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Ozgun G, Yaras T, Akman B, Özden-Yılmaz G, Landman N, Karakülah G, van Lohuizen M, Senturk S, Erkek-Ozhan S. Retinoids and EZH2 inhibitors cooperate to orchestrate anti-oncogenic effects on bladder cancer cells. Cancer Gene Ther 2024; 31:537-551. [PMID: 38233533 DOI: 10.1038/s41417-024-00725-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 01/04/2024] [Accepted: 01/04/2024] [Indexed: 01/19/2024]
Abstract
The highly mutated nature of bladder cancers harboring mutations in chromatin regulatory genes opposing Polycomb-mediated repression highlights the importance of targeting EZH2 in bladder cancer. Furthermore, the critical role of the retinoic acid signaling pathway in the development and homeostasis of the urothelium, and the anti-oncogenic effects of retinoids are well established. Therefore, our aim is to simultaneously target EZH2 and retinoic acid signaling in bladder cancer to potentiate the therapeutic response. Here we report that this coordinated targeting strategy stimulates an anti-oncogenic profile, as reflected by inducing a synergistic reduction in cell viability that was associated with increased apoptosis and cell cycle arrest in a cooperative and orchestrated manner. This study characterized anti-oncogenic transcriptional reprogramming centered on the transcriptional regulator CHOP by stimulating the endoplasmic reticulum stress response. We further portrayed a molecular mechanism whereby EZH2 maintains H3K27me3-mediated repression of a subset of genes involved in unfolded protein responses, reflecting the molecular mechanism underlying this co-targeting strategy. These findings highlight the importance of co-targeting the EZH2 and retinoic acid pathway in bladder cancers and encourage the design of novel treatments employing retinoids coupled with EZH2 inhibitors in bladder carcinoma.
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Affiliation(s)
- Gizem Ozgun
- Izmir Biomedicine and Genome Center, Izmir, Turkey
- Izmir International Biomedicine and Genome Institute, Dokuz Eylul University, Izmir, Turkey
| | - Tutku Yaras
- Izmir Biomedicine and Genome Center, Izmir, Turkey
- Izmir International Biomedicine and Genome Institute, Dokuz Eylul University, Izmir, Turkey
| | - Burcu Akman
- Izmir Biomedicine and Genome Center, Izmir, Turkey
| | - Gülden Özden-Yılmaz
- Izmir Biomedicine and Genome Center, Izmir, Turkey
- Izmir International Biomedicine and Genome Institute, Dokuz Eylul University, Izmir, Turkey
| | - Nick Landman
- Division of Molecular Genetics, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Gökhan Karakülah
- Izmir Biomedicine and Genome Center, Izmir, Turkey
- Izmir International Biomedicine and Genome Institute, Dokuz Eylul University, Izmir, Turkey
| | - Maarten van Lohuizen
- Division of Molecular Genetics, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Serif Senturk
- Izmir Biomedicine and Genome Center, Izmir, Turkey
- Izmir International Biomedicine and Genome Institute, Dokuz Eylul University, Izmir, Turkey
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2
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Landman N, Hulsman D, Badhai J, Kopparam J, Puppe J, Pandey GK, van Lohuizen M. Combination of EZH2 and ATM inhibition in BAP1-deficient mesothelioma. Br J Cancer 2024:10.1038/s41416-024-02661-3. [PMID: 38519707 DOI: 10.1038/s41416-024-02661-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 03/11/2024] [Accepted: 03/13/2024] [Indexed: 03/25/2024] Open
Abstract
BACKGROUND More than half of mesothelioma tumours show alterations in the tumour suppressor gene BAP1. BAP1-deficient mesothelioma is shown to be sensitive to EZH2 inhibition in preclinical settings but only showed modest efficacy in clinical trial. Adding a second inhibitor could potentially elevate EZH2i treatment efficacy while preventing acquired resistance at the same time. METHODS A focused drug synergy screen consisting of 20 drugs was performed by combining EZH2 inhibition with a panel of anti-cancer compounds in mesothelioma cell lines. The compounds used are under preclinical investigation or already used in the clinic. The synergistic potential of the combinations was assessed by using the Bliss model. To validate our findings, in vivo xenograft experiments were performed. RESULTS Combining EZH2i with ATMi was found to have synergistic potential against BAP1-deficient mesothelioma in our drug screen, which was validated in clonogenicity assays. Tumour growth inhibition potential was significantly increased in BAP1-deficient xenografts. In addition, we observe lower ATM levels upon depletion of BAP1 and hypothesise that this might be mediated by E2F1. CONCLUSIONS We demonstrated the efficacy of the combination of ATM and EZH2 inhibition against BAP1-deficient mesothelioma in preclinical models, indicating the potential of this combination as a novel treatment modality using BAP1 as a biomarker.
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Affiliation(s)
- Nick Landman
- Division of Molecular Genetics, The Netherlands Cancer Institute, Plesmanlaan 121, Amsterdam, The Netherlands
- Oncode Institute, Jaarbeursplein 6, Utrecht, The Netherlands
| | - Danielle Hulsman
- Division of Molecular Genetics, The Netherlands Cancer Institute, Plesmanlaan 121, Amsterdam, The Netherlands
- Oncode Institute, Jaarbeursplein 6, Utrecht, The Netherlands
| | - Jitendra Badhai
- Division of Molecular Genetics, The Netherlands Cancer Institute, Plesmanlaan 121, Amsterdam, The Netherlands
- Oncode Institute, Jaarbeursplein 6, Utrecht, The Netherlands
| | - Jawahar Kopparam
- Division of Molecular Genetics, The Netherlands Cancer Institute, Plesmanlaan 121, Amsterdam, The Netherlands
- Oncode Institute, Jaarbeursplein 6, Utrecht, The Netherlands
| | - Julian Puppe
- Department of Obstetrics and Gynaecology, University Hospital of Cologne, Kerpener Str. 34, Cologne, Germany
| | - Gaurav Kumar Pandey
- Division of Molecular Genetics, The Netherlands Cancer Institute, Plesmanlaan 121, Amsterdam, The Netherlands.
- Oncode Institute, Jaarbeursplein 6, Utrecht, The Netherlands.
- Department of Zoology, Banaras Hindu University, Varanasi, Uttar Pradesh, India.
| | - Maarten van Lohuizen
- Division of Molecular Genetics, The Netherlands Cancer Institute, Plesmanlaan 121, Amsterdam, The Netherlands.
- Oncode Institute, Jaarbeursplein 6, Utrecht, The Netherlands.
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3
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Badhai J, Landman N, Pandey GK, Song JY, Hulsman D, Krijgsman O, Chandrasekaran G, Berns A, van Lohuizen M. Combined Inhibition of EZH2 and FGFR is Synergistic in BAP1-deficient Malignant Mesothelioma. Cancer Res Commun 2024; 4:18-27. [PMID: 38054839 PMCID: PMC10763530 DOI: 10.1158/2767-9764.crc-23-0276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 10/02/2023] [Accepted: 11/30/2023] [Indexed: 12/07/2023]
Abstract
Malignant mesothelioma is a highly aggressive tumor with a survival of only 4-18 months after diagnosis. Treatment options for this disease are limited. Immune checkpoint blockade using ipilimumab and nivolumab has recently been approved as a frontline therapy, but this led to only a small improvement in overall patient survival. As more than half of patients with mesothelioma have alterations in the gene encoding for BAP1 this could be a potential marker for targeted therapies. In this study, we investigated the synergistic potential of combining EZH2 inhibition together with FGFR inhibition for treatment of BAP1-deficient malignancies. The efficacy of the combination was evaluated using human and murine preclinical models of mesothelioma and uveal melanoma in vitro. The efficacy of the combination was further validated in vivo by using BAP1-deficient mesothelioma xenografts and autochthonous mouse models. In vitro data showed sensitivity to the combined inhibition in BAP1-deficient mesothelioma and uveal melanoma tumor cell lines but not for BAP1-proficient subtypes. In vivo data showed susceptibility to the combination of BAP1-deficient xenografts and demonstrated an increase of survival in autochthonous models of mesothelioma. These results highlight the potential of this novel drug combination for the treatment of mesothelioma using BAP1 as a biomarker. Given these encouraging preclinical results, it will be important to clinically explore dual EZH2/FGFR inhibition in patients with BAP1-deficient malignant mesothelioma and justify further exploration in other BAP1 loss-associated tumors. SIGNIFICANCE Despite the recent approval of immunotherapy, malignant mesothelioma has limited treatment options and poor prognosis. Here, we observe that EZH2 inhibitors dramatically enhance the efficacy of FGFR inhibition, sensitising BAP1-mutant mesothelioma and uveal melanoma cells. The striking synergy of EZH2 and FGFR inhibition supports clinical investigations for BAP1-mutant tumors.
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Affiliation(s)
- Jitendra Badhai
- Division of Molecular Genetics, The Netherlands Cancer Institute, Plesmanlaan, Amsterdam, the Netherlands
- Oncode Institute, Jaarbeursplein, Utrecht, the Netherlands
| | - Nick Landman
- Division of Molecular Genetics, The Netherlands Cancer Institute, Plesmanlaan, Amsterdam, the Netherlands
- Oncode Institute, Jaarbeursplein, Utrecht, the Netherlands
| | - Gaurav Kumar Pandey
- Division of Molecular Genetics, The Netherlands Cancer Institute, Plesmanlaan, Amsterdam, the Netherlands
- Oncode Institute, Jaarbeursplein, Utrecht, the Netherlands
- Department of Zoology, Banaras Hindu University, Varanasi, India
| | - Ji-Ying Song
- Department of Experimental Animal Pathology, The Netherlands Cancer Institute, Plesmanlaan, Amsterdam, the Netherlands
| | - Danielle Hulsman
- Division of Molecular Genetics, The Netherlands Cancer Institute, Plesmanlaan, Amsterdam, the Netherlands
- Oncode Institute, Jaarbeursplein, Utrecht, the Netherlands
| | - Oscar Krijgsman
- Division of Molecular Oncology and Immunology, The Netherlands Cancer Institute, Plesmanlaan, Amsterdam, the Netherlands
| | - Gayathri Chandrasekaran
- Division of Molecular Genetics, The Netherlands Cancer Institute, Plesmanlaan, Amsterdam, the Netherlands
- Oncode Institute, Jaarbeursplein, Utrecht, the Netherlands
| | - Anton Berns
- Division of Molecular Genetics, The Netherlands Cancer Institute, Plesmanlaan, Amsterdam, the Netherlands
- Oncode Institute, Jaarbeursplein, Utrecht, the Netherlands
| | - Maarten van Lohuizen
- Division of Molecular Genetics, The Netherlands Cancer Institute, Plesmanlaan, Amsterdam, the Netherlands
- Oncode Institute, Jaarbeursplein, Utrecht, the Netherlands
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4
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Pandey GK, Landman N, Neikes HK, Hulsman D, Lieftink C, Beijersbergen R, Kolluri KK, Janes SM, Vermeulen M, Badhai J, van Lohuizen M. Genetic screens reveal new targetable vulnerabilities in BAP1-deficient mesothelioma. Cell Rep Med 2023; 4:100915. [PMID: 36657447 PMCID: PMC9975229 DOI: 10.1016/j.xcrm.2022.100915] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 12/06/2022] [Accepted: 12/30/2022] [Indexed: 01/19/2023]
Abstract
More than half of patients with malignant mesothelioma show alterations in the BAP1 tumor-suppressor gene. Being a member of the Polycomb repressive deubiquitinating (PR-DUB) complex, BAP1 loss results in an altered epigenome, which may create new vulnerabilities that remain largely unknown. Here, we performed a CRISPR-Cas9 kinome screen in mesothelioma cells that identified two kinases in the mevalonate/cholesterol biosynthesis pathway. Furthermore, our analysis of chromatin, expression, and genetic perturbation data in mesothelioma cells suggests a dependency on PR complex 2 (PRC2)-mediated silencing. Pharmacological inhibition of PRC2 elevates the expression of cholesterol biosynthesis genes only in BAP1-deficient mesothelioma, thereby sensitizing these cells to the combined targeting of PRC2 and the mevalonate pathway. Finally, by subjecting autochthonous Bap1-deficient mesothelioma mice or xenografts to mevalonate pathway inhibition (zoledronic acid) and PRC2 inhibition (tazemetostat), we demonstrate a potent anti-tumor effect, suggesting a targeted combination therapy for Bap1-deficient mesothelioma.
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Affiliation(s)
- Gaurav Kumar Pandey
- Division of Molecular Genetics, The Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, the Netherlands; Oncode Institute, Utrecht, the Netherlands
| | - Nick Landman
- Division of Molecular Genetics, The Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, the Netherlands; Oncode Institute, Utrecht, the Netherlands
| | - Hannah K Neikes
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University Nijmegen, Nijmegen, the Netherlands; Oncode Institute, Utrecht, the Netherlands
| | - Danielle Hulsman
- Division of Molecular Genetics, The Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, the Netherlands
| | - Cor Lieftink
- Division of Molecular Carcinogenesis, NKI Robotics and Screening Center, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Roderick Beijersbergen
- Division of Molecular Carcinogenesis, NKI Robotics and Screening Center, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Krishna Kalyan Kolluri
- Lung for Living Research Centre, UCL Respiratory, University College London, Rayne Building, London, UK
| | - Sam M Janes
- Lung for Living Research Centre, UCL Respiratory, University College London, Rayne Building, London, UK
| | - Michiel Vermeulen
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University Nijmegen, Nijmegen, the Netherlands; Oncode Institute, Utrecht, the Netherlands
| | - Jitendra Badhai
- Division of Molecular Genetics, The Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, the Netherlands; Oncode Institute, Utrecht, the Netherlands.
| | - Maarten van Lohuizen
- Division of Molecular Genetics, The Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, the Netherlands; Oncode Institute, Utrecht, the Netherlands.
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5
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Ratz L, Brambillasca C, Bartke L, Huetzen MA, Goergens J, Leidecker O, Jachimowicz RD, van de Ven M, Proost N, Siteur B, de Korte-Grimmerink R, Bouwman P, Pulver EM, de Bruijn R, Isensee J, Hucho T, Pandey G, van Lohuizen M, Mallmann P, Reinhardt HC, Jonkers J, Puppe J. Combined inhibition of EZH2 and ATM is synthetic lethal in BRCA1-deficient breast cancer. Breast Cancer Res 2022; 24:41. [PMID: 35715861 PMCID: PMC9206299 DOI: 10.1186/s13058-022-01534-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 06/02/2021] [Accepted: 06/01/2022] [Indexed: 11/25/2022] Open
Abstract
Background The majority of BRCA1-mutant breast cancers are characterized by a triple-negative phenotype and a basal-like molecular subtype, associated with aggressive clinical behavior. Current treatment options are limited, highlighting the need for the development of novel targeted therapies for this tumor subtype. Methods Our group previously showed that EZH2 is functionally relevant in BRCA1-deficient breast tumors and blocking EZH2 enzymatic activity could be a potent treatment strategy. To validate the role of EZH2 as a therapeutic target and to identify new synergistic drug combinations, we performed a high-throughput drug combination screen in various cell lines derived from BRCA1-deficient and -proficient mouse mammary tumors.
Results We identified the combined inhibition of EZH2 and the proximal DNA damage response kinase ATM as a novel synthetic lethality-based therapy for the treatment of BRCA1-deficient breast tumors. We show that the combined treatment with the EZH2 inhibitor GSK126 and the ATM inhibitor AZD1390 led to reduced colony formation, increased genotoxic stress, and apoptosis-mediated cell death in BRCA1-deficient mammary tumor cells in vitro. These findings were corroborated by in vivo experiments showing that simultaneous inhibition of EZH2 and ATM significantly increased anti-tumor activity in mice bearing BRCA1-deficient mammary tumors.
Conclusion Taken together, we identified a synthetic lethal interaction between EZH2 and ATM and propose this synergistic interaction as a novel molecular combination for the treatment of BRCA1-mutant breast cancer. Supplementary Information The online version contains supplementary material available at 10.1186/s13058-022-01534-y.
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Affiliation(s)
- Leonie Ratz
- Department of Obstetrics and Gynecology, University Hospital of Cologne, Kerpener Str. 34, 50931, Cologne, Germany.
| | - Chiara Brambillasca
- Division of Molecular Pathology, Netherlands Cancer Institute, Amsterdam, The Netherlands.,Oncode Institute, Amsterdam, The Netherlands
| | - Leandra Bartke
- Department of Obstetrics and Gynecology, University Hospital of Cologne, Kerpener Str. 34, 50931, Cologne, Germany
| | - Maxim A Huetzen
- Max Planck Research Group Mechanisms of DNA Repair, Max Planck Institute for Biology of Ageing, Cologne, Germany.,Department I of Internal Medicine, Center for Integrated Oncology Aachen Bonn Cologne and Duesseldorf, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany.,Cologne Excellence Cluster on Cellular Stress Responses in Ageing-Associated Diseases, University of Cologne, Cologne, Germany.,Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany
| | - Jonas Goergens
- Max Planck Research Group Mechanisms of DNA Repair, Max Planck Institute for Biology of Ageing, Cologne, Germany.,Department I of Internal Medicine, Center for Integrated Oncology Aachen Bonn Cologne and Duesseldorf, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany.,Cologne Excellence Cluster on Cellular Stress Responses in Ageing-Associated Diseases, University of Cologne, Cologne, Germany.,Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany
| | - Orsolya Leidecker
- Max Planck Research Group Mechanisms of DNA Repair, Max Planck Institute for Biology of Ageing, Cologne, Germany.,Department I of Internal Medicine, Center for Integrated Oncology Aachen Bonn Cologne and Duesseldorf, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany.,Cologne Excellence Cluster on Cellular Stress Responses in Ageing-Associated Diseases, University of Cologne, Cologne, Germany.,Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany
| | - Ron D Jachimowicz
- Max Planck Research Group Mechanisms of DNA Repair, Max Planck Institute for Biology of Ageing, Cologne, Germany.,Department I of Internal Medicine, Center for Integrated Oncology Aachen Bonn Cologne and Duesseldorf, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany.,Cologne Excellence Cluster on Cellular Stress Responses in Ageing-Associated Diseases, University of Cologne, Cologne, Germany.,Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany
| | - Marieke van de Ven
- Oncode Institute, Amsterdam, The Netherlands.,Mouse Clinic for Cancer and Ageing, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Natalie Proost
- Mouse Clinic for Cancer and Ageing, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Bjørn Siteur
- Mouse Clinic for Cancer and Ageing, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | | | - Peter Bouwman
- Oncode Institute, Amsterdam, The Netherlands.,Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University, Leiden, The Netherlands
| | - Emilia M Pulver
- Division of Molecular Pathology, Netherlands Cancer Institute, Amsterdam, The Netherlands.,Oncode Institute, Amsterdam, The Netherlands
| | - Roebi de Bruijn
- Division of Molecular Pathology, Netherlands Cancer Institute, Amsterdam, The Netherlands.,Oncode Institute, Amsterdam, The Netherlands.,Division of Molecular Carcinogenesis, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Jörg Isensee
- Translational Pain Research, Department of Anaesthesiology and Intensive Care Medicine, University Hospital Cologne, Faculty of Medicine, University Cologne, Cologne, Germany
| | - Tim Hucho
- Translational Pain Research, Department of Anaesthesiology and Intensive Care Medicine, University Hospital Cologne, Faculty of Medicine, University Cologne, Cologne, Germany
| | - Gaurav Pandey
- Mouse Clinic for Cancer and Ageing, Netherlands Cancer Institute, Amsterdam, The Netherlands.,Division of Molecular Genetics, Cancer Genomics Centre Netherlands, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Maarten van Lohuizen
- Mouse Clinic for Cancer and Ageing, Netherlands Cancer Institute, Amsterdam, The Netherlands.,Division of Molecular Genetics, Cancer Genomics Centre Netherlands, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Peter Mallmann
- Department of Obstetrics and Gynecology, University Hospital of Cologne, Kerpener Str. 34, 50931, Cologne, Germany
| | - Hans Christian Reinhardt
- Department of Hematology and Stem Cell Transplantation, University Hospital Essen, University Duisburg-Essen, German Cancer Consortium (DKTK Partner Site Essen), Essen, Germany
| | - Jos Jonkers
- Division of Molecular Pathology, Netherlands Cancer Institute, Amsterdam, The Netherlands.,Oncode Institute, Amsterdam, The Netherlands.,Mouse Clinic for Cancer and Ageing, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Julian Puppe
- Department of Obstetrics and Gynecology, University Hospital of Cologne, Kerpener Str. 34, 50931, Cologne, Germany.
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6
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Mbefo M, Berger A, Schouwey K, Gérard X, Kostic C, Beryozkin A, Sharon D, Dolfuss H, Munier F, Tran HV, van Lohuizen M, Beltran WA, Arsenijevic Y. Enhancer of Zeste Homolog 2 (EZH2) Contributes to Rod Photoreceptor Death Process in Several Forms of Retinal Degeneration and Its Activity Can Serve as a Biomarker for Therapy Efficacy. Int J Mol Sci 2021; 22:ijms22179331. [PMID: 34502238 PMCID: PMC8430630 DOI: 10.3390/ijms22179331] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [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] [Received: 07/26/2021] [Revised: 08/18/2021] [Accepted: 08/25/2021] [Indexed: 12/15/2022] Open
Abstract
Inherited retinal dystrophies (IRD) are due to various gene mutations. Each mutated gene instigates a specific cell homeostasis disruption, leading to a modification in gene expression and retinal degeneration. We previously demonstrated that the polycomb-repressive complex-1 (PRC1) markedly contributes to the cell death process. To better understand these mechanisms, we herein study the role of PRC2, specifically EZH2, which often initiates the gene inhibition by PRC1. We observed that the epigenetic mark H3K27me3 generated by EZH2 was progressively and strongly expressed in some individual photoreceptors and that the H3K27me3-positive cell number increased before cell death. H3K27me3 accumulation occurs between early (accumulation of cGMP) and late (CDK4 expression) events of retinal degeneration. EZH2 hyperactivity was observed in four recessive and two dominant mouse models of retinal degeneration, as well as two dog models and one IRD patient. Acute pharmacological EZH2 inhibition by intravitreal injection decreased the appearance of H3K27me3 marks and the number of TUNEL-positive cells revealing that EZH2 contributes to the cell death process. Finally, we observed that the absence of the H3K27me3 mark is a biomarker of gene therapy treatment efficacy in XLRPA2 dog model. PRC2 and PRC1 are therefore important actors in the degenerative process of multiple forms of IRD.
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Affiliation(s)
- Martial Mbefo
- Unit of Retinal Degeneration and Regeneration, Department of Ophthalmology, University of Lausanne, Fondation Asile des Aveugles, 1004 Lausanne, Switzerland; (M.M.); (A.B.); (K.S.); (X.G.); (C.K.)
| | - Adeline Berger
- Unit of Retinal Degeneration and Regeneration, Department of Ophthalmology, University of Lausanne, Fondation Asile des Aveugles, 1004 Lausanne, Switzerland; (M.M.); (A.B.); (K.S.); (X.G.); (C.K.)
| | - Karine Schouwey
- Unit of Retinal Degeneration and Regeneration, Department of Ophthalmology, University of Lausanne, Fondation Asile des Aveugles, 1004 Lausanne, Switzerland; (M.M.); (A.B.); (K.S.); (X.G.); (C.K.)
| | - Xavier Gérard
- Unit of Retinal Degeneration and Regeneration, Department of Ophthalmology, University of Lausanne, Fondation Asile des Aveugles, 1004 Lausanne, Switzerland; (M.M.); (A.B.); (K.S.); (X.G.); (C.K.)
| | - Corinne Kostic
- Unit of Retinal Degeneration and Regeneration, Department of Ophthalmology, University of Lausanne, Fondation Asile des Aveugles, 1004 Lausanne, Switzerland; (M.M.); (A.B.); (K.S.); (X.G.); (C.K.)
| | - Avigail Beryozkin
- Hadassah Medical Center, Faculty of Medicine, The Hebrew University Jerusalem, Jerusalem 91120, Israel; (A.B.); (D.S.)
| | - Dror Sharon
- Hadassah Medical Center, Faculty of Medicine, The Hebrew University Jerusalem, Jerusalem 91120, Israel; (A.B.); (D.S.)
| | - Hélène Dolfuss
- UMR_S 1112, Laboratoire de Génétique Médicales, University of Strasbourg, CEDEX, 67084 Strasbourg, France;
| | - Francis Munier
- Unit of Oculogenetics, Department of Ophthalmology, University of Lausanne, Fondation Asile des Aveugles, 1004 Lausanne, Switzerland; (F.M.); (H.V.T.)
| | - Hoai Viet Tran
- Unit of Oculogenetics, Department of Ophthalmology, University of Lausanne, Fondation Asile des Aveugles, 1004 Lausanne, Switzerland; (F.M.); (H.V.T.)
| | | | - William A. Beltran
- Division of Experimental Retinal Therapies, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA;
| | - Yvan Arsenijevic
- Unit of Retinal Degeneration and Regeneration, Department of Ophthalmology, University of Lausanne, Fondation Asile des Aveugles, 1004 Lausanne, Switzerland; (M.M.); (A.B.); (K.S.); (X.G.); (C.K.)
- Correspondence:
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7
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Badhai J, Pandey GK, Song JY, Krijgsman O, Bhaskaran R, Chandrasekaran G, Kwon MC, Bombardelli L, Monkhorst K, Grasso C, Zevenhoven J, van der Vliet J, Cozijnsen M, Krimpenfort P, Peeper D, van Lohuizen M, Berns A. Combined deletion of Bap1, Nf2, and Cdkn2ab causes rapid onset of malignant mesothelioma in mice. J Exp Med 2021; 217:151644. [PMID: 32271879 PMCID: PMC7971132 DOI: 10.1084/jem.20191257] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Revised: 12/09/2019] [Accepted: 02/26/2020] [Indexed: 12/26/2022] Open
Abstract
We have generated mouse models of malignant mesothelioma (MM) based upon disruption of the Bap1, Nf2, and Cdkn2ab tumor suppressor loci in various combinations as also frequently observed in human MM. Inactivation of all three loci in the mesothelial lining of the thoracic cavity leads to a highly aggressive MM that recapitulates the histological features and gene expression profile observed in human patients. The tumors also show a similar inflammatory phenotype. Bap1 deletion alone does not cause MM but dramatically accelerates MM development when combined with Nf2 and Cdkn2ab (hereafter BNC) disruption. The accelerated tumor development is accompanied by increased Polycomb repression and EZH2-mediated redistribution of H3K27me3 toward promoter sites with concomitant activation of PI3K and MAPK pathways. Treatment of BNC tumor–bearing mice with cisplatin and pemetrexed, the current frontline treatment, prolongs survival. This makes the autochthonous mouse model described here very well suited to explore the pathogenesis of MM and validate new treatment regimens for MM, including immunotherapy.
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Affiliation(s)
- Jitendra Badhai
- Oncode Institute, Division of Molecular Genetics, The Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Gaurav Kumar Pandey
- Oncode Institute, Division of Molecular Genetics, The Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Ji-Ying Song
- Department of Experimental Animal Pathology, The Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Oscar Krijgsman
- Oncode Institute, Division of Molecular Oncology and Immunology, The Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Rajith Bhaskaran
- Oncode Institute, Division of Molecular Genetics, The Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Gayathri Chandrasekaran
- Oncode Institute, Division of Molecular Genetics, The Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Min-Chul Kwon
- Division of Molecular Genetics, The Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Lorenzo Bombardelli
- Oncode Institute, Division of Molecular Genetics, The Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Kim Monkhorst
- Department of Pathology, The Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Cristoforo Grasso
- Division of Molecular Genetics, The Netherlands Cancer Institute, Amsterdam, Netherlands
| | - John Zevenhoven
- Division of Molecular Genetics, The Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Jan van der Vliet
- Division of Molecular Genetics, The Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Miranda Cozijnsen
- Division of Molecular Genetics, The Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Paul Krimpenfort
- Division of Molecular Genetics, The Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Daniel Peeper
- Oncode Institute, Division of Molecular Oncology and Immunology, The Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Maarten van Lohuizen
- Oncode Institute, Division of Molecular Genetics, The Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Anton Berns
- Oncode Institute, Division of Molecular Genetics, The Netherlands Cancer Institute, Amsterdam, Netherlands
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8
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van den Berk P, Lancini C, Company C, Serresi M, Sanchez-Bailon MP, Hulsman D, Pritchard C, Song JY, Schmitt MJ, Tanger E, Popp O, Mertins P, Huijbers IJ, Jacobs H, van Lohuizen M, Gargiulo G, Citterio E. USP15 Deubiquitinase Safeguards Hematopoiesis and Genome Integrity in Hematopoietic Stem Cells and Leukemia Cells. Cell Rep 2020; 33:108533. [PMID: 33378683 PMCID: PMC7788286 DOI: 10.1016/j.celrep.2020.108533] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Revised: 07/28/2020] [Accepted: 11/25/2020] [Indexed: 12/22/2022] Open
Abstract
Altering ubiquitination by disruption of deubiquitinating enzymes (DUBs) affects hematopoietic stem cell (HSC) maintenance. However, comprehensive knowledge of DUB function during hematopoiesis in vivo is lacking. Here, we systematically inactivate DUBs in mouse hematopoietic progenitors using in vivo small hairpin RNA (shRNA) screens. We find that multiple DUBs may be individually required for hematopoiesis and identify ubiquitin-specific protease 15 (USP15) as essential for HSC maintenance in vitro and in transplantations and Usp15 knockout (KO) mice in vivo. USP15 is highly expressed in human hematopoietic tissues and leukemias. USP15 depletion in murine progenitors and leukemia cells impairs in vitro expansion and increases genotoxic stress. In leukemia cells, USP15 interacts with and stabilizes FUS (fused in sarcoma), a known DNA repair factor, directly linking USP15 to the DNA damage response (DDR). Our study underscores the importance of DUBs in preserving normal hematopoiesis and uncovers USP15 as a critical DUB in safeguarding genome integrity in HSCs and leukemia cells. In vivo shRNAs screens for deubiquitinases identify regulators of murine hematopoiesis Usp15 deletion compromises HSC maintenance and reconstitution potential in vivo USP15 loss affects genome integrity and growth of mHSPCs and human leukemia cells In human leukemia cells, USP15 stabilizes its interactor, FUS, a DNA repair factor
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Affiliation(s)
- Paul van den Berk
- Division of Tumor Biology and Immunology, the Netherlands Cancer Institute, Plesmanlaan 121, Amsterdam 1066 CX, the Netherlands
| | - Cesare Lancini
- Division of Molecular Genetics, the Netherlands Cancer Institute, Plesmanlaan 121, Amsterdam 1066 CX, the Netherlands
| | - Carlos Company
- Max-Delbrück-Center for Molecular Medicine (MDC), Robert-Rössle-Str. 10, 13092 Berlin, Germany
| | - Michela Serresi
- Max-Delbrück-Center for Molecular Medicine (MDC), Robert-Rössle-Str. 10, 13092 Berlin, Germany
| | | | - Danielle Hulsman
- Division of Molecular Genetics, the Netherlands Cancer Institute, Plesmanlaan 121, Amsterdam 1066 CX, the Netherlands; ONCODE Institute, Utrecht, the Netherlands
| | - Colin Pritchard
- Transgenic Core Facility, Mouse Clinic for Cancer and Aging (MCCA), the Netherlands Cancer Institute, Plesmanlaan 121, Amsterdam 1066 CX, the Netherlands
| | - Ji-Ying Song
- Division of Experimental Animal Pathology, the Netherlands Cancer Institute, Plesmanlaan 121, Amsterdam 1066 CX, the Netherlands
| | - Matthias Jürgen Schmitt
- Max-Delbrück-Center for Molecular Medicine (MDC), Robert-Rössle-Str. 10, 13092 Berlin, Germany
| | - Ellen Tanger
- Division of Molecular Genetics, the Netherlands Cancer Institute, Plesmanlaan 121, Amsterdam 1066 CX, the Netherlands
| | - Oliver Popp
- Proteomics Platform, Max Delbrück Center for Molecular Medicine in the Helmholtz Association and Berlin Institute of Health, Robert Rössle Strasse 10, 13125 Berlin, Germany
| | - Philipp Mertins
- Proteomics Platform, Max Delbrück Center for Molecular Medicine in the Helmholtz Association and Berlin Institute of Health, Robert Rössle Strasse 10, 13125 Berlin, Germany
| | - Ivo J Huijbers
- Transgenic Core Facility, Mouse Clinic for Cancer and Aging (MCCA), the Netherlands Cancer Institute, Plesmanlaan 121, Amsterdam 1066 CX, the Netherlands
| | - Heinz Jacobs
- Division of Tumor Biology and Immunology, the Netherlands Cancer Institute, Plesmanlaan 121, Amsterdam 1066 CX, the Netherlands
| | - Maarten van Lohuizen
- Division of Molecular Genetics, the Netherlands Cancer Institute, Plesmanlaan 121, Amsterdam 1066 CX, the Netherlands; ONCODE Institute, Utrecht, the Netherlands
| | - Gaetano Gargiulo
- Max-Delbrück-Center for Molecular Medicine (MDC), Robert-Rössle-Str. 10, 13092 Berlin, Germany.
| | - Elisabetta Citterio
- Division of Molecular Genetics, the Netherlands Cancer Institute, Plesmanlaan 121, Amsterdam 1066 CX, the Netherlands; ONCODE Institute, Utrecht, the Netherlands.
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9
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Gisler S, Maia ARR, Chandrasekaran G, Kopparam J, van Lohuizen M. A genome-wide enrichment screen identifies NUMA1-loss as a resistance mechanism against mitotic cell-death induced by BMI1 inhibition. PLoS One 2020; 15:e0227592. [PMID: 32343689 PMCID: PMC7188281 DOI: 10.1371/journal.pone.0227592] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Accepted: 03/24/2020] [Indexed: 02/02/2023] Open
Abstract
BMI1 is a core protein of the polycomb repressive complex 1 (PRC1) that is overexpressed in several cancer types, making it a promising target for cancer therapies. However, the underlying mechanisms and interactions associated with BMI1-induced tumorigenesis are often context-dependent and complex. Here, we performed a drug resistance screen on mutagenized human haploid HAP1 cells treated with BMI1 inhibitor PTC-318 to find new genetic and mechanistic features associated with BMI1-dependent cancer cell proliferation. Our screen identified NUMA1-mutations as the most significant inducer of PTC-318 cell death resistance. Independent validations on NUMA1-proficient HAP1 and non-small cell lung cancer cell lines exposed to BMI1 inhibition by PTC-318 or BMI1 knockdown resulted in cell death following mitotic arrest. Interestingly, cells with CRISPR-Cas9 derived NUMA1 knockout also showed a mitotic arrest phenotype following BMI1 inhibition but, contrary to cells with wildtype NUMA1, these cells were resistant to BMI1-dependent cell death. The current study brings new insights to BMI1 inhibition-induced mitotic lethality in cancer cells and presents a previously unknown role of NUMA1 in this process.
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Affiliation(s)
- Santiago Gisler
- Division of Molecular Genetics, Oncode and The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Ana Rita R. Maia
- Division of Cell Biology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Gayathri Chandrasekaran
- Division of Molecular Genetics, Oncode and The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Jawahar Kopparam
- Division of Molecular Genetics, Oncode and The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Maarten van Lohuizen
- Division of Molecular Genetics, Oncode and The Netherlands Cancer Institute, Amsterdam, The Netherlands
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10
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Puppe J, Opdam M, Schouten PC, Jóźwiak K, Lips E, Severson T, van de Ven M, Brambillasca C, Bouwman P, van Tellingen O, Bernards R, Wesseling J, Eichler C, Thangarajah F, Malter W, Pandey GK, Ozretić L, Caldas C, van Lohuizen M, Hauptmann M, Rhiem K, Hahnen E, Reinhardt HC, Büttner R, Mallmann P, Schömig-Markiefka B, Schmutzler R, Linn S, Jonkers J. EZH2 Is Overexpressed in BRCA1-like Breast Tumors and Predictive for Sensitivity to High-Dose Platinum-Based Chemotherapy. Clin Cancer Res 2019; 25:4351-4362. [PMID: 31036541 DOI: 10.1158/1078-0432.ccr-18-4024] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Revised: 02/25/2019] [Accepted: 04/24/2019] [Indexed: 11/16/2022]
Abstract
PURPOSE BRCA1-deficient breast cancers carry a specific DNA copy-number signature ("BRCA1-like") and are hypersensitive to DNA double-strand break (DSB) inducing compounds. Here, we explored whether (i) EZH2 is overexpressed in human BRCA1-deficient breast tumors and might predict sensitivity to DSB-inducing drugs; (ii) EZH2 inhibition potentiates cisplatin efficacy in Brca1-deficient murine mammary tumors. EXPERIMENTAL DESIGN EZH2 expression was analyzed in 497 breast cancers using IHC or RNA sequencing. We classified 370 tumors by copy-number profiles as BRCA1-like or non-BRCA1-like and examined its association with EZH2 expression. Additionally, we assessed BRCA1 loss through mutation or promoter methylation status and investigated the predictive value of EZH2 expression in a study population of breast cancer patients treated with adjuvant high-dose platinum-based chemotherapy compared with standard anthracycline-based chemotherapy. To explore whether EZH2 inhibition by GSK126 enhances sensitivity to platinum drugs in EZH2-overexpressing breast cancers we used a Brca1-deficient mouse model. RESULTS The highest EZH2 expression was found in BRCA1-associated tumors harboring a BRCA1 mutation, BRCA1-promoter methylation or were classified as BRCA1 like. We observed a greater benefit from high-dose platinum-based chemotherapy in BRCA1-like and non-BRCA1-like patients with high EZH2 expression. Combined treatment with the EZH2 inhibitor GSK126 and cisplatin decreased cell proliferation and improved survival in Brca1-deficient mice in comparison with single agents. CONCLUSIONS Our findings demonstrate that EZH2 is expressed at significantly higher levels in BRCA1-deficient breast cancers. EZH2 overexpression can identify patients with breast cancer who benefit significantly from intensified DSB-inducing platinum-based chemotherapy independent of BRCA1-like status. EZH2 inhibition improves the antitumor effect of platinum drugs in Brca1-deficient breast tumors in vivo.
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Affiliation(s)
- Julian Puppe
- Division of Molecular Pathology, The Netherlands Cancer Institute, Amsterdam, the Netherlands.
- Department of Obstetrics and Gynecology, Medical Faculty, University Hospital Cologne, Cologne, Germany
- Center of Familial Breast and Ovarian Cancer, University Hospital of Cologne, Cologne, Germany
| | - Mark Opdam
- Division of Molecular Pathology, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Philip C Schouten
- Division of Molecular Pathology, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Katarzyna Jóźwiak
- Department of Epidemiology and Biostatistics, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Esther Lips
- Division of Molecular Pathology, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Tesa Severson
- Division of Molecular Pathology, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Marieke van de Ven
- Division of Molecular Pathology, The Netherlands Cancer Institute, Amsterdam, the Netherlands
- Oncode Institute, Utrecht, the Netherlands
| | - Chiara Brambillasca
- Division of Molecular Pathology, The Netherlands Cancer Institute, Amsterdam, the Netherlands
- Oncode Institute, Utrecht, the Netherlands
| | - Peter Bouwman
- Division of Molecular Pathology, The Netherlands Cancer Institute, Amsterdam, the Netherlands
- Oncode Institute, Utrecht, the Netherlands
| | - Olaf van Tellingen
- Division of Pharmacology, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - René Bernards
- Oncode Institute, Utrecht, the Netherlands
- Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Jelle Wesseling
- Division of Molecular Pathology, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Christian Eichler
- Department of Obstetrics and Gynecology, Medical Faculty, University Hospital Cologne, Cologne, Germany
| | - Fabinshy Thangarajah
- Department of Obstetrics and Gynecology, Medical Faculty, University Hospital Cologne, Cologne, Germany
| | - Wolfram Malter
- Department of Obstetrics and Gynecology, Medical Faculty, University Hospital Cologne, Cologne, Germany
| | - Gaurav Kumar Pandey
- Oncode Institute, Utrecht, the Netherlands
- Division of Molecular Genetics, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Luka Ozretić
- Department of Pathology, University Hospital of Cologne, Cologne, Germany
| | | | - Maarten van Lohuizen
- Oncode Institute, Utrecht, the Netherlands
- Division of Molecular Genetics, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Michael Hauptmann
- Department of Epidemiology and Biostatistics, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Kerstin Rhiem
- Center of Familial Breast and Ovarian Cancer, University Hospital of Cologne, Cologne, Germany
| | - Eric Hahnen
- Center of Familial Breast and Ovarian Cancer, University Hospital of Cologne, Cologne, Germany
| | | | - Reinhard Büttner
- Department of Pathology, University Hospital of Cologne, Cologne, Germany
| | - Peter Mallmann
- Department of Obstetrics and Gynecology, Medical Faculty, University Hospital Cologne, Cologne, Germany
| | | | - Rita Schmutzler
- Center of Familial Breast and Ovarian Cancer, University Hospital of Cologne, Cologne, Germany
| | - Sabine Linn
- Division of Molecular Pathology, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Jos Jonkers
- Division of Molecular Pathology, The Netherlands Cancer Institute, Amsterdam, the Netherlands
- Center of Familial Breast and Ovarian Cancer, University Hospital of Cologne, Cologne, Germany
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11
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Gisler S, Gonçalves JP, Akhtar W, de Jong J, Pindyurin AV, Wessels LFA, van Lohuizen M. Multiplexed Cas9 targeting reveals genomic location effects and gRNA-based staggered breaks influencing mutation efficiency. Nat Commun 2019; 10:1598. [PMID: 30962441 PMCID: PMC6453899 DOI: 10.1038/s41467-019-09551-w] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Accepted: 03/14/2019] [Indexed: 12/16/2022] Open
Abstract
Understanding the impact of guide RNA (gRNA) and genomic locus on CRISPR-Cas9 activity is crucial to design effective gene editing assays. However, it is challenging to profile Cas9 activity in the endogenous cellular environment. Here we leverage our TRIP technology to integrate ~ 1k barcoded reporter genes in the genomes of mouse embryonic stem cells. We target the integrated reporters (IRs) using RNA-guided Cas9 and characterize induced mutations by sequencing. We report that gRNA-sequence and IR locus explain most variation in mutation efficiency. Predominant insertions of a gRNA-specific nucleotide are consistent with template-dependent repair of staggered DNA ends with 1-bp 5' overhangs. We confirm that such staggered ends are induced by Cas9 in mouse pre-B cells. To explain observed insertions, we propose a model generating primarily blunt and occasionally staggered DNA ends. Mutation patterns indicate that gRNA-sequence controls the fraction of staggered ends, which could be used to optimize Cas9-based insertion efficiency.
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Affiliation(s)
- Santiago Gisler
- Division of Molecular Genetics, Oncode and The Netherlands Cancer Institute, Plesmanlaan 121, Amsterdam, 1066 CX, The Netherlands
| | - Joana P Gonçalves
- Department of Intelligent Systems, Delft University of Technology, Van Mourik Broekmanweg 6, Delft, 2628 XE, The Netherlands
- Division of Molecular Carcinogenesis, Oncode and The Netherlands Cancer Institute, Plesmanlaan 121, Amsterdam, 1066 CX, The Netherlands
| | - Waseem Akhtar
- Division of Molecular Genetics, Oncode and The Netherlands Cancer Institute, Plesmanlaan 121, Amsterdam, 1066 CX, The Netherlands
| | - Johann de Jong
- Division of Molecular Carcinogenesis, Oncode and The Netherlands Cancer Institute, Plesmanlaan 121, Amsterdam, 1066 CX, The Netherlands
- Data & Translational Sciences Group, UCB Biosciences GmbH, Alfred-Nobel-Straße 10, Monheim am Rhein, 40789, Germany
| | - Alexey V Pindyurin
- Institute of Molecular and Cellular Biology, Siberian Branch of Russian Academy of Sciences, Acad. Lavrentiev Ave. 8, Novosibirsk, 630090, Russia
- Division of Gene Regulation, Oncode and The Netherlands Cancer Institute, Plesmanlaan 121, Amsterdam, 1066 CX, The Netherlands
| | - Lodewyk F A Wessels
- Department of Intelligent Systems, Delft University of Technology, Van Mourik Broekmanweg 6, Delft, 2628 XE, The Netherlands.
- Division of Molecular Carcinogenesis, Oncode and The Netherlands Cancer Institute, Plesmanlaan 121, Amsterdam, 1066 CX, The Netherlands.
| | - Maarten van Lohuizen
- Division of Molecular Genetics, Oncode and The Netherlands Cancer Institute, Plesmanlaan 121, Amsterdam, 1066 CX, The Netherlands.
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12
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Serresi M, Siteur B, Hulsman D, Company C, Schmitt MJ, Lieftink C, Morris B, Cesaroni M, Proost N, Beijersbergen RL, van Lohuizen M, Gargiulo G. Ezh2 inhibition in Kras-driven lung cancer amplifies inflammation and associated vulnerabilities. J Exp Med 2018; 215:3115-3135. [PMID: 30487290 PMCID: PMC6279402 DOI: 10.1084/jem.20180801] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Revised: 08/31/2018] [Accepted: 11/01/2018] [Indexed: 12/24/2022] Open
Abstract
Kras-driven non–small-cell-lung cancers (NSCLCs) are a leading cause of death with limited therapeutic options. Serresi et al. show that inhibiting Ezh2 in orthotopic KrasG12D-driven NSCLC unleashes an inflammatory response rewiring tumor progression and amplifying associated vulnerabilities that could be therapeutically exploited. Kras-driven non–small-cell lung cancers (NSCLCs) are a leading cause of death with limited therapeutic options. Many NSCLCs exhibit high levels of Ezh2, the enzymatic subunit of polycomb repressive complex 2 (PRC2). We tested Ezh2 inhibitors as single agents or before chemotherapy in mice with orthotopic Kras-driven NSCLC grafts, which homogeneously express Ezh2. These tumors display sensitivity to EZH2 inhibition by GSK126 but also amplify an inflammatory program involving signaling through NF-κB and genes residing in PRC2-regulated chromatin. During this process, tumor cells overcome GSK126 antiproliferative effects. We identified oncogenes that may mediate progression through an in vivo RNAi screen aimed at targets of PRC2/NF-κB. An in vitro compound screening linked GSK126-driven inflammation and therapeutic vulnerability in human cells to regulation of RNA synthesis and proteostasis. Interestingly, GSK126-treated NSCLCs in vivo also showed an enhanced response to a combination of nimesulide and bortezomib. Thus, Ezh2 inhibition may restrict cell proliferation and promote defined adaptive responses. Targeting these responses potentially improves outcomes in Kras-driven NSCLCs.
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Affiliation(s)
- Michela Serresi
- Molecular Oncology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Bjorn Siteur
- Mouse Cancer Clinic, Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Danielle Hulsman
- Division of Molecular Genetics and Cancer Genomics Centre, Netherlands Cancer Institute, Amsterdam, Netherlands.,Oncode Institute, Utrecht, Netherlands
| | - Carlos Company
- Molecular Oncology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Matthias J Schmitt
- Molecular Oncology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Cor Lieftink
- Division of Molecular Carcinogenesis and Netherlands Cancer Institute Robotics and Screening Center, Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Ben Morris
- Division of Molecular Carcinogenesis and Netherlands Cancer Institute Robotics and Screening Center, Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Matteo Cesaroni
- Fels Institute, Temple University School of Medicine, Philadelphia, PA
| | - Natalie Proost
- Mouse Cancer Clinic, Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Roderick L Beijersbergen
- Division of Molecular Carcinogenesis and Netherlands Cancer Institute Robotics and Screening Center, Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Maarten van Lohuizen
- Division of Molecular Genetics and Cancer Genomics Centre, Netherlands Cancer Institute, Amsterdam, Netherlands .,Oncode Institute, Utrecht, Netherlands
| | - Gaetano Gargiulo
- Molecular Oncology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
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13
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Koppens MAJ, Bounova G, Cornelissen-Steijger P, de Vries N, Sansom OJ, Wessels LFA, van Lohuizen M. Large variety in a panel of human colon cancer organoids in response to EZH2 inhibition. Oncotarget 2016; 7:69816-69828. [PMID: 27634879 PMCID: PMC5342517 DOI: 10.18632/oncotarget.12002] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [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] [Received: 06/06/2016] [Accepted: 09/04/2016] [Indexed: 01/28/2023] Open
Abstract
EZH2 inhibitors have gained great interest for their use as anti-cancer therapeutics. However, most research has focused on EZH2 mutant cancers and recently adverse effects of EZH2 inactivation have come to light. To determine whether colorectal cancer cells respond to EZH2 inhibition and to explore which factors influence the degree of response, we treated a panel of 20 organoid lines derived from human colon tumors with different concentrations of the EZH2 inhibitor GSK126. The resulting responses were associated with mutation status, gene expression and responses to other drugs. We found that the response to GSK126 treatment greatly varied between organoid lines. Response associated with the mutation status of ATRX and PAX2, and correlated with BIK expression. It also correlated well with response to Nutlin-3a which inhibits MDM2-p53 interaction thereby activating p53 signaling. Sensitivity to EZH2 ablation depended on the presence of wild type p53, as tumor organoids became resistant when p53 was mutated or knocked down. Our exploratory study provides insight into which genetic factors predict sensitivity to EZH2 inhibition. In addition, we show that the response to EZH2 inhibition requires wild type p53. We conclude that a subset of colorectal cancer patients may benefit from EZH2-targeting therapies.
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Affiliation(s)
- Martijn AJ Koppens
- Division of Molecular Genetics, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Gergana Bounova
- Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | | | - Nienke de Vries
- Division of Molecular Genetics, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Owen J Sansom
- Cancer Research UK Beatson Institute, Glasgow, United Kingdom
| | - Lodewyk FA Wessels
- Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, Amsterdam, The Netherlands
- Department of EEMCS, Delft University of Technology, Delft, The Netherlands
- Cancer Genomics Centre Netherlands (CGC.nl), The Netherlands
| | - Maarten van Lohuizen
- Division of Molecular Genetics, The Netherlands Cancer Institute, Amsterdam, The Netherlands
- Cancer Genomics Centre Netherlands (CGC.nl), The Netherlands
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14
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Koppens MAJ, Bounova G, Gargiulo G, Tanger E, Janssen H, Cornelissen-Steijger P, Blom M, Song JY, Wessels LFA, van Lohuizen M. Deletion of Polycomb Repressive Complex 2 From Mouse Intestine Causes Loss of Stem Cells. Gastroenterology 2016; 151:684-697.e12. [PMID: 27342214 DOI: 10.1053/j.gastro.2016.06.020] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Revised: 06/03/2016] [Accepted: 06/13/2016] [Indexed: 12/30/2022]
Abstract
BACKGROUND & AIMS The polycomb repressive complex 2 (PRC2) regulates differentiation by contributing to repression of gene expression and thereby stabilizing the fate of stem cells and their progeny. PRC2 helps to maintain adult stem cell populations, but little is known about its functions in intestinal stem cells. We studied phenotypes of mice with intestine-specific deletion of the PRC2 proteins embryonic ectoderm development (EED) (a subunit required for PRC2 function) and enhancer of zeste homolog 2 (EZH2) (a histone methyltransferase). METHODS We performed studies of AhCre;EedLoxP/LoxP (EED knockout) mice and AhCre;Ezh2LoxP/LoxP (EZH2 knockout) mice, which have intestine-specific disruption in EED and EZH2, respectively. Small intestinal crypts were isolated and subsequently cultured to grow organoids. Intestines and organoids were analyzed by immunohistochemical, in situ hybridization, RNA sequence, and chromatin immunoprecipitation methods. RESULTS Intestines of EED knockout mice had massive crypt degeneration and lower numbers of proliferating cells compared with wild-type control mice. Cdkn2a became derepressed and we detected increased levels of P21. We did not observe any differences between EZH2 knockout and control mice. Intestinal crypts from EED knockout mice had signs of aberrant differentiation of uncommitted crypt cells-these differentiated toward the secretory cell lineage. Furthermore, crypts from EED-knockout mice had impaired Wnt signaling and concomitant loss of intestinal stem cells, this phenotype was not reversed upon ectopic stimulation of Wnt and Notch signaling in organoids. Analysis of gene expression patterns from intestinal tissues of EED knockout mice showed dysregulation of several genes involved in Wnt signaling. Wnt signaling was regulated directly by PRC2. CONCLUSIONS In intestinal tissues of mice, PRC2 maintains small intestinal stem cells by promoting proliferation and preventing differentiation in the intestinal stem cell compartment. PRC2 controls gene expression in multiple signaling pathways that regulate intestinal homeostasis. Sequencing data are available in the genomics data repository GEO under reference series GSE81578; RNA sequencing data are available under subseries GSE81576; and ChIP sequencing data are available under subseries GSE81577.
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Affiliation(s)
- Martijn A J Koppens
- Division of Molecular Genetics, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Gergana Bounova
- Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Gaetano Gargiulo
- Division of Molecular Genetics, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Ellen Tanger
- Division of Molecular Genetics, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Hans Janssen
- Division of Cell Biology II, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | | | - Marleen Blom
- Transgenic Core Facility, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Ji-Ying Song
- Department of Experimental Animal Pathology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Lodewyk F A Wessels
- Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, Amsterdam, The Netherlands; Department of Electrical Engineering, Mathematics and Computer Science, Delft University of Technology, Delft, The Netherlands; Cancer Genomics Centre Netherlands, Utrecht, The Netherlands
| | - Maarten van Lohuizen
- Division of Molecular Genetics, The Netherlands Cancer Institute, Amsterdam, The Netherlands; Cancer Genomics Centre Netherlands, Utrecht, The Netherlands.
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15
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Serresi M, Siteur B, Cesaroni M, Proost N, Hulsman D, van Lohuizen M, Gargiulo G. Abstract LB-204: Neoadjuvant Ezh2 inhibition amplifies an inflammatory program and sensitizes Kras-driven NSCLC to anti-NF-κB inhibition. Cancer Res 2016. [DOI: 10.1158/1538-7445.am2016-lb-204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Kras mutant non-small cell lung cancer (NSCLC) is a leading cause of death but has limited therapeutic options. We investigated the impact of Polycomb repressive complex 2 (PRC2) inhibitors as single agent or as neoadjuvant treatment for subsequent anti-inflammatory therapy. Using orthotopic grafts, we show that Kras cells highly expressing the PRC2 enzymatic component Ezh2 display sensitivity to its inhibition. Ezh2 inhibition leads to transcriptional amplification of an inflammatory program involving NF-kB. Pharmacological inhibition of Ezh2 rerouted Kras tumor progression towards exploiting PRC2/NF-kB target genes as inferred by in vivo RNAi screen but also enhanced the response of Kras NSCLC to a combination of Nimesulide and Bortezomib. These data suggest that low PRC2 levels in Kras-driven NSCLC promote an epigenetic switch, providing a rationale for exploring a novel therapeutic option in which Ezh2 simultaneously acts as biomarker for therapeutic decision and as a neoadjuvant target for therapy.
Citation Format: Michela Serresi, Bjorn Siteur, Matteo Cesaroni, Natalie Proost, Danielle Hulsman, Maarten van Lohuizen, Gaetano Gargiulo. Neoadjuvant Ezh2 inhibition amplifies an inflammatory program and sensitizes Kras-driven NSCLC to anti-NF-κB inhibition. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr LB-204.
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Affiliation(s)
| | - Bjorn Siteur
- 1The Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Matteo Cesaroni
- 2Fels Institute, Temple University School of Medicine, Philadelphia, PA
| | - Natalie Proost
- 1The Netherlands Cancer Institute, Amsterdam, Netherlands
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Miles DC, de Vries NA, Gisler S, Lieftink C, Akhtar W, Gogola E, Pawlitzky I, Hulsman D, Tanger E, Koppens M, Beijersbergen RL, van Lohuizen M. TRIM28 is an Epigenetic Barrier to Induced Pluripotent Stem Cell Reprogramming. Stem Cells 2016; 35:147-157. [PMID: 27350605 DOI: 10.1002/stem.2453] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2016] [Accepted: 06/07/2016] [Indexed: 01/12/2023]
Abstract
Since the discovery of induced pluripotent stem cells there has been intense interest in understanding the mechanisms that allow a somatic cell to be reprogrammed back to a pluripotent state. Several groups have studied the alterations in gene expression that occur as somatic cells modify their genome to that of an embryonic stem cell. Underpinning many of the gene expression changes are modifications to the epigenetic profile of the associated chromatin. We have used a large-scale shRNA screen to identify epigenetic modifiers that act as barriers to reprogramming. We have uncovered an important role for TRIM28 in cells resisting transition between somatic and pluripotent states. TRIM28 achieves this by maintaining the H3K9me3 repressed state and keeping endogenous retroviruses (ERVs) silenced. We propose that knockdown of TRIM28 during reprogramming results in more plastic H3K9me3 domains, dysregulation of genes nearby H3K9me3 marks, and up regulation of ERVs, thus facilitating the transition through reprogramming. Stem Cells 2017;35:147-157.
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Affiliation(s)
- Denise Catherine Miles
- Division of Molecular Genetics, NKI Robotics and Screening Center, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Nienke Alexandra de Vries
- Division of Molecular Genetics, NKI Robotics and Screening Center, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Santiago Gisler
- Division of Molecular Genetics, NKI Robotics and Screening Center, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Cor Lieftink
- Division of Molecular Carcinogenesis, NKI Robotics and Screening Center, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Waseem Akhtar
- Division of Molecular Genetics, NKI Robotics and Screening Center, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Ewa Gogola
- Division of Molecular of Molecular Pathology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Inka Pawlitzky
- Division of Molecular Genetics, NKI Robotics and Screening Center, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Danielle Hulsman
- Division of Molecular Genetics, NKI Robotics and Screening Center, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Ellen Tanger
- Division of Molecular Genetics, NKI Robotics and Screening Center, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Martijn Koppens
- Division of Molecular Genetics, NKI Robotics and Screening Center, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Roderick Leonardus Beijersbergen
- Division of Molecular Carcinogenesis, NKI Robotics and Screening Center, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Maarten van Lohuizen
- Division of Molecular Genetics, NKI Robotics and Screening Center, The Netherlands Cancer Institute, Amsterdam, The Netherlands.,Cancer Genomics Centre (CGC.nl), Amsterdam, The Netherlands
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Serresi M, Gargiulo G, Proost N, Siteur B, Cesaroni M, Koppens M, Xie H, Sutherland K, Hulsman D, Citterio E, Orkin S, Berns A, Lohuizen MV. Abstract IA05: Polycomb repressive complex-2 is a barrier to Kras-driven inflammation and epithelial-mesenchymal transition in non-small cell lung cancer. Mol Cancer Res 2016. [DOI: 10.1158/1557-3125.devbiolca15-ia05] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Polycomb repressive complexes (PRC) are frequently implicated in human cancer acting either as oncogenes or tumor suppressors. Here we show that PRC2 is a critical regulator of Kras-driven non-small-cell lung cancer (NSCLC) progression. Modulation of PRC2 by either Ezh2 overexpression or Eed deletion enhances Kras-driven adenomagenesis and inflammation, respectively. Eed-loss-driven inflammation leads to massive macrophage recruitment and marked decline in tissue function. Additional Trp53 inactivation activates a cell autonomous epithelial-to- mesenchymal transition (EMT) program leading to an invasive mucinous adenocarcinoma. A switch between methylated/acetylated chromatin underlies the tumor phenotypic evolution, prominently involving genes controlled by Hippo/Wnt-signaling. Our observations in the mouse models were conserved in human cells. Importantly, PRC2 inactivation results in context-dependent phenotypic alterations, with implications for its therapeutic application.
Citation Format: Michela Serresi, Gaetano Gargiulo, Nathalie Proost, Bjorn Siteur, Matteo Cesaroni, Martijn Koppens, Huafeng Xie, Kate Sutherland, Danielle Hulsman, Elisabetta Citterio, Stuart Orkin, Anton Berns, Maarten van Lohuizen. Polycomb repressive complex-2 is a barrier to Kras-driven inflammation and epithelial-mesenchymal transition in non-small cell lung cancer. [abstract]. In: Proceedings of the AACR Special Conference: Developmental Biology and Cancer; Nov 30-Dec 3, 2015; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Res 2016;14(4_Suppl):Abstract nr IA05.
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Affiliation(s)
- Michela Serresi
- 1The Netherlands Cancer Institute, Amsterdam, The Netherlands,
| | | | - Nathalie Proost
- 1The Netherlands Cancer Institute, Amsterdam, The Netherlands,
| | - Bjorn Siteur
- 1The Netherlands Cancer Institute, Amsterdam, The Netherlands,
| | - Matteo Cesaroni
- 2Fels Institute, Temple University School of Medicine, Philadelphia, PA,
| | - Martijn Koppens
- 1The Netherlands Cancer Institute, Amsterdam, The Netherlands,
| | - Huafeng Xie
- 3Dana-Farber Cancer Institute/Harvard Medical School, Boston, MA,
| | - Kate Sutherland
- 1The Netherlands Cancer Institute, Amsterdam, The Netherlands,
| | | | | | - Stuart Orkin
- 3Dana-Farber Cancer Institute/Harvard Medical School, Boston, MA,
| | - Anton Berns
- 1The Netherlands Cancer Institute, Amsterdam, The Netherlands,
| | - Maarten van Lohuizen
- 4The Netherlands Cancer Institute/Cancer Genomics Centre Netherlands, Amsterdam, The Netherlands
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Serresi M, Gargiulo G, Proost N, Siteur B, Cesaroni M, Koppens M, Xie H, Sutherland KD, Hulsman D, Citterio E, Orkin S, Berns A, van Lohuizen M. Polycomb Repressive Complex 2 Is a Barrier to KRAS-Driven Inflammation and Epithelial-Mesenchymal Transition in Non-Small-Cell Lung Cancer. Cancer Cell 2016; 29:17-31. [PMID: 26766588 DOI: 10.1016/j.ccell.2015.12.006] [Citation(s) in RCA: 73] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/12/2015] [Revised: 09/07/2015] [Accepted: 12/14/2015] [Indexed: 01/12/2023]
Abstract
Polycomb repressive complexes (PRC) are frequently implicated in human cancer, acting either as oncogenes or tumor suppressors. Here, we show that PRC2 is a critical regulator of KRAS-driven non-small cell lung cancer progression. Modulation of PRC2 by either Ezh2 overexpression or Eed deletion enhances KRAS-driven adenomagenesis and inflammation, respectively. Eed-loss-driven inflammation leads to massive macrophage recruitment and marked decline in tissue function. Additional Trp53 inactivation activates a cell-autonomous epithelial-to-mesenchymal transition program leading to an invasive mucinous adenocarcinoma. A switch between methylated/acetylated chromatin underlies the tumor phenotypic evolution, prominently involving genes controlled by Hippo/Wnt signaling. Our observations in the mouse models were conserved in human cells. Importantly, PRC2 inactivation results in context-dependent phenotypic alterations, with implications for its therapeutic application.
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Affiliation(s)
- Michela Serresi
- Division of Molecular Genetics, Centre for Biomedical Genetics, The Netherlands Cancer Institute, 1066 CX Amsterdam, the Netherlands
| | - Gaetano Gargiulo
- Division of Molecular Genetics, Centre for Biomedical Genetics, The Netherlands Cancer Institute, 1066 CX Amsterdam, the Netherlands.
| | - Natalie Proost
- Division of Molecular Genetics, Centre for Biomedical Genetics, The Netherlands Cancer Institute, 1066 CX Amsterdam, the Netherlands
| | - Bjorn Siteur
- Mouse Clinic Intervention Unit, The Netherlands Cancer Institute, 1066 CX Amsterdam, the Netherlands
| | - Matteo Cesaroni
- The Fels Institute, Temple University School of Medicine, Philadelphia, PA 19140, USA
| | - Martijn Koppens
- Division of Molecular Genetics, Centre for Biomedical Genetics, The Netherlands Cancer Institute, 1066 CX Amsterdam, the Netherlands
| | - Huafeng Xie
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Division of Hematology/Oncology, Boston Children's Hospital, Harvard Stem Cell Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Kate D Sutherland
- Division of Molecular Genetics, Centre for Biomedical Genetics, The Netherlands Cancer Institute, 1066 CX Amsterdam, the Netherlands
| | - Danielle Hulsman
- Division of Molecular Genetics, Centre for Biomedical Genetics, The Netherlands Cancer Institute, 1066 CX Amsterdam, the Netherlands
| | - Elisabetta Citterio
- Division of Molecular Genetics, Centre for Biomedical Genetics, The Netherlands Cancer Institute, 1066 CX Amsterdam, the Netherlands
| | - Stuart Orkin
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Division of Hematology/Oncology, Boston Children's Hospital, Harvard Stem Cell Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Anton Berns
- Division of Molecular Genetics, Centre for Biomedical Genetics, The Netherlands Cancer Institute, 1066 CX Amsterdam, the Netherlands
| | - Maarten van Lohuizen
- Division of Molecular Genetics, Centre for Biomedical Genetics, The Netherlands Cancer Institute, 1066 CX Amsterdam, the Netherlands; Cancer Genomics Centre (CGC.nl), Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands.
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de Jong J, Wessels LFA, van Lohuizen M, de Ridder J, Akhtar W. Applications of DNA integrating elements: Facing the bias bully. Mob Genet Elements 2015; 4:1-6. [PMID: 26442173 PMCID: PMC4588226 DOI: 10.4161/2159256x.2014.992694] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [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: 10/01/2014] [Revised: 11/19/2014] [Accepted: 11/25/2014] [Indexed: 12/17/2022] Open
Abstract
Retroviruses and DNA transposons are an important part of molecular biologists' toolbox. The applications of these elements range from functional genomics to oncogene discovery and gene therapy. However, these elements do not integrate uniformly across the genome, which is an important limitation to their use. A number of genetic and epigenetic factors have been shown to shape the integration preference of these elements. Insight into integration bias can significantly enhance the analysis and interpretation of results obtained using these elements. For three different applications, we outline how bias can affect results, and can potentially be addressed.
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Affiliation(s)
- Johann de Jong
- Computational Cancer Biology Group; Division of Molecular Carcinogenesis; The Netherlands Cancer Institute ; Amsterdam, The Netherlands
| | - Lodewyk F A Wessels
- Computational Cancer Biology Group; Division of Molecular Carcinogenesis; The Netherlands Cancer Institute ; Amsterdam, The Netherlands ; Delft Bioinformatics Lab; TU Delft ; Delft, The Netherlands
| | - Maarten van Lohuizen
- Division of Molecular Genetics; The Netherlands Cancer Institute ; Amsterdam, The Netherlands
| | | | - Waseem Akhtar
- Division of Molecular Genetics; The Netherlands Cancer Institute ; Amsterdam, The Netherlands
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Abstract
Loss-of-function (LOF) experiments targeting multiple genes during tumorigenesis can be implemented using pooled shRNA libraries. RNAi screens in animal models rely on the use of multiple shRNAs to simultaneously disrupt gene function, as well as to serve as barcodes for cell fate outcomes during tumorigenesis. Here we provide a protocol for performing RNAi screens in orthotopic mouse tumor models, referring to glioma and lung adenocarcinoma as specific examples. The protocol aims to provide guidelines for applying RNAi to a diverse spectrum of solid tumors and to highlight crucial considerations when designing and performing these studies. It covers shRNA library assembly and packaging into lentiviral particles, and transduction into tumor-initiating cells (TICs), followed by in vivo transplantation, tumor DNA recovery, sequencing and analysis. Depending on the target genes and tumor model, tumor suppressors and oncogenes can be identified or biological pathways can be dissected in 6-9 weeks.
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Affiliation(s)
- Gaetano Gargiulo
- Division of Molecular Genetics, the Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Michela Serresi
- Division of Molecular Genetics, the Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Matteo Cesaroni
- Fels Institute, Temple University School of Medicine, Philadelphia, Pennsylvania, USA
| | - Danielle Hulsman
- Division of Molecular Genetics, the Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Maarten van Lohuizen
- 1] Division of Molecular Genetics, the Netherlands Cancer Institute, Amsterdam, the Netherlands. [2] Cancer Genomics Centre, the Netherlands
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21
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Lohuizen MV. Abstract SY35-01: Unexpected results of prolonged EZH2 inhibition in an in vivo model for glioblastoma. Cancer Res 2014. [DOI: 10.1158/1538-7445.am2014-sy35-01] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Repressive Polycomb-group (Pc-G) protein complexes and the counteracting Trithorax-group (Trx-G) of nucleosome remodeling factors are involved in the dynamic maintenance of proper gene expression patterns during development, acting at the level of chromatin structure. As such, they are important controllers of cell fate and differentiation. When deregulated, these master switches of gene expression are strongly implicated in formation of a diverse set of cancers. Examples are the Pc-G gene Bmi1 and Ezh2 which are overexpressed in many cancers including glioblastoma. However, recently Ezh2 has also been found to be mutated/inactivated in other forms of cancer, suggesting a highly context-dependent role as either an oncogene or tumor suppressor. An outstanding question is how to identify among the many Pc-G bound genes the cancer-relevant ones. Hereto we have recently successfully combined stringent ChIP-seq with custom shRNAi library screening in in vivo models for glioblastoma. As Ezh2 is associated with poor prognosis and metastasis in many cancer settings there is an increasing interest for development of selective Ezh2 inhibitors as potential new ways for epigenetic cancer therapy. We have developed conditional shRNAi inhibition in mouse models for aggressive glioma to study the effects of Ezh2 inhibition on tumor initiation and maintenance. Whereas initial tumor regression upon Ezh2 inhibition was observed in vivo, prolonged Ezh2 inhibition caused unexpected profound changes in tumor plasticity, differentiation status with important consequences for tumor progression and treatment options, which will be discussed.
Selected references:
1. Sophia W.M. Bruggeman, Danielle Hulsman, Ellen Tanger, Tessa Buckle, Marleen Blom, John Zevenhoven, Olaf van Tellingen and Maarten van Lohuizen. Bmi1 controls tumor development in an Ink4a/Arf-independent manner in a mouse model for glioma. Cancer Cell 2007, 12, 328-341.
2. Gargiulo G, Cesaroni M, Serresi M, de Vries N, Hulsman D, Bruggeman SW, Lancini C, van Lohuizen M. In vivo RNAi screen for BMI1 targets identifies TGF-β/BMP-ER stress pathways as key regulators of neural- and malignant glioma-stem cell homeostasis. Cancer Cell. 2013 May 13;23(5):660-76
Citation Format: Maarten van Lohuizen. Unexpected results of prolonged EZH2 inhibition in an in vivo model for glioblastoma. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr SY35-01. doi:10.1158/1538-7445.AM2014-SY35-01
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Fujimura YI, Isono KI, Vidal M, Endoh M, Kajita H, Mizutani-Koseki Y, Takihara Y, van Lohuizen M, Otte A, Jenuwein T, Deschamps J, Koseki H. Distinct roles of Polycomb group gene products in transcriptionally repressed and active domains of Hoxb8. Development 2014. [DOI: 10.1242/dev.115667] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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23
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Lancini C, van den Berk PC, Vissers JH, Gargiulo G, Song JY, Hulsman D, Serresi M, Tanger E, Blom M, Vens C, van Lohuizen M, Jacobs H, Citterio E. Tight regulation of ubiquitin-mediated DNA damage response by USP3 preserves the functional integrity of hematopoietic stem cells. J Biophys Biochem Cytol 2014. [DOI: 10.1083/jcb.2064oia143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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24
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Lancini C, van den Berk PCM, Vissers JHA, Gargiulo G, Song JY, Hulsman D, Serresi M, Tanger E, Blom M, Vens C, van Lohuizen M, Jacobs H, Citterio E. Tight regulation of ubiquitin-mediated DNA damage response by USP3 preserves the functional integrity of hematopoietic stem cells. ACTA ACUST UNITED AC 2014; 211:1759-77. [PMID: 25113974 PMCID: PMC4144738 DOI: 10.1084/jem.20131436] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
In vivo deletion of USP3, a deubiquitinating enzyme involved in DNA damage repair, increases the incidence of spontaneous cancer and impairs the proliferation and repopulation ability of HSCs. Histone ubiquitination at DNA breaks is required for activation of the DNA damage response (DDR) and DNA repair. How the dynamic removal of this modification by deubiquitinating enzymes (DUBs) impacts genome maintenance in vivo is largely unknown. To address this question, we generated mice deficient for Ub-specific protease 3 (USP3; Usp3Δ/Δ), a histone H2A DUB which negatively regulates ubiquitin-dependent DDR signaling. Notably, USP3 deletion increased the levels of histone ubiquitination in adult tissues, reduced the hematopoietic stem cell (HSC) reserves over time, and shortened animal life span. Mechanistically, our data show that USP3 is important in HSC homeostasis, preserving HSC self-renewal, and repopulation potential in vivo and proliferation in vitro. A defective DDR and unresolved spontaneous DNA damage contribute to cell cycle restriction of Usp3Δ/Δ HSCs. Beyond the hematopoietic system, Usp3Δ/Δ animals spontaneously developed tumors, and primary Usp3Δ/Δ cells failed to preserve chromosomal integrity. These findings broadly support the regulation of chromatin ubiquitination as a key pathway in preserving tissue function through modulation of the response to genotoxic stress.
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Affiliation(s)
- Cesare Lancini
- Division of Molecular Genetics, Division of Biological Stress Response, and Division of Experimental Animal Pathology, The Netherlands Cancer Institute, 1066 CX Amsterdam, Netherlands
| | - Paul C M van den Berk
- Division of Molecular Genetics, Division of Biological Stress Response, and Division of Experimental Animal Pathology, The Netherlands Cancer Institute, 1066 CX Amsterdam, Netherlands
| | - Joseph H A Vissers
- Division of Molecular Genetics, Division of Biological Stress Response, and Division of Experimental Animal Pathology, The Netherlands Cancer Institute, 1066 CX Amsterdam, Netherlands
| | - Gaetano Gargiulo
- Division of Molecular Genetics, Division of Biological Stress Response, and Division of Experimental Animal Pathology, The Netherlands Cancer Institute, 1066 CX Amsterdam, Netherlands
| | - Ji-Ying Song
- Division of Molecular Genetics, Division of Biological Stress Response, and Division of Experimental Animal Pathology, The Netherlands Cancer Institute, 1066 CX Amsterdam, Netherlands
| | - Danielle Hulsman
- Division of Molecular Genetics, Division of Biological Stress Response, and Division of Experimental Animal Pathology, The Netherlands Cancer Institute, 1066 CX Amsterdam, Netherlands
| | - Michela Serresi
- Division of Molecular Genetics, Division of Biological Stress Response, and Division of Experimental Animal Pathology, The Netherlands Cancer Institute, 1066 CX Amsterdam, Netherlands
| | - Ellen Tanger
- Division of Molecular Genetics, Division of Biological Stress Response, and Division of Experimental Animal Pathology, The Netherlands Cancer Institute, 1066 CX Amsterdam, Netherlands
| | - Marleen Blom
- Division of Molecular Genetics, Division of Biological Stress Response, and Division of Experimental Animal Pathology, The Netherlands Cancer Institute, 1066 CX Amsterdam, Netherlands
| | - Conchita Vens
- Division of Molecular Genetics, Division of Biological Stress Response, and Division of Experimental Animal Pathology, The Netherlands Cancer Institute, 1066 CX Amsterdam, Netherlands
| | - Maarten van Lohuizen
- Division of Molecular Genetics, Division of Biological Stress Response, and Division of Experimental Animal Pathology, The Netherlands Cancer Institute, 1066 CX Amsterdam, Netherlands
| | - Heinz Jacobs
- Division of Molecular Genetics, Division of Biological Stress Response, and Division of Experimental Animal Pathology, The Netherlands Cancer Institute, 1066 CX Amsterdam, Netherlands
| | - Elisabetta Citterio
- Division of Molecular Genetics, Division of Biological Stress Response, and Division of Experimental Animal Pathology, The Netherlands Cancer Institute, 1066 CX Amsterdam, Netherlands
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Michalak EM, Nacerddine K, Pietersen A, Beuger V, Pawlitzky I, Cornelissen-Steijger P, Wientjens E, Tanger E, Seibler J, van Lohuizen M, Jonkers J. Polycomb group gene Ezh2 regulates mammary gland morphogenesis and maintains the luminal progenitor pool. Stem Cells 2014; 31:1910-20. [PMID: 23712803 DOI: 10.1002/stem.1437] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2013] [Revised: 04/08/2013] [Accepted: 04/29/2013] [Indexed: 01/19/2023]
Abstract
Specification of the cellular hierarchy in the mammary gland involves complex signaling that remains poorly defined. Polycomb group proteins are known to contribute to the maintenance of stem cell identity through epigenetic modifications, leading to stable alterations in gene expression. The polycomb protein family member EZH2 is known to be important for stem cell maintenance in multiple tissues, but its role in mammary gland development and differentiation remains unknown. Our analyses show that EZH2 is predominantly expressed in luminal cells of the mouse mammary epithelium. As mammary gland development occurs mostly after birth, the analysis of EZH2 gene function in postnatal development is precluded by embryonic lethality of conventional EZH2 knockout mice. To investigate the role of EZH2 in normal mammary gland epithelium, we have generated novel transgenic mice that express doxycycline-regulatable short hairpin (sh) RNAs directed against Ezh2. Knockdown of EZH2 results in delayed outgrowth of the mammary epithelium during puberty, due to impaired terminal end bud formation and ductal elongation. Furthermore, our results demonstrate that EZH2 is required to maintain the luminal cell pool and may limit differentiation of luminal progenitors into CD61(+) differentiated luminal cells, suggesting a role for EZH2 in mammary luminal cell fate determination. Consistent with this, EZH2 knockdown reduced lobuloalveolar expansion during pregnancy, suggesting EZH2 is required for the differentiation of luminal progenitors to alveolar cells.
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Affiliation(s)
- Ewa Malgorzata Michalak
- Division of Molecular Pathology and Cancer Genomics Centre, Netherlands Cancer Institute, Amsterdam, The Netherlands
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de Jong J, Akhtar W, Badhai J, Rust AG, Rad R, Hilkens J, Berns A, van Lohuizen M, Wessels LFA, de Ridder J. Chromatin landscapes of retroviral and transposon integration profiles. PLoS Genet 2014; 10:e1004250. [PMID: 24721906 PMCID: PMC3983033 DOI: 10.1371/journal.pgen.1004250] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2013] [Accepted: 02/04/2014] [Indexed: 12/16/2022] Open
Abstract
The ability of retroviruses and transposons to insert their genetic material into host DNA makes them widely used tools in molecular biology, cancer research and gene therapy. However, these systems have biases that may strongly affect research outcomes. To address this issue, we generated very large datasets consisting of to unselected integrations in the mouse genome for the Sleeping Beauty (SB) and piggyBac (PB) transposons, and the Mouse Mammary Tumor Virus (MMTV). We analyzed (epi)genomic features to generate bias maps at both local and genome-wide scales. MMTV showed a remarkably uniform distribution of integrations across the genome. More distinct preferences were observed for the two transposons, with PB showing remarkable resemblance to bias profiles of the Murine Leukemia Virus. Furthermore, we present a model where target site selection is directed at multiple scales. At a large scale, target site selection is similar across systems, and defined by domain-oriented features, namely expression of proximal genes, proximity to CpG islands and to genic features, chromatin compaction and replication timing. Notable differences between the systems are mainly observed at smaller scales, and are directed by a diverse range of features. To study the effect of these biases on integration sites occupied under selective pressure, we turned to insertional mutagenesis (IM) screens. In IM screens, putative cancer genes are identified by finding frequently targeted genomic regions, or Common Integration Sites (CISs). Within three recently completed IM screens, we identified 7%–33% putative false positive CISs, which are likely not the result of the oncogenic selection process. Moreover, results indicate that PB, compared to SB, is more suited to tag oncogenes. Retroviruses and transposons are widely used in cancer research and gene therapy. However, these systems show integration biases that may strongly affect results. To address this issue, we generated very large datasets consisting of to unselected integrations for the Sleeping Beauty and piggyBac transposons, and the Mouse Mammary Tumor Virus (MMTV). We analyzed (epi)genomic features to generate bias maps at local and genome-wide scales. MMTV showed a remarkably uniform distribution of integrations across the genome, and a striking similarity was observed between piggyBac and the Murine Leukemia Virus. Moreover, we find that target site selection is directed at multiple scales. At larger scales, it is similar across systems, and directed by a set of domain-oriented features, including chromatin compaction, replication timing, and CpG islands. Notable differences between systems are defined at smaller scales by a diverse range of epigenetic features. As a practical application of our findings, we determined that three recent insertional mutagenesis screens - commonly used for cancer gene discovery - contained 7%–33% putative false positive integration hotspots.
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Affiliation(s)
- Johann de Jong
- Computational Cancer Biology Group, Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, Amsterdam, The Netherlands
- Netherlands Consortium for Systems Biology, Amsterdam, The Netherlands
| | - Waseem Akhtar
- Netherlands Consortium for Systems Biology, Amsterdam, The Netherlands
- Division of Molecular Genetics, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Jitendra Badhai
- Division of Molecular Genetics, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Alistair G. Rust
- Wellcome Trust Sanger Institute, Genome Campus, Hinxton-Cambridge, United Kingdom
| | - Roland Rad
- Department of Medicine II; Klinikum Rechts der Isar; Technische Universität München, German Cancer Research Center (DKFZ), Heidelberg, & German Cancer Consortium (DKTK), Heidelberg, Germany
| | - John Hilkens
- Division of Molecular Genetics, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Anton Berns
- Division of Molecular Genetics, The Netherlands Cancer Institute, Amsterdam, The Netherlands
- Skoltech Center for Stem Cell Research, Skolkovo Institute for Science and Technology, Skolkovo, Odintsovsky, Moscow, Russia
| | - Maarten van Lohuizen
- Netherlands Consortium for Systems Biology, Amsterdam, The Netherlands
- Division of Molecular Genetics, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Lodewyk F. A. Wessels
- Computational Cancer Biology Group, Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, Amsterdam, The Netherlands
- Netherlands Consortium for Systems Biology, Amsterdam, The Netherlands
- Delft Bioinformatics Lab, Faculty of EEMCS, TU Delft, Delft, The Netherlands
- * E-mail: (LFAW); (JdR)
| | - Jeroen de Ridder
- Delft Bioinformatics Lab, Faculty of EEMCS, TU Delft, Delft, The Netherlands
- * E-mail: (LFAW); (JdR)
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Akhtar W, de Jong J, Pindyurin AV, Pagie L, Meuleman W, de Ridder J, Berns A, Wessels LFA, van Lohuizen M, van Steensel B. Chromatin position effects assayed by thousands of reporters integrated in parallel. Cell 2013; 154:914-27. [PMID: 23953119 DOI: 10.1016/j.cell.2013.07.018] [Citation(s) in RCA: 221] [Impact Index Per Article: 20.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2013] [Revised: 05/31/2013] [Accepted: 07/12/2013] [Indexed: 12/11/2022]
Abstract
Reporter genes integrated into the genome are a powerful tool to reveal effects of regulatory elements and local chromatin context on gene expression. However, so far such reporter assays have been of low throughput. Here, we describe a multiplexing approach for the parallel monitoring of transcriptional activity of thousands of randomly integrated reporters. More than 27,000 distinct reporter integrations in mouse embryonic stem cells, obtained with two different promoters, show ∼1,000-fold variation in expression levels. Data analysis indicates that lamina-associated domains act as attenuators of transcription, likely by reducing access of transcription factors to binding sites. Furthermore, chromatin compaction is predictive of reporter activity. We also found evidence for crosstalk between neighboring genes and estimate that enhancers can influence gene expression on average over ∼20 kb. The multiplexed reporter assay is highly flexible in design and can be modified to query a wide range of aspects of gene regulation.
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Affiliation(s)
- Waseem Akhtar
- Division of Molecular Genetics, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
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Gargiulo G, Cesaroni M, Serresi M, de Vries N, Hulsman D, Bruggeman SW, Lancini C, van Lohuizen M. In vivo RNAi screen for BMI1 targets identifies TGF-β/BMP-ER stress pathways as key regulators of neural- and malignant glioma-stem cell homeostasis. Cancer Cell 2013; 23:660-76. [PMID: 23680149 DOI: 10.1016/j.ccr.2013.03.030] [Citation(s) in RCA: 147] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/06/2012] [Revised: 01/10/2013] [Accepted: 03/29/2013] [Indexed: 01/26/2023]
Abstract
In mouse and human neural progenitor and glioblastoma "stem-like" cells, we identified key targets of the Polycomb-group protein BMI1 by combining ChIP-seq with in vivo RNAi screening. We discovered that Bmi1 is important in the cellular response to the transforming growth factor-β/bone morphogenetic protein (TGF-β/BMP) and endoplasmic reticulum (ER) stress pathways, in part converging on the Atf3 transcriptional repressor. We show that Atf3 is a tumor-suppressor gene inactivated in human glioblastoma multiforme together with Cbx7 and a few other candidates. Acting downstream of the ER stress and BMP pathways, ATF3 binds to cell-type-specific accessible chromatin preloaded with AP1 and participates in the inhibition of critical oncogenic networks. Our data support the feasibility of combining ChIP-seq and RNAi screens in solid tumors and highlight multiple p16(INK4a)/p19(ARF)-independent functions for Bmi1 in development and cancer.
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Affiliation(s)
- Gaetano Gargiulo
- Division of Molecular Genetics and Centre for Biomedical Genetics, The Netherlands Cancer Institute, 1066CX Amsterdam, The Netherlands
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29
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Abstract
Polycomb group (PcG) genes encode chromatin modifiers that are involved in the maintenance of cell identity and in proliferation, processes that are often deregulated in cancer. Interestingly, besides a role in epigenetic gene silencing, recent studies have begun to uncover a function for PcG proteins in the cellular response to DNA damage. In particular, PcG proteins have been shown to accumulate at sites of DNA double-strand breaks (DSBs). Several signaling pathways contribute to the recruitment of PcG proteins to DSBs, where they catalyze the ubiquitylation of histone H2A. The relevance of these findings is supported by the fact that loss of PcG genes decreases the efficiency of cells to repair DSBs and renders them sensitive to ionizing radiation. The recruitment of PcG proteins to DNA breaks suggests that they have a function in coordinating gene silencing and DNA repair at the chromatin flanking DNA lesions. In this Commentary, we discuss the current knowledge of the mechanisms that allow PcG proteins to exert their positive functions in genome maintenance.
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Affiliation(s)
- Joseph H A Vissers
- Division of Molecular Genetics, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
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30
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Yokobayashi S, Liang CY, Kohler H, Nestorov P, Liu Z, Vidal M, van Lohuizen M, Roloff TC, Peters AHFM. PRC1 coordinates timing of sexual differentiation of female primordial germ cells. Nature 2013; 495:236-40. [PMID: 23486062 DOI: 10.1038/nature11918] [Citation(s) in RCA: 90] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2012] [Accepted: 01/16/2013] [Indexed: 01/05/2023]
Abstract
In mammals, sex differentiation of primordial germ cells (PGCs) is determined by extrinsic cues from the environment. In mouse female PGCs, expression of stimulated by retinoic acid gene 8 (Stra8) and meiosis are induced in response to retinoic acid provided from the mesonephroi. Given the widespread role of retinoic acid signalling during development, the molecular mechanisms that enable PGCs to express Stra8 and enter meiosis in a timely manner are unknown. Here we identify gene-dosage-dependent roles in PGC development for Ring1 and Rnf2, two central components of the Polycomb repressive complex 1 (PRC1). Both paralogues are essential for PGC development between days 10.5 and 11.5 of gestation. Rnf2 is subsequently required in female PGCs to maintain high levels of Oct4 (also known as Pou5f1) and Nanog expression, and to prevent premature induction of meiotic gene expression and entry into meiotic prophase. Chemical inhibition of retinoic acid signalling partially suppresses precocious Oct4 downregulation and Stra8 activation in Rnf2-deficient female PGCs. Chromatin immunoprecipitation analyses show that Stra8 is a direct target of PRC1 and PRC2 in PGCs. These data demonstrate the importance of PRC1 gene dosage in PGC development and in coordinating the timing of sex differentiation of female PGCs by antagonizing extrinsic retinoic acid signalling.
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Affiliation(s)
- Shihori Yokobayashi
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, CH-4058 Basel, Switzerland
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31
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van der Velden YU, Wang L, van Lohuizen M, Haramis APG. The Polycomb group protein Ring1b is essential for pectoral fin development. Development 2012; 139:2210-20. [PMID: 22619390 DOI: 10.1242/dev.077156] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Polycomb group (PcG) proteins are transcriptional repressors that mediate epigenetic gene silencing by chromatin modification. PcG-mediated gene repression is implicated in development, cell differentiation, stem-cell fate maintenance and cancer. However, analysis of the roles of PcG proteins in orchestrating vertebrate developmental programs in vivo has been hampered by the early embryonic lethality of several PcG gene knockouts in mice. Here, we demonstrate that zebrafish Ring1b, the E3 ligase in Polycomb Repressive Complex 1 (PRC1), is essential for pectoral fin development. We show that differentiation of lateral plate mesoderm (LPM) cells into presumptive pectoral fin precursors is initiated normally in ring1b mutants, but fin bud outgrowth is impaired. Fgf signaling, which is essential for migration, proliferation and cell-fate maintenance during fin development, is not sufficiently activated in ring1b mutants. Exogenous application of FGF4, as well as enhanced stimulation of Fgf signaling by overactivated Wnt signaling in apc mutants, partially restores the fin developmental program. These results reveal that, in the absence of functional Ring1b, fin bud cells fail to execute the pectoral fin developmental program. Together, our results demonstrate that PcG-mediated gene regulation is essential for sustained Fgf signaling in vertebrate limb development.
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Affiliation(s)
- Yme U van der Velden
- Department of Molecular Genetics, Netherlands Cancer Institute, Amsterdam, The Netherlands
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32
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Nacerddine K, Beaudry JB, Ginjala V, Westerman B, Mattiroli F, Song JY, van der Poel H, Ponz OB, Pritchard C, Cornelissen-Steijger P, Zevenhoven J, Tanger E, Sixma TK, Ganesan S, van Lohuizen M. Akt-mediated phosphorylation of Bmi1 modulates its oncogenic potential, E3 ligase activity, and DNA damage repair activity in mouse prostate cancer. J Clin Invest 2012; 122:1920-32. [PMID: 22505453 DOI: 10.1172/jci57477] [Citation(s) in RCA: 87] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2011] [Accepted: 02/29/2012] [Indexed: 11/17/2022] Open
Abstract
Prostate cancer (PCa) is a major lethal malignancy in men, but the molecular events and their interplay underlying prostate carcinogenesis remain poorly understood. Epigenetic events and the upregulation of polycomb group silencing proteins including Bmi1 have been described to occur during PCa progression. Here, we found that conditional overexpression of Bmi1 in mice induced prostatic intraepithelial neoplasia, and elicited invasive adenocarcinoma when combined with PTEN haploinsufficiency. In addition, Bmi1 and the PI3K/Akt pathway were coactivated in a substantial fraction of human high-grade tumors. We found that Akt mediated Bmi1 phosphorylation, enhancing its oncogenic potential in an Ink4a/Arf-independent manner. This process also modulated the DNA damage response and affected genomic stability. Together, our findings demonstrate the etiological role of Bmi1 in PCa, unravel an oncogenic collaboration between Bmi1 and the PI3K/Akt pathway, and provide mechanistic insights into the modulation of Bmi1 function by phosphorylation during prostate carcinogenesis.
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Affiliation(s)
- Karim Nacerddine
- Division of Molecular Genetics and Center for Biomedical Genetics, The Netherlands Cancer Institute, Amsterdam, The Netherlands
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33
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Tolhuis B, Blom M, van Lohuizen M. Chromosome conformation capture on chip in single Drosophila melanogaster tissues. Methods 2012; 58:231-42. [PMID: 22525789 DOI: 10.1016/j.ymeth.2012.04.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2011] [Revised: 03/27/2012] [Accepted: 04/04/2012] [Indexed: 11/17/2022] Open
Abstract
Chromosomes are protein-DNA complexes that encode life. In a cell nucleus, chromosomes are folded in a highly specific manner, which connects strongly to some of their paramount functions, such as DNA replication and gene transcription. Chromosome conformation capture methodologies allow researchers to detect chromosome folding, by quantitatively measuring which genomic sequences are in close proximity in nuclear space. Here, we describe a modified chromosome conformation capture on chip (4C) protocol, which is specifically designed for detection of chromosome folding in a single Drosophila melanogaster tissue. Our protocol enables 4C analyses on a limited number of cells, which is crucial for fly tissues, because these contain relatively low numbers of cells. We used this protocol to demonstrate that target genes of Polycomb group proteins interact with each other in nuclear space of third instar larval brain cells. Major benefits of using D. melanogaster in 4C studies are: (1) powerful and tractable genetic approaches can be incorporated; (2) short generation time allows use of complex genotypes; and (3) compact and well annotated genome. We anticipate that our sensitized 4C method will be generally applicable to detect chromosome folding in other fly tissues.
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Affiliation(s)
- Bas Tolhuis
- Division of Molecular Genetics and the Centre for Biomedical Genetics, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands.
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34
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van Lohuizen M. Abstract SY20-02: Role of Polycomb repressors in stem cells, cancer, DNA repair and iPS cell reprogramming. Cancer Res 2012. [DOI: 10.1158/1538-7445.am2012-sy20-02] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Repressive Polycomb-group (Pc-G) protein complexes and the counteracting Trithorax-group (Trx-G) of nucleosome remodeling factors are involved in the dynamic maintenance of proper gene expression patterns during development, acting at the level of chromatin structure. As such, they are important controllers of cell fate. When deregulated, these master switches of gene expression are strongly implicated in formation of a diverse set of cancers, including leukemia, breast cancer, prostate cancer and glioblastoma. To identify critical Polycomb targets and pathways implicated in brain cancer we performed comprehensive Bmi1-ChIP-seq profiling of mouse and human glioma ‘stem-like’ cells followed by in vivo shRNAi-library screening. These studies revealed a critical cross-talk between the BMP/TGFβ signaling pathways and Bmi1 and also provided new candidate tumor suppressors and non-coding RNAs associated with gliomagenesis. Furthermore, we have characterized in detail an essential E3-ubiquitin ligase activity in the PRC1 Polycomb complex that consists of a functional Ring1B-Bmi1 heterodimer. This E3 ligase activity is required for maintenance of Polycomb repression in normal- and cancer stem cells and hence offers potential novel ways to target cancer stem cells or tumor reforming cells in which the activity of this E3 ligase is hyperactivated. This is further substantiated by dynamic regulation of the Ring1B.Bmi1 E3 ligase activity which also has implications for a novel link between Polycomb silencing and control of Double-Strand DNA repair. Lastly, our recent studies revealed an unanticipated important role for Polycomb repression in the process of cellular ‘iPS’ cell reprogramming. The implications of these findings for stem cell biology, development, and possibilities for new translational approaches to cancer will be discussed.
Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr SY20-02. doi:1538-7445.AM2012-SY20-02
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35
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Posfai E, Kunzmann R, Brochard V, Salvaing J, Cabuy E, Roloff TC, Liu Z, Tardat M, van Lohuizen M, Vidal M, Beaujean N, Peters AHFM. Polycomb function during oogenesis is required for mouse embryonic development. Genes Dev 2012; 26:920-32. [PMID: 22499591 DOI: 10.1101/gad.188094.112] [Citation(s) in RCA: 100] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
In mammals, totipotent embryos are formed by fusion of highly differentiated gametes. Acquisition of totipotency concurs with chromatin remodeling of parental genomes, changes in the maternal transcriptome and proteome, and zygotic genome activation (ZGA). The inefficiency of reprogramming somatic nuclei in reproductive cloning suggests that intergenerational inheritance of germline chromatin contributes to developmental proficiency after natural conception. Here we show that Ring1 and Rnf2, components of Polycomb-repressive complex 1 (PRC1), serve redundant transcriptional functions during oogenesis that are essential for proper ZGA, replication and cell cycle progression in early embryos, and development beyond the two-cell stage. Exchange of chromosomes between control and Ring1/Rnf2-deficient metaphase II oocytes reveal cytoplasmic and chromosome-based contributions by PRC1 to embryonic development. Our results strongly support a model in which Polycomb acts in the female germline to establish developmental competence for the following generation by silencing differentiation-inducing genes and defining appropriate chromatin states.
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Affiliation(s)
- Eszter Posfai
- Friedrich Miescher Institute for Biomedical Research, CH-4058 Basel, Switzerland
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36
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Baradaran-Heravi A, Cho KS, Tolhuis B, Sanyal M, Morozova O, Morimoto M, Elizondo LI, Bridgewater D, Lubieniecka J, Beirnes K, Myung C, Leung D, Fam HK, Choi K, Huang Y, Dionis KY, Zonana J, Keller K, Stenzel P, Mayfield C, Lücke T, Bokenkamp A, Marra MA, van Lohuizen M, Lewis DB, Shaw C, Boerkoel CF. Penetrance of biallelic SMARCAL1 mutations is associated with environmental and genetic disturbances of gene expression. Hum Mol Genet 2012; 21:2572-87. [PMID: 22378147 DOI: 10.1093/hmg/dds083] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Biallelic mutations of the DNA annealing helicase SMARCAL1 (SWI/SNF-related, matrix-associated, actin-dependent regulator of chromatin, subfamily a-like 1) cause Schimke immuno-osseous dysplasia (SIOD, MIM 242900), an incompletely penetrant autosomal recessive disorder. Using human, Drosophila and mouse models, we show that the proteins encoded by SMARCAL1 orthologs localize to transcriptionally active chromatin and modulate gene expression. We also show that, as found in SIOD patients, deficiency of the SMARCAL1 orthologs alone is insufficient to cause disease in fruit flies and mice, although such deficiency causes modest diffuse alterations in gene expression. Rather, disease manifests when SMARCAL1 deficiency interacts with genetic and environmental factors that further alter gene expression. We conclude that the SMARCAL1 annealing helicase buffers fluctuations in gene expression and that alterations in gene expression contribute to the penetrance of SIOD.
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Affiliation(s)
- Alireza Baradaran-Heravi
- Department of Medical Genetics, Child and Family Research Institute, University of British Columbia, Vancouver, British Columbia, Canada
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37
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Westerman BA, Braat AK, Taub N, Potman M, Vissers JH, Blom M, Verhoeven E, Stoop H, Gillis A, Velds A, Nijkamp W, Beijersbergen R, Huber LA, Looijenga LH, van Lohuizen M. A genome-wide RNAi screen in mouse embryonic stem cells identifies Mp1 as a key mediator of differentiation. J Biophys Biochem Cytol 2011. [DOI: 10.1083/jcb1956oia9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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38
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Westerman BA, Braat AK, Taub N, Potman M, Vissers JHA, Blom M, Verhoeven E, Stoop H, Gillis A, Velds A, Nijkamp W, Beijersbergen R, Huber LA, Looijenga LHJ, van Lohuizen M. A genome-wide RNAi screen in mouse embryonic stem cells identifies Mp1 as a key mediator of differentiation. ACTA ACUST UNITED AC 2011; 208:2675-89. [PMID: 22143885 PMCID: PMC3244037 DOI: 10.1084/jem.20102037] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Despite intense investigation of intrinsic and extrinsic factors that regulate pluripotency, the process of initial fate commitment of embryonic stem (ES) cells is still poorly understood. We used a genome-wide short hairpin RNA screen in mouse ES cells to identify genes that are essential for initiation of differentiation. Knockdown of the scaffolding protein Mek binding protein 1 (Mp1, also known as Lamtor3 or Map2k1ip1) stimulated self-renewal of ES cells, blocked differentiation, and promoted proliferation. Fibroblast growth factor 4 (FGF4) signaling is required for initial fate commitment of ES cells. Knockdown of Mp1 inhibited FGF4-induced differentiation but did not alter FGF4-driven proliferation. This uncoupling of differentiation and proliferation was also observed when oncogenic Ras isoforms were overexpressed in ES cells. Knockdown of Mp1 redirected FGF4 signaling from differentiation toward pluripotency and up-regulated the pluripotency-related genes Esrrb, Rex1, Tcl1, and Sox2. We also found that human germ cell tumors (GCTs) express low amounts of Mp1 in the invasive embryonic carcinoma and seminoma histologies and higher amounts of Mp1 in the noninvasive carcinoma in situ precursor and differentiated components. Knockdown of Mp1 in invasive GCT cells resulted in resistance to differentiation, thereby showing a functional role for Mp1 both in normal differentiation of ES cells and in germ cell cancer.
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Affiliation(s)
- Bart A Westerman
- Division of Molecular Genetics, the Netherlands Cancer Institute, 1066 CX Amsterdam, Netherlands
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39
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de Jong J, de Ridder J, van der Weyden L, Sun N, van Uitert M, Berns A, van Lohuizen M, Jonkers J, Adams DJ, Wessels LFA. Computational identification of insertional mutagenesis targets for cancer gene discovery. Nucleic Acids Res 2011; 39:e105. [PMID: 21652642 PMCID: PMC3159484 DOI: 10.1093/nar/gkr447] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Insertional mutagenesis is a potent forward genetic screening technique used to identify candidate cancer genes in mouse model systems. An important, yet unresolved issue in the analysis of these screens, is the identification of the genes affected by the insertions. To address this, we developed Kernel Convolved Rule Based Mapping (KC-RBM). KC-RBM exploits distance, orientation and insertion density across tumors to automatically map integration sites to target genes. We perform the first genome-wide evaluation of the association of insertion occurrences with aberrant gene expression of the predicted targets in both retroviral and transposon data sets. We demonstrate the efficiency of KC-RBM by showing its superior performance over existing approaches in recovering true positives from a list of independently, manually curated cancer genes. The results of this work will significantly enhance the accuracy and speed of cancer gene discovery in forward genetic screens. KC-RBM is available as R-package.
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Affiliation(s)
- Johann de Jong
- Bioinformatics and Statistics, The Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, The Netherlands
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40
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Tolhuis B, Blom M, Kerkhoven RM, Pagie L, Teunissen H, Nieuwland M, Simonis M, de Laat W, van Lohuizen M, van Steensel B. Interactions among Polycomb domains are guided by chromosome architecture. PLoS Genet 2011; 7:e1001343. [PMID: 21455484 PMCID: PMC3063757 DOI: 10.1371/journal.pgen.1001343] [Citation(s) in RCA: 147] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2010] [Accepted: 02/16/2011] [Indexed: 01/15/2023] Open
Abstract
Polycomb group (PcG) proteins bind and regulate hundreds of genes. Previous evidence has suggested that long-range chromatin interactions may contribute to the regulation of PcG target genes. Here, we adapted the Chromosome Conformation Capture on Chip (4C) assay to systematically map chromosomal interactions in Drosophila melanogaster larval brain tissue. Our results demonstrate that PcG target genes interact extensively with each other in nuclear space. These interactions are highly specific for PcG target genes, because non-target genes with either low or high expression show distinct interactions. Notably, interactions are mostly limited to genes on the same chromosome arm, and we demonstrate that a topological rather than a sequence-based mechanism is responsible for this constraint. Our results demonstrate that many interactions among PcG target genes exist and that these interactions are guided by overall chromosome architecture.
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Affiliation(s)
- Bas Tolhuis
- Division of Molecular Genetics and Centre for Biomedical Genetics, Netherlands Cancer Institute, Amsterdam, The Netherlands.
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41
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Peric-Hupkes D, Meuleman W, Pagie L, Bruggeman SWM, Solovei I, Brugman W, Gräf S, Flicek P, Kerkhoven RM, van Lohuizen M, Reinders M, Wessels L, van Steensel B. Molecular maps of the reorganization of genome-nuclear lamina interactions during differentiation. Mol Cell 2010; 38:603-13. [PMID: 20513434 DOI: 10.1016/j.molcel.2010.03.016] [Citation(s) in RCA: 743] [Impact Index Per Article: 53.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2009] [Revised: 02/08/2010] [Accepted: 03/10/2010] [Indexed: 11/15/2022]
Abstract
The three-dimensional organization of chromosomes within the nucleus and its dynamics during differentiation are largely unknown. To visualize this process in molecular detail, we generated high-resolution maps of genome-nuclear lamina interactions during subsequent differentiation of mouse embryonic stem cells via lineage-committed neural precursor cells into terminally differentiated astrocytes. This reveals that a basal chromosome architecture present in embryonic stem cells is cumulatively altered at hundreds of sites during lineage commitment and subsequent terminal differentiation. This remodeling involves both individual transcription units and multigene regions and affects many genes that determine cellular identity. Often, genes that move away from the lamina are concomitantly activated; many others, however, remain inactive yet become unlocked for activation in a next differentiation step. These results suggest that lamina-genome interactions are widely involved in the control of gene expression programs during lineage commitment and terminal differentiation.
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Affiliation(s)
- Daan Peric-Hupkes
- Division of Gene Regulation, Netherlands Cancer Institute, Amsterdam, The Netherlands
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42
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de Vries NA, Bruggeman SW, Hulsman D, de Vries HI, Zevenhoven J, Buckle T, Hamans BC, Leenders WP, Beijnen JH, van Lohuizen M, Berns AJM, van Tellingen O. Rapid and robust transgenic high-grade glioma mouse models for therapy intervention studies. Clin Cancer Res 2010; 16:3431-41. [PMID: 20472681 DOI: 10.1158/1078-0432.ccr-09-3414] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
PURPOSE To develop a transgenic mouse model of glioma that can be conveniently used for testing therapy intervention strategies. High-grade glioma is a devastating and uniformly fatal disease for which better therapy is urgently needed. Typical for high-grade glioma is that glioma cells infiltrate extensively into surrounding pivotal brain structures, thereby rendering current treatments largely ineffective. Evaluation of novel therapies requires the availability of appropriate glioma mouse models. EXPERIMENTAL DESIGN High-grade gliomas were induced by stereotactic intracranial injection of lentiviral GFAP-Cre or CMV-Cre vectors into compound LoxP-conditional mice, resulting in K-Ras(v12) expression and loss of p16(Ink4a)/p19(Arf) with or without concomitant loss of p53 or Pten. RESULTS Tumors reproduced many of the features that are characteristic for human high-grade gliomas, including invasiveness and blood-brain barrier functionality. Especially, CMV-Cre injection into p53;Ink4a/Arf;K-Ras(v12) mice resulted in high-grade glioma with a short tumor latency (2-3 weeks) and full penetrance. Early detection and follow-up was accomplished by noninvasive bioluminescence imaging, and the practical utility for therapy intervention was shown in a study with temozolomide. CONCLUSION We have developed a realistic high-grade glioma model that can be used with almost the same convenience as traditional xenograft models, thus allowing its implementation at the forefront of preclinical evaluation of new treatments.
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Affiliation(s)
- Nienke A de Vries
- Department of Clinical Chemistry/Preclinical Pharmacology, The Netherlands Cancer Institute/Antoni van Leeuwenhoek Hospital, Amsterdam, the Netherlands
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43
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de Vries NA, Bruggeman SW, de Vries HI, Zevenhoven J, Buckle T, Hamans BC, Leenders WP, Beijnen JH, van Lohuizen M, Berns AJ, van Tellingen O. Abstract 4187: A rapid and robust transgenic high-grade glioma mouse model for therapy-intervention studies. Cancer Res 2010. [DOI: 10.1158/1538-7445.am10-4187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
High-grade glioma is a devastating and uniformly fatal disease for which better therapy is urgently needed. Glioma cells extensively infiltrate into surrounding pivotal brain structures, thereby rendering current treatments largely ineffective. Evaluation of novel therapies requires the availability of appropriate glioma mouse models. We here present a novel transgenic mouse model of high-grade glioma that can be conveniently used for testing therapy-intervention strategies.
High-grade gliomas were induced by stereotactic intracranial injection of self-deleting lentiviral GFAP-Cre or CMV-Cre vectors into adult immune-competent compound LoxP-conditional mice, resulting in localized expression of K-Rasv12 in conjunction with loss of p16Ink4a/p19Arf with or without concomitant loss of p53 or Pten. Tumors have been characterized by histology, immune-histochemistry and magnetic resonance imaging and reproduced many of the features that are characteristic for human high-grade gliomas, including invasiveness and blood-brain barrier functionality. We are currently assessing which molecular alterations in cell signaling pathways have occurred.
Especially CMV-Cre injection into p53;Ink4a/Arf;K-Rasv12 mice resulted in grade IV (glioblastoma multiforme) with a short tumor latency (2-3 weeks) and full penetrance. Early detection and follow-up of tumor growth can be accomplished conveniently by non-invasive bioluminescence imaging and the practical utility for therapy-intervention has been demonstrated in a study with temozolomide. Temozolomide delayed tumor progression modestly but significantly in line with what is observed in patients. Importantly, this novel model can be used with almost the same convenience as traditional xenograft models, thus allowing the implementation of realistic high grade glioma models at the forefront of preclinical evaluation. We expect that this model will be particularly useful to assess the potential clinical utility of agents that may augment temozolomide cytotoxicity, such as PARP-inhibitors or Wee1 kinase inhibitors, but also for agents targeting activated RAS and/or PI3K-Akt-mTor signaling pathways.
Note: This abstract was not presented at the AACR 101st Annual Meeting 2010 because the presenter was unable to attend.
Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 4187.
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Affiliation(s)
| | | | | | | | - Tessa Buckle
- 1Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Bob C. Hamans
- 2Radboud University Nijmegen Medical Centre, Nijmegen, Netherlands
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Koudijs MJ, Kool J, Sie D, Prasetyanti P, Cuppen E, Berns A, Hilkens J, van Lohuizen M, Adams D, Jonkers J. Abstract 2208: High-resolution analysis of insertional mutagenesis screens to study genetic interactions in heterogeneous tumors. Cancer Res 2010. [DOI: 10.1158/1538-7445.am10-2208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Insertional mutagenesis (IM) screens in genetically engineered mouse models of cancer are a powerful tool to identify genes or regions in the genome contributing to tumorigenesis. Current methods to identify the integration sites are not quantitative and do not give information about the clonality of a given insertion in a tumor. Consequently, the results of IM screens are hard to interpret since the obtained data are incomplete and highly biased due to technical variation.
We have developed and optimized a next-generation sequencing-based method for ultra high-throughput analysis of insertional mutations in a less biased and quantitative manner. Integration sites of retroviral or transposon based insertional mutagens are amplified using Splinkerette-mediated PCR and subsequent 454 sequencing. In contrast to current protocols, based on restriction enzyme (RE) fragmentation, we randomly shear gDNA, which allows a random ligation of the Splinkerette. This enables us to generate randomly sized amplicons per integration, which reduces amplification- and sequencing bias compared to amplicons with a fixed length per integration using RE based methods. Since Splinkerette ligation can occur at every base pair, we can determine the amount of cells containing the given insertion by counting unique ligation points, each representing a unique chromosome, and thereby a cell, in the tumor. This latter feature, addressing clonality of an insertional mutagen, will allow the identification of both clonal and sub-clonal mutations in genetically heterogeneous tumors. More importantly, we are now able to study co-occurring mutations, e.g. underlying synthetic lethality, which cannot be performed reliably using the current method.
The insertional mutagenesis data obtained with the improved method will represent the biological situation of a given integration within a tumor, thereby facilitating subsequent validation experiments. Additionally, data obtained from our retroviral- and transposon-based screens in various mouse models of cancer will serve as a catalogue of cancer-relevant mutations that can be used for cross-species comparative analysis of the large numbers of mutations found in human breast cancer.
Note: This abstract was not presented at the AACR 101st Annual Meeting 2010 because the presenter was unable to attend.
Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 2208.
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Affiliation(s)
| | - Jaap Kool
- 1Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Daoud Sie
- 1Netherlands Cancer Institute, Amsterdam, Netherlands
| | | | - Edwin Cuppen
- 2Hubrecht Institute and University Medical Center Utrecht, Utrecht, Netherlands
| | - Anton Berns
- 1Netherlands Cancer Institute, Amsterdam, Netherlands
| | - John Hilkens
- 1Netherlands Cancer Institute, Amsterdam, Netherlands
| | | | - David Adams
- 3Wellcome Trust Sanger Institute, Hinxton, United Kingdom
| | - Jos Jonkers
- 1Netherlands Cancer Institute, Amsterdam, Netherlands
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Mattison J, Kool J, Uren AG, de Ridder J, Wessels L, Jonkers J, Bignell GR, Butler A, Rust AG, Brosch M, Wilson CH, van der Weyden L, Largaespada DA, Stratton MR, Futreal PA, van Lohuizen M, Berns A, Collier LS, Hubbard T, Adams DJ. Novel candidate cancer genes identified by a large-scale cross-species comparative oncogenomics approach. Cancer Res 2010; 70:883-95. [PMID: 20103622 DOI: 10.1158/0008-5472.can-09-1737] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Comparative genomic hybridization (CGH) can reveal important disease genes but the large regions identified could sometimes contain hundreds of genes. Here we combine high-resolution CGH analysis of 598 human cancer cell lines with insertion sites isolated from 1,005 mouse tumors induced with the murine leukemia virus (MuLV). This cross-species oncogenomic analysis revealed candidate tumor suppressor genes and oncogenes mutated in both human and mouse tumors, making them strong candidates for novel cancer genes. A significant number of these genes contained binding sites for the stem cell transcription factors Oct4 and Nanog. Notably, mice carrying tumors with insertions in or near stem cell module genes, which are thought to participate in cell self-renewal, died significantly faster than mice without these insertions. A comparison of the profile we identified to that induced with the Sleeping Beauty (SB) transposon system revealed significant differences in the profile of recurrently mutated genes. Collectively, this work provides a rich catalogue of new candidate cancer genes for functional analysis.
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Affiliation(s)
- Jenny Mattison
- The Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, United Kingdom
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Kool J, Uren AG, Martins CP, Sie D, de Ridder J, Turner G, van Uitert M, Matentzoglu K, Lagcher W, Krimpenfort P, Gadiot J, Pritchard C, Lenz J, Lund AH, Jonkers J, Rogers J, Adams DJ, Wessels L, Berns A, van Lohuizen M. Insertional mutagenesis in mice deficient for p15Ink4b, p16Ink4a, p21Cip1, and p27Kip1 reveals cancer gene interactions and correlations with tumor phenotypes. Cancer Res 2010; 70:520-31. [PMID: 20068150 DOI: 10.1158/0008-5472.can-09-2736] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
The cyclin dependent kinase (CDK) inhibitors p15, p16, p21, and p27 are frequently deleted, silenced, or downregulated in many malignancies. Inactivation of CDK inhibitors predisposes mice to tumor development, showing that these genes function as tumor suppressors. Here, we describe high-throughput murine leukemia virus insertional mutagenesis screens in mice that are deficient for one or two CDK inhibitors. We retrieved 9,117 retroviral insertions from 476 lymphomas to define hundreds of loci that are mutated more frequently than expected by chance. Many of these loci are skewed toward a specific genetic context of predisposing germline and somatic mutations. We also found associations between these loci with gender, age of tumor onset, and lymphocyte lineage (B or T cell). Comparison of retroviral insertion sites with single nucleotide polymorphisms associated with chronic lymphocytic leukemia revealed a significant overlap between the datasets. Together, our findings highlight the importance of genetic context within large-scale mutation detection studies, and they show a novel use for insertional mutagenesis data in prioritizing disease-associated genes that emerge from genome-wide association studies.
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Affiliation(s)
- Jaap Kool
- Division of Molecular Genetics, The Centre of Biomedical Genetics, Academic Medical Center and Cancer Genomics Centre, Netherlands Cancer Institute, 1066CX, Amsterdam, the Netherlands
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Puppe J, Drost R, Liu X, Joosse SA, Evers B, Cornelissen-Steijger P, Nederlof P, Yu Q, Jonkers J, van Lohuizen M, Pietersen AM. BRCA1-deficient mammary tumor cells are dependent on EZH2 expression and sensitive to Polycomb Repressive Complex 2-inhibitor 3-deazaneplanocin A. Breast Cancer Res 2009; 11:R63. [PMID: 19709408 PMCID: PMC2750125 DOI: 10.1186/bcr2354] [Citation(s) in RCA: 90] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2009] [Revised: 08/06/2009] [Accepted: 08/26/2009] [Indexed: 11/26/2022] Open
Abstract
Introduction Treatment of breast cancer is becoming more individualized with the recognition of tumor subgroups that respond differently to available therapies. Breast cancer 1 gene (BRCA1)-deficient tumors are usually of the basal subtype and associated with poor survival rates, highlighting the need for more effective therapy. Methods We investigated a mouse model that closely mimics breast cancer arising in BRCA1-mutation carriers to better understand the molecular mechanism of tumor progression and tested whether targeting of the Polycomb-group protein EZH2 would be a putative therapy for BRCA1-deficient tumors. Results Gene expression analysis demonstrated that EZH2 is overexpressed in BRCA1-deficient mouse mammary tumors. By immunohistochemistry we show that an increase in EZH2 protein levels is also evident in tumors from BRCA1-mutation carriers. EZH2 is responsible for repression of genes driving differentiation and could thus be involved in the undifferentiated phenotype of these tumors. Importantly, we show that BRCA1-deficient cancer cells are selectively dependent on their elevated EZH2 levels. In addition, a chemical inhibitor of EZH2, 3-deazaneplanocin A (DZNep), is about 20-fold more effective in killing BRCA1-deficient cells compared to BRCA1-proficient mammary tumor cells. Conclusions We demonstrate by specific knock-down experiments that EZH2 overexpression is functionally relevant in BRCA1-deficient breast cancer cells. The effectiveness of a small molecule inhibitor indicates that EZH2 is a druggable target. The overexpression of EZH2 in all basal-like breast cancers warrants further investigation of the potential for targeting the genetic make-up of this particular breast cancer type.
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Affiliation(s)
- Julian Puppe
- Molecular Genetics and Cancer Genomics Centre, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands.
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Boukarabila H, Saurin AJ, Batsché E, Mossadegh N, van Lohuizen M, Otte AP, Pradel J, Muchardt C, Sieweke M, Duprez E. The PRC1 Polycomb group complex interacts with PLZF/RARA to mediate leukemic transformation. Genes Dev 2009; 23:1195-206. [PMID: 19451220 DOI: 10.1101/gad.512009] [Citation(s) in RCA: 108] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Ectopic repression of retinoic acid (RA) receptor target genes by PML/RARA and PLZF/RARA fusion proteins through aberrant recruitment of nuclear corepressor complexes drives cellular transformation and acute promyelocytic leukemia (APL) development. In the case of PML/RARA, this repression can be reversed through treatment with all-trans RA (ATRA), leading to leukemic remission. However, PLZF/RARA ectopic repression is insensitive to ATRA, resulting in persistence of the leukemic diseased state after treatment, a phenomenon that is still poorly understood. Here we show that, like PML/RARA, PLZF/RARA expression leads to recruitment of the Polycomb-repressive complex 2 (PRC2) Polycomb group (PcG) complex to RA response elements. However, unlike PML/RARA, PLZF/RARA directly interacts with the PcG protein Bmi-1 and forms a stable component of the PRC1 PcG complex, resulting in PLZF/RARA-dependent ectopic recruitment of PRC1 to RA response elements. Upon treatment with ATRA, ectopic recruitment of PRC2 by either PML/RARA or PLZF/RARA is lost, whereas PRC1 recruited by PLZF/RARA remains, resulting in persistent RA-insensitive gene repression. We further show that Bmi-1 is essential for the PLZF/RARA cellular transformation property and implicates a central role for PRC1 in PLZF/RARA-mediated myeloid leukemic development.
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Affiliation(s)
- Hanane Boukarabila
- Centre d'Immunologie de Marseille-Luminy (CIML), Université de la Méditerranée, Campus de Luminy, 13288 Marseille Cedex 09, France
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Prieur A, Nacerddine K, van Lohuizen M, Peeper DS. SUMOylation of DRIL1 directs its transcriptional activity towards leukocyte lineage-specific genes. PLoS One 2009; 4:e5542. [PMID: 19436740 PMCID: PMC2677661 DOI: 10.1371/journal.pone.0005542] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2009] [Accepted: 04/18/2009] [Indexed: 11/18/2022] Open
Abstract
DRIL1 is an ARID family transcription factor that can immortalize primary mouse fibroblasts, bypass RASV12-induced cellular senescence and collaborate with RASV12 or MYC in mediating oncogenic transformation. It also activates immunoglobulin heavy chain transcription and engages in heterodimer formation with E2F to stimulate E2F-dependent transcription. Little, however, is known about the regulation of DRIL1 activity. Recently, DRIL1 was found to interact with the SUMO-conjugating enzyme Ubc9, but the functional relevance of this association has not been assessed. Here, we show that DRIL1 is sumoylated both in vitro and in vivo at lysine 398. Moreover, we provide evidence that PIASy functions as a specific SUMO E3-ligase for DRIL1 and promotes its sumoylation both in vitro and in vivo. Furthermore, consistent with the subnuclear localization of PIASy in the Matrix-Associated Region (MAR), SUMO-modified DRIL1 species are found exclusively in the MAR fraction. This post-translational modification interferes neither with the subcellular localization nor the DNA-binding activity of the protein. In contrast, DRIL1 sumoylation impairs its interaction with E2F1 in vitro and modifies its transcriptional activity in vivo, driving transcription of subset of genes regulating leukocyte fate. Taken together, these results identify sumoylation as a novel post-translational modification of DRIL1 that represents an important mechanism for targeting and modulating DRIL1 transcriptional activity.
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Affiliation(s)
- Alexandre Prieur
- Department of Molecular Genetics, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Karim Nacerddine
- Department of Molecular Genetics, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Maarten van Lohuizen
- Department of Molecular Genetics, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Daniel S. Peeper
- Department of Molecular Genetics, The Netherlands Cancer Institute, Amsterdam, The Netherlands
- * E-mail:
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Bruggeman SWM, Hulsman D, van Lohuizen M. Bmi1 deficient neural stem cells have increased integrin dependent adhesion to self-secreted matrix. Biochim Biophys Acta Gen Subj 2009; 1790:351-60. [PMID: 19298843 DOI: 10.1016/j.bbagen.2009.03.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2008] [Revised: 02/25/2009] [Accepted: 03/02/2009] [Indexed: 10/21/2022]
Abstract
BACKGROUND Neural cells deficient for Polycomb group (PcG) protein Bmi1 are impaired in the formation and differentiation of high grade glioma, an incurable cancer of the brain. It was shown that mechanisms involved in cell adhesion and migration were specifically affected in these tumors. METHODS Using biochemical and cell biological approaches, we investigated the adhesive capacities of Bmi1;Ink4a/Arf deficient primary neural stem cells (NSCs). RESULTS Bmi1;Ink4a/Arf deficient NSCs have altered expression of Collagen-related genes, secrete increased amounts of extracellular matrix, and exhibit enhanced cell-matrix binding through the Beta-1 Integrin receptor. These traits are independent from the well described role of Bmi1 as repressor of the Ink4a/Arf tumor suppressor locus. CONCLUSION In addition to proliferative processes, Bmi1 controls the adhesive capacities of primary NSCs by modulating extracellular matrix secretion. GENERAL SIGNIFICANCE Since PcG protein Bmi1 is important for both normal development and tumorigenesis, it is vital to understand the complete network in which this protein acts. Whereas it is clear that control of Ink4a/Arf is a major Bmi1 function, there is evidence that other downstream mechanisms exist. Hence, our novel finding that Bmi1 also governs cell adhesion significantly contributes to our understanding of the PcG proteins.
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Affiliation(s)
- Sophia W M Bruggeman
- The Netherlands Cancer Institute, Division of Molecular Genetics, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
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