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Lee OW, Rodrigues C, Lin SH, Luo W, Jones K, Brown DW, Zhou W, Karlins E, Khan SM, Baulande S, Raynal V, Surdez D, Reynaud S, Rubio RA, Zaidi S, Grossetête S, Ballet S, Lapouble E, Laurence V, Pierron G, Gaspar N, Corradini N, Marec-Bérard P, Rothman N, Dagnall CL, Burdett L, Manning M, Wyatt K, Yeager M, Chari R, Leisenring WM, Kulozik AE, Kriebel J, Meitinger T, Strauch K, Kirchner T, Dirksen U, Mirabello L, Tucker MA, Tirode F, Armstrong GT, Bhatia S, Robison LL, Yasui Y, Romero-Pérez L, Hartmann W, Metzler M, Diver WR, Lori A, Freedman ND, Hoover RN, Morton LM, Chanock SJ, Grünewald TGP, Delattre O, Machiela MJ. Targeted long-read sequencing of the Ewing sarcoma 6p25.1 susceptibility locus identifies germline-somatic interactions with EWSR1-FLI1 binding. Am J Hum Genet 2023; 110:427-441. [PMID: 36787739 PMCID: PMC10027473 DOI: 10.1016/j.ajhg.2023.01.017] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 01/23/2023] [Indexed: 02/16/2023] Open
Abstract
Ewing sarcoma (EwS) is a rare bone and soft tissue malignancy driven by chromosomal translocations encoding chimeric transcription factors, such as EWSR1-FLI1, that bind GGAA motifs forming novel enhancers that alter nearby expression. We propose that germline microsatellite variation at the 6p25.1 EwS susceptibility locus could impact downstream gene expression and EwS biology. We performed targeted long-read sequencing of EwS blood DNA to characterize variation and genomic features important for EWSR1-FLI1 binding. We identified 50 microsatellite alleles at 6p25.1 and observed that EwS-affected individuals had longer alleles (>135 bp) with more GGAA repeats. The 6p25.1 GGAA microsatellite showed chromatin features of an EWSR1-FLI1 enhancer and regulated expression of RREB1, a transcription factor associated with RAS/MAPK signaling. RREB1 knockdown reduced proliferation and clonogenic potential and reduced expression of cell cycle and DNA replication genes. Our integrative analysis at 6p25.1 details increased binding of longer GGAA microsatellite alleles with acquired EWSR-FLI1 to promote Ewing sarcomagenesis by RREB1-mediated proliferation.
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Affiliation(s)
- Olivia W Lee
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA; Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Calvin Rodrigues
- Inserm U830, PSL Université, Research Center, Institut Curie, 75005 Paris, France; SIREDO Oncology Centre, Institut Curie, 75005 Paris, France
| | - Shu-Hong Lin
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Wen Luo
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA; Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc, Frederick, MD 21701, USA
| | - Kristine Jones
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA; Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc, Frederick, MD 21701, USA
| | - Derek W Brown
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Weiyin Zhou
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA; Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc, Frederick, MD 21701, USA
| | - Eric Karlins
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA; Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc, Frederick, MD 21701, USA
| | - Sairah M Khan
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Sylvain Baulande
- ICGex Next-Generation Sequencing Platform, PSL Université, Research Center, Institut Curie, 75005 Paris, France
| | - Virginie Raynal
- ICGex Next-Generation Sequencing Platform, PSL Université, Research Center, Institut Curie, 75005 Paris, France
| | - Didier Surdez
- Inserm U830, PSL Université, Research Center, Institut Curie, 75005 Paris, France; SIREDO Oncology Centre, Institut Curie, 75005 Paris, France; Balgrist University Hospital, Faculty of Medicine, University of Zurich (UZH), Zurich, Switzerland
| | - Stephanie Reynaud
- SIREDO Oncology Centre, Institut Curie, 75005 Paris, France; Unité de Génétique Somatique, Department of Genetics, Institut Curie Hospital, 75005 Paris, France
| | - Rebeca Alba Rubio
- Max-Eder Research Group for Pediatric Sarcoma Biology, Institute of Pathology, Faculty of Medicine, LMU, 80337 Munich, Germany
| | - Sakina Zaidi
- Inserm U830, PSL Université, Research Center, Institut Curie, 75005 Paris, France; SIREDO Oncology Centre, Institut Curie, 75005 Paris, France
| | - Sandrine Grossetête
- Inserm U830, PSL Université, Research Center, Institut Curie, 75005 Paris, France; SIREDO Oncology Centre, Institut Curie, 75005 Paris, France
| | - Stelly Ballet
- SIREDO Oncology Centre, Institut Curie, 75005 Paris, France; Unité de Génétique Somatique, Department of Genetics, Institut Curie Hospital, 75005 Paris, France
| | - Eve Lapouble
- SIREDO Oncology Centre, Institut Curie, 75005 Paris, France; Unité de Génétique Somatique, Department of Genetics, Institut Curie Hospital, 75005 Paris, France
| | | | - Gaelle Pierron
- SIREDO Oncology Centre, Institut Curie, 75005 Paris, France; Unité de Génétique Somatique, Department of Genetics, Institut Curie Hospital, 75005 Paris, France
| | - Nathalie Gaspar
- Department of Oncology for Child and Adolescent, Institut Gustave Roussy, 94800 Villejuif, France
| | - Nadège Corradini
- Institute for Paediatric Haematology and Oncology, Leon Bérard Cancer Centre, University of Lyon, 69008 Lyon, France
| | - Perrine Marec-Bérard
- Institute for Paediatric Haematology and Oncology, Leon Bérard Cancer Centre, University of Lyon, 69008 Lyon, France
| | - Nathaniel Rothman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Casey L Dagnall
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA; Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc, Frederick, MD 21701, USA
| | - Laurie Burdett
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA; Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc, Frederick, MD 21701, USA
| | - Michelle Manning
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA; Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc, Frederick, MD 21701, USA
| | - Kathleen Wyatt
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA; Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc, Frederick, MD 21701, USA
| | - Meredith Yeager
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA; Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc, Frederick, MD 21701, USA
| | - Raj Chari
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA; Genome Modification Core Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD 21701, USA
| | - Wendy M Leisenring
- Cancer Prevention and Clinical Statistics Programs, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Andreas E Kulozik
- University Children's Hospital of Heidelberg, 69120 Heidelberg, Germany
| | - Jennifer Kriebel
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany; Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany; German Center for Diabetes Research (DZD), 85764 München-Neuherberg, Germany
| | - Thomas Meitinger
- Institute of Human Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany; Institute of Human Genetics, Technische Universität München, 80333 Munich, Germany
| | - Konstantin Strauch
- Institute of Genetic Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany; Chair of Genetic Epidemiology, IBE, Faculty of Medicine, LMU, 80539 Munich, Germany
| | - Thomas Kirchner
- Division of Translational Pediatric Sarcoma Research, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), 69120 Heidelberg, Germany; Hopp-Children's Cancer Center (KiTZ), Heidelberg, Germany; Institute of Pathology, Faculty of Medicine, LMU, 80337 Munich, Germany
| | - Uta Dirksen
- University Children's Hospital of Essen, 45147 Essen, Germany
| | - Lisa Mirabello
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Margaret A Tucker
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Franck Tirode
- Inserm U830, PSL Université, Research Center, Institut Curie, 75005 Paris, France; SIREDO Oncology Centre, Institut Curie, 75005 Paris, France
| | - Gregory T Armstrong
- Department of Epidemiology and Cancer Control, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Smita Bhatia
- Institute for Cancer Outcomes and Survivorship, University of Alabama, Birmingham, AL 35294, USA
| | - Leslie L Robison
- Department of Epidemiology and Cancer Control, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Yutaka Yasui
- Department of Epidemiology and Cancer Control, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Laura Romero-Pérez
- Max-Eder Research Group for Pediatric Sarcoma Biology, Institute of Pathology, Faculty of Medicine, LMU, 80337 Munich, Germany; Division of Translational Pediatric Sarcoma Research, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), 69120 Heidelberg, Germany; Hopp-Children's Cancer Center (KiTZ), Heidelberg, Germany
| | - Wolfgang Hartmann
- Gerhard- Domagk Institute of Pathology, University Hospital of Münster, 48149 Münster, Germany
| | - Markus Metzler
- University Children's Hospital of Erlangen, 91054 Erlangen, Germany
| | - W Ryan Diver
- Department of Population Science, American Cancer Society, Atlanta, GA, USA
| | - Adriana Lori
- Department of Population Science, American Cancer Society, Atlanta, GA, USA
| | - Neal D Freedman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Robert N Hoover
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Lindsay M Morton
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Stephen J Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Thomas G P Grünewald
- Max-Eder Research Group for Pediatric Sarcoma Biology, Institute of Pathology, Faculty of Medicine, LMU, 80337 Munich, Germany; Division of Translational Pediatric Sarcoma Research, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), 69120 Heidelberg, Germany; Hopp-Children's Cancer Center (KiTZ), Heidelberg, Germany; Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Olivier Delattre
- Inserm U830, PSL Université, Research Center, Institut Curie, 75005 Paris, France; SIREDO Oncology Centre, Institut Curie, 75005 Paris, France.
| | - Mitchell J Machiela
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA.
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