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Ottema S, Mulet-Lazaro R, Erpelinck-Verschueren C, van Herk S, Havermans M, Arricibita Varea A, Vermeulen M, Beverloo HB, Gröschel S, Haferlach T, Haferlach C, J. Wouters B, Bindels E, Smeenk L, Delwel R. The leukemic oncogene EVI1 hijacks a MYC super-enhancer by CTCF-facilitated loops. Nat Commun 2021; 12:5679. [PMID: 34584081 PMCID: PMC8479123 DOI: 10.1038/s41467-021-25862-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Accepted: 09/02/2021] [Indexed: 02/08/2023] Open
Abstract
Chromosomal rearrangements are a frequent cause of oncogene deregulation in human malignancies. Overexpression of EVI1 is found in a subgroup of acute myeloid leukemia (AML) with 3q26 chromosomal rearrangements, which is often therapy resistant. In AMLs harboring a t(3;8)(q26;q24), we observed the translocation of a MYC super-enhancer (MYC SE) to the EVI1 locus. We generated an in vitro model mimicking a patient-based t(3;8)(q26;q24) using CRISPR-Cas9 technology and demonstrated hyperactivation of EVI1 by the hijacked MYC SE. This MYC SE contains multiple enhancer modules, of which only one recruits transcription factors active in early hematopoiesis. This enhancer module is critical for EVI1 overexpression as well as enhancer-promoter interaction. Multiple CTCF binding regions in the MYC SE facilitate this enhancer-promoter interaction, which also involves a CTCF binding site upstream of the EVI1 promoter. We hypothesize that this CTCF site acts as an enhancer-docking site in t(3;8) AML. Genomic analyses of other 3q26-rearranged AML patient cells point to a common mechanism by which EVI1 uses this docking site to hijack enhancers active in early hematopoiesis.
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Affiliation(s)
- Sophie Ottema
- grid.508717.c0000 0004 0637 3764Department of Hematology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands ,grid.499559.dOncode Institute, Utrecht, The Netherlands
| | - Roger Mulet-Lazaro
- grid.508717.c0000 0004 0637 3764Department of Hematology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands ,grid.499559.dOncode Institute, Utrecht, The Netherlands
| | - Claudia Erpelinck-Verschueren
- grid.508717.c0000 0004 0637 3764Department of Hematology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands ,grid.499559.dOncode Institute, Utrecht, The Netherlands
| | - Stanley van Herk
- grid.508717.c0000 0004 0637 3764Department of Hematology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands ,grid.499559.dOncode Institute, Utrecht, The Netherlands
| | - Marije Havermans
- grid.508717.c0000 0004 0637 3764Department of Hematology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands ,grid.499559.dOncode Institute, Utrecht, The Netherlands
| | - Andrea Arricibita Varea
- grid.508717.c0000 0004 0637 3764Department of Hematology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands ,grid.499559.dOncode Institute, Utrecht, The Netherlands
| | - Michael Vermeulen
- grid.508717.c0000 0004 0637 3764Department of Hematology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | - H. Berna Beverloo
- grid.5645.2000000040459992XDepartment of Clinical Genetics, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Stefan Gröschel
- grid.7497.d0000 0004 0492 0584A380, German Cancer Research Center, Heidelberg, Germany ,grid.5253.10000 0001 0328 4908Department of Internal Medicine V, Heidelberg University Hospital, Heidelberg, Germany
| | - Torsten Haferlach
- grid.420057.40000 0004 7553 8497Munich Leukemia Laboratory, Munich, Germany
| | - Claudia Haferlach
- grid.420057.40000 0004 7553 8497Munich Leukemia Laboratory, Munich, Germany
| | - Bas J. Wouters
- grid.508717.c0000 0004 0637 3764Department of Hematology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands ,grid.499559.dOncode Institute, Utrecht, The Netherlands
| | - Eric Bindels
- grid.508717.c0000 0004 0637 3764Department of Hematology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | - Leonie Smeenk
- grid.508717.c0000 0004 0637 3764Department of Hematology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands ,grid.499559.dOncode Institute, Utrecht, The Netherlands
| | - Ruud Delwel
- grid.508717.c0000 0004 0637 3764Department of Hematology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands ,grid.499559.dOncode Institute, Utrecht, The Netherlands
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Smeenk L, Ottema S, Mulet-Lazaro R, Ebert A, Havermans M, Arricibita Varea A, Fellner M, Pastoors D, van Herk S, Erpelinck-Verschueren C, Grob T, Hoogenboezem RM, Kavelaars FG, Matson DR, Bresnick EH, Bindels EM, Kentsis A, Zuber J, Delwel R. Selective requirement of MYB for oncogenic hyperactivation of a translocated enhancer in leukemia. Cancer Discov 2021; 11:2868-2883. [PMID: 33980539 DOI: 10.1158/2159-8290.cd-20-1793] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 04/26/2021] [Accepted: 05/07/2021] [Indexed: 11/16/2022]
Abstract
In acute myeloid leukemia (AML) with inv(3)(q21;q26) or t(3;3)(q21;q26), a translocated GATA2 enhancer drives oncogenic expression of EVI1. We generated an EVI1-GFP AML model and applied an unbiased CRISPR/Cas9 enhancer scan to uncover sequence motifs essential for EVI1 transcription. Using this approach, we pinpointed a single regulatory element in the translocated GATA2 enhancer that is critically required for aberrant EVI1 expression. This element contained a DNA binding motif for the transcription factor MYB which specifically occupied this site at the translocated allele and was dispensable for GATA2 expression. MYB knockout as well as peptidomimetic blockade of CBP/p300-dependent MYB functions resulted in downregulation of EVI1 but not of GATA2. Targeting MYB or mutating its DNA-binding motif within the GATA2 enhancer resulted in myeloid differentiation and cell death, suggesting that interference with MYB-driven EVI1 transcription provides a potential entry point for therapy of inv(3)/t(3;3) AMLs.
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Affiliation(s)
- Leonie Smeenk
- Hematology, Erasmus MC Cancer Institute and Oncode Institute
| | - Sophie Ottema
- Hematology, Erasmus MC Cancer Institute and Oncode Institute
| | | | - Anja Ebert
- Department of Molecular Biology and Genetics, Aarhus University
| | | | | | - Michaela Fellner
- Immunology and Cancer, Research Institute of Molecular Pathology
| | - Dorien Pastoors
- Hematology, Erasmus MC Cancer Institute and Oncode Institute
| | | | | | - Tim Grob
- Hematology, Erasmus MC Cancer Institute
| | | | | | - Daniel R Matson
- Cell and Regenerative Biology, Paul Carbone Comprehensive Cancer Center, University of Wisconsin School of Medicine and Public Health
| | - Emery H Bresnick
- Cell and Regenerative Biology, Paul Carbone Comprehensive Cancer Center, University of Wisconsin School of Medicine and Public Health
| | | | - Alex Kentsis
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center
| | - Johannes Zuber
- Immunology and Cancer, Research Institute of Molecular Pathology
| | - Ruud Delwel
- Hematology, Erasmus MC Cancer Institute and Oncode Institute
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van der Heijden M, Miedema DM, Waclaw B, Veenstra VL, Lecca MC, Nijman LE, van Dijk E, van Neerven SM, Lodestijn SC, Lenos KJ, de Groot NE, Prasetyanti PR, Arricibita Varea A, Winton DJ, Medema JP, Morrissey E, Ylstra B, Nowak MA, Bijlsma MF, Vermeulen L. Spatiotemporal regulation of clonogenicity in colorectal cancer xenografts. Proc Natl Acad Sci U S A 2019; 116:6140-6145. [PMID: 30850544 PMCID: PMC6442578 DOI: 10.1073/pnas.1813417116] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Cancer evolution is predominantly studied by focusing on differences in the genetic characteristics of malignant cells within tumors. However, the spatiotemporal dynamics of clonal outgrowth that underlie evolutionary trajectories remain largely unresolved. Here, we sought to unravel the clonal dynamics of colorectal cancer (CRC) expansion in space and time by using a color-based clonal tracing method. This method involves lentiviral red-green-blue (RGB) marking of cell populations, which enabled us to track individual cells and their clonal outgrowth during tumor initiation and growth in a xenograft model. We found that clonal expansion largely depends on the location of a clone, as small clones reside in the center and large clones mostly drive tumor growth at the border. These dynamics are recapitulated in a computational model, which confirms that the clone position within a tumor rather than cell-intrinsic features, is crucial for clonal outgrowth. We also found that no significant clonal loss occurs during tumor growth and clonal dispersal is limited in most models. Our results imply that, in addition to molecular features of clones such as (epi-)genetic differences between cells, clone location and the geometry of tumor growth are crucial for clonal expansion. Our findings suggest that either microenvironmental signals on the tumor border or differences in physical properties within the tumor, are major contributors to explain heterogeneous clonal expansion. Thus, this study provides further insights into the dynamics of solid tumor growth and progression, as well as the origins of tumor cell heterogeneity in a relevant model system.
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Affiliation(s)
- Maartje van der Heijden
- Laboratory for Experimental Oncology and Radiobiology, Center for Experimental and Molecular Medicine, Cancer Center Amsterdam, Amsterdam Gastroenterology & Metabolism, Amsterdam UMC, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands
| | - Daniël M Miedema
- Laboratory for Experimental Oncology and Radiobiology, Center for Experimental and Molecular Medicine, Cancer Center Amsterdam, Amsterdam Gastroenterology & Metabolism, Amsterdam UMC, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands
| | - Bartlomiej Waclaw
- School of Physics and Astronomy, The University of Edinburgh, EH9 3FD Edinburgh, United Kingdom
| | - Veronique L Veenstra
- Laboratory for Experimental Oncology and Radiobiology, Center for Experimental and Molecular Medicine, Cancer Center Amsterdam, Amsterdam Gastroenterology & Metabolism, Amsterdam UMC, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands
| | - Maria C Lecca
- Laboratory for Experimental Oncology and Radiobiology, Center for Experimental and Molecular Medicine, Cancer Center Amsterdam, Amsterdam Gastroenterology & Metabolism, Amsterdam UMC, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands
| | - Lisanne E Nijman
- Laboratory for Experimental Oncology and Radiobiology, Center for Experimental and Molecular Medicine, Cancer Center Amsterdam, Amsterdam Gastroenterology & Metabolism, Amsterdam UMC, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands
| | - Erik van Dijk
- Department of Pathology, Amsterdam UMC, Vrije Universiteit Amsterdam, 1081 HV Amsterdam, The Netherlands
| | - Sanne M van Neerven
- Laboratory for Experimental Oncology and Radiobiology, Center for Experimental and Molecular Medicine, Cancer Center Amsterdam, Amsterdam Gastroenterology & Metabolism, Amsterdam UMC, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands
| | - Sophie C Lodestijn
- Laboratory for Experimental Oncology and Radiobiology, Center for Experimental and Molecular Medicine, Cancer Center Amsterdam, Amsterdam Gastroenterology & Metabolism, Amsterdam UMC, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands
| | - Kristiaan J Lenos
- Laboratory for Experimental Oncology and Radiobiology, Center for Experimental and Molecular Medicine, Cancer Center Amsterdam, Amsterdam Gastroenterology & Metabolism, Amsterdam UMC, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands
| | - Nina E de Groot
- Laboratory for Experimental Oncology and Radiobiology, Center for Experimental and Molecular Medicine, Cancer Center Amsterdam, Amsterdam Gastroenterology & Metabolism, Amsterdam UMC, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands
| | - Pramudita R Prasetyanti
- Laboratory for Experimental Oncology and Radiobiology, Center for Experimental and Molecular Medicine, Cancer Center Amsterdam, Amsterdam Gastroenterology & Metabolism, Amsterdam UMC, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands
| | - Andrea Arricibita Varea
- Laboratory for Experimental Oncology and Radiobiology, Center for Experimental and Molecular Medicine, Cancer Center Amsterdam, Amsterdam Gastroenterology & Metabolism, Amsterdam UMC, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands
| | - Douglas J Winton
- Cancer Research UK, Cambridge Institute, University of Cambridge, CB2 0RE Cambridge, United Kingdom
| | - Jan Paul Medema
- Laboratory for Experimental Oncology and Radiobiology, Center for Experimental and Molecular Medicine, Cancer Center Amsterdam, Amsterdam Gastroenterology & Metabolism, Amsterdam UMC, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands
| | - Edward Morrissey
- Medical Research Council Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Headington, OX3 9DS Oxford, United Kingdom
| | - Bauke Ylstra
- Department of Pathology, Amsterdam UMC, Vrije Universiteit Amsterdam, 1081 HV Amsterdam, The Netherlands
| | - Martin A Nowak
- Program for Evolutionary Dynamics, Harvard University, Cambridge, MA 02138
| | - Maarten F Bijlsma
- Laboratory for Experimental Oncology and Radiobiology, Center for Experimental and Molecular Medicine, Cancer Center Amsterdam, Amsterdam Gastroenterology & Metabolism, Amsterdam UMC, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands
| | - Louis Vermeulen
- Laboratory for Experimental Oncology and Radiobiology, Center for Experimental and Molecular Medicine, Cancer Center Amsterdam, Amsterdam Gastroenterology & Metabolism, Amsterdam UMC, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands;
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