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Arabzade A, Zhao Y, Varadharajan S, Chen HC, Jessa S, Rivas B, Stuckert AJ, Solis M, Kardian A, Tlais D, Golbourn BJ, Stanton ACJ, Chan YS, Olson C, Karlin KL, Kong K, Kupp R, Hu B, Injac SG, Ngo M, Wang PR, De León LA, Sahm F, Kawauchi D, Pfister SM, Lin CY, Hodges HC, Singh I, Westbrook TF, Chintagumpala MM, Blaney SM, Parsons DW, Pajtler KW, Agnihotri S, Gilbertson RJ, Yi J, Jabado N, Kleinman CL, Bertrand KC, Deneen B, Mack SC. ZFTA-RELA Dictates Oncogenic Transcriptional Programs to Drive Aggressive Supratentorial Ependymoma. Cancer Discov 2021; 11:2200-2215. [PMID: 33741710 PMCID: PMC8418998 DOI: 10.1158/2159-8290.cd-20-1066] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [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: 07/22/2020] [Revised: 01/05/2021] [Accepted: 03/16/2021] [Indexed: 01/10/2023]
Abstract
More than 60% of supratentorial ependymomas harbor a ZFTA-RELA (ZRfus) gene fusion (formerly C11orf95-RELA). To study the biology of ZRfus, we developed an autochthonous mouse tumor model using in utero electroporation (IUE) of the embryonic mouse brain. Integrative epigenomic and transcriptomic mapping was performed on IUE-driven ZRfus tumors by CUT&RUN, chromatin immunoprecipitation sequencing, assay for transposase-accessible chromatin sequencing, and RNA sequencing and compared with human ZRfus-driven ependymoma. In addition to direct canonical NFκB pathway activation, ZRfus dictates a neoplastic transcriptional program and binds to thousands of unique sites across the genome that are enriched with PLAGL family transcription factor (TF) motifs. ZRfus activates gene expression programs through recruitment of transcriptional coactivators (Brd4, Ep300, Cbp, Pol2) that are amenable to pharmacologic inhibition. Downstream ZRfus target genes converge on developmental programs marked by PLAGL TF proteins, and activate neoplastic programs enriched in Mapk, focal adhesion, and gene imprinting networks. SIGNIFICANCE: Ependymomas are aggressive brain tumors. Although drivers of supratentorial ependymoma (ZFTA- and YAP1-associated gene fusions) have been discovered, their functions remain unclear. Our study investigates the biology of ZFTA-RELA-driven ependymoma, specifically mechanisms of transcriptional deregulation and direct downstream gene networks that may be leveraged for potential therapeutic testing.This article is highlighted in the In This Issue feature, p. 2113.
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Affiliation(s)
- Amir Arabzade
- Department of Chemical and Biomolecular Engineering, Rice University, Houston, Texas
- Department of Pediatrics, Division of Pediatric Hematology and Oncology, Texas Children's Cancer and Hematology Centers, Dan L. Duncan Cancer Center, Houston, Texas
- Therapeutic Innovation Center at Baylor College of Medicine, Houston, Texas
| | - Yanhua Zhao
- Department of Pediatrics, Division of Pediatric Hematology and Oncology, Texas Children's Cancer and Hematology Centers, Dan L. Duncan Cancer Center, Houston, Texas
- Therapeutic Innovation Center at Baylor College of Medicine, Houston, Texas
| | - Srinidhi Varadharajan
- Department of Pediatrics, Division of Pediatric Hematology and Oncology, Texas Children's Cancer and Hematology Centers, Dan L. Duncan Cancer Center, Houston, Texas
- Therapeutic Innovation Center at Baylor College of Medicine, Houston, Texas
| | - Hsiao-Chi Chen
- Department of Pediatrics, Division of Pediatric Hematology and Oncology, Texas Children's Cancer and Hematology Centers, Dan L. Duncan Cancer Center, Houston, Texas
- Therapeutic Innovation Center at Baylor College of Medicine, Houston, Texas
- Cancer and Cell Biology Program, Baylor College of Medicine, Dan L. Duncan Cancer Center, Houston, Texas
| | - Selin Jessa
- Quantitative Life Sciences, McGill University, Montreal, Quebec, Canada
| | - Bryan Rivas
- Department of Pediatrics, Division of Pediatric Hematology and Oncology, Texas Children's Cancer and Hematology Centers, Dan L. Duncan Cancer Center, Houston, Texas
- Therapeutic Innovation Center at Baylor College of Medicine, Houston, Texas
| | - Austin J Stuckert
- Department of Pediatrics, Division of Pediatric Hematology and Oncology, Texas Children's Cancer and Hematology Centers, Dan L. Duncan Cancer Center, Houston, Texas
- Therapeutic Innovation Center at Baylor College of Medicine, Houston, Texas
| | - Minerva Solis
- Department of Pediatrics, Division of Pediatric Hematology and Oncology, Texas Children's Cancer and Hematology Centers, Dan L. Duncan Cancer Center, Houston, Texas
- Therapeutic Innovation Center at Baylor College of Medicine, Houston, Texas
- Cancer and Cell Biology Program, Baylor College of Medicine, Dan L. Duncan Cancer Center, Houston, Texas
| | - Alisha Kardian
- Department of Pediatrics, Division of Pediatric Hematology and Oncology, Texas Children's Cancer and Hematology Centers, Dan L. Duncan Cancer Center, Houston, Texas
- Therapeutic Innovation Center at Baylor College of Medicine, Houston, Texas
- Cancer and Cell Biology Program, Baylor College of Medicine, Dan L. Duncan Cancer Center, Houston, Texas
| | - Dana Tlais
- Department of Pediatrics, Division of Pediatric Hematology and Oncology, Texas Children's Cancer and Hematology Centers, Dan L. Duncan Cancer Center, Houston, Texas
- Therapeutic Innovation Center at Baylor College of Medicine, Houston, Texas
| | - Brian J Golbourn
- Department of Neurological Surgery, UPMC Children's Hospital of Pittsburgh, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Ann-Catherine J Stanton
- Department of Neurological Surgery, UPMC Children's Hospital of Pittsburgh, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Yuen San Chan
- Therapeutic Innovation Center at Baylor College of Medicine, Houston, Texas
- Department of Molecular and Cellular Biology and Center for Precision Environmental Health, Baylor College of Medicine, Houston, Texas
- Department of Bioengineering, Rice University, Houston, Texas
- Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Calla Olson
- Therapeutic Innovation Center at Baylor College of Medicine, Houston, Texas
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
- Department of Biochemistry and Molecular Biology, Houston, Texas
| | - Kristen L Karlin
- Therapeutic Innovation Center at Baylor College of Medicine, Houston, Texas
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
- Department of Biochemistry and Molecular Biology, Houston, Texas
| | - Kathleen Kong
- Therapeutic Innovation Center at Baylor College of Medicine, Houston, Texas
| | - Robert Kupp
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Cambridge, England
- Department of Oncology, University of Cambridge, Hutchison/MRC Research Centre, Cambridge Biomedical Campus, Cambridge, England
| | - Baoli Hu
- Department of Neurological Surgery, UPMC Children's Hospital of Pittsburgh, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Sarah G Injac
- Department of Pediatrics, Division of Pediatric Hematology and Oncology, Texas Children's Cancer and Hematology Centers, Dan L. Duncan Cancer Center, Houston, Texas
- Therapeutic Innovation Center at Baylor College of Medicine, Houston, Texas
| | - Madeline Ngo
- Department of Chemical and Biomolecular Engineering, Rice University, Houston, Texas
| | - Peter R Wang
- Department of Chemical and Biomolecular Engineering, Rice University, Houston, Texas
| | - Luz A De León
- Department of Pediatrics, Division of Pediatric Hematology and Oncology, Texas Children's Cancer and Hematology Centers, Dan L. Duncan Cancer Center, Houston, Texas
| | - Felix Sahm
- Hopp-Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Neuropathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Daisuke Kawauchi
- Hopp-Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Biochemistry and Cellular Biology, National Center of Neurology and Psychiatry (NCNP), Tokyo, Japan
| | - Stefan M Pfister
- Hopp-Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Department of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
- Department of Pediatric Hematology and Oncology, Heidelberg University Hospital, Heidelberg, Germany
| | - Charles Y Lin
- Therapeutic Innovation Center at Baylor College of Medicine, Houston, Texas
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - H Courtney Hodges
- Therapeutic Innovation Center at Baylor College of Medicine, Houston, Texas
- Department of Molecular and Cellular Biology and Center for Precision Environmental Health, Baylor College of Medicine, Houston, Texas
- Department of Bioengineering, Rice University, Houston, Texas
- Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Irtisha Singh
- Department of Molecular and Cellular Medicine, College of Medicine, Texas A&M University Health Science Center, Bryan, Texas
| | - Thomas F Westbrook
- Therapeutic Innovation Center at Baylor College of Medicine, Houston, Texas
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
- Department of Biochemistry and Molecular Biology, Houston, Texas
| | - Murali M Chintagumpala
- Department of Pediatrics, Division of Pediatric Hematology and Oncology, Texas Children's Cancer and Hematology Centers, Dan L. Duncan Cancer Center, Houston, Texas
| | - Susan M Blaney
- Department of Pediatrics, Division of Pediatric Hematology and Oncology, Texas Children's Cancer and Hematology Centers, Dan L. Duncan Cancer Center, Houston, Texas
| | - Donald W Parsons
- Department of Pediatrics, Division of Pediatric Hematology and Oncology, Texas Children's Cancer and Hematology Centers, Dan L. Duncan Cancer Center, Houston, Texas
| | - Kristian W Pajtler
- Hopp-Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Department of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
- Department of Pediatric Hematology and Oncology, Heidelberg University Hospital, Heidelberg, Germany
| | - Sameer Agnihotri
- Department of Neurological Surgery, UPMC Children's Hospital of Pittsburgh, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Richard J Gilbertson
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Cambridge, England
- Department of Oncology, University of Cambridge, Hutchison/MRC Research Centre, Cambridge Biomedical Campus, Cambridge, England
| | - Joanna Yi
- Department of Pediatrics, Division of Pediatric Hematology and Oncology, Texas Children's Cancer and Hematology Centers, Dan L. Duncan Cancer Center, Houston, Texas
- Therapeutic Innovation Center at Baylor College of Medicine, Houston, Texas
| | - Nada Jabado
- Quantitative Life Sciences, McGill University, Montreal, Quebec, Canada
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada
| | - Claudia L Kleinman
- Quantitative Life Sciences, McGill University, Montreal, Quebec, Canada
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada
- Lady Davis Research Institute, Jewish General Hospital, Quebec, Canada
| | - Kelsey C Bertrand
- Department of Pediatrics, Division of Pediatric Hematology and Oncology, Texas Children's Cancer and Hematology Centers, Dan L. Duncan Cancer Center, Houston, Texas.
- Therapeutic Innovation Center at Baylor College of Medicine, Houston, Texas
| | - Benjamin Deneen
- Cancer and Cell Biology Program, Baylor College of Medicine, Dan L. Duncan Cancer Center, Houston, Texas.
- Program in Developmental Biology, Baylor College of Medicine, Houston, Texas
- Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, Texas
- Department of Neurosurgery, Baylor College of Medicine, Houston, Texas
| | - Stephen C Mack
- Department of Pediatrics, Division of Pediatric Hematology and Oncology, Texas Children's Cancer and Hematology Centers, Dan L. Duncan Cancer Center, Houston, Texas.
- Therapeutic Innovation Center at Baylor College of Medicine, Houston, Texas
- Cancer and Cell Biology Program, Baylor College of Medicine, Dan L. Duncan Cancer Center, Houston, Texas
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2
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Zheng T, Ghasemi DR, Okonechnikov K, Korshunov A, Sill M, Maass KK, Benites Goncalves da Silva P, Ryzhova M, Gojo J, Stichel D, Arabzade A, Kupp R, Benzel J, Taya S, Adachi T, Shiraishi R, Gerber NU, Sturm D, Ecker J, Sievers P, Selt F, Chapman R, Haberler C, Figarella-Branger D, Reifenberger G, Fleischhack G, Rutkowski S, Donson AM, Ramaswamy V, Capper D, Ellison DW, Herold-Mende CC, Schüller U, Brandner S, Driever PH, Kros JM, Snuderl M, Milde T, Grundy RG, Hoshino M, Mack SC, Gilbertson RJ, Jones DTW, Kool M, von Deimling A, Pfister SM, Sahm F, Kawauchi D, Pajtler KW. Cross-Species Genomics Reveals Oncogenic Dependencies in ZFTA/C11orf95 Fusion-Positive Supratentorial Ependymomas. Cancer Discov 2021; 11:2230-2247. [PMID: 33879448 DOI: 10.1158/2159-8290.cd-20-0963] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [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: 07/21/2020] [Revised: 02/16/2021] [Accepted: 04/16/2021] [Indexed: 11/16/2022]
Abstract
Molecular groups of supratentorial ependymomas comprise tumors with ZFTA-RELA or YAP1-involving fusions and fusion-negative subependymoma. However, occasionally supratentorial ependymomas cannot be readily assigned to any of these groups due to lack of detection of a typical fusion and/or ambiguous DNA methylation-based classification. An unbiased approach with a cohort of unprecedented size revealed distinct methylation clusters composed of tumors with ependymal but also various other histologic features containing alternative translocations that shared ZFTA as a partner gene. Somatic overexpression of ZFTA-associated fusion genes in the developing cerebral cortex is capable of inducing tumor formation in vivo, and cross-species comparative analyses identified GLI2 as a key downstream regulator of tumorigenesis in all tumors. Targeting GLI2 with arsenic trioxide caused extended survival of tumor-bearing animals, indicating a potential therapeutic vulnerability in ZFTA fusion-positive tumors. SIGNIFICANCE: ZFTA-RELA fusions are a hallmark feature of supratentorial ependymoma. We find that ZFTA acts as a partner for alternative transcriptional activators in oncogenic fusions of supratentorial tumors with various histologic characteristics. Establishing representative mouse models, we identify potential therapeutic targets shared by ZFTA fusion-positive tumors, such as GLI2.This article is highlighted in the In This Issue feature, p. 2113.
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Affiliation(s)
- Tuyu Zheng
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
- Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - David R Ghasemi
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Konstantin Okonechnikov
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Andrey Korshunov
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Neuropathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Martin Sill
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Kendra K Maass
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
- Department of Pediatric Oncology, Hematology, and Immunology, Heidelberg University Hospital, Heidelberg, Germany
| | - Patricia Benites Goncalves da Silva
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Marina Ryzhova
- Department of Neuropathology, NN Burdenko Neurosurgical Institute, Moscow, Russia
| | - Johannes Gojo
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Department of Pediatrics and Adolescent Medicine and Comprehensive Center for Pediatrics, Medical University of Vienna, Vienna, Austria
| | - Damian Stichel
- Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Neuropathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Amir Arabzade
- Department of Pediatrics, Division of Hematology and Oncology, Baylor College of Medicine, Texas Children's Hospital, Houston, Texas
- Department of Chemical and Biomolecular Engineering, Rice University, Houston, Texas
| | - Robert Kupp
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Cambridge, United Kingdom
| | - Julia Benzel
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
- Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Shinichiro Taya
- Department of Biochemistry and Cellular Biology, National Institute of Neuroscience, NCNP, Tokyo, Japan
| | - Toma Adachi
- Department of Biochemistry and Cellular Biology, National Institute of Neuroscience, NCNP, Tokyo, Japan
| | - Ryo Shiraishi
- Department of Biochemistry and Cellular Biology, National Institute of Neuroscience, NCNP, Tokyo, Japan
| | - Nicolas U Gerber
- Department of Oncology, University Children's Hospital, Zurich, Switzerland
| | - Dominik Sturm
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Department of Pediatric Oncology, Hematology, and Immunology, Heidelberg University Hospital, Heidelberg, Germany
- Pediatric Glioma Research Group, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Jonas Ecker
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Department of Pediatric Oncology, Hematology, and Immunology, Heidelberg University Hospital, Heidelberg, Germany
- Clinical Cooperation Unit Pediatric Oncology, German Cancer Research Center (DKFZ) and German Consortium for Translational Cancer Research (DKTK), Heidelberg, Germany
| | - Philipp Sievers
- Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Neuropathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Florian Selt
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Department of Pediatric Oncology, Hematology, and Immunology, Heidelberg University Hospital, Heidelberg, Germany
- Clinical Cooperation Unit Pediatric Oncology, German Cancer Research Center (DKFZ) and German Consortium for Translational Cancer Research (DKTK), Heidelberg, Germany
| | - Rebecca Chapman
- Children's Brain Tumour Research Centre, School of Medicine, University of Nottingham, Nottingham, United Kingdom
| | - Christine Haberler
- Division of Neuropathology and Neurochemistry, Department of Neurology, Medical University of Vienna, Vienna, Austria
| | | | - Guido Reifenberger
- Institute of Neuropathology, Heinrich Heine University, Medical Faculty, Duesseldorf, Germany
- German Cancer Consortium (DKTK), Partner Site Essen/Duesseldorf, Germany
| | - Gudrun Fleischhack
- Pediatric Oncology and Hematology, Pediatrics III, University Hospital of Essen, Essen, Germany
| | - Stefan Rutkowski
- Department of Paediatric Haematology and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Andrew M Donson
- University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | - Vijay Ramaswamy
- Department of Paediatrics, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - David Capper
- Department of Neuropathology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
- German Cancer Consortium (DKTK), Partner Site Berlin, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - David W Ellison
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | | | - Ulrich Schüller
- Department of Paediatric Haematology and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Research Institute, Children's Cancer Center Hamburg, Hamburg, Germany
- Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Sebastian Brandner
- Division of Neuropathology, UCL Queen Square Institute of Neurology and The National Hospital for Neurology and Neurosurgery, University College London Hospitals NHS Foundation Trust, London, United Kingdom
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London, UK
| | - Pablo Hernáiz Driever
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Johan M Kros
- Department of Pathology, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Matija Snuderl
- Division of Neuropathology, Department of Pathology, NYU Langone Health, New York, New York
| | - Till Milde
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Department of Pediatric Oncology, Hematology, and Immunology, Heidelberg University Hospital, Heidelberg, Germany
- Clinical Cooperation Unit Pediatric Oncology, German Cancer Research Center (DKFZ) and German Consortium for Translational Cancer Research (DKTK), Heidelberg, Germany
| | - Richard G Grundy
- Children's Brain Tumour Research Centre, School of Medicine, University of Nottingham, Nottingham, United Kingdom
| | - Mikio Hoshino
- Department of Biochemistry and Cellular Biology, National Institute of Neuroscience, NCNP, Tokyo, Japan
| | - Stephen C Mack
- Department of Pediatrics, Division of Hematology and Oncology, Baylor College of Medicine, Texas Children's Hospital, Houston, Texas
| | - Richard J Gilbertson
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Cambridge, United Kingdom
- Department of Oncology, University of Cambridge, Hutchison/MRC Research Centre, Cambridge, United Kingdom
| | - David T W Jones
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Pediatric Glioma Research Group, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Marcel Kool
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
- Princess Máxima Centre for Paediatric Oncology, Utrecht, the Netherlands
| | - Andreas von Deimling
- Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Neuropathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Stefan M Pfister
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
- Department of Pediatric Oncology, Hematology, and Immunology, Heidelberg University Hospital, Heidelberg, Germany
| | - Felix Sahm
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany.
- Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Neuropathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Daisuke Kawauchi
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany.
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
- Department of Biochemistry and Cellular Biology, National Institute of Neuroscience, NCNP, Tokyo, Japan
| | - Kristian W Pajtler
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany.
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
- Department of Pediatric Oncology, Hematology, and Immunology, Heidelberg University Hospital, Heidelberg, Germany
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3
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Kupp R, Ruff L, Terranova S, Nathan E, Ballereau S, Stark R, Sekhar Reddy Chilamakuri C, Hoffmann N, Wickham-Rahrmann K, Widdess M, Arabzade A, Zhao Y, Varadharajan S, Zheng T, Murugesan M, Pfister SM, Kawauchi D, Pajtler KW, Deneen B, Mack SC, Masih KE, Gryder BE, Khan J, Gilbertson RJ. ZFTA Translocations Constitute Ependymoma Chromatin Remodeling and Transcription Factors. Cancer Discov 2021; 11:2216-2229. [PMID: 33741711 PMCID: PMC8918067 DOI: 10.1158/2159-8290.cd-20-1052] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [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: 07/16/2020] [Revised: 01/06/2021] [Accepted: 03/16/2021] [Indexed: 11/16/2022]
Abstract
ZFTA (C11orf95)-a gene of unknown function-partners with a variety of transcriptional coactivators in translocations that drive supratentorial ependymoma, a frequently lethal brain tumor. Understanding the function of ZFTA is key to developing therapies that inhibit these fusion proteins. Here, using a combination of transcriptomics, chromatin immunoprecipitation sequencing, and proteomics, we interrogated a series of deletion-mutant genes to identify a tripartite transformation mechanism of ZFTA-containing fusions, including: spontaneous nuclear translocation, extensive chromatin binding, and SWI/SNF, SAGA, and NuA4/Tip60 HAT chromatin modifier complex recruitment. Thereby, ZFTA tethers fusion proteins across the genome, modifying chromatin to an active state and enabling its partner transcriptional coactivators to promote promiscuous expression of a transforming transcriptome. Using mouse models, we validate further those elements of ZFTA-fusion proteins that are critical for transformation-including ZFTA zinc fingers and partner gene transactivation domains-thereby unmasking vulnerabilities for therapeutic targeting. SIGNIFICANCE: Ependymomas are hard-to-treat brain tumors driven by translocations between ZFTA and a variety of transcriptional coactivators. We dissect the transforming mechanism of these fusion proteins and identify protein domains indispensable for tumorigenesis, thereby providing insights into the molecular basis of ependymoma tumorigenesis and vulnerabilities for therapeutic targeting.This article is highlighted in the In This Issue feature, p. 2113.
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Affiliation(s)
- Robert Kupp
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Cambridge, England
| | - Lisa Ruff
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Cambridge, England
| | - Sabrina Terranova
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Cambridge, England
| | - Erica Nathan
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Cambridge, England
| | - Stephane Ballereau
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Cambridge, England
| | - Rory Stark
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Cambridge, England
| | | | - Nadin Hoffmann
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Cambridge, England
| | | | - Marcus Widdess
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Cambridge, England
| | - Amir Arabzade
- Department of Pediatrics, Section of Hematology-Oncology, Baylor College of Medicine, Houston, Texas
| | - Yanhua Zhao
- Department of Pediatrics, Section of Hematology-Oncology, Baylor College of Medicine, Houston, Texas
| | - Srinidhi Varadharajan
- Department of Pediatrics, Section of Hematology-Oncology, Baylor College of Medicine, Houston, Texas
| | - Tuyu Zheng
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Mohankumar Murugesan
- Centre for Stem Cell Research, Christian Medical College Campus, Bagayam, Vellore, Tamil Nadu, India
| | - Stefan M Pfister
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Daisuke Kawauchi
- Department of Biochemistry and Cellular Biology, National Center of Neurology and Psychiatry (NCNP), Tokyo, Japan
| | - Kristian W Pajtler
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Benjamin Deneen
- Cancer and Cell Biology Program, Baylor College of Medicine, Dan L. Duncan Cancer Center, Houston, Texas
| | - Stephen C Mack
- Department of Pediatrics, Section of Hematology-Oncology, Baylor College of Medicine, Houston, Texas
| | - Katherine E Masih
- Genetics Branch, Center for Cancer Research, NCI, Bethesda, Maryland
| | - Berkley E Gryder
- Genetics Branch, Center for Cancer Research, NCI, Bethesda, Maryland
| | - Javed Khan
- Genetics Branch, Center for Cancer Research, NCI, Bethesda, Maryland
| | - Richard J Gilbertson
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Cambridge, England.
- Department of Oncology, University of Cambridge, Hutchison/MRC Research Centre, Cambridge Biomedical Campus, Cambridge, England
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Arabzade A, Zhao Y, Varadharajan S, Chen HC, Bertrand K, Deneen B, Mack S. EPEN-01. C11ORF95-RELA DICTATES ONCOGENIC TRANSCRIPTIONAL PROGRAMS TO DRIVE AGGRESSIVE SUPRATENTORIAL EPENDYMOMA. Neuro Oncol 2021. [PMCID: PMC8168166 DOI: 10.1093/neuonc/noab090.051] [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] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Abstract
Over 60% of supratentorial (ST) ependymomas harbor a gene fusion between C11orf95, an uncharacterized gene, and RELA (also known as p65), a main component of the NF-ĸB family of transcription factors. While its sufficiency to drive tumor has been established, the mechanism of tumorigenesis remains elusive. To tackle this question, we developed a natively forming mouse tumor model using in utero electroporation (IUE) of the embryonic mouse brain and performed integrative epigenomic and transcriptomic mapping. Our findings indicate that in addition to direct canonical NF-ĸB pathway activation, C11orf95-RELA (CRfus) dictates a neoplastic transcriptional program and binds to unique sites across the genome enriched with Plagl family transcription factor motifs. CRfus modulates the transcriptional landscape by recruiting transcription co-activators (Brd4, EP300, Cbp, Pol2) which are amenable to pharmacologic inhibition. Downstream CRfus target genes converge on developmental programs marked by Plagl family of transcription factors and activate neoplastic programs enriched in Mapk, focal adhesion, and gene imprinting networks, many of which contain previously unreported therapeutic leads in C11orf95-RELA ependymoma.
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Affiliation(s)
| | - Yanhua Zhao
- Baylor College of Medicine, Houston, TX, USA
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Stuckert A, Arabzade A, Zhao Y, Chen HC, Mack S. EPEN-02. FUNCTION AND DEPENDENCY OF NF-KB ACTIVITY IN C11ORF95-RELA FUSION EPENDYMOMA. Neuro Oncol 2021. [PMCID: PMC8168265 DOI: 10.1093/neuonc/noab090.052] [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] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Abstract
Introduction
Ependymoma is an aggressive type of pediatric brain tumor resistant to chemotherapy, with treatment to date limited to surgical resection and radiation. Thus, identification and validation of molecular targets that can translate into clinical trials in ependymoma is desperately needed to improve patient outcomes. Over 70% of supratentorial ependymoma are driven by an oncogenic fusion between C11orf95 and Rela (denoted CRFUS). CRFUS expression initiates ependymoma development in mice by potentially acting as an oncogenic transcription factor and disrupting gene expression programs. We hypothesized that specific CRFUS interacting proteins are required for tumor formation and could represent lead therapeutic targets.
Methods
To study CRFUS ependymoma, a natively-forming tumor model of CRFUS generated by in utero electroporation of the developing mouse brain was utilized. Tumor cells were isolated and then subjected to nuclear Rapid Immunoprecipitation and Mass Spectrometry Analysis of Endogenous Proteins (RIME) of HA-tagged CRFUS protein. Immunoprecipitation and Western Blot (IP-WB) were utilized to probe for leading protein interactions.
Results
We identified NF-kB proteins consistent with canonical Rela mediated transcription (NFKB1 and NFKB2) as well as novel protein interactomes that converged on RNA splicing and translational regulation. In addition, we identified a large series of novel chromatin-binding proteins as candidates potentially required for CRFUS mediated tumorigenesis.
Conclusions
Further study is ongoing to validate key CRFUS protein interaction dependency on tumor development. ChIP-Seq (chromatin immunoprecipitation with massively parallel DNA sequencing) and CUT&RUN (cleavage under target and release using nuclease) assays have been employed to further analyze the functional role of canonical Rela pathway members. By interrogating these mechanisms, novel therapeutic targets and pathways may be identified in parallel with dissecting the molecular basis of CRFUS driven ependymoma.
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Affiliation(s)
- Austin Stuckert
- Baylor College of Medicine, Houston, TX, USA
- Texas Children’s Hospital, Houston, TX, USA
| | - Amir Arabzade
- Rice University, Houston, TX, USA
- Baylor College of Medicine, Houston, TX, USA
| | - Yanhua Zhao
- Baylor College of Medicine, Houston, TX, USA
| | | | - Stephen Mack
- Baylor College of Medicine, Houston, TX, USA
- Texas Children’s Hospital, Houston, TX, USA
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Injac S, Rivas B, Arabzade A, Zhao Y, Parsons DW, Mack S. EMBR-09. EXAMINING THE ROLE OF THE DEVELOPMENTALLY ENCODED TRANSCRIPTION FACTOR, LHX9, IN GROUP 3 MEDULLOBLASTOMA. Neuro Oncol 2021. [PMCID: PMC8168115 DOI: 10.1093/neuonc/noab090.027] [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] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Medulloblastoma (MB) is the most common malignant brain tumor of childhood. Despite major advances in our understanding of the biology of MB, novel treatments remain urgently needed. Using a chemical-genomics driven drug repositioning strategy, we identified the cardiac glycoside family of compounds as potential treatments for Group 3 MB. We subsequently demonstrated that single-agent treatment with digoxin prolongs survival in a patient-derived xenograft model (PDOX) of Group 3 MB to a degree comparable to radiation therapy, a mainstay in the treatment of MB. Finally, we examined the mechanism of digoxin-mediated cell killing using RNA-seq. This work identified LHX9, a member of the LIM homeobox family of transcription factors, as the gene most significantly down-regulated following treatment (Huang and Injac et al, Sci Trans Medicine, 2018). Homologs of LHX9 play key roles in cerebellar development via spatially and temporally restricted expression and LHX9 has been proposed as a core transcription factor (TF) in the regulatory circuitry of Group 3 tumors. Loss of function of other core TFs has been shown to impact MB growth. The role of LHX9 in MB, however, has not been previously experimentally evaluated. We now report that knockdown of LHX9 in MB-derived cell lines results in marked growth inhibition. RNA-seq analysis of LHX9-depleted cells showed changes which included alterations in extracellular matrix-receptor interactions and TGFb signaling. These findings raise the possibility that loss of LHX9 plays a major role in digoxin-mediated cell killing and that LHX9 represents a key dependency required for the growth of Group 3 MB. Clinical targeting of core TFs would represent a novel approach to targeting this devastating disease.
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Affiliation(s)
- Sarah Injac
- Texas Children’s Cancer and Hematology Centers, Houston, TX, USA
- Baylor College of Medicine, Houston, TX, USA
| | - Bryan Rivas
- Texas Children’s Cancer and Hematology Centers, Houston, TX, USA
- Baylor College of Medicine, Houston, TX, USA
| | - Amir Arabzade
- Graduate Program in Chemical and Biomolecular Engineering, Rice University, Houston, TX, USA
- Texas Children’s Cancer and Hematology Centers, Houston, TX, USA
| | - Yanhau Zhao
- Texas Children’s Cancer and Hematology Centers, Houston, TX, USA
- Baylor College of Medicine, Houston, TX, USA
| | - D William Parsons
- Texas Children’s Cancer and Hematology Centers, Houston, TX, USA
- Baylor College of Medicine, Houston, TX, USA
| | - Stephen Mack
- Texas Children’s Cancer and Hematology Centers, Houston, TX, USA
- Baylor College of Medicine, Houston, TX, USA
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Arabzade A, Zhao Y, Varadharajan S, Chen HC, Stuckert A, Rivas B, Agnihotri S, Hodges C, Parsons D, Blaney S, Westbrook T, Lin C, Yi J, Deneen B, Bertrand K, Mack S. EPEN-30. C11ORF95-RELA FUSION PROTEIN ENGAGES NOVEL GENOMIC LOCI TO DRIVE MURINE EPENDYMOMA GROWTH. Neuro Oncol 2020. [PMCID: PMC7715611 DOI: 10.1093/neuonc/noaa222.166] [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] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
RATIONALE Over 70% of supratentorial (ST) ependymoma are characterized by an oncogenic fusion between C11ORF95 and RELA. C11ORF95-RELA fusion is frequently the sole genetic driver detected in ST ependymoma, thus ranking this genomic event as a lead target for therapeutic investigation. RELA is a transcription factor (TF) central to mediating NF-kB pathway activation in processes such as inflammation, cellular metabolism, and chemotaxis. HYPOTHESIS: We posited that C11ORF95-RELA acts as an oncogenic TF that aberrantly shapes the tumor epigenome to drive aberrant transcription. Approach: To this end we developed an in utero electroporation (IUE) mouse model of ependymoma to express C11ORF95-RELA during embryonic development. Our IUE approach allowed us to develop C11ORF95-RELA driven tumor models and cell lines. We comprehensively characterized the epigenome and transcriptome of C11ORF95-RELA fusion driven mouse cells by H3K27ac ChIP-seq, ATAC-seq, and RNA-seq. RESULTS This data revealed that: 1) C11ORF95-RELA directly engages ‘open’ chromatin and is enriched at regions with known RELA TF binding sites as well as novel genomic loci/motifs, 2) C11ORF95-RELA preferentially binds to both H3K27ac (active) enhancers and promoters, and 3) Bound C11ORF95-RELA promoter loci are associated with increased transcription of genes shared with human ependymoma. CONCLUSION Our findings shed light on the transcriptional mechanisms of C11ORF95-RELA, and reveal downstream targets that may represent cancer dependency genes and molecular targets.
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Affiliation(s)
| | - Yanhua Zhao
- Baylor College of Medicine, Houston, TX, USA
| | | | | | | | - Bryan Rivas
- Baylor College of Medicine, Houston, TX, USA
| | | | | | | | | | | | - Charles Lin
- Baylor College of Medicine, Houston, TX, USA
| | - Joanna Yi
- Baylor College of Medicine, Houston, TX, USA
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Arabzade A, Stuckert AJ, Bertrand KC, Mack SC. Invited Review: The role and contribution of transcriptional enhancers in brain cancer. Neuropathol Appl Neurobiol 2020; 46:48-56. [DOI: 10.1111/nan.12612] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 02/23/2020] [Accepted: 02/25/2020] [Indexed: 12/13/2022]
Affiliation(s)
- A. Arabzade
- Department of Chemical and Biomolecular Engineering Rice University Houston TX 77005 USA
| | - A. J. Stuckert
- Department of Pediatrics Division of Hematology and Oncology Baylor College of Medicine Texas Children’s Hospital Dan L. Duncan Cancer Center Houston TX 77030 USA
| | - K. C. Bertrand
- Department of Pediatrics Division of Hematology and Oncology Baylor College of Medicine Texas Children’s Hospital Dan L. Duncan Cancer Center Houston TX 77030 USA
| | - S. C. Mack
- Department of Pediatrics Division of Hematology and Oncology Baylor College of Medicine Texas Children’s Hospital Dan L. Duncan Cancer Center Houston TX 77030 USA
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