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Machiela MJ, Grünewald TG, Surdez D, Reynaud S, Mirabeau O, Karlins E, Rubio RA, Zaidi S, Grossetete-Lalami S, Ballet S, Lapouble E, Laurence V, Michon J, Pierron G, Kovar H, Gaspar N, Kontny U, González-Neira A, Picci P, Alonso J, Patino-Garcia A, Corradini N, Freedman ND, Rothman N, Dagnall CL, Burdett L, Jones K, Manning M, Wyatt K, Zhou W, Yeager M, Cox DG, Hoover RN, Khan J, Armstrong GT, Leisenring WM, Bhatia S, Robison LL, Dirksen U, Metzler M, Hartmann W, Strauch K, Kirchner T, Kulozik AE, Morton LM, Mirabello L, Tucker MA, Tirode F, Chanock S, Delattre O. Abstract A13: Genome-wide association study identifies multiple new loci associated with Ewing sarcoma susceptibility. Cancer Res 2018. [DOI: 10.1158/1538-7445.pedca17-a13] [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
Ewing sarcoma (EWS), a pediatric tumor predominantly occurring in children of European ancestry, is characterized by the EWSR1-FLI1 fusion oncogene. We performed a genome-wide association study (GWAS) of 749 EWS cases and 1,378 unaffected individuals of European ancestry. Our study replicated previously reported susceptibility loci at 1p36.22, 10q21.3, and 15q15.1 and identified new loci at 6p25.1, 8q24.23, 20p11.22, and 20p11.23 (P-values <5x10-8). Effect estimates exhibited odds ratios (ORs) in excess of 1.7, which is high for cancer GWAS, and striking in light of the rarity of EWS cases in familial cancer syndromes. In expression quantitative trait locus (eQTL) analyses, we observed altered expression patterns for plausible candidate genes at 6p25.1 with RREB1, a RAS-responsive element, and at 20p11.23 with KIZ, a centrosomal stabilization protein. The 20p11.22 locus is also near NKX2-2, a highly overexpressed gene in EWS. Interestingly, most loci reside near GGAA repeat sequences where binding of the EWSR1-FLI1 fusion protein occurs. The seven EWS susceptibility loci discovered in only 749 cases make EWS one of the most productive GWAS studied cancers when considering a locus-to-case discovery ratio. The substantive estimated ORs suggest a distinctive underlying genetic architecture for EWS in which moderate-risk SNPs likely constitute a significant fraction and may interact with EWSR1-FLI1 binding.
Citation Format: Mitchell J. Machiela, Thomas G.P. Grünewald, Didier Surdez, Stephanie Reynaud, Olivier Mirabeau, Eric Karlins, Rebeca Alba Rubio, Sakina Zaidi, Sandrine Grossetete-Lalami, Stelly Ballet, Eve Lapouble, Valérie Laurence, Jean Michon, Gaelle Pierron, Heinrich Kovar, Nathalie Gaspar, Udo Kontny, Anna González-Neira, Piero Picci, Javier Alonso, Ana Patino-Garcia, Nadège Corradini, Neal D. Freedman, Nathaniel Rothman, Casey L. Dagnall, Laurie Burdett, Kristine Jones, Michelle Manning, Kathleen Wyatt, Weiyin Zhou, Meredith Yeager, David G. Cox, Robert N. Hoover, Javed Khan, Gregory T. Armstrong, Wendy M. Leisenring, Smita Bhatia, Leslie L. Robison, Uta Dirksen, Markus Metzler, Wolfgang Hartmann, Konstantin Strauch, Thomas Kirchner, Andreas E. Kulozik, Lindsay M. Morton, Lisa Mirabello, Margaret A. Tucker, Franck Tirode, Stephen Chanock, Olivier Delattre. Genome-wide association study identifies multiple new loci associated with Ewing sarcoma susceptibility [abstract]. In: Proceedings of the AACR Special Conference: Pediatric Cancer Research: From Basic Science to the Clinic; 2017 Dec 3-6; Atlanta, Georgia. Philadelphia (PA): AACR; Cancer Res 2018;78(19 Suppl):Abstract nr A13.
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Affiliation(s)
- Mitchell J. Machiela
- 1Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD,
| | - Thomas G.P. Grünewald
- 2Max-Eder Research Group for Pediatric Sarcoma Biology, Institute of Pathology, Faculty of Medicine,, Munich, Germany,
| | - Didier Surdez
- 3Inserm U830, Équipe Labellisés LNCC, PSL université, Institut Curie, Paris, France,
| | | | | | - Eric Karlins
- 1Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD,
| | - Rebeca Alba Rubio
- 2Max-Eder Research Group for Pediatric Sarcoma Biology, Institute of Pathology, Faculty of Medicine,, Munich, Germany,
| | - Sakina Zaidi
- 4SIREDO Oncology Centre, Institut Curie, Paris, France,
| | | | - Stelly Ballet
- 4SIREDO Oncology Centre, Institut Curie, Paris, France,
| | - Eve Lapouble
- 4SIREDO Oncology Centre, Institut Curie, Paris, France,
| | | | - Jean Michon
- 4SIREDO Oncology Centre, Institut Curie, Paris, France,
| | | | - Heinrich Kovar
- 5Children’s Cancer Research Institute, St. Anna Kinderkrebsforschung, Vienna, Austria,
| | - Nathalie Gaspar
- 6Service de Pédiatrie, Institut Gustave Roussy, Villejuif, France,
| | - Udo Kontny
- 7Division of Pediatric Hematology Oncology and Stem Cell Transplantation, RWTH Aachen University, Aachen, Germany,
| | - Anna González-Neira
- 8Human Cancer Genetics Programme, Spanish National Cancer Research Centre, Madrid, Spain,
| | - Piero Picci
- 9Laboratorio di Oncologia Sperimentale, Istituto Ortopedico Rizzoli di Bologna, Bologna, Italy,
| | - Javier Alonso
- 10Instituto de Investigación de Enfermedades Raras, Instituto de Salud Carlos III, Majadahonda, Spain,
| | - Ana Patino-Garcia
- 11Laboratory of Pediatrics, University of Navarra, University Clinic of Navarra, IdiSNA, Pamplona, Spain,
| | | | - Neal D. Freedman
- 1Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD,
| | - Nathaniel Rothman
- 1Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD,
| | - Casey L. Dagnall
- 1Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD,
| | - Laurie Burdett
- 1Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD,
| | - Kristine Jones
- 1Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD,
| | - Michelle Manning
- 1Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD,
| | - Kathleen Wyatt
- 1Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD,
| | - Weiyin Zhou
- 1Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD,
| | - Meredith Yeager
- 1Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD,
| | - David G. Cox
- 13Centre Léon Bérard, INSERM U1052, Lyon, France,
| | - Robert N. Hoover
- 1Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD,
| | - Javed Khan
- 14Genetics Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD,
| | - Gregory T. Armstrong
- 15Department of Epidemiology and Cancer Control, St. Jude Children’s Research Hospital, Memphis, TN,
| | - Wendy M. Leisenring
- 16Cancer Prevention and Clinical Statistics Programs, Fred Hutchinson Cancer Research Center, Seattle, WA,
| | - Smita Bhatia
- 17Institute for Cancer Outcomes and Survivorship, University of Alabama at Birmingham, Birmingham, AL,
| | - Leslie L. Robison
- 15Department of Epidemiology and Cancer Control, St. Jude Children’s Research Hospital, Memphis, TN,
| | - Uta Dirksen
- 18University Children’s Hospital of Essen, Essen, Germany,
| | - Markus Metzler
- 19University Children’s Hospital of Erlangen, Erlangen, Germany,
| | - Wolfgang Hartmann
- 20Gerhard-Domagk Institute of Pathology, University Hospital of Münster, Münster, Germany,
| | | | - Thomas Kirchner
- 22Institute of Pathology, Faculty of Medicine, LMU Munich, Munich, Germany,
| | | | - Lindsay M. Morton
- 1Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD,
| | - Lisa Mirabello
- 1Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD,
| | - Margaret A. Tucker
- 1Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD,
| | - Franck Tirode
- 4SIREDO Oncology Centre, Institut Curie, Paris, France,
| | - Stephen Chanock
- 1Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD,
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Machiela MJ, Grünewald TG, Surdez D, Reynaud S, Mirabeau O, Karlins E, Rubio RA, Zaidi S, Grossetete-Lalami S, Ballet S, Lapouble E, Laurence V, Michon J, Pierron G, Kovar H, Gaspar N, Kontny U, González-Neira A, Picci P, Alonso J, Patino-Garcia A, Corradini N, Freedman ND, Rothman N, Dagnall CL, Burdette L, Jones K, Manning M, Wyatt K, Zhou W, Yeager M, Cox DG, Hoover RN, Khan J, Armstrong GT, Leisenring WM, Bhatia S, Robison LL, Dirksen U, Metzler M, Hartmann W, Strauch K, Kirchner T, Kulozik AE, Morton LM, Mirabello L, Tucker MA, Tirode F, Chanock SJ, Delattre O. Abstract 2970: Multiple new susceptibility loci identified in genome-wide association study of Ewing sarcoma. Cancer Res 2018. [DOI: 10.1158/1538-7445.am2018-2970] [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
Ewing sarcoma (EWS) is a rare pediatric tumor predominantly occurring in children of European ancestry and is characterized by the pathognomonic EWSR1-FLI1 fusion oncogene. To identify germline susceptibility loci associated with EWS risk, we performed a genome-wide association study (GWAS) meta-analysis of 749 EWS cases and 1,378 unaffected individuals of European ancestry from sample collections within the Institut Curie, National Cancer Institute and the Childhood Cancer Survivor Study. Our study replicated previously reported susceptibility loci at 1p36.22, 10q21.3 and 15q15.1 as well as identified novel loci at 6p25.1, 8q24.23, 20p11.22 and 20p11.23 (P-values<5×10-8). These seven EWS susceptibility loci discovered in only 749 cases make EWS one of the most productive GWAS studied cancers when considering a locus to case discovery ratio. All estimated effect estimates were high for cancer GWAS with odds ratios in excess of 1.7 observed. These high per allele effects among relatively common germline variants are striking in light of the rarity of EWS cases and lack of evidence of EWS as part of a familial cancer syndrome and therefore suggest a distinctive genetic architecture for EWS. Interestingly, in silico bioinformatics analysis identified that most EWS susceptibility loci reside near GGAA nucleotide repeat sequences where binding of the EWSR1-FLI1 fusion protein occurs. ChIP-seq analyses confirmed in vivo binding of EWSR1-FLI1, suggesting germline variation in these regions could alter EWSR1-FLI1 binding and potentially deregulate neighboring genes. To identify genes with allele specific expression differences, we carried out expression quantitative trait locus (eQTL) analyses at each identified EWS susceptibility locus. We identified eQTLs for plausible candidate genes at 6p25.1 with RREB1, a RAS-responsive element, and at 20p11.23 with KIZ, a centrosomal stabilization protein. We also noted the 20p11.22 locus is near NKX2-2, a highly overexpressed gene in EWS, although no eQTL was observed in our expression data. Furthermore, knockdown of EWSR1-FLI1 in EWS cell lines indicated a more than 2-fold difference in expression of RREB1 and NKX2-2, further supporting the role of specific regulation of these genes by EWSR1-FLI1 and suggesting RREB1 and NKX2-2 may be transcription factors involved in core regulatory circuitries of EWS. Overall, our study suggests a distinctive underlying genetic architecture for EWS in which moderate risk common germline variants interact with EWSR1-FLI1 binding to alter expression of nearby target genes.
Citation Format: Mitchell J. Machiela, Thomas G. Grünewald, Didier Surdez, Stephanie Reynaud, Olivier Mirabeau, Eric Karlins, Rebeca Alba Rubio, Sakina Zaidi, Sandrine Grossetete-Lalami, Stelly Ballet, Eve Lapouble, Valérie Laurence, Jean Michon, Gaelle Pierron, Heinrich Kovar, Nathalie Gaspar, Udo Kontny, Anna González-Neira, Piero Picci, Javier Alonso, Ana Patino-Garcia, Nadège Corradini, Neal D. Freedman, Nathaniel Rothman, Casey L. Dagnall, Laurie Burdette, Kristine Jones, Michelle Manning, Kathleen Wyatt, Weiyin Zhou, Meredith Yeager, David G. Cox, Robert N. Hoover, Javed Khan, Gregory T. Armstrong, Wendy M. Leisenring, Smita Bhatia, Leslie L. Robison, Uta Dirksen, Markus Metzler, Wolfgang Hartmann, Konstantin Strauch, Thomas Kirchner, Andreas E. Kulozik, Lindsay M. Morton, Lisa Mirabello, Margaret A. Tucker, Franck Tirode, Stephen J. Chanock, Olivier Delattre. Multiple new susceptibility loci identified in genome-wide association study of Ewing sarcoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 2970.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | - Heinrich Kovar
- 4Children's Cancer Research Institute, St. Anna Kinderkrebsforschung, Austria
| | | | | | | | - Piero Picci
- 8Istituto Ortopedico Rizzoli di Bologna, Italy
| | - Javier Alonso
- 9Instituto de Investigación de Enfermedades Raras, Spain
| | | | | | | | | | | | | | | | | | | | | | | | | | | | - Javed Khan
- 1National Cancer Institute, Bethesda, MD
| | | | | | | | | | - Uta Dirksen
- 16University Children's Hospital of Essen, Germany
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Sheffield NC, Tirode F, Grossetete-Lalami S, Datlinger P, Schönegger A, Hadler J, Walder D, Ambros IM, Amaral AT, Álava ED, Schallmoser K, Strunk D, Rinner B, Liegl-Atzwanger B, Huppertz B, Leithner A, Dirksen U, Ambros P, Delattre O, Kovar H, Bock C, Tomazou EM. Abstract PR13: DNA methylation mapping and computational modeling in a large Ewing sarcoma cohort identifies principles of tumor heterogeneity and their impact on clinical phenotypes. Cancer Res 2016. [DOI: 10.1158/1538-7445.pedca15-pr13] [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
Ewing sarcoma is an excellent model for studying the role of epigenetic deregulation and tumor heterogeneity, given its low mutation rates and the well-defined oncogenic driver. We have recently shown that the fusion oncogene EWS-FLI1 induces widespread epigenetic rewiring in proximal and distal enhancers (Tomazou et al. Cell Reports 2015). In the current study, we validate the clinical relevance of our results in a large cohort of primary tumors, and we explore the prevalence, characteristics, and clinical impact of epigenetic tumor heterogeneity in Ewing sarcoma.
We used reduced representation bisulfite sequencing (RRBS) to generate genome-wide profiles of DNA methylation in 141 Ewing sarcoma primary tumors, 17 Ewing sarcoma cell lines, and 32 primary mesenchymal stem cell (MSC) samples. Deep sequencing resulted in DNA methylation measurements for an average of 3.5 million unique CpGs per sample with excellent data quality (>98% bisulfite conversion efficiency). In addition, for three primary tumors we generated comprehensive reference epigenome maps using whole genome bisulfite sequencing (WGBS) and ChIP-seq for seven histone marks (H3K4me3, H3K4me1, H3K27me3, H3K27ac, H3K56ac, H3K36me3, and H3K9me3).
We show that DNA methylation data can be used to infer enhancer activity differences among tumors, allowing us to exploit our large primary tumor dataset to systematically compare the regulation of EWS-FLI1 correlated and anticorrelated enhancers. We also identified Ewing-specific DNA methylation patterns. For example, Ewing sarcoma samples consistently show higher DNA methylation than MSCs at AP-1 binding sites, but lower DNA methylation at EWS-FLI1 binding sites.
To explore epigenetic heterogeneity within individual tumors, we developed a bioinformatic algorithm that quantifies DNA methylation disorder. Using individual reads containing multiple DNA methylation measurements from single cells, we assign scores at single-nucleotide resolution. This method uses a probabilistic model to account for overall methylation rate and expected disorder levels. By evaluating the likelihood of the data in a model that assumes that the DNA methylation status of a CpG is independent of the methylation status of a nearby CpG, we identify extremely heterogeneous as well as highly epigenetically conserved genomic elements. These different region types show distinct patterns of enrichment for regulatory modes and transcription factor binding.
We also compared the observed DNA methylation disorder in 141 Ewing tumors to those observed in 17 Ewing sarcoma cell lines, 32 primary MSC samples, and several hundred additional tumor and normal samples that are unrelated to Ewing sarcoma. This analysis identified Ewing-specific patterns of DNA methylation heterogeneity and stratifies patients based on epigenetic heterogeneity.
Our dataset constitutes the largest available resource of genome-scale DNA methylation maps in a solid pediatric tumor. It strongly confirms the relevance of enhancer reprogramming and tumor heterogeneity in Ewing sarcoma, and it constitutes a starting point to develop DNA methylation biomarkers for prognosis and patient stratification.
This study is supported by the Austrian National Bank (OeNB project #15714) and the Kapsch group (https://www.kapsch.net/).
This abstract is also presented as Poster A24.
Citation Format: Nathan C. Sheffield, Franck Tirode, Sandrine Grossetete-Lalami, Paul Datlinger, Andreas Schönegger, Johanna Hadler, Diana Walder, Ingeborg M. Ambros, Ana Teresa Amaral, Enrique de Álava, Katharina Schallmoser, Dirk Strunk, Beate Rinner, Bernadette Liegl-Atzwanger, Berthold Huppertz, Andreas Leithner, Uta Dirksen, Peter Ambros, Olivier Delattre, Heinrich Kovar, Christoph Bock, Eleni M. Tomazou. DNA methylation mapping and computational modeling in a large Ewing sarcoma cohort identifies principles of tumor heterogeneity and their impact on clinical phenotypes. [abstract]. In: Proceedings of the AACR Special Conference on Advances in Pediatric Cancer Research: From Mechanisms and Models to Treatment and Survivorship; 2015 Nov 9-12; Fort Lauderdale, FL. Philadelphia (PA): AACR; Cancer Res 2016;76(5 Suppl):Abstract nr PR13.
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Affiliation(s)
- Nathan C. Sheffield
- 1CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria,
| | - Franck Tirode
- 2Centre de Recherche, Institut Curie, Paris, France,
| | | | - Paul Datlinger
- 1CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria,
| | - Andreas Schönegger
- 1CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria,
| | - Johanna Hadler
- 1CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria,
| | - Diana Walder
- 3Children's Cancer Research Institute, St. Anna Kinderkrebsforschung, Vienna, Austria,
| | - Ingeborg M. Ambros
- 3Children's Cancer Research Institute, St. Anna Kinderkrebsforschung, Vienna, Austria,
| | - Ana Teresa Amaral
- 4Instituto de Biomedicina de Sevilla - Hospital Universitario Virgen del Rocío, Sevilla, Spain,
| | - Enrique de Álava
- 4Instituto de Biomedicina de Sevilla - Hospital Universitario Virgen del Rocío, Sevilla, Spain,
| | - Katharina Schallmoser
- 5Spinal Cord Injury and Tissue Regeneration Center Salzburg, Paracelsus Medical University, Salzburg, Austria,
| | - Dirk Strunk
- 5Spinal Cord Injury and Tissue Regeneration Center Salzburg, Paracelsus Medical University, Salzburg, Austria,
| | - Beate Rinner
- 6Center for Medical Research, Medical University of Graz, Graz, Austria,
| | | | - Berthold Huppertz
- 8Organizational Unit of Research Infrastructure, Biobank Graz, Medical University of Graz, Graz, Austria,
| | - Andreas Leithner
- 9Department of Orthopedic Surgery, Medical University of Graz, Graz, Austria,
| | - Uta Dirksen
- 10University Hospital Münster, Department of Pediatrics and Pediatric Hematology and Oncology, Münster, Germany
| | - Peter Ambros
- 3Children's Cancer Research Institute, St. Anna Kinderkrebsforschung, Vienna, Austria,
| | | | - Heinrich Kovar
- 3Children's Cancer Research Institute, St. Anna Kinderkrebsforschung, Vienna, Austria,
| | - Christoph Bock
- 1CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria,
| | - Eleni M. Tomazou
- 3Children's Cancer Research Institute, St. Anna Kinderkrebsforschung, Vienna, Austria,
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