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Grünewald TGP, Bernard V, Gilardi-Hebenstreit P, Raynal V, Surdez D, Aynaud MM, Mirabeau O, Cidre-Aranaz F, Tirode F, Zaidi S, Perot G, Jonker AH, Lucchesi C, Le Deley MC, Oberlin O, Marec-Bérard P, Véron AS, Reynaud S, Lapouble E, Boeva V, Rio Frio T, Alonso J, Bhatia S, Pierron G, Cancel-Tassin G, Cussenot O, Cox DG, Morton LM, Machiela MJ, Chanock SJ, Charnay P, Delattre O. Chimeric EWSR1-FLI1 regulates the Ewing sarcoma susceptibility gene EGR2 via a GGAA microsatellite. Nat Genet 2015. [PMID: 26214589 DOI: 10.1038/ng.3363] [Citation(s) in RCA: 120] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Deciphering the ways in which somatic mutations and germline susceptibility variants cooperate to promote cancer is challenging. Ewing sarcoma is characterized by fusions between EWSR1 and members of the ETS gene family, usually EWSR1-FLI1, leading to the generation of oncogenic transcription factors that bind DNA at GGAA motifs. A recent genome-wide association study identified susceptibility variants near EGR2. Here we found that EGR2 knockdown inhibited proliferation, clonogenicity and spheroidal growth in vitro and induced regression of Ewing sarcoma xenografts. Targeted germline deep sequencing of the EGR2 locus in affected subjects and controls identified 291 Ewing-associated SNPs. At rs79965208, the A risk allele connected adjacent GGAA repeats by converting an interspaced GGAT motif into a GGAA motif, thereby increasing the number of consecutive GGAA motifs and thus the EWSR1-FLI1-dependent enhancer activity of this sequence, with epigenetic characteristics of an active regulatory element. EWSR1-FLI1 preferentially bound to the A risk allele, which increased global and allele-specific EGR2 expression. Collectively, our findings establish cooperation between a dominant oncogene and a susceptibility variant that regulates a major driver of Ewing sarcomagenesis.
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Affiliation(s)
- Thomas G P Grünewald
- Genetics and Biology of Cancers Unit, Institut Curie, PSL Research University, Paris, France.,INSERM U830, Institut Curie Research Center, Paris, France
| | - Virginie Bernard
- Institut Curie Genomics of Excellence (ICGex) Platform, Institut Curie Research Center, Paris, France
| | - Pascale Gilardi-Hebenstreit
- École Normale Supérieure (ENS), Institut de Biologie de l'ENS (IBENS), INSERM U1024, CNRS UMR8197, Paris, France
| | - Virginie Raynal
- Genetics and Biology of Cancers Unit, Institut Curie, PSL Research University, Paris, France.,INSERM U830, Institut Curie Research Center, Paris, France.,Institut Curie Genomics of Excellence (ICGex) Platform, Institut Curie Research Center, Paris, France
| | - Didier Surdez
- Genetics and Biology of Cancers Unit, Institut Curie, PSL Research University, Paris, France.,INSERM U830, Institut Curie Research Center, Paris, France
| | - Marie-Ming Aynaud
- Genetics and Biology of Cancers Unit, Institut Curie, PSL Research University, Paris, France.,INSERM U830, Institut Curie Research Center, Paris, France
| | - Olivier Mirabeau
- Genetics and Biology of Cancers Unit, Institut Curie, PSL Research University, Paris, France.,INSERM U830, Institut Curie Research Center, Paris, France
| | - Florencia Cidre-Aranaz
- Instituto de Investigación de Enfermedades Raras, Instituto de Salud Carlos III, Madrid, Spain
| | - Franck Tirode
- Genetics and Biology of Cancers Unit, Institut Curie, PSL Research University, Paris, France.,INSERM U830, Institut Curie Research Center, Paris, France
| | - Sakina Zaidi
- Genetics and Biology of Cancers Unit, Institut Curie, PSL Research University, Paris, France.,INSERM U830, Institut Curie Research Center, Paris, France
| | - Gaëlle Perot
- INSERM U916 Biology of Sarcomas, Institut Bergonié, Bordeaux, France
| | - Anneliene H Jonker
- Genetics and Biology of Cancers Unit, Institut Curie, PSL Research University, Paris, France.,INSERM U830, Institut Curie Research Center, Paris, France
| | - Carlo Lucchesi
- Genetics and Biology of Cancers Unit, Institut Curie, PSL Research University, Paris, France.,INSERM U830, Institut Curie Research Center, Paris, France
| | - Marie-Cécile Le Deley
- Département d'Epidémiologie et de Biostatistiques, Institut Gustave Roussy, Villejuif, France
| | - Odile Oberlin
- Département de Pédiatrie, Institut Gustave Roussy, Villejuif, France
| | - Perrine Marec-Bérard
- Institute for Pediatric Hematology and Oncology, Leon-Bérard Cancer Center, University of Lyon, Lyon, France
| | - Amélie S Véron
- INSERM U1052, Léon-Bérard Cancer Centre, Cancer Research Center of Lyon, Lyon, France
| | - Stephanie Reynaud
- Unité Génétique Somatique (UGS), Institut Curie Centre Hospitalier, Paris, France
| | - Eve Lapouble
- Unité Génétique Somatique (UGS), Institut Curie Centre Hospitalier, Paris, France
| | - Valentina Boeva
- INSERM U900, Bioinformatics, Biostatistics, Epidemiology and Computational Systems Biology of Cancer, Institut Curie Research Center, Paris, France.,Mines ParisTech, Fontainebleau, France
| | - Thomas Rio Frio
- Institut Curie Genomics of Excellence (ICGex) Platform, Institut Curie Research Center, Paris, France
| | - Javier Alonso
- Instituto de Investigación de Enfermedades Raras, Instituto de Salud Carlos III, Madrid, Spain
| | - Smita Bhatia
- Institute for Cancer Outcomes and Survivorship, School of Medicine, University of Alabama, Birmingham, Alabama, USA
| | - Gaëlle Pierron
- Unité Génétique Somatique (UGS), Institut Curie Centre Hospitalier, Paris, France
| | - Geraldine Cancel-Tassin
- Centre de Recherche sur les Pathologies Prostatiques (CeRePP)-Laboratory for Urology, Research Team 2, UPMC, Hôpital Tenon, Paris, France
| | - Olivier Cussenot
- Centre de Recherche sur les Pathologies Prostatiques (CeRePP)-Laboratory for Urology, Research Team 2, UPMC, Hôpital Tenon, Paris, France
| | - David G Cox
- INSERM U1052, Léon-Bérard Cancer Centre, Cancer Research Center of Lyon, Lyon, France
| | - Lindsay M Morton
- Division of Cancer Epidemiology and Genetics (DCEG), National Cancer Institute (NCI), Bethesda, Maryland, USA
| | - Mitchell J Machiela
- Division of Cancer Epidemiology and Genetics (DCEG), National Cancer Institute (NCI), Bethesda, Maryland, USA
| | - Stephen J Chanock
- Division of Cancer Epidemiology and Genetics (DCEG), National Cancer Institute (NCI), Bethesda, Maryland, USA
| | - Patrick Charnay
- École Normale Supérieure (ENS), Institut de Biologie de l'ENS (IBENS), INSERM U1024, CNRS UMR8197, Paris, France
| | - Olivier Delattre
- Genetics and Biology of Cancers Unit, Institut Curie, PSL Research University, Paris, France.,INSERM U830, Institut Curie Research Center, Paris, France.,Institut Curie Genomics of Excellence (ICGex) Platform, Institut Curie Research Center, Paris, France.,Unité Génétique Somatique (UGS), Institut Curie Centre Hospitalier, Paris, France
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Postel-Vinay S, Véron AS, Tirode F, Pierron G, Reynaud S, Kovar H, Oberlin O, Lapouble E, Ballet S, Lucchesi C, Kontny U, González-Neira A, Picci P, Alonso J, Patino-Garcia A, de Paillerets BB, Laud K, Dina C, Froguel P, Clavel-Chapelon F, Doz F, Michon J, Chanock SJ, Thomas G, Cox DG, Delattre O. Common variants near TARDBP and EGR2 are associated with susceptibility to Ewing sarcoma. Nat Genet 2012; 44:323-7. [PMID: 22327514 DOI: 10.1038/ng.1085] [Citation(s) in RCA: 130] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2011] [Accepted: 12/22/2011] [Indexed: 01/23/2023]
Abstract
Ewing sarcoma, a pediatric tumor characterized by EWSR1-ETS fusions, is predominantly observed in populations of European ancestry. We performed a genome-wide association study (GWAS) of 401 French individuals with Ewing sarcoma, 684 unaffected French individuals and 3,668 unaffected individuals of European descent and living in the United States. We identified candidate risk loci at 1p36.22, 10q21 and 15q15. We replicated these loci in two independent sets of cases and controls. Joint analysis identified associations with rs9430161 (P = 1.4 × 10(-20); odds ratio (OR) = 2.2) located 25 kb upstream of TARDBP, rs224278 (P = 4.0 × 10(-17); OR = 1.7) located 5 kb upstream of EGR2 and, to a lesser extent, rs4924410 at 15q15 (P = 6.6 × 10(-9); OR = 1.5). The major risk haplotypes were less prevalent in Africans, suggesting that these loci could contribute to geographical differences in Ewing sarcoma incidence. TARDBP shares structural similarities with EWSR1 and FUS, which encode RNA binding proteins, and EGR2 is a target gene of EWSR1-ETS. Variants at these loci were associated with expression levels of TARDBP, ADO (encoding cysteamine dioxygenase) and EGR2.
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Vellozo AF, Véron AS, Baa-Puyoulet P, Huerta-Cepas J, Cottret L, Febvay G, Calevro F, Rahbé Y, Douglas AE, Gabaldón T, Sagot MF, Charles H, Colella S. CycADS: an annotation database system to ease the development and update of BioCyc databases. Database (Oxford) 2011; 2011:bar008. [PMID: 21474551 PMCID: PMC3072769 DOI: 10.1093/database/bar008] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
In recent years, genomes from an increasing number of organisms have been sequenced, but their annotation remains a time-consuming process. The BioCyc databases offer a framework for the integrated analysis of metabolic networks. The Pathway tool software suite allows the automated construction of a database starting from an annotated genome, but it requires prior integration of all annotations into a specific summary file or into a GenBank file. To allow the easy creation and update of a BioCyc database starting from the multiple genome annotation resources available over time, we have developed an ad hoc data management system that we called Cyc Annotation Database System (CycADS). CycADS is centred on a specific database model and on a set of Java programs to import, filter and export relevant information. Data from GenBank and other annotation sources (including for example: KAAS, PRIAM, Blast2GO and PhylomeDB) are collected into a database to be subsequently filtered and extracted to generate a complete annotation file. This file is then used to build an enriched BioCyc database using the PathoLogic program of Pathway Tools. The CycADS pipeline for annotation management was used to build the AcypiCyc database for the pea aphid (Acyrthosiphon pisum) whose genome was recently sequenced. The AcypiCyc database webpage includes also, for comparative analyses, two other metabolic reconstruction BioCyc databases generated using CycADS: TricaCyc for Tribolium castaneum and DromeCyc for Drosophila melanogaster. Linked to its flexible design, CycADS offers a powerful software tool for the generation and regular updating of enriched BioCyc databases. The CycADS system is particularly suited for metabolic gene annotation and network reconstruction in newly sequenced genomes. Because of the uniform annotation used for metabolic network reconstruction, CycADS is particularly useful for comparative analysis of the metabolism of different organisms. Database URL:http://www.cycadsys.org
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Affiliation(s)
- Augusto F Vellozo
- UMR203 BF2I, Biologie Fonctionnelle Insectes et Interactions, INRA, INSA-Lyon, Université de Lyon, 20 av. A. Einstein, F-69621 Villeurbanne, France.
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