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Bischerour J, Bhullar S, Denby Wilkes C, Régnier V, Mathy N, Dubois E, Singh A, Swart E, Arnaiz O, Sperling L, Nowacki M, Bétermier M. Six domesticated PiggyBac transposases together carry out programmed DNA elimination in Paramecium. eLife 2018; 7:37927. [PMID: 30223944 PMCID: PMC6143343 DOI: 10.7554/elife.37927] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Accepted: 08/29/2018] [Indexed: 02/06/2023] Open
Abstract
The domestication of transposable elements has repeatedly occurred during evolution and domesticated transposases have often been implicated in programmed genome rearrangements, as remarkably illustrated in ciliates. In Paramecium, PiggyMac (Pgm), a domesticated PiggyBac transposase, carries out developmentally programmed DNA elimination, including the precise excision of tens of thousands of gene-interrupting germline Internal Eliminated Sequences (IESs). Here, we report the discovery of five groups of distant Pgm-like proteins (PgmLs), all able to interact with Pgm and essential for its nuclear localization and IES excision genome-wide. Unlike Pgm, PgmLs lack a conserved catalytic site, suggesting that they rather have an architectural function within a multi-component excision complex embedding Pgm. PgmL depletion can increase erroneous targeting of residual Pgm-mediated DNA cleavage, indicating that PgmLs contribute to accurately position the complex on IES ends. DNA rearrangements in Paramecium constitute a rare example of a biological process jointly managed by six distinct domesticated transposases.
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Affiliation(s)
- Julien Bischerour
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Simran Bhullar
- Institute of Cell Biology, University of Bern, Bern, Switzerland.,Institut de Biologie de l'Ecole Normale Supérieure, Paris, France
| | - Cyril Denby Wilkes
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Vinciane Régnier
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France.,Univ Paris Diderot, Paris, France
| | - Nathalie Mathy
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Emeline Dubois
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Aditi Singh
- Institute of Cell Biology, University of Bern, Bern, Switzerland
| | - Estienne Swart
- Institute of Cell Biology, University of Bern, Bern, Switzerland
| | - Olivier Arnaiz
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Linda Sperling
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Mariusz Nowacki
- Institute of Cell Biology, University of Bern, Bern, Switzerland
| | - Mireille Bétermier
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France
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52
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Wang J, Xie ZX, Ma Y, Chen XR, Huang YQ, He B, Bin Jia, Li BZ, Yuan YJ. Ring synthetic chromosome V SCRaMbLE. Nat Commun 2018; 9:3783. [PMID: 30224715 PMCID: PMC6141504 DOI: 10.1038/s41467-018-06216-y] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Accepted: 08/21/2018] [Indexed: 11/09/2022] Open
Abstract
Structural variations (SVs) exert important functional impacts on biological phenotypic diversity. Here we show a ring synthetic yeast chromosome V (ring_synV) can be used to continuously generate complex genomic variations and improve the production of prodeoxyviolacein (PDV) by applying Synthetic Chromosome Recombination and Modification by LoxP-mediated Evolution (SCRaMbLE) in haploid yeast cells. The SCRaMbLE of ring_synV generates aneuploid yeast strains with increased PDV productivity, and we identify aneuploid chromosome I, III, VI, XII, XIII, and ring_synV. The neochromosome of SCRaMbLEd ring_synV generated more unbalanced forms of variations, including duplication, insertions, and balanced forms of translocations and inversions than its linear form. Furthermore, of the 29 novel SVs detected, 11 prompted the PDV biosynthesis; and the deletion of uncharacterized gene YER182W is related to the improvement of the PDV. Overall, the SCRaMbLEing ring_synV embraces the evolution of the genome by modifying the chromosome number, structure, and organization, identifying targets for phenotypic comprehension.
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Affiliation(s)
- Juan Wang
- Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, 300072, Tianjin, People's Republic of China.,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, 300072, Tianjin, People's Republic of China
| | - Ze-Xiong Xie
- Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, 300072, Tianjin, People's Republic of China.,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, 300072, Tianjin, People's Republic of China
| | - Yuan Ma
- Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, 300072, Tianjin, People's Republic of China.,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, 300072, Tianjin, People's Republic of China
| | - Xiang-Rong Chen
- Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, 300072, Tianjin, People's Republic of China.,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, 300072, Tianjin, People's Republic of China
| | - Yao-Qing Huang
- Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, 300072, Tianjin, People's Republic of China.,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, 300072, Tianjin, People's Republic of China
| | - Bo He
- Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, 300072, Tianjin, People's Republic of China.,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, 300072, Tianjin, People's Republic of China
| | - Bin Jia
- Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, 300072, Tianjin, People's Republic of China.,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, 300072, Tianjin, People's Republic of China
| | - Bing-Zhi Li
- Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, 300072, Tianjin, People's Republic of China.,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, 300072, Tianjin, People's Republic of China
| | - Ying-Jin Yuan
- Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, 300072, Tianjin, People's Republic of China. .,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, 300072, Tianjin, People's Republic of China.
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53
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Ishak CA, Classon M, De Carvalho DD. Deregulation of Retroelements as an Emerging Therapeutic Opportunity in Cancer. Trends Cancer 2018; 4:583-597. [DOI: 10.1016/j.trecan.2018.05.008] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Revised: 05/22/2018] [Accepted: 05/24/2018] [Indexed: 12/26/2022]
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54
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Henssen AG, Reed C, Jiang E, Garcia HD, von Stebut J, MacArthur IC, Hundsdoerfer P, Kim JH, de Stanchina E, Kuwahara Y, Hosoi H, Ganem NJ, Dela Cruz F, Kung AL, Schulte JH, Petrini JH, Kentsis A. Therapeutic targeting of PGBD5-induced DNA repair dependency in pediatric solid tumors. Sci Transl Med 2018; 9:9/414/eaam9078. [PMID: 29093183 DOI: 10.1126/scitranslmed.aam9078] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Revised: 07/15/2017] [Accepted: 09/25/2017] [Indexed: 12/16/2022]
Abstract
Despite intense efforts, the cure rates of childhood and adult solid tumors are not satisfactory. Resistance to intensive chemotherapy is common, and targets for molecular therapies are largely undefined. We have found that the majority of childhood solid tumors, including rhabdoid tumors, neuroblastoma, medulloblastoma, and Ewing sarcoma, express an active DNA transposase, PGBD5, that can promote site-specific genomic rearrangements in human cells. Using functional genetic approaches, we discovered that mouse and human cells deficient in nonhomologous end joining (NHEJ) DNA repair cannot tolerate the expression of PGBD5. In a chemical screen of DNA damage signaling inhibitors, we identified AZD6738 as a specific sensitizer of PGBD5-dependent DNA damage and apoptosis. We found that expression of PGBD5, but not its nuclease activity-deficient mutant, was sufficient to induce sensitivity to AZD6738. Depletion of endogenous PGBD5 conferred resistance to AZD6738 in human tumor cells. PGBD5-expressing tumor cells accumulated unrepaired DNA damage in response to AZD6738 treatment and underwent apoptosis in both dividing and G1-phase cells in the absence of immediate DNA replication stress. Accordingly, AZD6738 exhibited nanomolar potency against most neuroblastoma, medulloblastoma, Ewing sarcoma, and rhabdoid tumor cells tested while sparing nontransformed human and mouse embryonic fibroblasts in vitro. Finally, treatment with AZD6738 induced apoptosis and regression of human neuroblastoma and medulloblastoma tumors engrafted in immunodeficient mice in vivo. This effect was potentiated by combined treatment with cisplatin, including substantial antitumor activity against patient-derived primary neuroblastoma xenografts. These findings delineate a therapeutically actionable synthetic dependency induced in PGBD5-expressing solid tumors.
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Affiliation(s)
- Anton G Henssen
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.,Berlin Institute of Health, 10178 Berlin, Germany.,Department of Pediatric Oncology and Hematology, Charité-Universitätsmedizin Berlin, 10117 Berlin, Germany.,German Cancer Consortium (DKTK), 10117 Berlin, Germany
| | - Casie Reed
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Eileen Jiang
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Heathcliff Dorado Garcia
- Department of Pediatric Oncology and Hematology, Charité-Universitätsmedizin Berlin, 10117 Berlin, Germany
| | - Jennifer von Stebut
- Department of Pediatric Oncology and Hematology, Charité-Universitätsmedizin Berlin, 10117 Berlin, Germany
| | - Ian C MacArthur
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Patrick Hundsdoerfer
- Berlin Institute of Health, 10178 Berlin, Germany.,Department of Pediatric Oncology and Hematology, Charité-Universitätsmedizin Berlin, 10117 Berlin, Germany
| | - Jun Hyun Kim
- Molecular Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Elisa de Stanchina
- Antitumor Assessment Core Facility, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Yasumichi Kuwahara
- Department of Biochemistry and Molecular Biology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Hajime Hosoi
- Department of Pediatrics, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Neil J Ganem
- Section of Hematology and Medical Oncology, Department of Pharmacology, Boston University School of Medicine, Boston, MA 02215, USA
| | - Filemon Dela Cruz
- Department of Pediatrics, Weill Cornell Medical College of Cornell University and Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Andrew L Kung
- Department of Pediatrics, Weill Cornell Medical College of Cornell University and Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Johannes H Schulte
- Berlin Institute of Health, 10178 Berlin, Germany.,Department of Pediatric Oncology and Hematology, Charité-Universitätsmedizin Berlin, 10117 Berlin, Germany.,German Cancer Consortium (DKTK), 10117 Berlin, Germany.,Deutsches Krebsforschungszentrum Heidelberg, 69120 Heidelberg, Germany
| | - John H Petrini
- Molecular Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Alex Kentsis
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA. .,Department of Pediatrics, Weill Cornell Medical College of Cornell University and Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
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55
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Watson S, Perrin V, Guillemot D, Reynaud S, Coindre JM, Karanian M, Guinebretière JM, Freneaux P, Le Loarer F, Bouvet M, Galmiche-Rolland L, Larousserie F, Longchampt E, Ranchere-Vince D, Pierron G, Delattre O, Tirode F. Transcriptomic definition of molecular subgroups of small round cell sarcomas. J Pathol 2018; 245:29-40. [PMID: 29431183 DOI: 10.1002/path.5053] [Citation(s) in RCA: 215] [Impact Index Per Article: 35.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Revised: 01/10/2018] [Accepted: 02/02/2018] [Indexed: 01/02/2023]
Abstract
Sarcoma represents a highly heterogeneous group of tumours. We report here the first unbiased and systematic search for gene fusions combined with unsupervised expression analysis of a series of 184 small round cell sarcomas. Fusion genes were detected in 59% of samples, with half of them being observed recurrently. We identified biologically homogeneous groups of tumours such as the CIC-fused (to DUX4, FOXO4 or NUTM1) and BCOR-rearranged (BCOR-CCNB3, BCOR-MAML3, ZC3H7B-BCOR, and BCOR internal duplication) tumour groups. VGLL2-fused tumours represented a more biologically and pathologically heterogeneous group. This study also refined the characteristics of some entities such as EWSR1-PATZ1 spindle cell sarcoma or FUS-NFATC2 bone tumours that are different from EWSR1-NFATC2 tumours and transcriptionally resemble CIC-fused tumour entities. We also describe a completely novel group of epithelioid and spindle-cell rhabdomyosarcomas characterized by EWSR1- or FUS-TFCP2 fusions. Finally, expression data identified some potentially new therapeutic targets or pathways. Copyright © 2018 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
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Affiliation(s)
- Sarah Watson
- INSERM U830, Laboratory of Genetics and Biology of Cancer, Paris, France.,Institut Curie, Paris Sciences et Lettres, Paris, France
| | - Virginie Perrin
- INSERM U830, Laboratory of Genetics and Biology of Cancer, Paris, France.,Institut Curie, Paris Sciences et Lettres, Paris, France
| | | | | | - Jean-Michel Coindre
- Institut Bergonié, Department of Pathology, Bordeaux, France.,Université Bordeaux 2, Bordeaux, France
| | - Marie Karanian
- Centre Leon Bérard, Department of Pathology, Lyon, France
| | | | - Paul Freneaux
- Département de Biologie des Tumeurs, Institut Curie, Service d'Anatomie Pathologique, Paris, France
| | - François Le Loarer
- Institut Bergonié, Department of Pathology, Bordeaux, France.,Université Bordeaux 2, Bordeaux, France
| | - Megane Bouvet
- Institut Curie, Unité de Génétique Somatique, Paris, France
| | - Louise Galmiche-Rolland
- Service d'Anatomie Pathologique, Hôpital Necker Enfants Malades, Paris, France.,Université Paris Descartes, Paris, France
| | | | - Elisabeth Longchampt
- Service d'Anatomie et de Cytologie Pathologiques, Hôpital Foch, Suresnes, France
| | | | - Gaelle Pierron
- Institut Curie, Unité de Génétique Somatique, Paris, France
| | - Olivier Delattre
- INSERM U830, Laboratory of Genetics and Biology of Cancer, Paris, France.,Institut Curie, Paris Sciences et Lettres, Paris, France.,Institut Curie, Unité de Génétique Somatique, Paris, France.,Ligue Contre le Cancer, Equipe Labellisée
| | - Franck Tirode
- INSERM U830, Laboratory of Genetics and Biology of Cancer, Paris, France.,Institut Curie, Paris Sciences et Lettres, Paris, France.,Univ Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Cancer Research Center of Lyon, Centre Léon Bérard, Lyon, France
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56
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Mack SC, Suzuki H, Taylor MD. Transposase-driven rearrangements in human tumors. Nat Genet 2017; 49:975-977. [PMID: 28656983 DOI: 10.1038/ng.3908] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
A new study shows that aberrant DNA transposase activity promotes structural alterations that are clonally selected to drive tumor development. This discovery uncovers novel mechanisms of tumor-suppressor gene inactivation and highlights a new approach to cancer gene identification.
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Affiliation(s)
- Stephen C Mack
- Cleveland Clinic, Stem Cell Biology and Regenerative Medicine, Cleveland, Ohio, USA
| | - Hiromichi Suzuki
- The Hospital for Sick Children, Department of Neurosurgery, Toronto, Ontario, Canada
| | - Michael D Taylor
- The Hospital for Sick Children, Department of Neurosurgery, Toronto, Ontario, Canada
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