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Therapeutic targeting of ependymoma as informed by oncogenic enhancer profiling

Nature volume 553, pages 101105 (04 January 2018) | Download Citation


Genomic sequencing has driven precision-based oncology therapy; however, the genetic drivers of many malignancies remain unknown or non-targetable, so alternative approaches to the identification of therapeutic leads are necessary. Ependymomas are chemotherapy-resistant brain tumours, which, despite genomic sequencing, lack effective molecular targets. Intracranial ependymomas are segregated on the basis of anatomical location (supratentorial region or posterior fossa) and further divided into distinct molecular subgroups that reflect differences in the age of onset, gender predominance and response to therapy1,2,3. The most common and aggressive subgroup, posterior fossa ependymoma group A (PF-EPN-A), occurs in young children and appears to lack recurrent somatic mutations2. Conversely, posterior fossa ependymoma group B (PF-EPN-B) tumours display frequent large-scale copy number gains and losses but have favourable clinical outcomes1,3. More than 70% of supratentorial ependymomas are defined by highly recurrent gene fusions in the NF-κB subunit gene RELA (ST-EPN-RELA), and a smaller number involve fusion of the gene encoding the transcriptional activator YAP1 (ST-EPN-YAP1)1,3,4. Subependymomas, a distinct histologic variant, can also be found within the supratetorial and posterior fossa compartments, and account for the majority of tumours in the molecular subgroups ST-EPN-SE and PF-EPN-SE. Here we describe mapping of active chromatin landscapes in 42 primary ependymomas in two non-overlapping primary ependymoma cohorts, with the goal of identifying essential super-enhancer-associated genes on which tumour cells depend. Enhancer regions revealed putative oncogenes, molecular targets and pathways; inhibition of these targets with small molecule inhibitors or short hairpin RNA diminished the proliferation of patient-derived neurospheres and increased survival in mouse models of ependymomas. Through profiling of transcriptional enhancers, our study provides a framework for target and drug discovery in other cancers that lack known genetic drivers and are therefore difficult to treat.

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This work was supported by an Alex's Lemonade Stand Young Investigator Award (S.C.M.), The CIHR Banting Fellowship (S.C.M.), The Cancer Prevention Research Institute of Texas (S.C.M., RR170023), Sibylle Assmus Award for Neurooncology (K.W.P.), the DKFZ-MOST (Ministry of Science, Technology & Space, Israel) program in cancer research (H.W.), James S. McDonnell Foundation (J.N.R.) and NIH grants: CA154130 (J.N.R.), R01 CA169117 (J.N.R.), R01 CA171652 (J.N.R.), R01 NS087913 (J.N.R.) and R01 NS089272 (J.N.R.). R.C.G. is supported by NIH grants T32GM00725 and F30CA217065. M.D.T. is supported by The Garron Family Chair in Childhood Cancer Research, and grants from the Pediatric Brain Tumour Foundation, Grand Challenge Award from CureSearch for Children’s Cancer, the National Institutes of Health (R01CA148699, R01CA159859), The Terry Fox Research Institute and Brainchild. M.D.T. is also supported by a Stand Up To Cancer St. Baldrick’s Pediatric Dream Team Translational Research Grant (SU2C-AACR-DT1113). Stand Up To Cancer is a program of the Entertainment Industry Foundation administered by the American Association for Cancer Research. We thank S. Archer for technical writing and editing expertise. In addition, we thank the High-Throughput Sequencing Unit of the DKFZ Genomics and Proteomics Core Facility for technical support and acknowledge technical assistance by M. Mauermann, T. Wedig, A. Wittmann and L. Siebert. Additional support came from the ICGC DE-Mining grant (#01KU1505). We thank The Children’s Hospital at Westmead (CHW) Tumour Bank for support of tumour samples (H.W.). We thank D. Schumick (Cleveland Clinic Art Department) and G. Hsu (https://www.hsubiomedicalvisual.com) for their assistance with creative artwork.

Author information

Author notes

    • Stephen C. Mack
    • , Kristian W. Pajtler
    •  & Lukas Chavez

    These authors contributed equally to this work.

    • Marcel Kool
    • , Michael D. Taylor
    •  & Jeremy N. Rich

    These authors jointly supervised this work.


  1. Department of Pediatrics, Baylor College of Medicine, Houston, Texas, USA

    • Stephen C. Mack
    •  & Kelsey C. Bertrand
  2. Department of Pediatric Hematolgy and Oncology, Texas Children’s Cancer and Hematology Centers, Houston, Texas, USA

    • Stephen C. Mack
    •  & Kelsey C. Bertrand
  3. Department of Stem Cell Biology and Regenerative Medicine, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio 44195, USA

    • Stephen C. Mack
    • , Xiuxing Wang
    • , Anne Song
    • , Christine Lee
    • , Qiulian Wu
    • , Tyler E. Miller
    • , Christopher G. Hubert
    • , Stephen Dombrowski
    • , Claudia L. L. Valentim
    • , Ryan C. Gimple
    • , Andrew Morton
    • , Leo Kim
    • , Briana C. Prager
    • , Susan Q. Ke
    • , Adam Tropper
    • , Sisi Lai
    • , Vaidehi Mahadev
    •  & Jeremy N. Rich
  4. Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine of Case Western Reserve University, Cleveland, Ohio 44195, USA

    • Stephen C. Mack
    • , Xiuxing Wang
    • , Anne Song
    • , Christine Lee
    • , Qiulian Wu
    • , Tyler E. Miller
    • , Christopher G. Hubert
    • , Stephen Dombrowski
    • , Claudia L. L. Valentim
    • , Ryan C. Gimple
    • , Andrew Morton
    • , Leo Kim
    • , Briana C. Prager
    • , Susan Q. Ke
    • , Adam Tropper
    • , Sisi Lai
    • , Vaidehi Mahadev
    •  & Jeremy N. Rich
  5. Hopp Children’s Cancer Center at the NCT Heidelberg (KiTZ), 69120 Heidelberg, Germany

    • Kristian W. Pajtler
    • , Lukas Chavez
    • , Konstantin Okonechnikov
    • , Serap Erkek
    • , Susanne N. Gröbner
    • , Till Milde
    • , Hendrik Witt
    • , David T. W. Jones
    • , Stefan M. Pfister
    •  & Marcel Kool
  6. Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany and German Cancer Consortium (DKTK), 69120 Heidelberg, Germany

    • Kristian W. Pajtler
    • , Lukas Chavez
    • , Konstantin Okonechnikov
    • , Serap Erkek
    • , Susanne N. Gröbner
    • , Hendrik Witt
    • , David T. W. Jones
    • , Stefan M. Pfister
    •  & Marcel Kool
  7. Department of Pediatric Oncology, Hematology and Immunology, Heidelberg University Hospital, 69120 Heidelberg, Germany

    • Kristian W. Pajtler
    • , Till Milde
    • , Hendrik Witt
    •  & Stefan M. Pfister
  8. Department of Medicine, Division of Medical Genetics, University of California – San Diego School of Medicine, La Jolla, California 92093, USA

    • Lukas Chavez
  9. Department of Pediatrics, Cleveland Clinic, Cleveland, Ohio 44195, USA

    • Kelsey C. Bertrand
    •  & Senthuran Vijayarajah
  10. Department of Medicine, Division of Regenerative Medicine, University of California – San Diego School of Medicine, La Jolla, California, USA

    • Xiuxing Wang
    • , Qiulian Wu
    • , Ryan C. Gimple
    • , Leo Kim
    • , Briana C. Prager
    •  & Jeremy N. Rich
  11. European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany

    • Serap Erkek
  12. Department of Genomic Sciences, University of Washington, Seattle, Washington 355065, USA

    • Alexander Federation
  13. Division of Neurosurgery, Program in Developmental and Stem Cell Biology, Arthur and Sonia Labatt Brain Tumour Research Centre, Hospital for Sick Children, Toronto, Ontario M5G 1X8, Canada

    • Xin Wang
    • , Laura McDonald
    • , Patrick Sin-Chan
    • , Kulandaimanuvel Antony Michaelraj
    • , Livia Garzia
    • , Laura Donovan
    • , Betty Luu
    • , John J. Y. Lee
    • , Xiaochong Wu
    • , Jennifer Zuccaro
    • , Yuan Thompson
    • , Borja L. Holgado
    • , Ian Scott
    • , Annie Huang
    • , Peter B. Dirks
    • , Eric Bouffet
    • , Vijay Ramaswamy
    • , James T. Rutka
    •  & Michael D. Taylor
  14. Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, Ohio 44106, USA

    • James J. Morrow
    • , Alina Saiakhova
    • , Daniel C. Factor
    • , Andrew Morton
    • , Yan Li
    •  & Peter C. Scacheri
  15. Department of Pathology, Case Western Reserve University, Cleveland, Ohio 44106, USA

    • Tyler E. Miller
    •  & Ryan C. Gimple
  16. Department of Neuropathology, NN Burdenko Neurosurgical Institute, 4th Tverskaya-Yamskaya 16, Moscow 125047, Russia

    • Marina Ryzhova
  17. Rose Ella Burkhardt Brain Tumor & Neuro-Oncology Center, Cleveland Clinic Neurological Institute, Department of Neurosurgery, Cleveland Clinic, Cleveland, Ohio 44195, USA

    • Stephen Dombrowski
    •  & Jeremy N. Rich
  18. Computational Biology Program, Ontario Institute for Cancer Research, Toronto, Ontario M5G 0A3, Canada

    • Jüri Reimand
  19. Department of Medical Biophysics, University of Toronto, Toronto, Ontario M5G 1L7, Canada

    • Jüri Reimand
    •  & Mathieu Lupien
  20. Department of Pediatrics, Division of Critical Care, University of Utah School of Medicine, Salt Lake City, Utah, USA

    • Senthuran Vijayarajah
  21. Department of Pediatrics, University of Utah School of Medicine, Salt Lake City, Utah, USA

    • Sylvia Doan
  22. Centro Andaluz de Biología del Desarrollo, Consejo Superior de Investigaciones Científicas and Universidad Pablo de Olavide, Sevilla, Spain

    • Ana Fernandez Miñan
  23. Department of Computational Molecular Biology, Max-Planck-Institute for Molecular Genetics, 14195 Berlin, Germany

    • Matthias Lienhard
  24. Division of Molecular Genetics, German Cancer Research Center (DKFZ), 69121 Heidelberg, Germany

    • Marc Zapatka
    • , Zhiqin Huang
    •  & Peter Lichter
  25. Department of Pathology, University Health Network, Toronto, Ontario M5G 1L7, Canada

    • Kenneth D. Aldape
  26. Preclinical Therapeutics and Drug Delivery Research Program, Fundacio Sant Joan de Deu, 08950 Barcelona, Spain

    • Angel M. Carcaboso
  27. Nationwide Children’s Hospital, Center for Childhood Cancer and Blood Diseases, Columbus, Ohio

    • Peter J. Houghton
  28. Duke University Medical Center, Department of Surgery, Durham, North Carolina, USA

    • Stephen T. Keir
  29. Clinical Cooperation Unit Pediatric Oncology, German Cancer Research Center (DKFZ), INF 280, D-69120 Heidelberg, Germany

    • Till Milde
  30. MOE Key Laboratory of Model Animal for Disease Study, Model Animal Research Center, Nanjing University, National Resource Centre for Mutant Mice, Nanjing, China

    • Chao-Jun Li
  31. Institute of Pathology and Southwest Cancer Center, Southwest Hospital, The Third Military Medical University, and The Key Laboratory of Tumor Immunopathology, The Ministry of Education of China, Chongqing, China

    • Xiu-Wu Bian
  32. Department of Surgery, Division of Neurosurgery, Faculty of Health Sciences, McMaster University, Hamilton, Ontario, Canada

    • Sheila K. Singh
  33. Novartis Institutes for Biomedical Research, Cambridge, Massachusetts 02139, USA

    • Annie Huang
    • , Eric Bouffet
    •  & James E. Bradner
  34. Division of Hematology and Oncology, Hospital for Sick Children, Toronto, Ontario M5G 1X8, Canada

    • Vijay Ramaswamy
  35. Departments of Paediatrics and Human Genetics, McGill University and the McGill University Health Centre Research Institute, Montreal, Quebec H3Z 2Z3, Canada

    • Nada Jabado
  36. Developmental Neurobiology, St Jude Children’s Research Hospital, Memphis, Tennessee, USA

    • Paul A. Northcott
  37. Department of Neuropathology, University of Heidelberg, 69120 Heidelberg, Germany

    • Andrey Korshunov
  38. Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), 69121 Heidelberg, Germany

    • Andrey Korshunov


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S.C.M., K.W.P. and L.C. designed, performed and analysed the majority of the experiments in this study. Q.W. performed genetic knockdown experiments along with in vivo drug studies. K.C.B. performed all of the ChIP QC including library preparations and pre- and post-qPCR for the entire cohort. A.F., K.O. and S.E. performed the transcription factor network mapping of the super enhancer data. J.J.M. and T.E.M. assisted with super enhancer analysis and overall interpretation of data and analysis. Xin W., L.M., A.F.M. and I.S. led all of the zebrafish experiments in terms of establishment, interpretation and analysis. L.G., A.M., Y.T. and B.L.H. performed timed mating and tissue isolation in developing mouse embryos. J.R. assisted with pathway analysis of super enhancers. J.J.Y.L. assisted with ChIP experiments and library preparations. A.S. guided analysis of super-enhancer-subgroup stratification. D.C.F. performed RNA-seq pre-processing and analysis. B.L. helped with tissue isolation, preparation and submission for ChIP sequencing and DNA methylation analysis. Xia.W. and L.G. directed breeding and establishment of meis1–GFP mice. C.L.L.V., R.C.G. K.A.M. and A.T. performed data integration and mining of drug databases and identification of lead therapeutic compounds. A.M. performed super-enhancer-saturation analysis. P.C.S. assisted with study design, data analysis interpretation and manuscript review. S.Q.K., J.Z., V.M. and S.L., assisted with qPCR of numerous targets in genetic knockdown and differentiation experiments. P.J.H., T.M., A.M.C., S.K.S. and S.T.K. provided ependymoma models, controls and helped design the study. Xiu.W., L.D., S.D., L.K. and B.C.P. assisted with normal NSC drug treatments with drug inhibitors used in this study. C.L., C.-J.L., X.-W.B., C.G.H., M.R., S.D., S.V., S.N.G., H.W., D.T.W.J., P.A.N., P.L., A.K., N.J., J.T.R., E.B., A.H., K.D.A., P.B.D., Y.L., M.L., Z.H., M.Z., V.R., J.E.B, S.M.P., P.S.-C. and P.C.S., assisted with data interpretation, manuscript preparation and review. M.D.T., J.N.R. and M.K. conceived, designed, interpreted and funded the study.

Competing interests

The authors declare no competing financial interests.

Corresponding authors

Correspondence to Marcel Kool or Michael D. Taylor or Jeremy N. Rich.

Reviewer Information Nature thanks S. Pomeroy, W. Weiss and the other anonymous reviewer(s) for their contribution to the peer review of this work.

Publisher's note: Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

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