PMCID: PMC6770227 DOI: 10.3390/ijms20184576] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Revised: 08/31/2019] [Accepted: 09/10/2019] [Indexed: 12/19/2022] Open
Abstract
Acute myeloid leukemia (AML) is a heterogeneous disease that is characterized by distinct cytogenetic or genetic abnormalities. Recent discoveries in cancer epigenetics demonstrated a critical role of epigenetic dysregulation in AML pathogenesis. Unlike genetic alterations, the reversible nature of epigenetic modifications is therapeutically attractive in cancer therapy. DNA methylation is an epigenetic modification that regulates gene expression and plays a pivotal role in mammalian development including hematopoiesis. DNA methyltransferases (DNMTs) and Ten-eleven-translocation (TET) dioxygenases are responsible for the dynamics of DNA methylation. Genetic alterations of DNMTs or TETs disrupt normal hematopoiesis and subsequently result in hematological malignancies. Emerging evidence reveals that the dysregulation of DNA methylation is a key event for AML initiation and progression. Importantly, aberrant DNA methylation is regarded as a hallmark of AML, which is heralded as a powerful epigenetic marker in early diagnosis, prognostic prediction, and therapeutic decision-making. In this review, we summarize the current knowledge of DNA methylation in normal hematopoiesis and AML pathogenesis. We also discuss the clinical implications of DNA methylation and the current therapeutic strategies of targeting DNA methylation in AML therapy.
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18
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Franzese O, Minotti L, Aguiari G, Corrà F, Cervellati C, Ferrari C, Volinia S, Bergamini CM, Bianchi N. Involvement of non-coding RNAs and transcription factors in the induction of Transglutaminase isoforms by ATRA. Amino Acids 2019; 51:1273-1288. [PMID: 31440819 DOI: 10.1007/s00726-019-02766-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Accepted: 07/24/2019] [Indexed: 01/02/2023]
Abstract
The multifunctional protein Transglutaminase type 2, is associated with cancer epithelial mesenchymal transition, invasiveness, stemness and drugs resistance. Several variant isoforms and non-coding RNAs are present in cancer and this report explored the expression of these transcripts of the TGM2 gene in cancer cell lines after induction with all-trans retinoic acid. The expression of truncated variants along with two long non-coding RNAs, was demonstrated. One of these is coded from the first intron and the Last Exon Variant is constituted by a sequence corresponding to the last three exons and the 3'UTR. Analysis of ChIP-seq data, from ENCODE project, highlighted factors interacting with intronic sequences, which could interfere with the progression of RNApol II at checkpoints, during the elongation process. Some relevant transcription factors, bound in an ATRA-dependent way, were found by RNA immunoprecipitation, notably GATA3 mainly enriched to Last Exon Variant non-coding RNA. The involvement of NMD in the regulation of the ratio among these transcripts was observed, as the prevalent recovering of Last Exon Variant to phUPF1-complexes, with decrease of the binding towards other selective targets. This study contributes to identify molecular mechanisms regulating the ratio among the variants and improves the knowledge about regulatory roles of the non-coding RNAs of the TGM2 gene.
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Affiliation(s)
- Ornella Franzese
- Department of Systems Medicine, School of Medicine, University of Rome Tor Vergata, Rome, Italy
| | - Linda Minotti
- Department of Morphology, Surgery and Experimental Medicine, University of Ferrara, Ferrara, Italy
| | - Gianluca Aguiari
- Department of Biomedical Sciences and Specialist Surgery, University of Ferrara, Via Luigi Borsari, 46, 44121, Ferrara, Italy
| | - Fabio Corrà
- Department of Morphology, Surgery and Experimental Medicine, University of Ferrara, Ferrara, Italy
| | - Carlo Cervellati
- Department of Biomedical Sciences and Specialist Surgery, University of Ferrara, Via Luigi Borsari, 46, 44121, Ferrara, Italy
| | - Carlo Ferrari
- Department of Clinical and Molecular Sciences, Marche Polytechnic University, Ancona, Italy
| | - Stefano Volinia
- Department of Morphology, Surgery and Experimental Medicine, University of Ferrara, Ferrara, Italy
| | - Carlo M Bergamini
- Department of Biomedical Sciences and Specialist Surgery, University of Ferrara, Via Luigi Borsari, 46, 44121, Ferrara, Italy.
| | - Nicoletta Bianchi
- Department of Biomedical Sciences and Specialist Surgery, University of Ferrara, Via Luigi Borsari, 46, 44121, Ferrara, Italy.
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19
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Wu RJ, Zheng RJ, Huang YQ, Ma XD. [Chidamide combined with chemotherapy for treatment of therapy-related acute myeloid leukemia secondary to peripheral T-cell lymphoma: a case report and literatures review]. ZHONGHUA XUE YE XUE ZA ZHI = ZHONGHUA XUEYEXUE ZAZHI 2019; 40:685-687. [PMID: 31495139 PMCID: PMC7342885 DOI: 10.3760/cma.j.issn.0253-2727.2019.08.013] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Download PDF] [Subscribe] [Scholar Register] [Received: 11/25/2018] [Indexed: 01/15/2023]
Affiliation(s)
- R J Wu
- Department of Hematology, Zhangzhou Affiliated Hospital of Fujian Medical University, Zhangzhou 363000, China
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20
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Wang G, Tian Y, Hu Q, Xiao X, Chen S. PML/RARa blocks the differentiation and promotes the proliferation of acute promyelocytic leukemia through activating MYB expression by transcriptional and epigenetic regulation mechanisms. J Cell Biochem 2019; 120:1210-1220. [PMID: 30335887 DOI: 10.1002/jcb.27077] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2018] [Accepted: 04/26/2018] [Indexed: 01/24/2023]
Abstract
The promyelocytic leukemia (PML)/retinoic acid receptor-alpha (RARα) onco-fusion protein that is generated from t(15;17) chromosome translocation is crucial for the leukemogenesis of acute promyelocytic leukemia (APL) and is well documented as a transcriptional repressor. To understand the relationship between PML/RARα and the oncogene in the development of APL, we investigate the regulation mechanism of PML/RARα to MYB proto-oncogene and the role of this regulation on the proliferation and differentiation of APL cells. Reverse transcription-quantitative polymerase chain reaction (RT-qPCR) assays show that MYB expression was significantly higher in PML/RARα positive cell lines. Microarray data verify that the MYB expression was significantly higher in APL patient samples than in normal promyelocyte samples. Further expression analysis from RT-qPCR and microarray data verifies that the expression of MYB is upregulated by PML/RARα. Transcriptional factor binding analysis shows that MYB is directly bound by PML/RARα and its cofactors. Luciferase assays show that PML/RARα transactivated MYB promoter activity through the RARα binding site and the coexistence of CCAAT enhancer binding protein ε. We also find that PML/RARα increases the acetylation level of the promoter region of MYB. Further evidence demonstrates that PML/RARα regulates MYB expression through long-range interaction. Functionally, PML/RARα increases the cell proliferation and blocks the differentiation through activating MYB expression. Collectively, this study uncovers a novel mechanism of PML/RARα-mediated transcriptional activation and enriches our knowledge of the onco-fusion protein-mediated transcription activation.
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Affiliation(s)
- Genjie Wang
- Department of Hematology, The First People's Hospital of Shangqiu, Shangqiu, China
| | - Ying Tian
- Department of Hematology, The First People's Hospital of Shangqiu, Shangqiu, China
| | - Qingzhu Hu
- Department of Hematology, The First People's Hospital of Shangqiu, Shangqiu, China
| | - Xichun Xiao
- Department of Hematology, The First People's Hospital of Shangqiu, Shangqiu, China
| | - Shuxia Chen
- Department of Hematology, The First People's Hospital of Shangqiu, Shangqiu, China
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21
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van der Kouwe E, Staber PB. RUNX1-ETO: Attacking the Epigenome for Genomic Instable Leukemia. Int J Mol Sci 2019; 20:E350. [PMID: 30654457 PMCID: PMC6358732 DOI: 10.3390/ijms20020350] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Revised: 01/09/2019] [Accepted: 01/11/2019] [Indexed: 12/29/2022] Open
Abstract
Oncogenic fusion protein RUNX1-ETO is the product of the t(8;21) translocation, responsible for the most common cytogenetic subtype of acute myeloid leukemia. RUNX1, a critical transcription factor in hematopoietic development, is fused with almost the entire ETO sequence with the ability to recruit a wide range of repressors. Past efforts in providing a comprehensive picture of the genome-wide localization and the target genes of RUNX1-ETO have been inconclusive in understanding the underlying mechanism by which it deregulates native RUNX1. In this review; we dissect the current data on the epigenetic impact of RUNX1 and RUNX1-ETO. Both share similarities however, in recent years, research focused on epigenetic factors to explain their differences. RUNX1-ETO impairs DNA repair mechanisms which compromises genomic stability and favors a mutator phenotype. Among an increasing pool of mutated factors, regulators of DNA methylation are frequently found in t(8;21) AML. Together with the alteration of both, histone markers and distal enhancer regulation, RUNX1-ETO might specifically disrupt normal chromatin structure. Epigenetic studies on the fusion protein uncovered new mechanisms contributing to leukemogenesis and hopefully will translate into clinical applications.
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Affiliation(s)
- Emiel van der Kouwe
- Department of Internal Medicine I, Division of Hematology and Hemostaseology, Medical University of Vienna, 1090 Vienna, Austria.
| | - Philipp Bernhard Staber
- Department of Internal Medicine I, Division of Hematology and Hemostaseology, Medical University of Vienna, 1090 Vienna, Austria.
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22
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Zhang S, Zhou W, Li Y, Yu S, Xue M, Qiao Y, Jian J, Liu B, Wang D. Co-expression of AML1-ETO and PML-RARa following treatment of de novo acute myeloid leukemia with AML1-ETO. Leuk Lymphoma 2018; 60:1316-1319. [PMID: 30328750 DOI: 10.1080/10428194.2018.1520991] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Affiliation(s)
- Shuling Zhang
- The First Clinical Medical College, Lanzhou University, Lanzhou, Gansu, China
| | - Wei Zhou
- Respiratory medicine department, Beijing Geriatric Hospital, Beijing, China
| | - Yanchun Li
- Department of Hematology, Shanxi Provincial People’s Hospital, Xian, Shanxi, China
| | - Shuili Yu
- People’s Hospital of Jingyuan County, Jingyuan, Baiyin, Gansu, China
| | - Mingming Xue
- The First Clinical Medical College, Lanzhou University, Lanzhou, Gansu, China
| | - Yanhong Qiao
- The First Clinical Medical College, Lanzhou University, Lanzhou, Gansu, China
| | - Jinli Jian
- The First Clinical Medical College, Lanzhou University, Lanzhou, Gansu, China
| | - Bei Liu
- The First Clinical Medical College, Lanzhou University, Lanzhou, Gansu, China
- Department of Hematology, The First Affiliated Hospital, Lanzhou University, Lanzhou, Gansu, China
| | - Degui Wang
- Department of Anatomy and Histology, Lanzhou University, School of Basic Medical Sciences, Lanzhou, China
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23
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Combined HAT/EZH2 modulation leads to cancer-selective cell death. Oncotarget 2018; 9:25630-25646. [PMID: 29876013 PMCID: PMC5986654 DOI: 10.18632/oncotarget.25428] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Accepted: 05/02/2018] [Indexed: 12/20/2022] Open
Abstract
Epigenetic alterations have been associated with both pathogenesis and progression of cancer. By screening of library compounds, we identified a novel hybrid epi-drug MC2884, a HAT/EZH2 inhibitor, able to induce bona fide cancer-selective cell death in both solid and hematological cancers in vitro, ex vivo and in vivo xenograft models. Anticancer action was due to an epigenome modulation by H3K27me3, H3K27ac, H3K9/14ac decrease, and to caspase-dependent apoptosis induction. MC2884 triggered mitochondrial pathway apoptosis by up-regulation of cleaved-BID, and strong down-regulation of BCL2. Even aggressive models of cancer, such as p53-/- or TET2-/- cells, responded to MC2884, suggesting MC2884 therapeutic potential also for the therapy of TP53 or TET2-deficient human cancers. MC2884 induced massive apoptosis in ex vivo human primary leukemia blasts with poor prognosis in vivo, by targeting BCL2 expression. MC2884-treatment reduced acetylation of the BCL2 promoter at higher level than combined p300 and EZH2 inhibition. This suggests a key role for BCL-2 reduction in potentiating responsiveness, also in combination therapy with BCL2 inhibitors. Finally, we identified both the mechanism of MC2884 action as well as a potential therapeutic scheme of its use. Altogether, this provides proof of concept for the use of epi-drugs coupled with epigenome analyses to 'personalize' precision medicine.
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24
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Singh AA, Petraglia F, Nebbioso A, Yi G, Conte M, Valente S, Mandoli A, Scisciola L, Lindeboom R, Kerstens H, Janssen-Megens EM, Pourfarzad F, Habibi E, Berentsen K, Kim B, Logie C, Heath S, Wierenga ATJ, Clarke L, Flicek P, Jansen JH, Kuijpers T, Yaspo ML, Valle VD, Bernard O, Gut I, Vellenga E, Stunnenberg HG, Mai A, Altucci L, Martens JHA. Multi-omics profiling reveals a distinctive epigenome signature for high-risk acute promyelocytic leukemia. Oncotarget 2018; 9:25647-25660. [PMID: 29876014 PMCID: PMC5986653 DOI: 10.18632/oncotarget.25429] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Accepted: 05/01/2018] [Indexed: 12/30/2022] Open
Abstract
Epigenomic alterations have been associated with both pathogenesis and progression of cancer. Here, we analyzed the epigenome of two high-risk APL (hrAPL) patients and compared it to non-high-risk APL cases. Despite the lack of common genetic signatures, we found that human hrAPL blasts from patients with extremely poor prognosis display specific patterns of histone H3 acetylation, specifically hyperacetylation at a common set of enhancer regions. In addition, unique profiles of the repressive marks H3K27me3 and DNA methylation were exposed in high-risk APLs. Epigenetic comparison with low/intermediate-risk APLs and AMLs revealed hrAPL-specific patterns of histone acetylation and DNA methylation, suggesting these could be further developed into markers for clinical identification. The epigenetic drug MC2884, a newly generated general HAT/EZH2 inhibitor, induces apoptosis of high-risk APL blasts and reshapes their epigenomes by targeting both active and repressive marks. Together, our analysis uncovers distinctive epigenome signatures of hrAPL patients, and provides proof of concept for use of epigenome profiling coupled to epigenetic drugs to ‘personalize’ precision medicine.
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Affiliation(s)
- Abhishek A Singh
- Department of Molecular Biology, Radboud University, Nijmegen, Netherlands
| | - Francesca Petraglia
- Dipartimento di Biochimica Biofisica e Patologia Generale, Università degli Studi della Campania Luigi Vanvitelli, Napoli, Italy
| | - Angela Nebbioso
- Dipartimento di Biochimica Biofisica e Patologia Generale, Università degli Studi della Campania Luigi Vanvitelli, Napoli, Italy
| | - Guoqiang Yi
- Department of Molecular Biology, Radboud University, Nijmegen, Netherlands
| | | | - Sergio Valente
- Dipartimento di Chimica e Tecnologie del Farmaco 'Sapienza' Università, Roma, Italy
| | - Amit Mandoli
- Department of Molecular Biology, Radboud University, Nijmegen, Netherlands
| | - Lucia Scisciola
- Dipartimento di Biochimica Biofisica e Patologia Generale, Università degli Studi della Campania Luigi Vanvitelli, Napoli, Italy
| | - Rik Lindeboom
- Department of Molecular Biology, Radboud University, Nijmegen, Netherlands
| | - Hinri Kerstens
- Department of Molecular Biology, Radboud University, Nijmegen, Netherlands
| | | | - Farzin Pourfarzad
- Department of Blood Cell Research, Sanquin Research and Landsteiner Laboratory, Academic Medical Center, University of Amsterdam, Amsterdam, Netherlands
| | - Ehsan Habibi
- Department of Molecular Biology, Radboud University, Nijmegen, Netherlands
| | - Kim Berentsen
- Department of Molecular Biology, Radboud University, Nijmegen, Netherlands
| | - Bowon Kim
- Department of Molecular Biology, Radboud University, Nijmegen, Netherlands
| | - Colin Logie
- Department of Molecular Biology, Radboud University, Nijmegen, Netherlands
| | - Simon Heath
- Centro Nacional de Análisis Genómico, Barcelona, Spain
| | - Albertus T J Wierenga
- Department of Hematology, University of Groningen and University Medical Center Groningen, Groningen, Netherlands
| | - Laura Clarke
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, United Kingdom
| | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, United Kingdom
| | - Joop H Jansen
- Department of Laboratory Medicine, Radboud UMC, Nijmegen, Netherlands
| | - Taco Kuijpers
- Department of Blood Cell Research, Sanquin Research and Landsteiner Laboratory, Academic Medical Center, University of Amsterdam, Amsterdam, Netherlands
| | | | - Veronique Della Valle
- INSERM U1170, Universtité Paris-Saclay, Institut Gustave Roussy, Equipe Labellisée Ligue Nationale Contre le Cancer (LNCC), Paris, France
| | - Olivier Bernard
- INSERM U1170, Universtité Paris-Saclay, Institut Gustave Roussy, Equipe Labellisée Ligue Nationale Contre le Cancer (LNCC), Paris, France
| | - Ivo Gut
- Centro Nacional de Análisis Genómico, Barcelona, Spain
| | - Edo Vellenga
- Department of Hematology, University of Groningen and University Medical Center Groningen, Groningen, Netherlands
| | | | - Antonello Mai
- Dipartimento di Chimica e Tecnologie del Farmaco 'Sapienza' Università, Roma, Italy.,Pasteur Institute, Cenci-Bolognetti Foundation, Sapienza University of Rome, Roma, Italy
| | - Lucia Altucci
- Dipartimento di Biochimica Biofisica e Patologia Generale, Università degli Studi della Campania Luigi Vanvitelli, Napoli, Italy
| | - Joost H A Martens
- Department of Molecular Biology, Radboud University, Nijmegen, Netherlands.,Dipartimento di Biochimica Biofisica e Patologia Generale, Università degli Studi della Campania Luigi Vanvitelli, Napoli, Italy
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25
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Methylation-associated silencing of BASP1 contributes to leukemogenesis in t(8;21) acute myeloid leukemia. Exp Mol Med 2018; 50:1-8. [PMID: 29674693 PMCID: PMC5938046 DOI: 10.1038/s12276-018-0067-4] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Revised: 12/06/2017] [Accepted: 01/02/2018] [Indexed: 12/20/2022] Open
Abstract
The AML1-ETO fusion protein (A/E), which results from the t(8;21) translocation, is considered to be a leukemia-initiating event. Identifying the mechanisms underlying the oncogenic activity of A/E remains a major challenge. In this study, we identified a specific down-regulation of brain acid-soluble protein 1 (BASP1) in t(8;21) acute myeloid leukemia (AML). A/E recognized AML1-binding sites and recruited DNA methyltransferase 3a (DNMT3a) to the BASP1 promoter sequence, which triggered DNA methylation-mediated silencing of BASP1. Ectopic expression of BASP1 inhibited proliferation and the colony-forming ability of A/E-positive AML cell lines and led to apoptosis and cell cycle arrest. The DNMT inhibitor decitabine up-regulated the expression of BASP1 in A/E-positive AML cell lines. In conclusion, our data suggest that BASP1 silencing via promoter methylation may be involved in A/E-mediated leukemogenesis and that BASP1 targeting may be an actionable therapeutic strategy in t(8;21) AML. A chromosomal rearrangement commonly observed in certain leukemias selectively inactivates a gene that otherwise thwarts cancerous growth. Between 7 and 12% of acute myeloid leukemia cases exhibit a dramatic alteration in chromosomal structure that results in the production of an abnormal fusion protein. Researchers led by Li Yu at the General Hospital of Shenzen University in China have learned that this protein promotes disease progression by switching off an important tumor suppressor. Yu and colleagues showed that it binds a genomic sequence that regulates the gene encoding a second protein called BASP1, dramatically reducing its production. This gene silencing facilitates tumor growth. Chemicals that reactivated BASP1 production slowed proliferation and initiated ‘self-destruct’ mechanisms in leukemia cells. These findings suggest that BASP1-oriented therapies could offer a fruitful avenue of treatment for some patients.
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26
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Singh AA, Mandoli A, Prange KHM, Laakso M, Martens JHA. AML associated oncofusion proteins PML-RARA, AML1-ETO and CBFB-MYH11 target RUNX/ETS-factor binding sites to modulate H3ac levels and drive leukemogenesis. Oncotarget 2017; 8:12855-12865. [PMID: 28030795 PMCID: PMC5355061 DOI: 10.18632/oncotarget.14150] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Accepted: 11/21/2016] [Indexed: 12/11/2022] Open
Abstract
Chromosomal translocations are one of the hallmarks of acute myeloid leukemia (AML), often leading to gene fusions and expression of an oncofusion protein. Over recent years it has become clear that most of the AML associated oncofusion proteins molecularly adopt distinct mechanisms for inducing leukemogenesis. Still these unique molecular properties of the chimeric proteins converge and give rise to a common pathogenic molecular mechanism. In the present study we compared genome-wide DNA binding and transcriptome data associated with AML1-ETO, CBFB-MYH11 and PML-RARA oncofusion protein expression to identify unique and common features. Our analyses revealed targeting of oncofusion binding sites to RUNX1 and ETS-factor occupied genomic regions. In addition, it revealed a highly comparable global histone acetylation pattern, similar expression of common target genes and related enrichment of several biological pathways critical for maintenance of AML, suggesting oncofusion proteins deregulate common gene programs despite their distinct binding signatures and mechanisms of action.
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Affiliation(s)
- Abhishek A Singh
- Radboud University, Department of Molecular Biology, Faculty of Science, Nijmegen Centre for Molecular Life Sciences, 6500 HB Nijmegen, The Netherlands
| | - Amit Mandoli
- Radboud University, Department of Molecular Biology, Faculty of Science, Nijmegen Centre for Molecular Life Sciences, 6500 HB Nijmegen, The Netherlands
| | - Koen H M Prange
- Radboud University, Department of Molecular Biology, Faculty of Science, Nijmegen Centre for Molecular Life Sciences, 6500 HB Nijmegen, The Netherlands
| | - Marko Laakso
- Genome Scale Biology Research Program, Research Programs Unit, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Joost H A Martens
- Radboud University, Department of Molecular Biology, Faculty of Science, Nijmegen Centre for Molecular Life Sciences, 6500 HB Nijmegen, The Netherlands
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27
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Lin S, Mulloy JC, Goyama S. RUNX1-ETO Leukemia. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 962:151-173. [PMID: 28299657 DOI: 10.1007/978-981-10-3233-2_11] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
AML1-ETO leukemia is the most common cytogenetic subtype of acute myeloid leukemia, defined by the presence of t(8;21). Remarkable progress has been achieved in understanding the molecular pathogenesis of AML1-ETO leukemia. Proteomic surveies have shown that AML-ETO forms a stable complex with several transcription factors, including E proteins. Genome-wide transcriptome and ChIP-seq analyses have revealed the genes directly regulated by AML1-ETO, such as CEBPA. Several lines of evidence suggest that AML1-ETO suppresses endogenous DNA repair in cells to promote mutagenesis, which facilitates acquisition of cooperating secondary events. Furthermore, it has become increasingly apparent that a delicate balance of AML1-ETO and native AML1 is important to sustain the malignant cell phenotype. Translation of these findings into the clinical setting is just beginning.
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Affiliation(s)
- Shan Lin
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - James C Mulloy
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Susumu Goyama
- Division of Cellular Therapy, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan.
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28
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Quin JE, Bujila I, Chérif M, Sanou GS, Qu Y, Vafa Homann M, Rolicka A, Sirima SB, O'Connell MA, Lennartsson A, Troye-Blomberg M, Nebie I, Östlund Farrants AK. Major transcriptional changes observed in the Fulani, an ethnic group less susceptible to malaria. eLife 2017; 6:29156. [PMID: 28923166 PMCID: PMC5629023 DOI: 10.7554/elife.29156] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Accepted: 09/05/2017] [Indexed: 12/12/2022] Open
Abstract
The Fulani ethnic group has relatively better protection from Plasmodium falciparum malaria, as reflected by fewer symptomatic cases of malaria, lower infection rates, and lower parasite densities compared to sympatric ethnic groups. However, the basis for this lower susceptibility to malaria by the Fulani is unknown. The incidence of classic malaria resistance genes are lower in the Fulani than in other sympatric ethnic populations, and targeted SNP analyses of other candidate genes involved in the immune response to malaria have not been able to account for the observed difference in the Fulani susceptibility to P.falciparum. Therefore, we have performed a pilot study to examine global transcription and DNA methylation patterns in specific immune cell populations in the Fulani to elucidate the mechanisms that confer the lower susceptibility to P.falciparum malaria. When we compared uninfected and infected Fulani individuals, in contrast to uninfected and infected individuals from the sympatric ethnic group Mossi, we observed a key difference: a strong transcriptional response was only detected in the monocyte fraction of the Fulani, where over 1000 genes were significantly differentially expressed upon P.falciparum infection.
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Affiliation(s)
- Jaclyn E Quin
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Ioana Bujila
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Mariama Chérif
- Centre National de Recherche et de Formation sur le Paludisme, Ouagadougou, Burkina Faso.,Université Polytechnique de Bobo-Dioulasso, Bobo-Dioulasso, Burkina Faso
| | - Guillaume S Sanou
- Centre National de Recherche et de Formation sur le Paludisme, Ouagadougou, Burkina Faso
| | - Ying Qu
- Department of Biosciences and Nutrition, Karolinska Institute, Stockholm, Sweden
| | - Manijeh Vafa Homann
- Unit of Infectious Diseases, Department of Medicine, Karolinska Institute, Stockholm, Sweden
| | - Anna Rolicka
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Sodiomon B Sirima
- Centre National de Recherche et de Formation sur le Paludisme, Ouagadougou, Burkina Faso
| | | | - Andreas Lennartsson
- Department of Biosciences and Nutrition, Karolinska Institute, Stockholm, Sweden
| | - Marita Troye-Blomberg
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Issa Nebie
- Centre National de Recherche et de Formation sur le Paludisme, Ouagadougou, Burkina Faso
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29
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Dirks RAM, Stunnenberg HG, Marks H. Genome-wide epigenomic profiling for biomarker discovery. Clin Epigenetics 2016; 8:122. [PMID: 27895806 PMCID: PMC5117701 DOI: 10.1186/s13148-016-0284-4] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2016] [Accepted: 11/02/2016] [Indexed: 12/24/2022] Open
Abstract
A myriad of diseases is caused or characterized by alteration of epigenetic patterns, including changes in DNA methylation, post-translational histone modifications, or chromatin structure. These changes of the epigenome represent a highly interesting layer of information for disease stratification and for personalized medicine. Traditionally, epigenomic profiling required large amounts of cells, which are rarely available with clinical samples. Also, the cellular heterogeneity complicates analysis when profiling clinical samples for unbiased genome-wide biomarker discovery. Recent years saw great progress in miniaturization of genome-wide epigenomic profiling, enabling large-scale epigenetic biomarker screens for disease diagnosis, prognosis, and stratification on patient-derived samples. All main genome-wide profiling technologies have now been scaled down and/or are compatible with single-cell readout, including: (i) Bisulfite sequencing to determine DNA methylation at base-pair resolution, (ii) ChIP-Seq to identify protein binding sites on the genome, (iii) DNaseI-Seq/ATAC-Seq to profile open chromatin, and (iv) 4C-Seq and HiC-Seq to determine the spatial organization of chromosomes. In this review we provide an overview of current genome-wide epigenomic profiling technologies and main technological advances that allowed miniaturization of these assays down to single-cell level. For each of these technologies we evaluate their application for future biomarker discovery. We will focus on (i) compatibility of these technologies with methods used for clinical sample preservation, including methods used by biobanks that store large numbers of patient samples, and (ii) automation of these technologies for robust sample preparation and increased throughput.
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Affiliation(s)
- René A M Dirks
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University, 6500HB Nijmegen, The Netherlands
| | - Hendrik G Stunnenberg
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University, 6500HB Nijmegen, The Netherlands
| | - Hendrik Marks
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University, 6500HB Nijmegen, The Netherlands
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30
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Zhou L, Wang Q, Chen X, Fu L, Zhang X, Wang L, Deng A, Li D, Liu J, Lv N, Wang L, Li Y, Liu D, Yu L, Dou L. AML1-ETO promotes SIRT1 expression to enhance leukemogenesis of t(8;21) acute myeloid leukemia. Exp Hematol 2016; 46:62-69. [PMID: 27725192 DOI: 10.1016/j.exphem.2016.09.013] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Revised: 09/21/2016] [Accepted: 09/30/2016] [Indexed: 10/20/2022]
Abstract
Recently, SIRT1 was found to play an important role in a variety of solid and hematologic malignancies. The expression and function of SIRT1 may differ completely depending on cell type and gene subtype, and it can act as a tumor suppressor or oncogene. We describe how SIRT1 mRNA and protein levels are overexpressed in t(8;21) AML cells. AML1-ETO triggers the activation of SIRT1 by binding at AML1 binding sites on the SIRT1 promoter. Pharmacologic targeting or RNAi-mediated inhibition of SIRT1 induces G1 arrest, apoptosis, and proliferation inhibition that is more sensitive in AML1-ETO-positive than AML1-ETO-negative cell lines. Our data suggest that targeting SIRT1 may be an attractive therapeutic strategy in t(8;21) AML.
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Affiliation(s)
- Lei Zhou
- Department of Hematology, Chinese PLA General Hospital, Beijing, China; Department of Hematology, No. 202 Hospital of PLA, Shenyang, China
| | - Qian Wang
- Department of Hematology, Chinese PLA General Hospital, Beijing, China; Department of Medical Oncology, Jinling Hospital, Medical School of Nanjing University, Nanjing, China
| | - Xiaosu Chen
- Department of Hematology, Chinese PLA General Hospital, Beijing, China; School of Medicine, Nankai University, Tianjin, China
| | - Lin Fu
- Department of Hematology and Lymphoma Research Center, Peking University Third Hospital, Beijing, China
| | - Xiaodong Zhang
- Department of Hematology, No. 202 Hospital of PLA, Shenyang, China
| | - Lijun Wang
- Department of Hematology, Chinese PLA General Hospital, Beijing, China
| | - Ailing Deng
- Department of Hematology, Chinese PLA General Hospital, Beijing, China
| | - Dandan Li
- Department of Hematology, Chinese PLA General Hospital, Beijing, China; Beijing Shijitan Hospital, Beijing, China
| | - Jing Liu
- Department of Hematology, Chinese PLA General Hospital, Beijing, China
| | - Na Lv
- Department of Hematology, Chinese PLA General Hospital, Beijing, China
| | - Lili Wang
- Department of Hematology, Chinese PLA General Hospital, Beijing, China
| | - Yonghui Li
- Department of Hematology, Chinese PLA General Hospital, Beijing, China
| | - Daihong Liu
- Department of Hematology, Chinese PLA General Hospital, Beijing, China
| | - Li Yu
- Department of Hematology, Chinese PLA General Hospital, Beijing, China.
| | - Liping Dou
- Department of Hematology, Chinese PLA General Hospital, Beijing, China.
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31
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Logie C, Stunnenberg HG. Epigenetic memory: A macrophage perspective. Semin Immunol 2016; 28:359-67. [DOI: 10.1016/j.smim.2016.06.003] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/09/2016] [Revised: 06/16/2016] [Accepted: 06/23/2016] [Indexed: 01/02/2023]
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32
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Abstract
Histone posttranslational modifications represent a versatile set of epigenetic marks involved not only in dynamic cellular processes, such as transcription and DNA repair, but also in the stable maintenance of repressive chromatin. In this article, we review many of the key and newly identified histone modifications known to be deregulated in cancer and how this impacts function. The latter part of the article addresses the challenges and current status of the epigenetic drug development process as it applies to cancer therapeutics.
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Affiliation(s)
- James E Audia
- Constellation Pharmaceuticals, Cambridge, Massachusetts 02142
| | - Robert M Campbell
- Eli Lilly and Company, Lilly Corporate Center, Indianapolis, Indiana 46285
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33
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Chen M, Zhu N, Liu X, Laurent B, Tang Z, Eng R, Shi Y, Armstrong SA, Roeder RG. JMJD1C is required for the survival of acute myeloid leukemia by functioning as a coactivator for key transcription factors. Genes Dev 2016; 29:2123-39. [PMID: 26494788 PMCID: PMC4617977 DOI: 10.1101/gad.267278.115] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
RUNX1-RUNX1T1 (formerly AML1-ETO), a transcription factor generated by the t(8;21) translocation in acute myeloid leukemia (AML), dictates a leukemic program by increasing self-renewal and inhibiting differentiation. Here we demonstrate that the histone demethylase JMJD1C functions as a coactivator for RUNX1-RUNX1T1 and is required for its transcriptional program. JMJD1C is directly recruited by RUNX1-RUNX1T1 to its target genes and regulates their expression by maintaining low H3K9 dimethyl (H3K9me2) levels. Analyses in JMJD1C knockout mice also establish a JMJD1C requirement for RUNX1-RUNX1T1's ability to increase proliferation. We also show a critical role for JMJD1C in the survival of multiple human AML cell lines, suggesting that it is required for leukemic programs in different AML cell types through its association with key transcription factors.
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Affiliation(s)
- Mo Chen
- Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, New York, New York 10065, USA
| | - Nan Zhu
- Human Oncology and Pathogenesis Program, Memorial Sloan-Kettering Cancer Center, New York, New York 10065, USA
| | - Xiaochuan Liu
- Department of Microbiology, Biochemistry, and Molecular Genetics, Rutgers University, Newark, New Jersey 07103, USA
| | - Benoit Laurent
- Division of Newborn Medicine, Epigenetics Program, Department of Medicine, Boston Children's Hospital, Boston, Massachusetts 02115, USA; Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Zhanyun Tang
- Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, New York, New York 10065, USA
| | - Rowena Eng
- Human Oncology and Pathogenesis Program, Memorial Sloan-Kettering Cancer Center, New York, New York 10065, USA
| | - Yang Shi
- Division of Newborn Medicine, Epigenetics Program, Department of Medicine, Boston Children's Hospital, Boston, Massachusetts 02115, USA; Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Scott A Armstrong
- Human Oncology and Pathogenesis Program, Memorial Sloan-Kettering Cancer Center, New York, New York 10065, USA
| | - Robert G Roeder
- Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, New York, New York 10065, USA
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Brettingham-Moore KH, Taberlay PC, Holloway AF. Interplay between Transcription Factors and the Epigenome: Insight from the Role of RUNX1 in Leukemia. Front Immunol 2015; 6:499. [PMID: 26483790 PMCID: PMC4586508 DOI: 10.3389/fimmu.2015.00499] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2015] [Accepted: 09/14/2015] [Indexed: 01/13/2023] Open
Abstract
The genome has the ability to respond in a precise and co-ordinated manner to cellular signals. It achieves this through the concerted actions of transcription factors and the chromatin platform, which are targets of the signaling pathways. Our understanding of the molecular mechanisms through which transcription factors and the chromatin landscape each control gene activity has expanded dramatically over recent years, and attention has now turned to understanding the complex, multifaceted interplay between these regulatory layers in normal and disease states. It has become apparent that transcription factors as well as the components and modifiers of the epigenetic machinery are frequent targets of genomic alterations in cancer cells. Through the study of these factors, we can gain unique insight into the dynamic interplay between transcription factors and the epigenome, and how their dysregulation leads to aberrant gene expression programs in cancer. Here, we will highlight how these factors normally co-operate to establish and maintain the transcriptional and epigenetic landscape of cells, and how this is reprogramed in cancer, focusing on the RUNX1 transcription factor and oncogenic derivative RUNX1–ETO in leukemia as paradigms of transcriptional and epigenetic reprograming.
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Affiliation(s)
| | - Phillippa C Taberlay
- Genomics and Epigenetics Program, The Garvan Institute of Medical Research , Sydney, NSW , Australia
| | - Adele F Holloway
- School of Medicine, University of Tasmania , Hobart, TAS , Australia
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35
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The oncofusion protein FUS-ERG targets key hematopoietic regulators and modulates the all-trans retinoic acid signaling pathway in t(16;21) acute myeloid leukemia. Oncogene 2015; 35:1965-76. [PMID: 26148230 PMCID: PMC4833872 DOI: 10.1038/onc.2015.261] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2014] [Revised: 04/28/2015] [Accepted: 06/05/2015] [Indexed: 01/08/2023]
Abstract
The ETS transcription factor ERG has been implicated as a major regulator of both normal and aberrant hematopoiesis. In acute myeloid leukemias harboring t(16;21), ERG function is deregulated due to a fusion with FUS/TLS resulting in the expression of a FUS–ERG oncofusion protein. How this oncofusion protein deregulates the normal ERG transcription program is unclear. Here, we show that FUS–ERG acts in the context of a heptad of proteins (ERG, FLI1, GATA2, LYL1, LMO2, RUNX1 and TAL1) central to proper expression of genes involved in maintaining a stem cell hematopoietic phenotype. Moreover, in t(16;21) FUS–ERG co-occupies genomic regions bound by the nuclear receptor heterodimer RXR:RARA inhibiting target gene expression and interfering with hematopoietic differentiation. All-trans retinoic acid treatment of t(16;21) cells as well as FUS–ERG knockdown alleviate the myeloid-differentiation block. Together, the results suggest that FUS–ERG acts as a transcriptional repressor of the retinoic acid signaling pathway.
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36
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Woodcroft MW, Nanan K, Thompson P, Tyryshkin K, Smith SP, Slany RK, LeBrun DP. Retrovirus-Mediated Expression of E2A-PBX1 Blocks Lymphoid Fate but Permits Retention of Myeloid Potential in Early Hematopoietic Progenitors. PLoS One 2015; 10:e0130495. [PMID: 26098938 PMCID: PMC4476730 DOI: 10.1371/journal.pone.0130495] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2014] [Accepted: 05/20/2015] [Indexed: 11/19/2022] Open
Abstract
The oncogenic transcription factor E2A-PBX1 is expressed consequent to chromosomal translocation 1;19 and is an important oncogenic driver in cases of pre-B-cell acute lymphoblastic leukemia (ALL). Elucidating the mechanism by which E2A-PBX1 induces lymphoid leukemia would be expedited by the availability of a tractable experimental model in which enforced expression of E2A-PBX1 in hematopoietic progenitors induces pre-B-cell ALL. However, hematopoietic reconstitution of irradiated mice with bone marrow infected with E2A-PBX1-expressing retroviruses consistently gives rise to myeloid, not lymphoid, leukemia. Here, we elucidate the hematopoietic consequences of forced E2A-PBX1 expression in primary murine hematopoietic progenitors. We show that introducing E2A-PBX1 into multipotent progenitors permits the retention of myeloid potential but imposes a dense barrier to lymphoid development prior to the common lymphoid progenitor stage, thus helping to explain the eventual development of myeloid, and not lymphoid, leukemia in transplanted mice. Our findings also indicate that E2A-PBX1 enforces the aberrant, persistent expression of some genes that would normally have been down-regulated in the subsequent course of hematopoietic maturation. We show that enforced expression of one such gene, Hoxa9, a proto-oncogene associated with myeloid leukemia, partially reproduces the phenotype produced by E2A-PBX1 itself. Existing evidence suggests that the 1;19 translocation event takes place in committed B-lymphoid progenitors. However, we find that retrovirus-enforced expression of E2A-PBX1 in committed pro-B-cells results in cell cycle arrest and apoptosis. Our findings indicate that the neoplastic phenotype induced by E2A-PBX1 is determined by the developmental stage of the cell into which the oncoprotein is introduced.
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Affiliation(s)
- Mark W. Woodcroft
- Department of Pathology and Molecular Medicine, Queen's University, Kingston, Ontario, Canada
| | - Kyster Nanan
- Department of Pathology and Molecular Medicine, Queen's University, Kingston, Ontario, Canada
| | - Patrick Thompson
- Department of Pathology and Molecular Medicine, Queen's University, Kingston, Ontario, Canada
| | - Kathrin Tyryshkin
- Department of Pathology and Molecular Medicine, Queen's University, Kingston, Ontario, Canada
| | - Steven P. Smith
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Ontario, Canada
| | - Robert K. Slany
- Department of Genetics, University Erlangen, Erlangen, Germany
| | - David P. LeBrun
- Department of Pathology and Molecular Medicine, Queen's University, Kingston, Ontario, Canada
- * E-mail:
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37
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Trombly DJ, Whitfield TW, Padmanabhan S, Gordon JAR, Lian JB, van Wijnen AJ, Zaidi SK, Stein JL, Stein GS. Genome-wide co-occupancy of AML1-ETO and N-CoR defines the t(8;21) AML signature in leukemic cells. BMC Genomics 2015; 16:309. [PMID: 25928846 PMCID: PMC4434520 DOI: 10.1186/s12864-015-1445-0] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2014] [Accepted: 03/06/2015] [Indexed: 11/10/2022] Open
Abstract
Background Many leukemias result from chromosomal rearrangements. The t(8;21) chromosomal translocation produces AML1-ETO, an oncogenic fusion protein that compromises the function of AML1, a transcription factor critical for myeloid cell differentiation. Because of the pressing need for new therapies in the treatment of acute myleoid leukemia, we investigated the genome-wide occupancy of AML1-ETO in leukemic cells to discover novel regulatory mechanisms involving AML-ETO bound genes. Results We report the co-localization of AML1-ETO with the N-CoR co-repressor to be primarily on genomic regions distal to transcriptional start sites (TSSs). These regions exhibit over-representation of the motif for PU.1, a key hematopoietic regulator and member of the ETS family of transcription factors. A significant discovery of our study is that genes co-occupied by AML1-ETO and N-CoR (e.g., TYROBP and LAPTM5) are associated with the leukemic phenotype, as determined by analyses of gene ontology and by the observation that these genes are predominantly up-regulated upon AML1-ETO depletion. In contrast, the AML1-ETO/p300 gene network is less responsive to AML1-ETO depletion and less associated with the differentiation block characteristic of leukemic cells. Furthermore, a substantial fraction of AML1-ETO/p300 co-localization occurs near TSSs in promoter regions associated with transcriptionally active loci. Conclusions Our findings establish a novel and dominant t(8;21) AML leukemia signature characterized by occupancy of AML1-ETO/N-CoR at promoter-distal genomic regions enriched in motifs for myeloid differentiation factors, thus providing mechanistic insight into the leukemic phenotype. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1445-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Daniel J Trombly
- Department of Cell and Developmental Biology, University of Massachusetts Medical School, 55 Lake Avenue North, Worcester, MA, 01655, USA.
| | - Troy W Whitfield
- Department of Cell and Developmental Biology, University of Massachusetts Medical School, 55 Lake Avenue North, Worcester, MA, 01655, USA. .,Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, 55 Lake Avenue North, Worcester, MA, 01655, USA.
| | - Srivatsan Padmanabhan
- Department of Cell and Developmental Biology, University of Massachusetts Medical School, 55 Lake Avenue North, Worcester, MA, 01655, USA.
| | - Jonathan A R Gordon
- Department of Biochemistry and Vermont Cancer Center, University of Vermont College of Medicine, 89 Beaumont Avenue, Burlington, VT, 05405, USA. .,Department of Cell and Developmental Biology, University of Massachusetts Medical School, 55 Lake Avenue North, Worcester, MA, 01655, USA.
| | - Jane B Lian
- Department of Biochemistry and Vermont Cancer Center, University of Vermont College of Medicine, 89 Beaumont Avenue, Burlington, VT, 05405, USA. .,Department of Cell and Developmental Biology, University of Massachusetts Medical School, 55 Lake Avenue North, Worcester, MA, 01655, USA.
| | - Andre J van Wijnen
- Department of Cell and Developmental Biology, University of Massachusetts Medical School, 55 Lake Avenue North, Worcester, MA, 01655, USA. .,Current address: Biomedical Sciences, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA.
| | - Sayyed K Zaidi
- Department of Biochemistry and Vermont Cancer Center, University of Vermont College of Medicine, 89 Beaumont Avenue, Burlington, VT, 05405, USA. .,Department of Cell and Developmental Biology, University of Massachusetts Medical School, 55 Lake Avenue North, Worcester, MA, 01655, USA.
| | - Janet L Stein
- Department of Biochemistry and Vermont Cancer Center, University of Vermont College of Medicine, 89 Beaumont Avenue, Burlington, VT, 05405, USA. .,Department of Cell and Developmental Biology, University of Massachusetts Medical School, 55 Lake Avenue North, Worcester, MA, 01655, USA.
| | - Gary S Stein
- Department of Biochemistry and Vermont Cancer Center, University of Vermont College of Medicine, 89 Beaumont Avenue, Burlington, VT, 05405, USA. .,Department of Cell and Developmental Biology, University of Massachusetts Medical School, 55 Lake Avenue North, Worcester, MA, 01655, USA.
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38
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D'Amato L, Dell'Aversana C, Conte M, Ciotta A, Scisciola L, Carissimo A, Nebbioso A, Altucci L. ARHGEF3 controls HDACi-induced differentiation via RhoA-dependent pathways in acute myeloid leukemias. Epigenetics 2015; 10:6-18. [PMID: 25494542 DOI: 10.4161/15592294.2014.988035] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Altered expression and activity of histone deacetylases (HDACs) have been correlated with tumorigenesis. Inhibitors of HDACs (HDACi) induce acetylation of histone and non-histone proteins affecting gene expression, cell cycle progression, cell migration, terminal differentiation and cell death. Here, we analyzed the regulation of ARHGEF3, a RhoA-specific guanine nucleotide exchange factor, by the HDACi MS275 (entinostat). MS275 is a well-known benzamide-based HDACi, which induces differentiation of the monoblastic-like human histiocytic lymphoma cell line U937 to monocytes/macrophages. Incubation of U937 cells with MS275 resulted in an up regulation of ARHGEF3, followed by a significant enhancement of the marker of macrophage differentiation CD68. ARHGEF3 protein is primarily nuclear, but MS275 treatment rapidly induced its translocation into the cytoplasm. ARHGEF3 cytoplasmic localization is associated with activation of the RhoA/Rho-associated Kinase (ROCK) pathway. In addition to cytoskeletal rearrangements orchestrated by RhoA, we showed that ARHGEF3/RhoA-dependent signals involve activation of SAPK/JNK and then Elk1 transcription factor. Importantly, MS275-induced CD68 expression was blocked by exposure of U937 cells to exoenzyme C3 transferase and Y27632, inhibitors of Rho and ROCK respectively. Moreover, ARHGEF3 silencing prevented RhoA activation leading to a reduction in SAPK/JNK phosphorylation, Elk1 activation and CD68 expression, suggesting a crucial role for ARHGEF3 in myeloid differentiation. Taken together, our results demonstrate that ARHGEF3 modulates acute myeloid leukemia differentiation through activation of RhoA and pathways directly controlled by small GTPase family proteins. The finding that GEF protein modulation by HDAC inhibition impacts on cell differentiation may be important for understanding the antitumor mechanism(s) by which HDACi treatment stimulates differentiation in cancer.
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Affiliation(s)
- Loredana D'Amato
- a Dipartimento di Biochimica, Biofisica e Patologia Generale ; Seconda Università di Napoli ; Napoli , Italy
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39
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Chen PB, Zhu LJ, Hainer SJ, McCannell KN, Fazzio TG. Unbiased chromatin accessibility profiling by RED-seq uncovers unique features of nucleosome variants in vivo. BMC Genomics 2014; 15:1104. [PMID: 25494698 PMCID: PMC4378318 DOI: 10.1186/1471-2164-15-1104] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2014] [Accepted: 12/10/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Differential accessibility of DNA to nuclear proteins underlies the regulation of numerous cellular processes. Although DNA accessibility is primarily determined by the presence or absence of nucleosomes, differences in nucleosome composition or dynamics may also regulate accessibility. Methods for mapping nucleosome positions and occupancies genome-wide (MNase-seq) have uncovered the nucleosome landscapes of many different cell types and organisms. Conversely, methods specialized for the detection of large nucleosome-free regions of chromatin (DNase-seq, FAIRE-seq) have uncovered numerous gene regulatory elements. However, these methods are less successful in measuring the accessibility of DNA sequences within nucelosome arrays. RESULTS Here we probe the genome-wide accessibility of multiple cell types in an unbiased manner using restriction endonuclease digestion of chromatin coupled to deep sequencing (RED-seq). Using this method, we identified differences in chromatin accessibility between populations of cells, not only in nucleosome-depleted regions of the genome (e.g., enhancers and promoters), but also within the majority of the genome that is packaged into nucleosome arrays. Furthermore, we identified both large differences in chromatin accessibility in distinct cell lineages and subtle but significant changes during differentiation of mouse embryonic stem cells (ESCs). Most significantly, using RED-seq, we identified differences in accessibility among nucleosomes harboring well-studied histone variants, and show that these differences depend on factors required for their deposition. CONCLUSIONS Using an unbiased method to probe chromatin accessibility genome-wide, we uncover unique features of chromatin structure that are not observed using more widely-utilized methods. We demonstrate that different types of nucleosomes within mammalian cells exhibit different degrees of accessibility. These findings provide significant insight into the regulation of DNA accessibility.
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Affiliation(s)
| | | | | | | | - Thomas G Fazzio
- Program in Gene Function and Expression, University of Massachusetts Medical School, Worcester, MA 01605, USA.
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40
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Ptasinska A, Assi SA, Martinez-Soria N, Imperato MR, Piper J, Cauchy P, Pickin A, James SR, Hoogenkamp M, Williamson D, Wu M, Tenen DG, Ott S, Westhead DR, Cockerill PN, Heidenreich O, Bonifer C. Identification of a dynamic core transcriptional network in t(8;21) AML that regulates differentiation block and self-renewal. Cell Rep 2014; 8:1974-1988. [PMID: 25242324 PMCID: PMC4487811 DOI: 10.1016/j.celrep.2014.08.024] [Citation(s) in RCA: 96] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2014] [Revised: 06/19/2014] [Accepted: 08/12/2014] [Indexed: 11/29/2022] Open
Abstract
Oncogenic transcription factors such as RUNX1/ETO, which is generated by the chromosomal translocation t(8;21), subvert normal blood cell development by impairing differentiation and driving malignant self-renewal. Here, we use digital footprinting and chromatin immunoprecipitation sequencing (ChIP-seq) to identify the core RUNX1/ETO-responsive transcriptional network of t(8;21) cells. We show that the transcriptional program underlying leukemic propagation is regulated by a dynamic equilibrium between RUNX1/ETO and RUNX1 complexes, which bind to identical DNA sites in a mutually exclusive fashion. Perturbation of this equilibrium in t(8;21) cells by RUNX1/ETO depletion leads to a global redistribution of transcription factor complexes within preexisting open chromatin, resulting in the formation of a transcriptional network that drives myeloid differentiation. Our work demonstrates on a genome-wide level that the extent of impaired myeloid differentiation in t(8;21) is controlled by the dynamic balance between RUNX1/ETO and RUNX1 activities through the repression of transcription factors that drive differentiation. RUNX1/ETO drives a t(8;21)-specific transcriptional network RUNX1/ETO and RUNX1 dynamically compete for the same genomic sites RUNX1/ETO targets transcription factor complexes that control differentiation RUNX1/ETO depletion activates a transcriptional network dominated by C/EBPα
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Affiliation(s)
- Anetta Ptasinska
- School of Cancer Sciences, College of Medicine and Dentistry, University of Birmingham, Birmingham B15 2TT, UK
| | - Salam A Assi
- School of Cancer Sciences, College of Medicine and Dentistry, University of Birmingham, Birmingham B15 2TT, UK; School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Natalia Martinez-Soria
- Northern Institute for Cancer Research, University of Newcastle, Newcastle upon Tyne NE2 4HH, UK
| | - Maria Rosaria Imperato
- School of Cancer Sciences, College of Medicine and Dentistry, University of Birmingham, Birmingham B15 2TT, UK
| | - Jason Piper
- Warwick Systems Biology Centre, University of Warwick, Coventry CV4 7AL, UK
| | - Pierre Cauchy
- School of Cancer Sciences, College of Medicine and Dentistry, University of Birmingham, Birmingham B15 2TT, UK
| | - Anna Pickin
- School of Cancer Sciences, College of Medicine and Dentistry, University of Birmingham, Birmingham B15 2TT, UK
| | - Sally R James
- Section of Experimental Haematology, Leeds Institute for Molecular Medicine, University of Leeds, Leeds LS2 9JT, UK
| | - Maarten Hoogenkamp
- School of Cancer Sciences, College of Medicine and Dentistry, University of Birmingham, Birmingham B15 2TT, UK
| | - Dan Williamson
- Northern Institute for Cancer Research, University of Newcastle, Newcastle upon Tyne NE2 4HH, UK
| | - Mengchu Wu
- Cancer Science Institute, National University of Singapore, Republic of Singapore, Singapore 117456, Singapore
| | - Daniel G Tenen
- Cancer Science Institute, National University of Singapore, Republic of Singapore, Singapore 117456, Singapore
| | - Sascha Ott
- Warwick Systems Biology Centre, University of Warwick, Coventry CV4 7AL, UK
| | - David R Westhead
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Peter N Cockerill
- School of Cancer Sciences, College of Medicine and Dentistry, University of Birmingham, Birmingham B15 2TT, UK
| | - Olaf Heidenreich
- Northern Institute for Cancer Research, University of Newcastle, Newcastle upon Tyne NE2 4HH, UK.
| | - Constanze Bonifer
- School of Cancer Sciences, College of Medicine and Dentistry, University of Birmingham, Birmingham B15 2TT, UK.
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41
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Stunnenberg HG, Hubner NC. Genomics meets proteomics: identifying the culprits in disease. Hum Genet 2014; 133:689-700. [PMID: 24135908 PMCID: PMC4021166 DOI: 10.1007/s00439-013-1376-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2013] [Accepted: 10/01/2013] [Indexed: 12/20/2022]
Abstract
Genome-wide association studies (GWAS) revealed genomic risk loci that potentially have an impact on disease and phenotypic traits. This extensive resource holds great promise in providing novel directions for personalized medicine, including disease risk prediction, prevention and targeted medication. One of the major challenges that researchers face on the path between the initial identification of an association and precision treatment of patients is the comprehension of the biological mechanisms that underlie these associations. Currently, the focus to solve these questions lies on the integrative analysis of system-wide data on global genome variation, gene expression, transcription factor binding, epigenetic profiles and chromatin conformation. The generation of this data mainly relies on next-generation sequencing. However, due to multiple recent developments, mass spectrometry-based proteomics now offers additional, by the GWAS field so far hardly recognized possibilities for the identification of functional genome variants and, in particular, for the identification and characterization of (differentially) bound protein complexes as well as physiological target genes. In this review, we introduce these proteomics advances and suggest how they might be integrated in post-GWAS workflows. We argue that the combination of highly complementary techniques is powerful and can provide an unbiased, detailed picture of GWAS loci and their mechanistic involvement in disease.
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Affiliation(s)
- Hendrik G. Stunnenberg
- Department of Molecular Biology, Faculty of Science, Nijmegen Centre for Molecular Life Sciences, Radboud University Nijmegen, 6525 GA Nijmegen, The Netherlands
| | - Nina C. Hubner
- Department of Molecular Biology, Faculty of Science, Nijmegen Centre for Molecular Life Sciences, Radboud University Nijmegen, 6525 GA Nijmegen, The Netherlands
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42
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Breig O, Bras S, Martinez Soria N, Osman D, Heidenreich O, Haenlin M, Waltzer L. Pontin is a critical regulator for AML1-ETO-induced leukemia. Leukemia 2014; 28:1271-9. [PMID: 24342949 DOI: 10.1038/leu.2013.376] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2013] [Revised: 12/05/2013] [Accepted: 12/11/2013] [Indexed: 01/07/2023]
Abstract
The oncogenic fusion protein AML1-ETO, also known as RUNX1-RUNX1T1 is generated by the t(8;21)(q22;q22) translocation, one of the most frequent chromosomal rearrangements in acute myeloid leukemia (AML). Identifying the genes that cooperate with or are required for the oncogenic activity of this chimeric transcription factor remains a major challenge. Our previous studies showed that Drosophila provides a genuine model to study how AML1-ETO promotes leukemia. Here, using an in vivo RNA interference screen for suppressors of AML1-ETO activity, we identified pontin/RUVBL1 as a gene required for AML1-ETO-induced lethality and blood cell proliferation in Drosophila. We further show that PONTIN inhibition strongly impaired the growth of human t(8;21)(+) or AML1-ETO-expressing leukemic blood cells. Interestingly, AML1-ETO promoted the transcription of PONTIN. Moreover, transcriptome analysis in Kasumi-1 cells revealed a strong correlation between PONTIN and AML1-ETO gene signatures and demonstrated that PONTIN chiefly regulated the expression of genes implicated in cell cycle progression. Concordantly, PONTIN depletion inhibited leukemic self-renewal and caused cell cycle arrest. All together our data suggest that the upregulation of PONTIN by AML1-ETO participate in the oncogenic growth of t(8;21) cells.
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MESH Headings
- ATPases Associated with Diverse Cellular Activities
- Animals
- Biomarkers, Tumor/genetics
- Biomarkers, Tumor/metabolism
- Blotting, Western
- Carrier Proteins/antagonists & inhibitors
- Carrier Proteins/genetics
- Carrier Proteins/metabolism
- Cell Cycle
- Cell Proliferation
- Chromosomes, Human, Pair 21/genetics
- Chromosomes, Human, Pair 8/genetics
- Core Binding Factor Alpha 2 Subunit/genetics
- Core Binding Factor Alpha 2 Subunit/metabolism
- DNA Helicases/antagonists & inhibitors
- DNA Helicases/genetics
- DNA Helicases/metabolism
- Drosophila melanogaster/genetics
- Drosophila melanogaster/growth & development
- Female
- Gene Expression Profiling
- Gene Expression Regulation, Neoplastic
- Humans
- Leukemia, Myeloid, Acute/etiology
- Leukemia, Myeloid, Acute/metabolism
- Leukemia, Myeloid, Acute/pathology
- Male
- Oligonucleotide Array Sequence Analysis
- Oncogene Proteins, Fusion/genetics
- Oncogene Proteins, Fusion/metabolism
- RNA, Messenger/genetics
- RNA, Small Interfering/genetics
- RUNX1 Translocation Partner 1 Protein
- Real-Time Polymerase Chain Reaction
- Reverse Transcriptase Polymerase Chain Reaction
- Translocation, Genetic
- Tumor Cells, Cultured
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Affiliation(s)
- O Breig
- CNRS, CBD UMR5547, Université de Toulouse, UPS, CBD (Centre de Biologie du Développement), Bâtiment 4R3, 118 route de Narbonne, Toulouse, France
| | - S Bras
- CNRS, CBD UMR5547, Université de Toulouse, UPS, CBD (Centre de Biologie du Développement), Bâtiment 4R3, 118 route de Narbonne, Toulouse, France
| | - N Martinez Soria
- Northern Institute for Cancer Research, University of Newcastle, Newcastle upon Tyne, UK
| | - D Osman
- CNRS, CBD UMR5547, Université de Toulouse, UPS, CBD (Centre de Biologie du Développement), Bâtiment 4R3, 118 route de Narbonne, Toulouse, France
| | - O Heidenreich
- Northern Institute for Cancer Research, University of Newcastle, Newcastle upon Tyne, UK
| | - M Haenlin
- CNRS, CBD UMR5547, Université de Toulouse, UPS, CBD (Centre de Biologie du Développement), Bâtiment 4R3, 118 route de Narbonne, Toulouse, France
| | - L Waltzer
- CNRS, CBD UMR5547, Université de Toulouse, UPS, CBD (Centre de Biologie du Développement), Bâtiment 4R3, 118 route de Narbonne, Toulouse, France
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43
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Prange KHM, Singh AA, Martens JHA. The genome-wide molecular signature of transcription factors in leukemia. Exp Hematol 2014; 42:637-50. [PMID: 24814246 DOI: 10.1016/j.exphem.2014.04.012] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2014] [Revised: 04/22/2014] [Accepted: 04/23/2014] [Indexed: 01/08/2023]
Abstract
Transcription factors control expression of genes essential for the normal functioning of the hematopoietic system and regulate development of distinct blood cell types. During leukemogenesis, aberrant regulation of transcription factors such as RUNX1, CBFβ, MLL, C/EBPα, SPI1, GATA, and TAL1 is central to the disease. Here, we will discuss the mechanisms of transcription factor deregulation in leukemia and how in recent years next-generation sequencing approaches have helped to elucidate the molecular role of many of these aberrantly expressed transcription factors. We will focus on the complexes in which these factors reside, the role of posttranslational modification of these factors, their involvement in setting up higher order chromatin structures, and their influence on the local epigenetic environment. We suggest that only comprehensive knowledge on all these aspects will increase our understanding of aberrant gene expression in leukemia as well as open new entry points for therapeutic intervention.
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Affiliation(s)
- Koen H M Prange
- Department of Molecular Biology, Faculty of Science, Nijmegen Centre for Molecular Life Sciences, Radboud University, Nijmegen, The Netherlands
| | - Abhishek A Singh
- Department of Molecular Biology, Faculty of Science, Nijmegen Centre for Molecular Life Sciences, Radboud University, Nijmegen, The Netherlands
| | - Joost H A Martens
- Department of Molecular Biology, Faculty of Science, Nijmegen Centre for Molecular Life Sciences, Radboud University, Nijmegen, The Netherlands.
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44
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White BS, DiPersio JF. Genomic tools in acute myeloid leukemia: From the bench to the bedside. Cancer 2014; 120:1134-44. [PMID: 24474533 DOI: 10.1002/cncr.28552] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2013] [Accepted: 11/14/2013] [Indexed: 12/28/2022]
Abstract
Since its use in the initial characterization of an acute myeloid leukemia (AML) genome, next-generation sequencing (NGS) has continued to molecularly refine the disease. Here, the authors review the spectrum of NGS applications that have subsequently delineated the prognostic significance and biologic consequences of these mutations. Furthermore, the role of this technology in providing a high-resolution glimpse of AML clonal heterogeneity, which may inform future choice of targeted therapy, is discussed. Although obstacles remain in applying these techniques clinically, they have already had an impact on patient care.
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Affiliation(s)
- Brian S White
- Department of Internal Medicine, Division of Oncology, Washington University School of Medicine, St. Louis, Missouri; The Genome Institute, Washington University, St. Louis, Missouri
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Fu L, Huang W, Jing Y, Jiang M, Zhao Y, Shi J, Huang S, Xue X, Zhang Q, Tang J, Dou L, Wang L, Nervi C, Li Y, Yu L. AML1-ETO triggers epigenetic activation of early growth response gene l, inducing apoptosis in t(8;21) acute myeloid leukemia. FEBS J 2014; 281:1123-31. [PMID: 24314118 DOI: 10.1111/febs.12673] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2013] [Revised: 11/06/2013] [Accepted: 12/02/2013] [Indexed: 11/30/2022]
Abstract
The t(8;21)(q22;q22) translocation is the most common chromosomal translocation in acute myeloid leukemia (AML), and it gives rise to acute myeloid gene 1 (AML1)-myeloid transforming gene 8 (ETO)-positive AML, which has a relatively favorable prognosis. However, the molecular mechanism related to a favorable prognosis in AML1-ETO-positive AML is still not fully understood. Our results show that the AML1-ETO fusion protein triggered activation of early growth response gene l (EGR1) by binding at AML1-binding sites on the EGR1 promoter and, subsequently, recruiting acetyltransferase P300, which is known to acetylate histones. However, AML1-ETO could not recruit DNA methyltransferases and histone deacetylases; therefore, EGR1 expression was affected by histone acetylation but not by DNA methylation. Both transcription and translation of EGR1 were higher in AML1-ETO-positive AML cell lines than in AML1-ETO-negative AML cell lines, owing to acetylation. Furthermore, when AML1-ETO-positive AML cell lines were treated with C646 (P300 inhibitor) and trichostatin A (histone deacetylase inhibitor), EGR1 expression was significantly decreased and increased, respectively. In addition, treatment with 5-azacytidine (methyltransferase inhibitor) did not cause any significant change in EGR1 expression. Overexpression of EGR1 inhibited cell proliferation and promoted apoptosis, and EGR1 knockout promoted cell proliferation. Thus, EGR1 could be a novel prognostic factor for a favorable outcome in AML1-ETO-positive AML. The results of our study may explain the molecular mechanisms underlying the favorable prognosis in AML1-ETO-positive AML.
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Affiliation(s)
- Lin Fu
- Department of Hematology, Chinese PLA General Hospital, Beijing, China; Nankai University School of Medicine, Tianjin, China
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Mandoli A, Singh AA, Jansen PWTC, Wierenga ATJ, Riahi H, Franci G, Prange K, Saeed S, Vellenga E, Vermeulen M, Stunnenberg HG, Martens JHA. CBFB-MYH11/RUNX1 together with a compendium of hematopoietic regulators, chromatin modifiers and basal transcription factors occupies self-renewal genes in inv(16) acute myeloid leukemia. Leukemia 2013; 28:770-8. [PMID: 24002588 DOI: 10.1038/leu.2013.257] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2013] [Revised: 08/19/2013] [Accepted: 08/22/2013] [Indexed: 11/09/2022]
Abstract
Different mechanisms for CBFβ-MYH11 function in acute myeloid leukemia with inv(16) have been proposed such as tethering of RUNX1 outside the nucleus, interference with transcription factor complex assembly and recruitment of histone deacetylases, all resulting in transcriptional repression of RUNX1 target genes. Here, through genome-wide CBFβ-MYH11-binding site analysis and quantitative interaction proteomics, we found that CBFβ-MYH11 localizes to RUNX1 occupied promoters, where it interacts with TAL1, FLI1 and TBP-associated factors (TAFs) in the context of the hematopoietic transcription factors ERG, GATA2 and PU.1/SPI1 and the coregulators EP300 and HDAC1. Transcriptional analysis revealed that upon fusion protein knockdown, a small subset of the CBFβ-MYH11 target genes show increased expression, confirming a role in transcriptional repression. However, the majority of CBFβ-MYH11 target genes, including genes implicated in hematopoietic stem cell self-renewal such as ID1, LMO1 and JAG1, are actively transcribed and repressed upon fusion protein knockdown. Together these results suggest an essential role for CBFβ-MYH11 in regulating the expression of genes involved in maintaining a stem cell phenotype.
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Affiliation(s)
- A Mandoli
- Department of Molecular Biology, Faculty of Science, Nijmegen Centre for Molecular Life Sciences, Radboud University, Nijmegen, The Netherlands
| | - A A Singh
- Department of Molecular Biology, Faculty of Science, Nijmegen Centre for Molecular Life Sciences, Radboud University, Nijmegen, The Netherlands
| | - P W T C Jansen
- Department of Molecular Cancer Research, UMC Utrecht, Utrecht, The Netherlands
| | - A T J Wierenga
- 1] Department of Hematology, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands [2] Department of Laboratory Medicine University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
| | - H Riahi
- Department of Molecular Biology, Faculty of Science, Nijmegen Centre for Molecular Life Sciences, Radboud University, Nijmegen, The Netherlands
| | - G Franci
- Dipartimento di Biochimica, Biofisica e Patologia Generale, Seconda Università degli Studi di Napoli, Napoli, Italy
| | - K Prange
- Department of Molecular Biology, Faculty of Science, Nijmegen Centre for Molecular Life Sciences, Radboud University, Nijmegen, The Netherlands
| | - S Saeed
- Department of Molecular Biology, Faculty of Science, Nijmegen Centre for Molecular Life Sciences, Radboud University, Nijmegen, The Netherlands
| | - E Vellenga
- Department of Hematology, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
| | - M Vermeulen
- Department of Molecular Cancer Research, UMC Utrecht, Utrecht, The Netherlands
| | - H G Stunnenberg
- Department of Molecular Biology, Faculty of Science, Nijmegen Centre for Molecular Life Sciences, Radboud University, Nijmegen, The Netherlands
| | - J H A Martens
- Department of Molecular Biology, Faculty of Science, Nijmegen Centre for Molecular Life Sciences, Radboud University, Nijmegen, The Netherlands
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Origins of aberrant DNA methylation in acute myeloid leukemia. Leukemia 2013; 28:1-14. [DOI: 10.1038/leu.2013.242] [Citation(s) in RCA: 87] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2013] [Revised: 08/06/2013] [Accepted: 08/09/2013] [Indexed: 01/02/2023]
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Martin FL. Epigenetic influences in the aetiology of cancers arising from breast and prostate: a hypothesised transgenerational evolution in chromatin accessibility. ISRN ONCOLOGY 2013; 2013:624794. [PMID: 23431470 PMCID: PMC3574745 DOI: 10.1155/2013/624794] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/09/2012] [Accepted: 12/26/2012] [Indexed: 01/12/2023]
Abstract
Epidemiological studies have consistently supported the notion that environmental and/or dietary factors play a central role in the aetiology of cancers of the breast and prostate. However, for more than five decades investigators have failed to identify a single cause-and-effect factor, which could be implicated; identification of a causative entity would allow the implementation of an intervention strategy in at-risk populations. This suggests a more complex pathoaetiology for these cancer sites, compared to others. When one examines the increases or decreases in incidence of specific cancers amongst migrant populations, it is notable that disease arising in colon or stomach requires one or at most two generations to exhibit a change in incidence to match that of high-incidence regions, whereas for breast or prostate cancer, at least three generations are required. This generational threshold could suggest a requirement for nonmutation-driven epigenetic alterations in the F0/F1 generations (parental/offspring adopting a more westernized lifestyle), which then predisposes the inherited genome of subsequent generations to mutagenic/genotoxic alterations leading to the development of sporadic cancer in these target sites. As such, individual susceptibility to carcinogen insult would not be based per se on polymorphisms in activating/detoxifying/repair enzymes, but on elevated accessibility of crucial target genes (e.g., oncogenes, tumour suppressor genes) or hotspots therein to mutation events. This could be termed a genomic susceptibility organizational structure (SOS). Several exposures including alcohol and heavy metals are epigens (i.e., modifiers of the epigenome), whereas others are mutagenic/genotoxic, for example, heterocyclic aromatic amines; humans are continuously and variously exposed to mixtures of these agents. Within such a transgenerational multistage model of cancer development, determining the interaction between epigenetic modification to generate a genomic SOS and genotoxic insult will facilitate a new level of understanding in the aetiology of cancer.
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Affiliation(s)
- Francis L. Martin
- Centre for Biophotonics, Lancaster Environment Centre, Lancaster University, Bailrigg, Lancaster LA1 4YQ, UK
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DNA methylation changes are a late event in acute promyelocytic leukemia and coincide with loss of transcription factor binding. Blood 2013; 121:178-87. [DOI: 10.1182/blood-2012-08-448860] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Abstract
The origin of aberrant DNA methylation in cancer remains largely unknown. In the present study, we elucidated the DNA methylome in primary acute promyelocytic leukemia (APL) and the role of promyelocytic leukemia–retinoic acid receptor α (PML-RARα) in establishing these patterns. Cells from APL patients showed increased genome-wide DNA methylation with higher variability than healthy CD34+ cells, promyelocytes, and remission BM cells. A core set of differentially methylated regions in APL was identified. Age at diagnosis, Sanz score, and Flt3-mutation status characterized methylation subtypes. Transcription factor–binding sites (eg, the c-myc–binding sites) were associated with low methylation. However, SUZ12- and REST-binding sites identified in embryonic stem cells were preferentially DNA hypermethylated in APL cells. Unexpectedly, PML-RARα–binding sites were also protected from aberrant DNA methylation in APL cells. Consistent with this, myeloid cells from preleukemic PML-RARα knock-in mice did not show altered DNA methylation and the expression of PML-RARα in hematopoietic progenitor cells prevented differentiation without affecting DNA methylation. Treatment of APL blasts with all-trans retinoic acid also did not result in immediate DNA methylation changes. The results of the present study suggest that aberrant DNA methylation is associated with leukemia phenotype but is not required for PML-RARα–mediated initiation of leukemogenesis.
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