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Kardian A, Sun H, Ippagunta S, Laboe N, Chen HC, Emanus E, Varadharajan S, Zheng T, Holcomb B, Connelly P, Connelly JP, Wang M, Lowe K, Pruett-Miller SM, Bertrand KC, Deneen B, Mack SC. Dominant Malignant Clones Leverage Lineage Restricted Epigenomic Programs to Drive Ependymoma Development. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.12.607603. [PMID: 39211123 PMCID: PMC11361245 DOI: 10.1101/2024.08.12.607603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/04/2024]
Abstract
ZFTA-RELA is the most recurrent genetic alteration seen in pediatric supratentorial ependymoma (EPN) and is sufficient to initiate tumors in mice. Despite ZFTA-RELA's potent oncogenic potential, ZFTA-RELA gene fusions are observed exclusively in childhood EPN, with tumors located distinctly in the supratentorial region of the central nervous system (CNS). We hypothesized that specific chromatin modules accessible during brain development would render distinct cell lineage programs at direct risk of transformation by ZFTA-RELA. To this end, we performed combined single cell ATAC and RNA-seq analysis (scMultiome) of the developing mouse forebrain as compared to ZR-driven mouse and human EPN. We demonstrate that specific developmental lineage programs present in radial glial cells and regulated by Plagl family transcription factors are at risk of neoplastic transformation. Binding of this chromatin network by ZFTA-RELA or other PLAGL family motif targeting fusion proteins leads to persistent chromatin accessibility at oncogenic loci and oncogene expression. Cross-species analysis of mouse and human EPN reveals significant cell type heterogeneity mirroring incomplete neurogenic and gliogenic differentiation, with a small percentage of cycling intermediate progenitor-like cells that establish a putative tumor cell hierarchy. In vivo lineage tracing studies reveal single neoplastic clones that aggressively dominate tumor growth and establish the entire EPN cellular hierarchy. These findings unravel developmental epigenomic states critical for fusion oncoprotein driven transformation and elucidate how these states continue to shape tumor progression. HIGHLIGHTS 1. Specific chromatin modules accessible during brain development render distinct cell lineage programs at risk of transformation by pediatric fusion oncoproteins.2. Cross-species single cell ATAC and RNA (scMultiome) of mouse and human ependymoma (EPN) reveals diverse patterns of lineage differentiation programs that restrain oncogenic transformation.3. Early intermediate progenitor-like EPN cells establish a tumor cell hierarchy that mirrors neural differentiation programs.4. ZFTA-RELA transformation is compatible with distinct developmental epigenetic states requiring precise 'goldilocks' levels of fusion oncoprotein expression.5. Dominant tumor clones establish the entire EPN cellular hierarchy that reflects normal gliogenic and neurogenic differentiation programs.
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2
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Kardian AS, Mack S. The Intersection of Epigenetic Alterations and Developmental State in Pediatric Ependymomas. Dev Neurosci 2024:000537694. [PMID: 38527429 DOI: 10.1159/000537694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 02/03/2024] [Indexed: 03/27/2024] Open
Abstract
BACKGROUND Ependymomas are the third most common brain cancer in children and have no targeted therapies. They are divided into at least 9 major subtypes based on molecular characteristics and major drivers and have few genetic mutations compared to the adult form of this disease, leading to investigation of other mechanisms. SUMMARY Epigenetic alterations such as transcriptional programs activated by oncofusion proteins and alterations in histone modifications play an important role in development of this disease. Evidence suggests these alterations interact with the developmental epigenetic programs in the cell of origin to initiate neoplastic transformation and later disease progression, perhaps by keeping a portion of tumor cells in a developmental, proliferative state. KEY MESSAGES To better understand this disease, research on its developmental origins and associated epigenetic states needs to be further pursued. This could lead to better treatments, which are currently lacking due to the difficult-to-drug nature of known drivers such as fusion proteins. Epigenetic and developmental states characteristic of these tumors may not just be potential therapeutic targets, but used as a tool to find new avenues of treatment.
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3
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Rossi S, Barresi S, Colafati GS, Genovese S, Tancredi C, Costabile V, Patrizi S, Giovannoni I, Asioli S, Poliani PL, Gardiman MP, Cardoni A, Del Baldo G, Antonelli M, Gianno F, Piccirilli E, Catino G, Martucci L, Quacquarini D, Toni F, Melchionda F, Viscardi E, Zucchelli M, Dal Pos S, Gatti E, Liserre R, Schiavello E, Diomedi-Camassei F, Carai A, Mastronuzzi A, Gessi M, Giannini C, Novelli A, Onetti Muda A, Miele E, Alesi V, Alaggio R. PATZ1-Rearranged Tumors of the Central Nervous System: Characterization of a Pediatric Series of Seven Cases. Mod Pathol 2024; 37:100387. [PMID: 38007157 DOI: 10.1016/j.modpat.2023.100387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 10/28/2023] [Accepted: 11/06/2023] [Indexed: 11/27/2023]
Abstract
PATZ1-rearranged sarcomas are well-recognized tumors as part of the family of round cell sarcoma with EWSR1-non-ETS fusions. Whether PATZ1-rearranged central nervous system (CNS) tumors are a distinct tumor type is debatable. We thoroughly characterized a pediatric series of PATZ1-rearranged CNS tumors by chromosome microarray analysis (CMA), DNA methylation analysis, gene expression profiling and, when frozen tissue is available, optical genome mapping (OGM). The series consisted of 7 cases (M:F=1.3:1, 1-17 years, median 12). On MRI, the tumors were supratentorial in close relation to the lateral ventricles (intraventricular or iuxtaventricular), preferentially located in the occipital lobe. Two major histologic groups were identified: one (4 cases) with an overall glial appearance, indicated as "neuroepithelial" (NET) by analogy with the corresponding methylation class (MC); the other (3 cases) with a predominant spindle cell sarcoma morphology, indicated as "sarcomatous" (SM). A single distinct methylation cluster encompassing both groups was identified by multidimensional scaling analysis. Despite the epigenetic homogeneity, unsupervised clustering analysis of gene expression profiles revealed 2 distinct transcriptional subgroups correlating with the histologic phenotypes. Interestingly, genes implicated in epithelial-mesenchymal transition and extracellular matrix composition were enriched in the subgroup associated to the SM phenotype. The combined use of CMA and OGM enabled the identification of chromosome 22 chromothripsis in all cases suitable for the analyses, explaining the physical association of PATZ1 to EWSR1 or MN1. Six patients are currently disease-free (median follow-up 30 months, range 12-92). One patient of the SM group developed spinal metastases at 26 months from diagnosis and is currently receiving multimodal therapy (42 months). Our data suggest that PATZ1-CNS tumors are defined by chromosome 22 chromothripsis as causative of PATZ1 fusion, show peculiar MRI features (eg, relation to lateral ventricles, supratentorial frequently posterior site), and, although epigenetically homogenous, encompass 2 distinct histologic and transcriptional subgroups.
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Affiliation(s)
- Sabrina Rossi
- Pathology Unit, Department of Laboratories, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy.
| | - Sabina Barresi
- Pathology Unit, Department of Laboratories, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Giovanna Stefania Colafati
- Imaging Department, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy; Department of Neuroscience, Imaging and Clinical Sciences (DNISC), University "Gabriele D'Annunzio" of Chieti-Pescara, Chieti, Italy
| | - Silvia Genovese
- Laboratory of Medical Genetics, Translational Cytogenomics Research Unit, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Chantal Tancredi
- Pathology Unit, Department of Laboratories, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Valentino Costabile
- Multimodal Research Area, Unit of Microbiology and Diagnostics in Immunology, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Sara Patrizi
- Onco-Hematology, Cell Therapy, Gene Therapies and Hemopoietic Transplant, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Isabella Giovannoni
- Pathology Unit, Department of Laboratories, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Sofia Asioli
- Department of Biomedical and Neuromotor Sciences (DIBINEM)-Surgical Pathology Section-Alma Mater Studiorum - University of Bologna, Bologna, Italy
| | - Pietro Luigi Poliani
- Pathology Unit, San Raffaele Hospital Scientific Institute, Vita-Salute San Raffaele University, Milan, Italy
| | - Marina Paola Gardiman
- Surgical Pathology and Cytopathology Unit, Department of Medicine, University Hospital of Padua, Padua, Italy
| | - Antonello Cardoni
- Pathology Unit, Department of Laboratories, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Giada Del Baldo
- Onco-Hematology, Cell Therapy, Gene Therapies and Hemopoietic Transplant, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Manila Antonelli
- Department of Radiology, Oncology and Anatomic Pathology, University La Sapienza, Rome, Italy
| | - Francesca Gianno
- Department of Radiology, Oncology and Anatomic Pathology, University La Sapienza, Rome, Italy; IRCCS Neuromed, Pozzilli, Isernia, Italy
| | - Eleonora Piccirilli
- Imaging Department, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy; Department of Neuroscience, Imaging and Clinical Sciences (DNISC), University "Gabriele D'Annunzio" of Chieti-Pescara, Chieti, Italy
| | - Giorgia Catino
- Laboratory of Medical Genetics, Translational Cytogenomics Research Unit, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Licia Martucci
- Laboratory of Medical Genetics, Translational Cytogenomics Research Unit, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Denise Quacquarini
- Pathology Unit, Department of Laboratories, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Francesco Toni
- Neuroradiology Unit, IRCCS Istituto delle Scienze Neurologiche di Bologna, Bologna, Italy
| | - Fraia Melchionda
- SSD Oncoematologia Pediatrica, IRCCS AOU Policlinico S.Orsola, Bologna, Italy
| | - Elisabetta Viscardi
- Department of Pediatrics, Azienda Ospedale-Università di Padova, Padova, Italy
| | - Mino Zucchelli
- Paediatric Neurosurgery, IRCCS Istituto delle Scienze Neurologiche di Bologna, Bologna, Italy
| | - Sandro Dal Pos
- Department of Radiology, Azienda Ospedale-Università di Padova, Padova, Italy
| | - Enza Gatti
- Department of Radiology, Neuroradiology Unit, ASST Spedali Civili University Hospital, Brescia, Italy
| | - Roberto Liserre
- Department of Radiology, Neuroradiology Unit, ASST Spedali Civili University Hospital, Brescia, Italy
| | - Elisabetta Schiavello
- Pediatric Oncology Unit, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | | | - Andrea Carai
- Neurosurgery Unit, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Angela Mastronuzzi
- Onco-Hematology, Cell Therapy, Gene Therapies and Hemopoietic Transplant, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Marco Gessi
- Neuropathology Unit, Pathology Division, Fondazione Policlinico Universitario A. Gemelli IRCCS, Università Cattolica S.Cuore, Rome, Italy
| | - Caterina Giannini
- Department of Biomedical and Neuromotor Sciences (DIBINEM)-Surgical Pathology Section-Alma Mater Studiorum - University of Bologna, Bologna, Italy; Department of Anatomic Pathology, Mayo Clinic, Rochester, Minnesota
| | - Antonio Novelli
- Laboratory of Medical Genetics, Translational Cytogenomics Research Unit, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | | | - Evelina Miele
- Onco-Hematology, Cell Therapy, Gene Therapies and Hemopoietic Transplant, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy.
| | - Viola Alesi
- Laboratory of Medical Genetics, Translational Cytogenomics Research Unit, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Rita Alaggio
- Pathology Unit, Department of Laboratories, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy; Department of Medico-surgical Sciences and Biotechnologies, Sapienza University, Rome, Italy
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4
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Pohl LC, Leitheiser M, Obrecht D, Schweizer L, Wefers AK, Eckhardt A, Raffeld M, Sturm D, Pajtler KW, Rutkowski S, Fukuoka K, Ichimura K, Bockmayr M, Schüller U. Molecular characteristics and improved survival prediction in a cohort of 2023 ependymomas. Acta Neuropathol 2024; 147:24. [PMID: 38265522 PMCID: PMC10808151 DOI: 10.1007/s00401-023-02674-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 12/04/2023] [Accepted: 12/21/2023] [Indexed: 01/25/2024]
Abstract
The diagnosis of ependymoma has moved from a purely histopathological review with limited prognostic value to an integrated diagnosis, relying heavily on molecular information. However, as the integrated approach is still novel and some molecular ependymoma subtypes are quite rare, few studies have correlated integrated pathology and clinical outcome, often focusing on small series of single molecular types. We collected data from 2023 ependymomas as classified by DNA methylation profiling, consisting of 1736 previously published and 287 unpublished methylation profiles. Methylation data and clinical information were correlated, and an integrated model was developed to predict progression-free survival. Patients with EPN-PFA, EPN-ZFTA, and EPN-MYCN tumors showed the worst outcome with 10-year overall survival rates of 56%, 62%, and 32%, respectively. EPN-PFA harbored chromosome 1q gains and/or 6q losses as markers for worse survival. In supratentorial EPN-ZFTA, a combined loss of CDKN2A and B indicated worse survival, whereas a single loss did not. Twelve out of 200 EPN-ZFTA (6%) were located in the posterior fossa, and these tumors relapsed or progressed even earlier than supratentorial tumors with a combined loss of CDKN2A/B. Patients with MPE and PF-SE, generally regarded as non-aggressive tumors, only had a 10-year progression-free survival of 59% and 65%, respectively. For the prediction of the 5-year progression-free survival, Kaplan-Meier estimators based on the molecular subtype, a Support Vector Machine based on methylation, and an integrated model based on clinical factors, CNV data, and predicted methylation scores achieved balanced accuracies of 66%, 68%, and 73%, respectively. Excluding samples with low prediction scores resulted in balanced accuracies of over 80%. In sum, our large-scale analysis of ependymomas provides robust information about molecular features and their clinical meaning. Our data are particularly relevant for rare and hardly explored tumor subtypes and seemingly benign variants that display higher recurrence rates than previously believed.
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Affiliation(s)
- Lara C Pohl
- Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Research Institute Children's Cancer Center Hamburg, Hamburg, Germany
| | - Maximilian Leitheiser
- Institute of Pathology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- Institute of Pathology, Ludwig Maximilians University Hospital Munich, Munich, Germany
| | - Denise Obrecht
- Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Leonille Schweizer
- Institute of Neurology (Edinger Institute), University Hospital Frankfurt, Goethe University, Frankfurt am Main, Germany
- German Cancer Consortium (DKTK), Partner Site Frankfurt/Mainz, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Frankfurt Cancer Institute (FCI), Frankfurt am Main, Germany
| | - Annika K Wefers
- Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Alicia Eckhardt
- Research Institute Children's Cancer Center Hamburg, Hamburg, Germany
- Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Department of Radiotherapy and Radiation Oncology, Hubertus Wald Tumor Center-University Cancer Center Hamburg, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Mark Raffeld
- Laboratory of Pathology, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Dominik Sturm
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Glioma Research, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
- Department of Pediatric Oncology, Hematology and Immunology, Heidelberg University Hospital, Heidelberg, Germany
| | - 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
- KiTZ Clinical Trial Unit, Department of Pediatric Oncology, Hematology, Immunology and Pulmonology, Heidelberg University Hospital, Heidelberg, Germany
| | - Stefan Rutkowski
- Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Kohei Fukuoka
- Department of Hematology/Oncology, Saitama Children's Medical Center, Saitama, Japan
| | - Koichi Ichimura
- Department of Brain Disease Translational Research, Graduate School of Medicine, Juntendo University, 2-1-1 Hongo, Bunkyo-Ku, Tokyo, 113-8421, Japan
| | - Michael Bockmayr
- Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.
- Research Institute Children's Cancer Center Hamburg, Hamburg, Germany.
- Institute of Pathology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany.
| | - Ulrich Schüller
- Department of Pediatric Hematology 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.
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5
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Chapman RJ, Ghasemi DR, Andreiuolo F, Zschernack V, Espariat AT, Buttarelli FR, Giangaspero F, Grill J, Haberler C, Paine SML, Scott I, Jacques TS, Sill M, Pfister S, Kilday JP, Leblond P, Massimino M, Witt H, Modena P, Varlet P, Pietsch T, Grundy RG, Pajtler KW, Ritzmann TA. Optimizing biomarkers for accurate ependymoma diagnosis, prognostication, and stratification within International Clinical Trials: A BIOMECA study. Neuro Oncol 2023; 25:1871-1882. [PMID: 36916248 PMCID: PMC10547510 DOI: 10.1093/neuonc/noad055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Indexed: 03/14/2023] Open
Abstract
BACKGROUND Accurate identification of brain tumor molecular subgroups is increasingly important. We aimed to establish the most accurate and reproducible ependymoma subgroup biomarker detection techniques, across 147 cases from International Society of Pediatric Oncology (SIOP) Ependymoma II trial participants, enrolled in the pan-European "Biomarkers of Ependymoma in Children and Adolescents (BIOMECA)" study. METHODS Across 6 European BIOMECA laboratories, we evaluated epigenetic profiling (DNA methylation array); immunohistochemistry (IHC) for nuclear p65-RELA, H3K27me3, and Tenascin-C; copy number analysis via fluorescent in situ hybridization (FISH) and MLPA (1q, CDKN2A), and MIP and DNA methylation array (genome-wide copy number evaluation); analysis of ZFTA- and YAP1-fusions by RT-PCR and sequencing, Nanostring and break-apart FISH. RESULTS DNA Methylation profiling classified 65.3% (n = 96/147) of cases as EPN-PFA and 15% (n = 22/147) as ST-ZFTA fusion-positive. Immunohistochemical loss of H3K27me3 was a reproducible and accurate surrogate marker for EPN-PFA (sensitivity 99%-100% across 3 centers). IHC for p65-RELA, FISH, and RNA-based analyses effectively identified ZFTA- and YAP-fused supratentorial ependymomas. Detection of 1q gain using FISH exhibited only 57% inter-center concordance and low sensitivity and specificity while MIP, MLPA, and DNA methylation-based approaches demonstrated greater accuracy. CONCLUSIONS We confirm, in a prospective trial cohort, that H3K27me3 immunohistochemistry is a robust EPN-PFA biomarker. Tenascin-C should be abandoned as a PFA marker. DNA methylation and MIP arrays are effective tools for copy number analysis of 1q gain, 6q, and CDKN2A loss while FISH is inadequate. Fusion detection was successful, but rare novel fusions need more extensive technologies. Finally, we propose test sets to guide future diagnostic approaches.
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Affiliation(s)
- Rebecca J Chapman
- Children’s Brain Tumour Research Centre, University of Nottingham, Nottingham, UK
| | - David R Ghasemi
- Hopp Children’s Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neuro-oncology, German Cancer Research Center (DKFZ) and German Consortium for Translational Cancer Research (DKTK), Heidelberg, Germany
- Department of Pediatric Oncology, Hematology, Immunology and Pulmonology, Heidelberg University Hospital, Heidelberg, Germany
| | - Felipe Andreiuolo
- Department of Neuropathology, DGNN Brain Tumor Reference Center, University of Bonn, Bonn, Germany
- Instituto Estadual do Cerebro Paulo Niemeyer, Rio de Janerio, Brazil
- IDOR Institute, Rio de Janeiro, Brazil
| | - Valentina Zschernack
- Department of Neuropathology, DGNN Brain Tumor Reference Center, University of Bonn, Bonn, Germany
| | - Arnault Tauziede Espariat
- Departement de Neuropathologie, Hopital Sainte-Anne, Paris, France
- INSERM Unit 981 and Department of Pediatric and Adolescent Oncology, Gustave Roussy, Villejuif, France
| | - Francesca R Buttarelli
- Department of Radiological, Oncological and Anatomo-Pathological Sciences, Sapienza University of Rome, Rome, Italy
| | - Felice Giangaspero
- Department of Radiological, Oncological and Anatomo-Pathological Sciences, Sapienza University of Rome, Rome, Italy
- IRCCS Neuromed, Pozzilli, Italy
| | - Jacques Grill
- INSERM Unit 981 and Department of Pediatric and Adolescent Oncology, Gustave Roussy, Villejuif, France
| | - Christine Haberler
- Division of Neuropathology and Neurochemistry, Department of Neurology, Medical University of Vienna, Vienna, Austria
| | - Simon M L Paine
- Department of Neuropathology, Nottingham University Hospital, Nottingham, UK
| | - Ian Scott
- Department of Neuropathology, Nottingham University Hospital, Nottingham, UK
| | - Thomas S Jacques
- Developmental Biology and Cancer Programme, UCL GOS Institute of Child Health, London, UK
- Department of Histopathology, Great Ormond Street Hospital for Children, London, UK
| | - Martin Sill
- Hopp Children’s Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
| | - Stefan Pfister
- Hopp Children’s Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neuro-oncology, German Cancer Research Center (DKFZ) and German Consortium for Translational Cancer Research (DKTK), Heidelberg, Germany
- Department of Pediatric Oncology, Hematology, Immunology and Pulmonology, Heidelberg University Hospital, Heidelberg, Germany
| | - John-Paul Kilday
- Children’s Brain Tumour Research Network (CBTRN), Royal Manchester Children’s Hospital, Manchester, UK
- The Centre for Paediatric, Teenage and Young Adult Cancer, Institute of Cancer Sciences, University of Manchester, Manchester, UK
| | - Pierre Leblond
- Institute of Hematology and Pediatric Oncology (IHOPe), Leon Berard Comprehensive Cancer Center, Lyon, France
| | - Maura Massimino
- Paediatric Unit, Fondazione Istituto Di Ricovero e Cura a Carattere Scientifico, Istituto Nazionale dei Tumori, Milano, Italy
| | - Hendrik Witt
- Hopp Children’s Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neuro-oncology, German Cancer Research Center (DKFZ) and German Consortium for Translational Cancer Research (DKTK), Heidelberg, Germany
- Department of Pediatric Oncology, Hematology, Immunology and Pulmonology, Heidelberg University Hospital, Heidelberg, Germany
| | | | - Pascale Varlet
- Departement de Neuropathologie, Hopital Sainte-Anne, Paris, France
- INSERM Unit 981 and Department of Pediatric and Adolescent Oncology, Gustave Roussy, Villejuif, France
| | - Torsten Pietsch
- Department of Neuropathology, DGNN Brain Tumor Reference Center, University of Bonn, Bonn, Germany
| | - Richard G Grundy
- Children’s Brain Tumour Research Centre, University of Nottingham, Nottingham, UK
| | - Kristian W Pajtler
- Children’s Brain Tumour Research Centre, University of Nottingham, Nottingham, UK
- Hopp Children’s Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neuro-oncology, German Cancer Research Center (DKFZ) and German Consortium for Translational Cancer Research (DKTK), Heidelberg, Germany
- Department of Pediatric Oncology, Hematology, Immunology and Pulmonology, Heidelberg University Hospital, Heidelberg, Germany
| | - Timothy A Ritzmann
- Children’s Brain Tumour Research Centre, University of Nottingham, Nottingham, UK
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6
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Boop SH, Shimony N, Boop FA. Review and update on pediatric ependymoma. Childs Nerv Syst 2023; 39:2667-2673. [PMID: 37493720 DOI: 10.1007/s00381-023-06091-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 07/17/2023] [Indexed: 07/27/2023]
Abstract
Since our last Special Annual Issue dedicated to the topic of ependymoma in 2009, critical advancements have been made in the understanding of this disease which is largely confined to childhood. In the era of molecular profiling, the prior classification of ependymoma based on histology has become largely irrelevant, with multiple new subtypes of this disease now being described in the newest 2021 WHO CNS Tumor Classification System. Despite our advancements in understanding the underlying biology of these tumors, the mainstays of treatment-gross total surgical resection followed by confocal radiation therapy-have continued to yield the best treatment results across multiple studies and centers. Here, we provide an update on our understanding of the advancements made in tumor biology, surgical, and oncologic management of this disease. As we move into an era of more personalized medicine, it is critical to reflect on our historical understanding of different disease entities, to better understand the future directions of our treatments.
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Affiliation(s)
- Scott H Boop
- Department of Neurological Surgery, University of Washington, Seattle, WA, USA
| | - Nir Shimony
- Department of Surgery, St. Jude Children's Research Hospital, Memphis, TN, USA
- Le Bonheur Neuroscience Institute, LeBonheur Children's Hospital, Memphis, TN, USA
- Department of Neurological Surgery, University of Tennessee Health Science Center, Memphis, TN, USA
- Department of Neurosurgery, Johns Hopkins University, Baltimore, MD, USA
- Semmes Murphey Clinic, Memphis, TN, USA
| | - Frederick A Boop
- Department of Neurological Surgery, University of Tennessee Health Science Center, Memphis, TN, USA.
- Global Program, St. Jude Children's Research Hospital, Memphis, TN, USA.
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7
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de Sousa GR, Salomão KB, Nagano LFP, Riemondy KA, Chagas PS, Veronez LC, Saggioro FP, Marie SKN, Yunes JA, Cardinalli IA, Brandalise SR, de Paula Queiroz RG, Scrideli CA, Donson AM, Foreman NK, Tone LG, Valera ET. Identification of HDAC4 as a potential therapeutic target and prognostic biomarker for ZFTA-fused ependymomas. Cancer Gene Ther 2023; 30:1105-1113. [PMID: 37041276 DOI: 10.1038/s41417-023-00616-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 03/21/2023] [Accepted: 03/28/2023] [Indexed: 04/13/2023]
Abstract
Members of the HDAC family are predictive biomarkers and regulate the tumorigenesis in several cancers. However, the role of these genes in the biology of intracranial ependymomas (EPNs) remains unexplored. Here, an analysis of eighteen HDACs genes in an EPN transcriptomic dataset, revealed significantly higher levels of HDAC4 in supratentorial ZFTA fusion (ST-ZFTA) compared with ST-YAP1 fusion and posterior fossa EPNs, while HDAC7 and SIRT2 were downregulated in ST-ZFTA. HDAC4 was also overexpressed in ST-ZFTA as measured by single-cell RNA-Seq, quantitative real time-polymerase chain reaction, and immunohistochemistry. Survival analyses showed a significantly worse outcome for EPNs with higher HDAC4 and SIRT1 mRNA levels. Ontology enrichment analysis showed an HDAC4-high signature consistent with viral processes while collagen-containing extracellular matrix and cell-cell junction were enriched in those with an HDAC4-low signature. Immune gene analysis demonstrated a correlation between HDAC4 expression and low levels of NK resting cells. Several small molecules compounds targeting HDAC4 and ABCG2, were predicted by in silico analysis to be effective against HDAC4-high ZFTA. Our results provide novel insights into the biology of the HDAC family in intracranial ependymomas and reveal HDAC4 as a prognostic marker and potential therapeutic target in ST-ZFTA.
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Affiliation(s)
- Graziella R de Sousa
- Department of Genetics, Ribeirão Preto Medical School, 3900, Bandeirantes Avenue, Ribeirão Preto, SP, 14049-900, Brazil.
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA.
| | - Karina B Salomão
- Department of Pediatrics, Ribeirão Preto Medical School, 3900, Bandeirantes Avenue, Ribeirão Preto, SP, 14049-900, Brazil
| | - Luis F P Nagano
- Department of Genetics, Ribeirão Preto Medical School, 3900, Bandeirantes Avenue, Ribeirão Preto, SP, 14049-900, Brazil
| | - Kent A Riemondy
- RNA Bioscience Initiative, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA
| | - Pablo S Chagas
- Department of Genetics, Ribeirão Preto Medical School, 3900, Bandeirantes Avenue, Ribeirão Preto, SP, 14049-900, Brazil
- Department of Clinical Analyses, Toxicology and Food Sciences, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, SP, Brazil
| | - Luciana C Veronez
- Department of Pediatrics, Ribeirão Preto Medical School, 3900, Bandeirantes Avenue, Ribeirão Preto, SP, 14049-900, Brazil
| | - Fabiano P Saggioro
- Department of Pathology, Ribeirão Preto Medical School, 3900, Bandeirantes Avenue, Ribeirão Preto, SP, 14049-900, Brazil
| | - Suely K N Marie
- Laboratory of Molecular and Cellular Biology (LIM 15), Department of Neurology, Faculdade de Medicina FMUSP, Universidade de São Paulo, São Paulo, 01246-903, SP, Brazil
| | | | | | | | - Rosane G de Paula Queiroz
- Department of Pediatrics, Ribeirão Preto Medical School, 3900, Bandeirantes Avenue, Ribeirão Preto, SP, 14049-900, Brazil
| | - Carlos A Scrideli
- Department of Genetics, Ribeirão Preto Medical School, 3900, Bandeirantes Avenue, Ribeirão Preto, SP, 14049-900, Brazil
- Department of Pediatrics, Ribeirão Preto Medical School, 3900, Bandeirantes Avenue, Ribeirão Preto, SP, 14049-900, Brazil
| | - Andrew M Donson
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA
- Morgan Adams Foundation Pediatric Brain Tumor Research Program, Children's Hospital Colorado, Aurora, CO, 80045, USA
| | - Nicholas K Foreman
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA
- Morgan Adams Foundation Pediatric Brain Tumor Research Program, Children's Hospital Colorado, Aurora, CO, 80045, USA
| | - Luiz G Tone
- Department of Genetics, Ribeirão Preto Medical School, 3900, Bandeirantes Avenue, Ribeirão Preto, SP, 14049-900, Brazil
- Department of Pediatrics, Ribeirão Preto Medical School, 3900, Bandeirantes Avenue, Ribeirão Preto, SP, 14049-900, Brazil
| | - Elvis T Valera
- Department of Pediatrics, Ribeirão Preto Medical School, 3900, Bandeirantes Avenue, Ribeirão Preto, SP, 14049-900, Brazil
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8
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Yamaguchi J, Ohka F, Motomura K, Saito R. Latest classification of ependymoma in the molecular era and advances in its treatment: a review. Jpn J Clin Oncol 2023; 53:653-663. [PMID: 37288489 DOI: 10.1093/jjco/hyad056] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 05/19/2023] [Indexed: 06/09/2023] Open
Abstract
Ependymoma is a rare central nervous system (CNS) tumour occurring in all age groups and is one of the most common paediatric malignant brain tumours. Unlike other malignant brain tumours, ependymomas have few identified point mutations and genetic and epigenetic features. With advances in molecular understanding, the latest 2021 World Health Organization (WHO) classification of CNS tumours divided ependymomas into 10 diagnostic categories based on the histology, molecular information and location; this accurately reflected the prognosis and biology of this tumour. Although maximal surgical resection followed by radiotherapy is considered the standard treatment method, and chemotherapy is considered ineffective, the validation of the role of these treatment modalities continues. Although the rarity and long-term clinical course of ependymoma make designing and conducting prospective clinical trials challenging, knowledge is steadily accumulating and progress is being made. Much of the clinical knowledge obtained from clinical trials to date was based on the previous histology-based WHO classifications, and the addition of new molecular information may lead to more complex treatment strategies. Therefore, this review presents the latest findings on the molecular classification of ependymomas and advances in its treatment.
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Affiliation(s)
- Junya Yamaguchi
- Department of Neurosurgery, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Fumiharu Ohka
- Department of Neurosurgery, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Kazuya Motomura
- Department of Neurosurgery, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Ryuta Saito
- Department of Neurosurgery, Nagoya University Graduate School of Medicine, Nagoya, Japan
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9
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Gubbiotti MA, Madsen PJ, Tucker AM, Abdullaev Z, Aldape K, Shekdar K, Yang A, Minturn JE, Santi M, Viaene AN. ZFTA-fused supratentorial ependymoma with a novel fusion partner, DUX4. J Neuropathol Exp Neurol 2023; 82:668-671. [PMID: 37218333 PMCID: PMC10501467 DOI: 10.1093/jnen/nlad038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/24/2023] Open
Affiliation(s)
- Maria A Gubbiotti
- Department of Pathology and Laboratory Medicine, Hospital of the University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Peter J Madsen
- Department of Neurosurgery, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Alexander M Tucker
- Department of Neurosurgery, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Zied Abdullaev
- Department of Pathology and Laboratory Medicine, Hospital of the University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Kenneth Aldape
- Laboratory of Pathology and Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA
| | - Karuna Shekdar
- Department of Radiology, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Adeline Yang
- Department of Pediatrics, Division of Oncology, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Jane E Minturn
- Department of Pediatrics, Division of Oncology, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Mariarita Santi
- Department of Pathology and Laboratory Medicine, Hospital of the University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Angela N Viaene
- Department of Pathology and Laboratory Medicine, Hospital of the University of Pennsylvania, Philadelphia, Pennsylvania, USA
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10
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Bertrand KC, Klimo P. Recent Advancements in Ependymoma: Challenges and Therapeutic Opportunities. Pediatr Neurosurg 2023; 58:307-312. [PMID: 37231859 DOI: 10.1159/000530868] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 04/14/2023] [Indexed: 05/27/2023]
Abstract
BACKGROUND Ependymoma is one of the most common malignant pediatric brain tumors and can be difficult to treat. Over the last decade, much progress has been made in the understanding of the underlying molecular drivers within this group of tumors, but clinical outcomes remain unchanged. SUMMARY Here, we review the most recent molecular advances in pediatric ependymoma, evaluate results of recent clinical trials and discuss the ongoing challenges in the field and questions that remain. KEY MESSAGES The field of ependymoma has vastly changed over the last several decades with ten distinct molecular subgroups now described, but much progress needs to be made in developing new therapeutic strategies and targets.
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Affiliation(s)
- Kelsey C Bertrand
- Division of Neuro-oncology, Department of Oncology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA,
| | - Paul Klimo
- Department of Surgery, St Jude Children's Research Hospital, Memphis, Tennessee, USA
- Department of Neurosurgery, University of Tennessee Health and Science Center, Memphis, Tennessee, USA
- Le Bonheur Neuroscience Institute, Le Bonheur Children's Hospital, Memphis, Tennessee, USA
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11
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Okonechnikov K, Camgöz A, Chapman O, Wani S, Park DE, Hübner JM, Chakraborty A, Pagadala M, Bump R, Chandran S, Kraft K, Acuna-Hidalgo R, Reid D, Sikkink K, Mauermann M, Juarez EF, Jenseit A, Robinson JT, Pajtler KW, Milde T, Jäger N, Fiesel P, Morgan L, Sridhar S, Coufal NG, Levy M, Malicki D, Hobbs C, Kingsmore S, Nahas S, Snuderl M, Crawford J, Wechsler-Reya RJ, Davidson TB, Cotter J, Michaiel G, Fleischhack G, Mundlos S, Schmitt A, Carter H, Michealraj KA, Kumar SA, Taylor MD, Rich J, Buchholz F, Mesirov JP, Pfister SM, Ay F, Dixon JR, Kool M, Chavez L. 3D genome mapping identifies subgroup-specific chromosome conformations and tumor-dependency genes in ependymoma. Nat Commun 2023; 14:2300. [PMID: 37085539 PMCID: PMC10121654 DOI: 10.1038/s41467-023-38044-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Accepted: 04/13/2023] [Indexed: 04/23/2023] Open
Abstract
Ependymoma is a tumor of the brain or spinal cord. The two most common and aggressive molecular groups of ependymoma are the supratentorial ZFTA-fusion associated and the posterior fossa ependymoma group A. In both groups, tumors occur mainly in young children and frequently recur after treatment. Although molecular mechanisms underlying these diseases have recently been uncovered, they remain difficult to target and innovative therapeutic approaches are urgently needed. Here, we use genome-wide chromosome conformation capture (Hi-C), complemented with CTCF and H3K27ac ChIP-seq, as well as gene expression and DNA methylation analysis in primary and relapsed ependymoma tumors, to identify chromosomal conformations and regulatory mechanisms associated with aberrant gene expression. In particular, we observe the formation of new topologically associating domains ('neo-TADs') caused by structural variants, group-specific 3D chromatin loops, and the replacement of CTCF insulators by DNA hyper-methylation. Through inhibition experiments, we validate that genes implicated by these 3D genome conformations are essential for the survival of patient-derived ependymoma models in a group-specific manner. Thus, this study extends our ability to reveal tumor-dependency genes by 3D genome conformations even in tumors that lack targetable genetic alterations.
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Affiliation(s)
- Konstantin Okonechnikov
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Aylin Camgöz
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
- National Center for Tumor Diseases (NCT): German Cancer Research Center (DKFZ) Heidelberg, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Helmholtz-Zentrum Dresden-Rossendorf (HZDR), Dresden, Germany
| | - Owen Chapman
- Division of Genomics and Precision Medicine, Department of Medicine, University of California San Diego (UCSD), San Diego, USA
| | - Sameena Wani
- Division of Genomics and Precision Medicine, Department of Medicine, University of California San Diego (UCSD), San Diego, USA
| | - Donglim Esther Park
- Division of Regenerative Medicine, Department of Medicine, University of California, San Diego, La Jolla, CA, 92037, USA
- Sanford Consortium for Regenerative Medicine, 2880 Torrey Pines Scenic Drive, La Jolla, CA, 92037, USA
| | - Jens-Martin Hübner
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Abhijit Chakraborty
- Centers for Cancer Immunotherapy and Autoimmunity, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Meghana Pagadala
- Division of Genomics and Precision Medicine, Department of Medicine, University of California San Diego (UCSD), San Diego, USA
| | - Rosalind Bump
- Peptide Biology Labs, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Sahaana Chandran
- Peptide Biology Labs, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Katerina Kraft
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA
| | - Rocio Acuna-Hidalgo
- Max Planck Institute for Molecular Genetics, Berlin, Germany
- Institute for Medical Genetics and Human Genetics, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Derek Reid
- Arima Genomics, Inc, San Diego, CA, 92121, USA
| | | | - Monika Mauermann
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Edwin F Juarez
- Division of Genomics and Precision Medicine, Department of Medicine, University of California San Diego (UCSD), San Diego, USA
| | - Anne Jenseit
- Hopp Children's Cancer Center (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
| | - James T Robinson
- Division of Genomics and Precision Medicine, Department of Medicine, University of California San Diego (UCSD), San Diego, USA
| | - Kristian W Pajtler
- Hopp Children's Cancer Center (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
| | - Till Milde
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany
- Department of Pediatric Oncology, Hematology and Immunology, Heidelberg University Hospital, Heidelberg, Germany
- CCU Pediatric Oncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Natalie Jäger
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Petra Fiesel
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany
- CCU Neuropathology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Ling Morgan
- Division of Genomics and Precision Medicine, Department of Medicine, University of California San Diego (UCSD), San Diego, USA
| | - Sunita Sridhar
- Division of Genomics and Precision Medicine, Department of Medicine, University of California San Diego (UCSD), San Diego, USA
| | - Nicole G Coufal
- Sanford Consortium for Regenerative Medicine, 2880 Torrey Pines Scenic Drive, La Jolla, CA, 92037, USA
- Department of Pediatrics, University of California, San Diego, San Diego, CA, 92093, USA
| | - Michael Levy
- Neurosurgery, University of California San Diego - Rady Children's Hospital, San Diego, CA, 92123, USA
| | - Denise Malicki
- Pathology, University of California San Diego - Rady Children's Hospital, San Diego, CA, 92123, USA
| | - Charlotte Hobbs
- Rady Children's Institute for Genomic Medicine, San Diego, CA, 92123, USA
| | - Stephen Kingsmore
- Rady Children's Institute for Genomic Medicine, San Diego, CA, 92123, USA
| | - Shareef Nahas
- Rady Children's Institute for Genomic Medicine, San Diego, CA, 92123, USA
| | - Matija Snuderl
- Department of Pathology, NYU Langone Health, NYU Grossman School of Medicine, 550 First Ave, New York, NY, 10016, USA
- Laura and Isaac Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
| | - John Crawford
- Department of Neurosciences, University of California San Diego - Rady Children's Hospital, San Diego, CA, 92123, USA
| | - Robert J Wechsler-Reya
- Sanford Consortium for Regenerative Medicine, 2880 Torrey Pines Scenic Drive, La Jolla, CA, 92037, USA
- Department of Pediatrics, University of California, San Diego, San Diego, CA, 92093, USA
- Tumor Initiation and Maintenance Program, NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Tom Belle Davidson
- Division of Hematology-Oncology, Cancer and Blood Disease Institute and Department of Pediatrics, Children's Hospital Los Angeles, Los Angeles, California, USA
| | - Jennifer Cotter
- Division of Hematology-Oncology, Cancer and Blood Disease Institute and Department of Pediatrics, Children's Hospital Los Angeles, Los Angeles, California, USA
| | - George Michaiel
- Division of Hematology-Oncology, Cancer and Blood Disease Institute and Department of Pediatrics, Children's Hospital Los Angeles, Los Angeles, California, USA
| | - Gudrun Fleischhack
- German Cancer Consortium (DKTK), West German Cancer Center, Pediatrics III, University Hospital Essen, Essen, Germany
| | - Stefan Mundlos
- Max Planck Institute for Molecular Genetics, Berlin, Germany
| | | | - Hannah Carter
- Division of Genomics and Precision Medicine, Department of Medicine, University of California San Diego (UCSD), San Diego, USA
| | - Kulandaimanuvel Antony Michealraj
- Division of Neurosurgery, Arthur and Sonia Labatt Brain Tumor Research Center, Hospital for Sick Children, University of Toronto, Toronto, ONT, Canada
| | - Sachin A Kumar
- Division of Neurosurgery, Arthur and Sonia Labatt Brain Tumor Research Center, Hospital for Sick Children, University of Toronto, Toronto, ONT, Canada
| | - Michael D Taylor
- Division of Neurosurgery, Arthur and Sonia Labatt Brain Tumor Research Center, Hospital for Sick Children, University of Toronto, Toronto, ONT, Canada
| | - Jeremy Rich
- Division of Regenerative Medicine, Department of Medicine, University of California, San Diego, La Jolla, CA, 92037, USA
- Sanford Consortium for Regenerative Medicine, 2880 Torrey Pines Scenic Drive, La Jolla, CA, 92037, USA
- Department of Neurosciences, School of Medicine, University of California San Diego, La Jolla, CA, 92037, USA
| | - Frank Buchholz
- National Center for Tumor Diseases (NCT): German Cancer Research Center (DKFZ) Heidelberg, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Helmholtz-Zentrum Dresden-Rossendorf (HZDR), Dresden, Germany
- Medical Systems Biology, Medical Faculty and University Hospital Carl Gustav Carus, TU Dresden, 01307, Dresden, Germany
- German Cancer Research Center (DKFZ), Heidelberg and German Cancer Consortium (DKTK) Partner Site Dresden, Dresden, Germany
| | - Jill P Mesirov
- Division of Genomics and Precision Medicine, Department of Medicine, University of California San Diego (UCSD), San Diego, USA
- Moores Cancer Center, University of California San Diego (UCSD), La Jolla, CA, USA
| | - Stefan M Pfister
- Hopp Children's Cancer Center (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
| | - Ferhat Ay
- Centers for Cancer Immunotherapy and Autoimmunity, La Jolla Institute for Immunology, La Jolla, CA, USA
- Department of Pediatrics, University of California, San Diego, San Diego, CA, 92093, USA
| | - Jesse R Dixon
- Peptide Biology Labs, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Marcel Kool
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - Lukas Chavez
- Division of Genomics and Precision Medicine, Department of Medicine, University of California San Diego (UCSD), San Diego, USA.
- Rady Children's Institute for Genomic Medicine, San Diego, CA, 92123, USA.
- Tumor Initiation and Maintenance Program, NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA.
- Moores Cancer Center, University of California San Diego (UCSD), La Jolla, CA, USA.
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12
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Hwang EI, Hanson D, Filbin MG, Mack SC. Why haven't we solved intracranial pediatric ependymoma? Current questions and barriers to treatment advances. Neoplasia 2023; 39:100895. [PMID: 36944298 PMCID: PMC10036929 DOI: 10.1016/j.neo.2023.100895] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 02/20/2023] [Accepted: 02/28/2023] [Indexed: 03/22/2023]
Abstract
Pediatric intracranial ependymoma has seen a recent exponential expansion of biological findings, rapidly dividing the diagnosis into several subgroups, each with specific molecular and clinical characteristics. While such subdivision may complicate clinical conclusions from historical trials, this knowledge also provides an opportunity for interrogating the major clinical and biological questions preventing near-term translation into effective therapy for children with ependymoma. In this article, we briefly review some of the most critical clinical questions facing both patient management and the construct of future trials in childhood ependymoma, as well as explore some of the current barriers to efficient translation of preclinical discovery to the clinic.
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13
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de Almeida Magalhães T, Alencastro Veiga Cruzeiro G, Ribeiro de Sousa G, Englinger B, Fernando Peinado Nagano L, Ancliffe M, Rodrigues da Silva K, Jiang L, Gojo J, Cherry Liu Y, Carline B, Kuchibhotla M, Pinto Saggioro F, Kazue Nagahashi Marie S, Mieko Oba-Shinjo S, Andres Yunes J, Gomes de Paula Queiroz R, Alberto Scrideli C, Endersby R, Filbin MG, Silva Borges K, Salic A, Gonzaga Tone L, Valera ET. Activation of Hedgehog signaling by the oncogenic RELA fusion reveals a primary cilia-dependent vulnerability in supratentorial ependymoma. Neuro Oncol 2023; 25:185-198. [PMID: 35640920 PMCID: PMC9825332 DOI: 10.1093/neuonc/noac147] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Indexed: 01/13/2023] Open
Abstract
BACKGROUND Supratentorial RELA fusion (ST-RELA) ependymomas (EPNs) are resistant tumors without an approved chemotherapeutic treatment. Unfortunately, the molecular mechanisms that lead to chemoresistance traits of ST-RELA remain elusive. The aim of this study was to assess RELA fusion-dependent signaling modules, specifically the role of the Hedgehog (Hh) pathway as a novel targetable vulnerability in ST-RELA. METHODS Gene expression was analyzed in EPN from patient cohorts, by microarray, RNA-seq, qRT-PCR, and scRNA-seq. Inhibitors against Smoothened (SMO) (Sonidegib) and Aurora kinase A (AURKA) (Alisertib) were evaluated. Protein expression, primary cilia formation, and drug effects were assessed by immunoblot, immunofluorescence, and immunohistochemistry. RESULTS Hh components were selectively overexpressed in EPNs induced by the RELA fusion. Single-cell analysis showed that the Hh signature was primarily confined to undifferentiated, stem-like cell subpopulations. Sonidegib exhibited potent growth-inhibitory effects on ST-RELA cells, suggesting a key role in active Hh signaling; importantly, the effect of Sonidegib was reversed by primary cilia loss. We, thus, tested the effect of AURKA inhibition by Alisertib, to induce cilia stabilization/reassembly. Strikingly, Alisertib rescued ciliogenesis and synergized with Sonidegib in killing ST-RELA cells. Using a xenograft model, we show that cilia loss is a mechanism for acquiring resistance to the inhibitory effect of Sonidegib. However, Alisertib fails to rescue cilia and highlights the need for other strategies to promote cilia reassembly, for treating ST-RELA tumors. CONCLUSION Our study reveals a crucial role for the Hh pathway in ST-RELA tumor growth, and suggests that rescue of primary cilia represents a vulnerability of the ST-RELA EPNs.
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Affiliation(s)
- Taciani de Almeida Magalhães
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts, USA
| | - Gustavo Alencastro Veiga Cruzeiro
- Department of Pediatrics, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
- Department of Pediatric Oncology, Dana-Farber Boston Children’s Cancer and Blood Disorders Center, Boston, Massachusetts, USA
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA
| | - Graziella Ribeiro de Sousa
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Bernhard Englinger
- Department of Pediatric Oncology, Dana-Farber Boston Children’s Cancer and Blood Disorders Center, Boston, Massachusetts, USA
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA
- Department of Urology, Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
| | - Luis Fernando Peinado Nagano
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Mathew Ancliffe
- Brain Tumour Research Program, Telethon Kids Institute and the University of Western Australia, Nedlands, Western Australia, Australia
| | - Keteryne Rodrigues da Silva
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
- Brain Tumour Research Program, Telethon Kids Institute and the University of Western Australia, Nedlands, Western Australia, Australia
| | - Li Jiang
- Department of Pediatric Oncology, Dana-Farber Boston Children’s Cancer and Blood Disorders Center, Boston, Massachusetts, USA
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA
| | - Johannes Gojo
- Department of Pediatric Oncology, Dana-Farber Boston Children’s Cancer and Blood Disorders Center, Boston, Massachusetts, USA
- Department of Pediatrics and Adolescent Medicine, Comprehensive Center for Pediatrics, Medical University of Vienna, Vienna, Austria
| | - Yulu Cherry Liu
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts, USA
| | - Brooke Carline
- Brain Tumour Research Program, Telethon Kids Institute and the University of Western Australia, Nedlands, Western Australia, Australia
| | - Mani Kuchibhotla
- Brain Tumour Research Program, Telethon Kids Institute and the University of Western Australia, Nedlands, Western Australia, Australia
| | - Fabiano Pinto Saggioro
- Department of Pathology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Suely Kazue Nagahashi Marie
- Cellular and Molecular Biology Laboratory, Department of Neurology, Faculdade de Medicina (FMUSP), University of São Paulo, São Paulo, Brazil
| | - Sueli Mieko Oba-Shinjo
- Cellular and Molecular Biology Laboratory, Department of Neurology, Faculdade de Medicina (FMUSP), University of São Paulo, São Paulo, Brazil
| | - José Andres Yunes
- Molecular Biology Laboratory, Boldrini Children’s Center, Campinas, São Paulo, Brazil
| | | | - Carlos Alberto Scrideli
- Department of Pediatrics, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Raelene Endersby
- Brain Tumour Research Program, Telethon Kids Institute and the University of Western Australia, Nedlands, Western Australia, Australia
| | - Mariella G Filbin
- Department of Pediatric Oncology, Dana-Farber Boston Children’s Cancer and Blood Disorders Center, Boston, Massachusetts, USA
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA
| | - Kleiton Silva Borges
- Department of Pediatrics, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
- Division of Endocrinology, Boston Children’s Hospital, Boston, Massachusetts, USA
| | - Adrian Salic
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts, USA
| | - Luiz Gonzaga Tone
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
- Department of Pediatrics, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Elvis Terci Valera
- Department of Pediatrics, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
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14
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Zhao S, Li J, Zhang H, Qi L, Du Y, Kogiso M, Braun FK, Xiao S, Huang Y, Li J, Teo WY, Lindsay H, Baxter P, Su JMF, Adesina A, Laczik M, Genevini P, Veillard AC, Schvartzman S, Berguet G, Ding SR, Du L, Stephan C, Yang J, Davies PJA, Lu X, Chintagumpala M, Parsons DW, Perlaky L, Xia YF, Man TK, Huang Y, Sun D, Li XN. Epigenetic Alterations of Repeated Relapses in Patient-matched Childhood Ependymomas. Nat Commun 2022; 13:6689. [PMID: 36335125 PMCID: PMC9637194 DOI: 10.1038/s41467-022-34514-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 10/27/2022] [Indexed: 11/07/2022] Open
Abstract
Recurrence is frequent in pediatric ependymoma (EPN). Our longitudinal integrated analysis of 30 patient-matched repeated relapses (3.67 ± 1.76 times) over 13 years (5.8 ± 3.8) reveals stable molecular subtypes (RELA and PFA) and convergent DNA methylation reprogramming during serial relapses accompanied by increased orthotopic patient derived xenograft (PDX) (13/27) formation in the late recurrences. A set of differentially methylated CpGs (DMCs) and DNA methylation regions (DMRs) are found to persist in primary and relapse tumors (potential driver DMCs) and are acquired exclusively in the relapses (potential booster DMCs). Integrating with RNAseq reveals differentially expressed genes regulated by potential driver DMRs (CACNA1H, SLC12A7, RARA in RELA and HSPB8, GMPR, ITGB4 in PFA) and potential booster DMRs (PLEKHG1 in RELA and NOTCH, EPHA2, SUFU, FOXJ1 in PFA tumors). DMCs predicators of relapse are also identified in the primary tumors. This study provides a high-resolution epigenetic roadmap of serial EPN relapses and 13 orthotopic PDX models to facilitate biological and preclinical studies.
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Affiliation(s)
- Sibo Zhao
- grid.39382.330000 0001 2160 926XPre-clinical Neuro-oncology Research Program, Texas Children’s Hospital, Baylor College of Medicine, Houston, TX 77030 USA ,grid.39382.330000 0001 2160 926XTexas Children’s Cancer Center, Texas Children’s Hospital, Baylor College of Medicine, Houston, TX 77030 USA ,grid.413584.f0000 0004 0383 5679Jane and John Justin Neurosciences Center, Cook Children’s Medical Center, Fort Worth, TX 76104 USA ,grid.413584.f0000 0004 0383 5679Hematology and Oncology Center, Cook Children’s Medical Center, Fort Worth, TX 76104 USA
| | - Jia Li
- grid.264756.40000 0004 4687 2082Center for Epigenetics & Disease Prevention, Texas A&M University, Houston, TX 77030 USA ,grid.264756.40000 0004 4687 2082Center for Translational Cancer Research, Institute of Biosciences and Technology, Texas A&M University, Houston, TX 77030 USA ,grid.470124.4State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University; and Guangzhou Laboratory, Bioland, 510120 Guangzhou, Guangdong P. R. China
| | - Huiyuan Zhang
- grid.39382.330000 0001 2160 926XPre-clinical Neuro-oncology Research Program, Texas Children’s Hospital, Baylor College of Medicine, Houston, TX 77030 USA ,grid.39382.330000 0001 2160 926XTexas Children’s Cancer Center, Texas Children’s Hospital, Baylor College of Medicine, Houston, TX 77030 USA
| | - Lin Qi
- grid.39382.330000 0001 2160 926XPre-clinical Neuro-oncology Research Program, Texas Children’s Hospital, Baylor College of Medicine, Houston, TX 77030 USA ,grid.39382.330000 0001 2160 926XTexas Children’s Cancer Center, Texas Children’s Hospital, Baylor College of Medicine, Houston, TX 77030 USA ,grid.16753.360000 0001 2299 3507Program of Precision Medicine PDOX Modeling of Pediatric Tumors, Division of Hematology-Oncology, Neuro-Oncology & Stem Cell transplantation, Ann & Robert H. Lurie Children’s Hospital of Chicago; Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611 USA
| | - Yuchen Du
- grid.39382.330000 0001 2160 926XPre-clinical Neuro-oncology Research Program, Texas Children’s Hospital, Baylor College of Medicine, Houston, TX 77030 USA ,grid.39382.330000 0001 2160 926XTexas Children’s Cancer Center, Texas Children’s Hospital, Baylor College of Medicine, Houston, TX 77030 USA ,grid.16753.360000 0001 2299 3507Program of Precision Medicine PDOX Modeling of Pediatric Tumors, Division of Hematology-Oncology, Neuro-Oncology & Stem Cell transplantation, Ann & Robert H. Lurie Children’s Hospital of Chicago; Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611 USA
| | - Mari Kogiso
- grid.39382.330000 0001 2160 926XPre-clinical Neuro-oncology Research Program, Texas Children’s Hospital, Baylor College of Medicine, Houston, TX 77030 USA ,grid.39382.330000 0001 2160 926XTexas Children’s Cancer Center, Texas Children’s Hospital, Baylor College of Medicine, Houston, TX 77030 USA
| | - Frank K. Braun
- grid.39382.330000 0001 2160 926XPre-clinical Neuro-oncology Research Program, Texas Children’s Hospital, Baylor College of Medicine, Houston, TX 77030 USA ,grid.39382.330000 0001 2160 926XTexas Children’s Cancer Center, Texas Children’s Hospital, Baylor College of Medicine, Houston, TX 77030 USA
| | - Sophie Xiao
- grid.16753.360000 0001 2299 3507Program of Precision Medicine PDOX Modeling of Pediatric Tumors, Division of Hematology-Oncology, Neuro-Oncology & Stem Cell transplantation, Ann & Robert H. Lurie Children’s Hospital of Chicago; Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611 USA
| | - Yulun Huang
- grid.39382.330000 0001 2160 926XPre-clinical Neuro-oncology Research Program, Texas Children’s Hospital, Baylor College of Medicine, Houston, TX 77030 USA ,grid.39382.330000 0001 2160 926XTexas Children’s Cancer Center, Texas Children’s Hospital, Baylor College of Medicine, Houston, TX 77030 USA ,grid.263761.70000 0001 0198 0694Department of Neurosurgery and Brain and Nerve Research Laboratory, the First Affiliated Hospital, and Department of Neurosurgery, Dushu Lake Hospital, Suzhou Medical College, Soochow University, 215007 Suzhou, P. R. China
| | - Jianfang Li
- grid.264756.40000 0004 4687 2082Center for Epigenetics & Disease Prevention, Texas A&M University, Houston, TX 77030 USA
| | - Wan-Yee Teo
- grid.410724.40000 0004 0620 9745Humphrey Oei Institute of Cancer Research, National Cancer Center Singapore, Singapore, 169610 Singapore ,grid.428397.30000 0004 0385 0924Cancer and Stem Cell Biology Program, Duke-NUS Medical School Singapore, Singapore, Singapore ,grid.414963.d0000 0000 8958 3388KK Women’s & Children’s Hospital Singapore, Singapore, Singapore ,grid.418812.60000 0004 0620 9243Institute of Molecular and Cell Biology, A*STAR, Singapore, Singapore
| | - Holly Lindsay
- grid.39382.330000 0001 2160 926XPre-clinical Neuro-oncology Research Program, Texas Children’s Hospital, Baylor College of Medicine, Houston, TX 77030 USA ,grid.39382.330000 0001 2160 926XTexas Children’s Cancer Center, Texas Children’s Hospital, Baylor College of Medicine, Houston, TX 77030 USA
| | - Patricia Baxter
- grid.39382.330000 0001 2160 926XTexas Children’s Cancer Center, Texas Children’s Hospital, Baylor College of Medicine, Houston, TX 77030 USA
| | - Jack M. F. Su
- grid.39382.330000 0001 2160 926XTexas Children’s Cancer Center, Texas Children’s Hospital, Baylor College of Medicine, Houston, TX 77030 USA
| | - Adekunle Adesina
- grid.39382.330000 0001 2160 926XDepartment of Pathology, Texas Children’s Hospital, Baylor College of Medicine, Houston, TX 77030 USA
| | - Miklós Laczik
- grid.424287.f0000 0004 0555 845XEpigenetic Services, Diagenode, Liège Belgium
| | - Paola Genevini
- grid.424287.f0000 0004 0555 845XEpigenetic Services, Diagenode, Liège Belgium
| | | | - Sol Schvartzman
- grid.424287.f0000 0004 0555 845XEpigenetic Services, Diagenode, Liège Belgium
| | - Geoffrey Berguet
- grid.424287.f0000 0004 0555 845XEpigenetic Services, Diagenode, Liège Belgium
| | - Shi-Rong Ding
- grid.488530.20000 0004 1803 6191State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine; Department of Radiation, Sun Yat-sen University Cancer Center, 510060 Guangzhou, Guangdong P. R. China
| | - Liping Du
- grid.16753.360000 0001 2299 3507Clinical Cytogenetic Laboratory, Department of Pathology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611 USA
| | - Clifford Stephan
- grid.264756.40000 0004 4687 2082Center for Translational Cancer Research, Institute of Biosciences and Technology, Texas A&M University, Houston, TX 77030 USA
| | - Jianhua Yang
- grid.39382.330000 0001 2160 926XTexas Children’s Cancer Center, Texas Children’s Hospital, Baylor College of Medicine, Houston, TX 77030 USA
| | - Peter J. A. Davies
- grid.264756.40000 0004 4687 2082Center for Translational Cancer Research, Institute of Biosciences and Technology, Texas A&M University, Houston, TX 77030 USA
| | - Xinyan Lu
- grid.16753.360000 0001 2299 3507Clinical Cytogenetic Laboratory, Department of Pathology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611 USA
| | - Murali Chintagumpala
- grid.39382.330000 0001 2160 926XTexas Children’s Cancer Center, Texas Children’s Hospital, Baylor College of Medicine, Houston, TX 77030 USA
| | - Donald William Parsons
- grid.39382.330000 0001 2160 926XTexas Children’s Cancer Center, Texas Children’s Hospital, Baylor College of Medicine, Houston, TX 77030 USA
| | - Laszlo Perlaky
- grid.39382.330000 0001 2160 926XTexas Children’s Cancer Center, Texas Children’s Hospital, Baylor College of Medicine, Houston, TX 77030 USA
| | - Yun-Fei Xia
- grid.488530.20000 0004 1803 6191State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine; Department of Radiation, Sun Yat-sen University Cancer Center, 510060 Guangzhou, Guangdong P. R. China
| | - Tsz-Kwong Man
- grid.39382.330000 0001 2160 926XTexas Children’s Cancer Center, Texas Children’s Hospital, Baylor College of Medicine, Houston, TX 77030 USA
| | - Yun Huang
- grid.264756.40000 0004 4687 2082Center for Epigenetics & Disease Prevention, Texas A&M University, Houston, TX 77030 USA
| | - Deqiang Sun
- grid.264756.40000 0004 4687 2082Center for Epigenetics & Disease Prevention, Texas A&M University, Houston, TX 77030 USA
| | - Xiao-Nan Li
- grid.39382.330000 0001 2160 926XPre-clinical Neuro-oncology Research Program, Texas Children’s Hospital, Baylor College of Medicine, Houston, TX 77030 USA ,grid.39382.330000 0001 2160 926XTexas Children’s Cancer Center, Texas Children’s Hospital, Baylor College of Medicine, Houston, TX 77030 USA ,grid.16753.360000 0001 2299 3507Program of Precision Medicine PDOX Modeling of Pediatric Tumors, Division of Hematology-Oncology, Neuro-Oncology & Stem Cell transplantation, Ann & Robert H. Lurie Children’s Hospital of Chicago; Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611 USA
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15
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Gonzalez Castro LN, Liu I, Filbin M. Characterizing the biology of primary brain tumors and their microenvironment via single-cell profiling methods. Neuro Oncol 2022; 25:234-247. [PMID: 36197833 PMCID: PMC9925698 DOI: 10.1093/neuonc/noac211] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Genomic and transcriptional heterogeneity is prevalent among the most common and aggressive primary brain tumors in children and adults. Over the past 20 years, advances in bioengineering, biochemistry and bioinformatics have enabled the development of an array of techniques to study tumor biology at single-cell resolution. The application of these techniques to study primary brain tumors has helped advance our understanding of their intra-tumoral heterogeneity and uncover new insights regarding their co-option of developmental programs and signaling from their microenvironment to promote tumor proliferation and invasion. These insights are currently being harnessed to develop new therapeutic approaches. Here we provide an overview of current single-cell techniques and discuss relevant biology and therapeutic insights uncovered by their application to primary brain tumors in children and adults.
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Affiliation(s)
- L Nicolas Gonzalez Castro
- Corresponding Author: L. Nicolas Gonzalez Castro, MD, PhD, Center for Neuro-Oncology, Dana-Farber Cancer Institute, Boston, MA, USA ()
| | | | - Mariella Filbin
- Pediatric Neuro-Oncology Program, Dana-Farber/Boston Children’s and Blood Disorders Center, Boston, MA, USA
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16
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Lindsay HB, Massimino M, Avula S, Stivaros S, Grundy R, Metrock K, Bhatia A, Fernández-Teijeiro A, Chiapparini L, Bennett J, Wright K, Hoffman LM, Smith A, Pajtler KW, Poussaint TY, Warren KE, Foreman NK, Mirsky DM. Response assessment in paediatric intracranial ependymoma: recommendations from the Response Assessment in Pediatric Neuro-Oncology (RAPNO) working group. Lancet Oncol 2022; 23:e393-e401. [DOI: 10.1016/s1470-2045(22)00222-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 03/31/2022] [Accepted: 04/05/2022] [Indexed: 10/16/2022]
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17
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Kresbach C, Neyazi S, Schüller U. Updates in the classification of ependymal neoplasms: The 2021 WHO Classification and beyond. Brain Pathol 2022; 32:e13068. [PMID: 35307892 PMCID: PMC9245931 DOI: 10.1111/bpa.13068] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 02/16/2022] [Accepted: 02/25/2022] [Indexed: 01/23/2023] Open
Abstract
Ependymal neoplasms occur at all ages and encompass multiple tumor types and subtypes that develop in the supratentorial compartment, the posterior fossa, or the spinal cord. Clinically, ependymomas represent a very heterogeneous group of tumors from rather benign subependymomas to very aggressive and often deadly childhood ependymomas of the posterior fossa. Newly identified biological markers and classification schemes, e. g. based on global DNA methylation profiling, have led to the definition of 10 types of ependymal tumors and an improved prediction of patients' outcome by applying the new classification system. While the exact genetic basis for several ependymoma types still remains unclear, the knowledge about ependymoma driving events has significantly increased within the last decade and contributed to a classification based on molecular characteristics and localization rather than histological features alone. Convincing evidence is now pointing towards gene fusions involving ZFTA or YAP1 causing the development of supratentorial ependymomas. Also, H3, EZHIP, or TERT mutations have been detected in a fraction of infratentorial ependymal tumors. Finally, MYCN amplifications have recently been identified in spinal ependymomas, in addition to the previously known mutations in NF2. This review summarizes how recent findings regarding biology, molecular tumor typing, and clinical outcome have impacted the classification of ependymomas as suggested by the updated 2021 WHO CNS tumor classification system. We focus on changes compared to the previous classification of 2016 and discuss how a formal grading could evolve in the future and guide clinicians to treat ependymoma patients.
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Affiliation(s)
- Catena Kresbach
- Department of Pediatric Hematology and OncologyUniversity Medical Center Hamburg‐EppendorfHamburgGermany
- Research Institute Children’s Cancer Center HamburgHamburgGermany
- Institute of NeuropathologyUniversity Medical Center Hamburg‐EppendorfHamburgGermany
| | - Sina Neyazi
- Department of Pediatric Hematology and OncologyUniversity Medical Center Hamburg‐EppendorfHamburgGermany
- Research Institute Children’s Cancer Center HamburgHamburgGermany
| | - Ulrich Schüller
- Department of Pediatric Hematology and OncologyUniversity Medical Center Hamburg‐EppendorfHamburgGermany
- Research Institute Children’s Cancer Center HamburgHamburgGermany
- Institute of NeuropathologyUniversity Medical Center Hamburg‐EppendorfHamburgGermany
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18
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Ritzmann TA, Chapman RJ, Kilday JP, Thorp N, Modena P, Dineen RA, Macarthur D, Mallucci C, Jaspan T, Pajtler KW, Giagnacovo M, Jacques TS, Paine SML, Ellison DW, Bouffet E, Grundy RG. SIOP Ependymoma I: Final results, long-term follow-up, and molecular analysis of the trial cohort-A BIOMECA Consortium Study. Neuro Oncol 2022; 24:936-948. [PMID: 35018471 PMCID: PMC9159435 DOI: 10.1093/neuonc/noac012] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND SIOP Ependymoma I was a non-randomised trial assessing event free and overall survival (EFS/OS) of non-metastatic intracranial ependymoma in children aged 3-21 years treated with a staged management strategy. A further aim was to assess the response rate (RR) of subtotally resected (STR) ependymoma to vincristine, etoposide, and cyclophosphamide (VEC). We report final results with 12-year follow-up and post hoc analyses of recently described biomarkers. METHODS Seventy-four participants were eligible. Children with gross total resection (GTR) received radiotherapy, whilst those with STR received VEC before radiotherapy. DNA methylation, 1q, hTERT, ReLA, Tenascin-C, H3K27me3, and pAKT status were evaluated. RESULTS Five- and ten-year EFS was 49.5% and 46.7%, OS was 69.3% and 60.5%. GTR was achieved in 33/74 (44.6%) and associated with improved EFS (P = .003, HR = 2.6, 95% confidence interval (CI) 1.4-5.1). Grade 3 tumours were associated with worse OS (P = .005, HR = 2.8, 95%CI 1.3-5.8). 1q gain and hTERT expression were associated with poorer EFS (P = .003, HR = 2.70, 95%CI 1.49-6.10 and P = .014, HR = 5.8, 95%CI 1.2-28) and H3K27me3 loss with worse OS (P = .003, HR = 4.6, 95%CI 1.5-13.2). Methylation profiles showed expected patterns. 12 participants with STR did not receive chemotherapy; a protocol violation. However, best chemotherapy RR was 65.5% (19/29, 95%CI 45.7-82.1), exceeding the prespecified 45%. CONCLUSIONS Participants with totally resected ependymoma had the best outcomes. RR of STR to VEC exceeded the pre-specified efficacy criterion. However, cases of inaccurate stratification highlighted the need for rapid central review. 1q gain, H3K27me3 loss, and hTERT expression were all associated with poorer survival outcomes.
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Affiliation(s)
- Timothy A Ritzmann
- Children’s Brain Tumour Research Centre, University of Nottingham, Nottingham, UK
- Nottingham University Hospitals NHS Trust, Nottingham, UK
| | - Rebecca J Chapman
- Children’s Brain Tumour Research Centre, University of Nottingham, Nottingham, UK
| | - John-Paul Kilday
- Children’s Brain Tumour Research Network (CBTRN), Royal Manchester Children’s Hospital, Manchester, UK
- The Centre for Paediatric, Teenage and Young Adult Cancer, University of Manchester, Manchester, UK
| | - Nicola Thorp
- The Clatterbridge Cancer Centre, Liverpool, UK
- The Christie Hospital Proton Beam Therapy Centre, Manchester, UK
| | | | - Robert A Dineen
- Children’s Brain Tumour Research Centre, University of Nottingham, Nottingham, UK
- Nottingham University Hospitals NHS Trust, Nottingham, UK
- NIHR Nottingham Biomedical Research Centre, Nottingham, UK
| | - Donald Macarthur
- Children’s Brain Tumour Research Centre, University of Nottingham, Nottingham, UK
- Nottingham University Hospitals NHS Trust, Nottingham, UK
| | - Conor Mallucci
- Alder Hey Children’s NHS Foundation Trust, Liverpool, UK
| | - Timothy Jaspan
- Nottingham University Hospitals NHS Trust, Nottingham, UK
| | - Kristian W Pajtler
- Hopp Children’s Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neuro-oncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
- Department of Pediatric Oncology, Hematology, and Immunology, University Hospital Heidelberg, Heidelberg, Germany
| | | | - Thomas S Jacques
- UCL GOS Institute of Child Health, London, UK
- Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Simon M L Paine
- Children’s Brain Tumour Research Centre, University of Nottingham, Nottingham, UK
- Nottingham University Hospitals NHS Trust, Nottingham, UK
| | - David W Ellison
- Department of Pathology, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | - Eric Bouffet
- The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Richard G Grundy
- Children’s Brain Tumour Research Centre, University of Nottingham, Nottingham, UK
- Nottingham University Hospitals NHS Trust, Nottingham, UK
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19
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Bromodomain and Extra-Terminal Protein Inhibitors: Biologic Insights and Therapeutic Potential in Pediatric Brain Tumors. Pharmaceuticals (Basel) 2022; 15:ph15060665. [PMID: 35745584 PMCID: PMC9227239 DOI: 10.3390/ph15060665] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 05/19/2022] [Accepted: 05/23/2022] [Indexed: 02/06/2023] Open
Abstract
Pediatric brain tumors have surpassed leukemia as the leading cause of cancer-related death in children. Several landmark studies from the last two decades have shown that many pediatric brain tumors are driven by epigenetic dysregulation within specific developmental contexts. One of the major determinants of epigenetic control is the histone code, which is orchestrated by a number of enzymes categorized as writers, erasers, and readers. Bromodomain and extra-terminal (BET) proteins are reader proteins that bind to acetylated lysines in histone tails and play a crucial role in regulating gene transcription. BET inhibitors have shown efficacy in a wide range of cancers, and a number have progressed to clinical phase testing. Here, we review the evidence for BET inhibitors in pediatric brain tumor experimental models, as well as their translational potential.
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20
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Wang W, Shiraishi R, Kawauchi D. Sonic Hedgehog Signaling in Cerebellar Development and Cancer. Front Cell Dev Biol 2022; 10:864035. [PMID: 35573667 PMCID: PMC9100414 DOI: 10.3389/fcell.2022.864035] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 03/28/2022] [Indexed: 12/30/2022] Open
Abstract
The sonic hedgehog (SHH) pathway regulates the development of the central nervous system in vertebrates. Aberrant regulation of SHH signaling pathways often causes neurodevelopmental diseases and brain tumors. In the cerebellum, SHH secreted by Purkinje cells is a potent mitogen for granule cell progenitors, which are the most abundant cell type in the mature brain. While a reduction in SHH signaling induces cerebellar structural abnormalities, such as hypoplasia in various genetic disorders, the constitutive activation of SHH signaling often induces medulloblastoma (MB), one of the most common pediatric malignant brain tumors. Based on the existing literature on canonical and non-canonical SHH signaling pathways, emerging basic and clinical studies are exploring novel therapeutic approaches for MB by targeting SHH signaling at distinct molecular levels. In this review, we discuss the present consensus on SHH signaling mechanisms, their roles in cerebellar development and tumorigenesis, and the recent advances in clinical trials for MB.
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Affiliation(s)
- Wanchen Wang
- Department of Biochemistry and Cellular Biology, National Center of Neurology and Psychiatry (NCNP), Tokyo, Japan
| | - Ryo Shiraishi
- Department of Biochemistry and Cellular Biology, National Center of Neurology and Psychiatry (NCNP), Tokyo, Japan
- Department of NCNP Brain Physiology and Pathology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Daisuke Kawauchi
- Department of Biochemistry and Cellular Biology, National Center of Neurology and Psychiatry (NCNP), Tokyo, Japan
- *Correspondence: Daisuke Kawauchi,
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21
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Okonechnikov KV, Ryzhova MV, Galstyan SA, Telysheva EN. [Application of high throughput sequencing in pediatric neurooncology]. Arkh Patol 2022; 84:58-63. [PMID: 35417950 DOI: 10.17116/patol20228402158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Over the past decade, next generation sequencing (NGS) has become the standard method in research of cancer genomics; currently NGS is entering a new stage - direct usage in clinical oncology to improve diagnostics and establish personalized tumor treatments. NGS allows to read the genome and it is successfully applied to detect mutations and other somatic changes (translocations, inversions, insertions and deletions, copy number variants) leading to the development of a tumor. With a focus on transcriptome sequencing allows to clearly identify differences in gene expression, improve the classification of tumors and detect somatic chimeras. All these possibilities are especially relevant for pediatric neurooncology filed in view of the existing limitations in treatment and the need for the most accurate identification of the key factors of tumor development. In this article, we describe sequencing technology basis, its application on brain tumor materials to improve diagnostics, and other relevant possibilities that can be considered for direct usage in medicine.
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Affiliation(s)
- K V Okonechnikov
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany.,NN Burdenko Neurosurgical Center, Moscow, Russia
| | - M V Ryzhova
- NN Burdenko Neurosurgical Center, Moscow, Russia
| | - S A Galstyan
- NN Burdenko Neurosurgical Center, Moscow, Russia
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22
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Roosen M, Odé Z, Bunt J, Kool M. The oncogenic fusion landscape in pediatric CNS neoplasms. Acta Neuropathol 2022; 143:427-451. [PMID: 35169893 PMCID: PMC8960661 DOI: 10.1007/s00401-022-02405-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 01/31/2022] [Accepted: 01/31/2022] [Indexed: 01/09/2023]
Abstract
Pediatric neoplasms in the central nervous system (CNS) are the leading cause of cancer-related deaths in children. Recent developments in molecular analyses have greatly contributed to a more accurate diagnosis and risk stratification of CNS tumors. Additionally, sequencing studies have identified various, often entity specific, tumor-driving events. In contrast to adult tumors, which often harbor multiple mutated oncogenic drivers, the number of mutated genes in pediatric cancers is much lower and many tumors can have a single oncogenic driver. Moreover, in children, much more than in adults, fusion proteins play an important role in driving tumorigenesis, and many different fusions have been identified as potential driver events in pediatric CNS neoplasms. However, a comprehensive overview of all the different reported oncogenic fusion proteins in pediatric CNS neoplasms is still lacking. A better understanding of the fusion proteins detected in these tumors and of the molecular mechanisms how these proteins drive tumorigenesis, could improve diagnosis and further benefit translational research into targeted therapies necessary to treat these distinct entities. In this review, we discuss the different oncogenic fusions reported in pediatric CNS neoplasms and their structure to create an overview of the variety of oncogenic fusion proteins to date, the tumor entities they occur in and their proposed mode of action.
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Affiliation(s)
- Mieke Roosen
- Princess Máxima Center for Pediatric Oncology, 3584CS, Utrecht, The Netherlands
| | - Zelda Odé
- Princess Máxima Center for Pediatric Oncology, 3584CS, Utrecht, The Netherlands
| | - Jens Bunt
- Princess Máxima Center for Pediatric Oncology, 3584CS, Utrecht, The Netherlands
| | - Marcel Kool
- Princess Máxima Center for Pediatric Oncology, 3584CS, Utrecht, The Netherlands.
- Hopp Children's Cancer Center (KiTZ), 69120, Heidelberg, Germany.
- Division of Pediatric Neurooncology, German Cancer Research Center DKFZ and German Cancer Consortium DKTK, 69120, Heidelberg, Germany.
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23
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Pfister SM, Reyes-Múgica M, Chan JKC, Hasle H, Lazar AJ, Rossi S, Ferrari A, Jarzembowski JA, Pritchard-Jones K, Hill DA, Jacques TS, Wesseling P, López Terrada DH, von Deimling A, Kratz CP, Cree IA, Alaggio R. A Summary of the Inaugural WHO Classification of Pediatric Tumors: Transitioning from the Optical into the Molecular Era. Cancer Discov 2022; 12:331-355. [PMID: 34921008 PMCID: PMC9401511 DOI: 10.1158/2159-8290.cd-21-1094] [Citation(s) in RCA: 79] [Impact Index Per Article: 39.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 10/28/2021] [Accepted: 11/18/2021] [Indexed: 01/07/2023]
Abstract
Pediatric tumors are uncommon, yet are the leading cause of cancer-related death in childhood. Tumor types, molecular characteristics, and pathogenesis are unique, often originating from a single genetic driver event. The specific diagnostic challenges of childhood tumors led to the development of the first World Health Organization (WHO) Classification of Pediatric Tumors. The classification is rooted in a multilayered approach, incorporating morphology, IHC, and molecular characteristics. The volume is organized according to organ sites and provides a single, state-of-the-art compendium of pediatric tumor types. A special emphasis was placed on "blastomas," which variably recapitulate the morphologic maturation of organs from which they originate. SIGNIFICANCE: In this review, we briefly summarize the main features and updates of each chapter of the inaugural WHO Classification of Pediatric Tumors, including its rapid transition from a mostly microscopic into a molecularly driven classification systematically taking recent discoveries in pediatric tumor genomics into account.
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Affiliation(s)
- 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 Hematology and Oncology, Heidelberg University Hospital, Heidelberg, Germany
| | - Miguel Reyes-Múgica
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
- Division of Pediatric Pathology, UPMC Children's Hospital of Pittsburgh, Pittsburgh, Pennsylvania
| | - John K C Chan
- Department of Pathology, Queen Elizabeth Hospital, Kowloon, Hong Kong, SAR China
| | - Henrik Hasle
- Department of Pediatrics and Adolescent Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Alexander J Lazar
- Departments of Pathology & Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Sabrina Rossi
- Pathology Unit, Department of Laboratories, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Andrea Ferrari
- Pediatric Oncology Unit, Fondazione IRCCS Istituto Nazionale Tumori, Milano, Italy
| | - Jason A Jarzembowski
- Department of Pathology, Children's Wisconsin and Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Kathy Pritchard-Jones
- Developmental Biology and Cancer Research & Teaching Department, UCL Great Ormond Street Institute of Child Health, University College London, London, United Kingdom
| | - D Ashley Hill
- Department of Pathology, Children's National Hospital, Genomics and Precision Medicine, George Washington University School of Medicine and Health Sciences, Washington, DC
| | - Thomas S Jacques
- Developmental Biology and Cancer Research & Teaching Department, UCL Great Ormond Street Institute of Child Health, London, United Kingdom
- Department of Histopathology, Great Ormond Street Hospital for Children NHS Foundation Trust, London, United Kingdom
| | - Pieter Wesseling
- Laboratory for Childhood Cancer Pathology, Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
- Department of Pathology, Amsterdam University Medical Centers/VUmc, Amsterdam, the Netherlands
| | - Dolores H López Terrada
- Department of Pathology, Texas Children's Hospital and Baylor College of Medicine, Houston, Texas
| | - Andreas von Deimling
- Department of Neuropathology, Heidelberg University Hospital, Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Christian P Kratz
- Department of Pediatric Hematology and Oncology, Hannover Medical School, Hannover, Germany
| | - Ian A Cree
- International Agency for Research on Cancer, World Health Organization, Lyon, France
| | - Rita Alaggio
- Pathology Unit, Department of Laboratories, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy.
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24
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Aboubakr O, Metais A, Berthaud C, Gigant P, Mehdi L, Pucelle N, Lacombe J, Hasty L, Chrétien F, Lechapt E, Varlet P, Tauziède-Espariat A. L1CAM Is Not a Reliable Diagnostic Biomarker for Distinguishing Supratentorial Ependymomas, ZFTA Fusion-Positive From Other Central Nervous System Tumors. J Neuropathol Exp Neurol 2022; 81:82-85. [DOI: 10.1093/jnen/nlab105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Oumaima Aboubakr
- Department of Neuropathology, GHU Paris-Psychiatry and Neurosciences, Sainte-Anne Hospital, Paris, France
| | - Alice Metais
- Department of Neuropathology, GHU Paris-Psychiatry and Neurosciences, Sainte-Anne Hospital, Paris, France
| | - Charlotte Berthaud
- Department of Neuropathology, GHU Paris-Psychiatry and Neurosciences, Sainte-Anne Hospital, Paris, France
| | - Priscille Gigant
- Department of Neuropathology, GHU Paris-Psychiatry and Neurosciences, Sainte-Anne Hospital, Paris, France
| | - Leïla Mehdi
- Department of Neuropathology, GHU Paris-Psychiatry and Neurosciences, Sainte-Anne Hospital, Paris, France
| | - Noémie Pucelle
- Department of Neuropathology, GHU Paris-Psychiatry and Neurosciences, Sainte-Anne Hospital, Paris, France
| | - Joëlle Lacombe
- Department of Neuropathology, GHU Paris-Psychiatry and Neurosciences, Sainte-Anne Hospital, Paris, France
| | - Lauren Hasty
- Department of Neuropathology, GHU Paris-Psychiatry and Neurosciences, Sainte-Anne Hospital, Paris, France
| | - Fabrice Chrétien
- Department of Neuropathology, GHU Paris-Psychiatry and Neurosciences, Sainte-Anne Hospital, Paris, France
- Université de Paris, Paris, France
| | - Emmanuèle Lechapt
- Department of Neuropathology, GHU Paris-Psychiatry and Neurosciences, Sainte-Anne Hospital, Paris, France
- Université de Paris, Paris, France
| | - Pascale Varlet
- Department of Neuropathology, GHU Paris-Psychiatry and Neurosciences, Sainte-Anne Hospital, Paris, France
- Université de Paris, Paris, France
- Institute of Psychiatry and Neurosciences de Paris (IPNP), UMR S1266, INSERM, IMA-BRAIN, Paris, France
| | - Arnault Tauziède-Espariat
- Department of Neuropathology, GHU Paris-Psychiatry and Neurosciences, Sainte-Anne Hospital, Paris, France
- Université de Paris, Paris, France
- Institute of Psychiatry and Neurosciences de Paris (IPNP), UMR S1266, INSERM, IMA-BRAIN, Paris, France
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25
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Jenseit A, Camgöz A, Pfister SM, Kool M. EZHIP: a new piece of the puzzle towards understanding pediatric posterior fossa ependymoma. Acta Neuropathol 2022; 143:1-13. [PMID: 34762160 PMCID: PMC8732814 DOI: 10.1007/s00401-021-02382-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 10/29/2021] [Accepted: 10/30/2021] [Indexed: 12/14/2022]
Abstract
Ependymomas (EPN) are tumors of the central nervous system (CNS) that can arise in the supratentorial brain (ST-EPN), hindbrain or posterior fossa (PF-EPN) or anywhere in the spinal cord (SP-EPN), both in children and adults. Molecular profiling studies have identified distinct groups and subtypes in each of these anatomical compartments. In this review, we give an overview on recent findings and new insights what is driving PFA ependymomas, which is the most common group. PFA ependymomas are characterized by a young median age at diagnosis, an overall balanced genome and a bad clinical outcome (56% 10-year overall survival). Sequencing studies revealed no fusion genes or other highly recurrently mutated genes, suggesting that the disease is epigenetically driven. Indeed, recent findings have shown that the characteristic global loss of the repressive histone 3 lysine 27 trimethylation (H3K27me3) mark in PFA ependymoma is caused by aberrant expression of the enhancer of zeste homolog inhibitory protein (EZHIP) or in rare cases by H3K27M mutations, which both inhibit EZH2 thereby preventing the polycomb repressive complex 2 (PRC2) from spreading H3K27me3. We present the current status of the ongoing work on EZHIP and its essential role in the epigenetic disturbance of PFA biology. Comparisons to the oncohistone H3K27M and its role in diffuse midline glioma (DMG) are drawn, highlighting similarities but also differences between the tumor entities and underlying mechanisms. A strong focus is to point out missing information and to present directions of further research that may result in new and improved therapies for PFA ependymoma patients.
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Affiliation(s)
- Anne Jenseit
- Hopp Children's Cancer Center (KITZ), Im Neuenheimer Feld 280, 69120, 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
| | - Aylin Camgöz
- Hopp Children's Cancer Center (KITZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
- National Center for Tumor Diseases (NCT), Dresden, Germany
| | - Stefan M Pfister
- Hopp Children's Cancer Center (KITZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
- Department of Hematology and Oncology, University Hospital Heidelberg, Heidelberg, Germany
| | - Marcel Kool
- Hopp Children's Cancer Center (KITZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany.
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany.
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands.
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Larrew T, Saway BF, Lowe SR, Olar A. Molecular Classification and Therapeutic Targets in Ependymoma. Cancers (Basel) 2021; 13:cancers13246218. [PMID: 34944845 PMCID: PMC8699461 DOI: 10.3390/cancers13246218] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 12/05/2021] [Accepted: 12/08/2021] [Indexed: 12/12/2022] Open
Abstract
Ependymoma is a biologically diverse tumor wherein molecular classification has superseded traditional histological grading based on its superior ability to characterize behavior, prognosis, and possible targeted therapies. The current, updated molecular classification of ependymoma consists of ten distinct subgroups spread evenly among the spinal, infratentorial, and supratentorial compartments, each with its own distinct clinical and molecular characteristics. In this review, the history, histopathology, standard of care, prognosis, oncogenic drivers, and hypothesized molecular targets for all subgroups of ependymoma are explored. This review emphasizes that despite the varied behavior of the ependymoma subgroups, it remains clear that research must be performed to further elucidate molecular targets for these tumors. Although not all ependymoma subgroups are oncologically aggressive, development of targeted therapies is essential, particularly for cases where surgical resection is not an option without causing significant morbidity. The development of molecular therapies must rely on building upon our current understanding of ependymoma oncogenesis, as well as cultivating transfer of knowledge based on malignancies with similar genomic alterations.
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Affiliation(s)
- Thomas Larrew
- Department of Neurosurgery, Medical University of South Carolina, Charleston, SC 29425, USA; (T.L.); (B.F.S.)
| | - Brian Fabian Saway
- Department of Neurosurgery, Medical University of South Carolina, Charleston, SC 29425, USA; (T.L.); (B.F.S.)
| | | | - Adriana Olar
- NOMIX Laboratories, Denver, CO 80218, USA
- Correspondence: or
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Cell-of-Origin and Genetic, Epigenetic, and Microenvironmental Factors Contribute to the Intra-Tumoral Heterogeneity of Pediatric Intracranial Ependymoma. Cancers (Basel) 2021; 13:cancers13236100. [PMID: 34885210 PMCID: PMC8657076 DOI: 10.3390/cancers13236100] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 11/24/2021] [Accepted: 12/01/2021] [Indexed: 02/07/2023] Open
Abstract
Intra-tumoral heterogeneity (ITH) is a complex multifaceted phenomenon that posits major challenges for the clinical management of cancer patients. Genetic, epigenetic, and microenvironmental factors are concurrent drivers of diversity among the distinct populations of cancer cells. ITH may also be installed by cancer stem cells (CSCs), that foster unidirectional hierarchy of cellular phenotypes or, alternatively, shift dynamically between distinct cellular states. Ependymoma (EPN), a molecularly heterogeneous group of tumors, shows a specific spatiotemporal distribution that suggests a link between ependymomagenesis and alterations of the biological processes involved in embryonic brain development. In children, EPN most often arises intra-cranially and is associated with an adverse outcome. Emerging evidence shows that EPN displays large intra-patient heterogeneity. In this review, after touching on EPN inter-tumoral heterogeneity, we focus on the sources of ITH in pediatric intra-cranial EPN in the framework of the CSC paradigm. We also examine how single-cell technology has shed new light on the complexity and developmental origins of EPN and the potential impact that this understanding may have on the therapeutic strategies against this deadly pediatric malignancy.
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28
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Sievers P, Henneken SC, Blume C, Sill M, Schrimpf D, Stichel D, Okonechnikov K, Reuss DE, Benzel J, Maaß KK, Kool M, Sturm D, Zheng T, Ghasemi DR, Kohlhof-Meinecke P, Cruz O, Suñol M, Lavarino C, Ruf V, Boldt HB, Pagès M, Pouget C, Schweizer L, Kranendonk MEG, Akhtar N, Bunkowski S, Stadelmann C, Schüller U, Mueller WC, Dohmen H, Acker T, Harter PN, Mawrin C, Beschorner R, Brandner S, Snuderl M, Abdullaev Z, Aldape K, Gilbert MR, Armstrong TS, Ellison DW, Capper D, Ichimura K, Reifenberger G, Grundy RG, Jabado N, Krskova L, Zapotocky M, Vicha A, Varlet P, Wesseling P, Rutkowski S, Korshunov A, Wick W, Pfister SM, Jones DTW, von Deimling A, Pajtler KW, Sahm F. Recurrent fusions in PLAGL1 define a distinct subset of pediatric-type supratentorial neuroepithelial tumors. Acta Neuropathol 2021; 142:827-839. [PMID: 34355256 PMCID: PMC8500895 DOI: 10.1007/s00401-021-02356-6] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 07/27/2021] [Accepted: 07/29/2021] [Indexed: 02/07/2023]
Abstract
Ependymomas encompass a heterogeneous group of central nervous system (CNS) neoplasms that occur along the entire neuroaxis. In recent years, extensive (epi-)genomic profiling efforts have identified several molecular groups of ependymoma that are characterized by distinct molecular alterations and/or patterns. Based on unsupervised visualization of a large cohort of genome-wide DNA methylation data, we identified a highly distinct group of pediatric-type tumors (n = 40) forming a cluster separate from all established CNS tumor types, of which a high proportion were histopathologically diagnosed as ependymoma. RNA sequencing revealed recurrent fusions involving the pleomorphic adenoma gene-like 1 (PLAGL1) gene in 19 of 20 of the samples analyzed, with the most common fusion being EWSR1:PLAGL1 (n = 13). Five tumors showed a PLAGL1:FOXO1 fusion and one a PLAGL1:EP300 fusion. High transcript levels of PLAGL1 were noted in these tumors, with concurrent overexpression of the imprinted genes H19 and IGF2, which are regulated by PLAGL1. Histopathological review of cases with sufficient material (n = 16) demonstrated a broad morphological spectrum of tumors with predominant ependymoma-like features. Immunohistochemically, tumors were GFAP positive and OLIG2- and SOX10 negative. In 3/16 of the cases, a dot-like positivity for EMA was detected. All tumors in our series were located in the supratentorial compartment. Median age of the patients at the time of diagnosis was 6.2 years. Median progression-free survival was 35 months (for 11 patients with data available). In summary, our findings suggest the existence of a novel group of supratentorial neuroepithelial tumors that are characterized by recurrent PLAGL1 fusions and enriched for pediatric patients.
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Affiliation(s)
- Philipp Sievers
- Department of Neuropathology, Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Sophie C Henneken
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Christina Blume
- Department of Neuropathology, Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
- Bioinformatics and Omics Data Analytics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Martin Sill
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Daniel Schrimpf
- Department of Neuropathology, Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Damian Stichel
- Department of Neuropathology, Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Konstantin Okonechnikov
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - David E Reuss
- Department of Neuropathology, Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Julia Benzel
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Kendra K Maaß
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Pediatric Oncology, Hematology, Immunology and Pulmonology, University Hospital Heidelberg, Heidelberg, Germany
| | - Marcel Kool
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - Dominik Sturm
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Department of Pediatric Oncology, Hematology, Immunology and Pulmonology, University Hospital Heidelberg, Heidelberg, Germany
- Pediatric Glioma Research Group, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Tuyu Zheng
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
- Faculty of Biosciences, Heidelberg University, 69117, Heidelberg, Germany
| | - David R Ghasemi
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | | | - Ofelia Cruz
- Department of Pediatric Oncology, Hospital Sant Joan de Déu, Esplugues de Llobregat, Barcelona, Spain
| | - Mariona Suñol
- Department of Pathology, Hospital Sant Joan de Déu, Esplugues de Llobregat, Barcelona, Spain
| | - Cinzia Lavarino
- Laboratory of Molecular Oncology, Hospital Sant Joan de Déu, Esplugues de Llobregat, Barcelona, Spain
| | - Viktoria Ruf
- Institute of Neuropathology, Ludwig-Maximilian University, Munich, Germany
| | - Henning B Boldt
- Department of Pathology, Odense University Hospital, Odense, Denmark
- Department of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Mélanie Pagès
- Department of Neuropathology, GHU Paris Psychiatry and Neurosciences, Sainte-Anne Hospital, Paris, France
- Laboratory of Translational Research in Pediatric Oncology, SIREDO, INSERM U830, Institut Curie, Paris Sciences Lettres University, Paris, France
| | | | - Leonille Schweizer
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Neuropathology, Berlin, Germany
- German Cancer Consortium (DKTK), Partner Site Berlin, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Mariëtte E G Kranendonk
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
- Department of Pathology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Noreen Akhtar
- Manchester Royal Infirmary, Manchester University NHS Foundation Trust, Manchester, UK
- Shaukat Khanum Memorial Cancer Hospital and Research Centre, Lahore, Pakistan
| | - Stephanie Bunkowski
- Institute for Neuropathology, University Medical Centre Göttingen, Göttingen, Germany
| | - Christine Stadelmann
- Institute for Neuropathology, University Medical Centre Göttingen, Göttingen, Germany
| | - Ulrich Schüller
- Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Research Institute Children's Cancer Center Hamburg, Hamburg, Germany
| | - Wolf C Mueller
- Paul-Flechsig Institute of Neuropathology, University Hospital and Faculty of Medicine, Leipzig, Germany
| | - Hildegard Dohmen
- Institute of Neuropathology, University of Giessen, Giessen, Germany
| | - Till Acker
- Institute of Neuropathology, University of Giessen, Giessen, Germany
| | - Patrick N Harter
- Frankfurt Cancer Institute (FCI), University Hospital, Goethe University Frankfurt am Main, Frankfurt am Main, Germany
- Institute of Neurology (Edinger-Institute), University Hospital, Goethe University Frankfurt am Main, Frankfurt am Main, Germany
- German Cancer Consortium (DKTK), Partner site Frankfurt/Mainz, Frankfurt am Main, Germany
- German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Christian Mawrin
- Department of Neuropathology, Otto-Von-Guericke University, Magdeburg, Germany
| | - Rudi Beschorner
- Department of Neuropathology, University of Tübingen, Tübingen, Germany
| | - Sebastian Brandner
- Division of Neuropathology, National Hospital for Neurology and Neurosurgery, University College London Hospitals NHS Foundation Trust, Queen Square, London, UK
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, Queen Square, London, UK
| | - Matija Snuderl
- Department of Pathology, NYU Langone Medical Center, New York, NY, USA
| | - Zied Abdullaev
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Kenneth Aldape
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Mark R Gilbert
- Neuro-Oncology Branch, National Cancer Institute, Bethesda, MD, USA
| | | | - David W Ellison
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - David Capper
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Neuropathology, Berlin, Germany
- German Cancer Consortium (DKTK), Partner Site Berlin, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Koichi Ichimura
- Division of Brain Tumor Translational Research, National Cancer Center Research Institute, Chuo-ku, Tokyo, Japan
| | - Guido Reifenberger
- Institute of Neuropathology, Heinrich Heine University, Düsseldorf, Germany
- German Cancer Consortium (DKTK), Partner Site Essen/Düsseldorf, Essen/Düsseldorf, Germany
| | - Richard G Grundy
- Children's Brain Tumour Research Centre, University of Nottingham, Nottingham, UK
| | - Nada Jabado
- Department of Human Genetics, McGill University, Montreal, QC, H3A 1B1, Canada
- Department of Pediatrics, McGill University, Montreal, QC, H4A 3J1, Canada
- The Research Institute of the McGill University Health Center, Montreal, QC, H4A 3J1, Canada
| | - Lenka Krskova
- Prague Brain Tumor Research Group, Second Faculty of Medicine, Charles University and University Hospital Motol, Prague, Czech Republic
- Department of Pathology and Molecular Medicine, Second Faculty of Medicine, Charles University and University Hospital Motol, Prague, Czech Republic
| | - Michal Zapotocky
- Prague Brain Tumor Research Group, Second Faculty of Medicine, Charles University and University Hospital Motol, Prague, Czech Republic
- Department of Pediatric Haematology and Oncology, Second Faculty of Medicine, Charles University and University Hospital Motol, Prague, Czech Republic
| | - Ales Vicha
- Prague Brain Tumor Research Group, Second Faculty of Medicine, Charles University and University Hospital Motol, Prague, Czech Republic
- Department of Pediatric Haematology and Oncology, Second Faculty of Medicine, Charles University and University Hospital Motol, Prague, Czech Republic
| | - Pascale Varlet
- Department of Neuropathology, GHU Paris Psychiatry and Neurosciences, Sainte-Anne Hospital, Paris, France
| | - Pieter Wesseling
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
- Department of Pathology, Amsterdam University Medical Centers, Location VUmc and Brain Tumor Center Amsterdam, Amsterdam, The Netherlands
| | - Stefan Rutkowski
- Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Andrey Korshunov
- Department of Neuropathology, Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
| | - Wolfgang Wick
- Clinical Cooperation Unit Neurooncology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Neurology and Neurooncology Program, National Center for Tumor Diseases, Heidelberg University Hospital, Heidelberg, Germany
| | - Stefan M Pfister
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Pediatric Oncology, Hematology, Immunology and Pulmonology, University Hospital Heidelberg, Heidelberg, Germany
| | - David T W Jones
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Pediatric Glioma Research Group, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Andreas von Deimling
- Department of Neuropathology, Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Kristian W Pajtler
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany.
- Division of Pediatric Neurooncology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany.
- Department of Pediatric Oncology, Hematology, Immunology and Pulmonology, University Hospital Heidelberg, Heidelberg, Germany.
| | - Felix Sahm
- Department of Neuropathology, Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany.
- Clinical Cooperation Unit Neuropathology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany.
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany.
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Zaytseva M, Papusha L, Novichkova G, Druy A. Molecular Stratification of Childhood Ependymomas as a Basis for Personalized Diagnostics and Treatment. Cancers (Basel) 2021; 13:cancers13194954. [PMID: 34638438 PMCID: PMC8507860 DOI: 10.3390/cancers13194954] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Revised: 09/27/2021] [Accepted: 09/29/2021] [Indexed: 01/07/2023] Open
Abstract
Ependymomas are among the most enigmatic tumors of the central nervous system, posing enormous challenges for pathologists and clinicians. Despite the efforts made, the treatment options are still limited to surgical resection and radiation therapy, while none of conventional chemotherapies is beneficial. While being histologically similar, ependymomas show considerable clinical and molecular diversity. Their histopathological evaluation alone is not sufficient for reliable diagnostics, prognosis, and choice of treatment strategy. The importance of integrated diagnosis for ependymomas is underscored in the recommendations of Consortium to Inform Molecular and Practical Approaches to CNS Tumor Taxonomy. These updated recommendations were adopted and implemented by WHO experts. This minireview highlights recent advances in comprehensive molecular-genetic characterization of ependymomas. Strong emphasis is made on the use of molecular approaches for verification and specification of histological diagnoses, as well as identification of prognostic markers for ependymomas in children.
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Affiliation(s)
- Margarita Zaytseva
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, 117997 Moscow, Russia; (L.P.); (G.N.); (A.D.)
- Correspondence:
| | - Ludmila Papusha
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, 117997 Moscow, Russia; (L.P.); (G.N.); (A.D.)
| | - Galina Novichkova
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, 117997 Moscow, Russia; (L.P.); (G.N.); (A.D.)
| | - Alexander Druy
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, 117997 Moscow, Russia; (L.P.); (G.N.); (A.D.)
- Research Institute of Medical Cell Technologies, 620026 Yekaterinburg, Russia
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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: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [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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31
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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: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [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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32
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Highlights from the Literature. Neuro Oncol 2021. [DOI: 10.1093/neuonc/noab171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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33
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Tauziède-Espariat A, Siegfried A, Nicaise Y, Kergrohen T, Sievers P, Vasiljevic A, Roux A, Dezamis E, Benevello C, Machet MC, Michalak S, Puiseux C, Llamas-Gutierrez F, Leblond P, Bourdeaut F, Grill J, Dufour C, Guerrini-Rousseau L, Abbou S, Dangouloff-Ros V, Boddaert N, Saffroy R, Hasty L, Wahler E, Pagès M, Andreiuolo F, Lechapt E, Chrétien F, Blauwblomme T, Beccaria K, Pallud J, Puget S, Uro-Coste E, Varlet P. Supratentorial non-RELA, ZFTA-fused ependymomas: a comprehensive phenotype genotype correlation highlighting the number of zinc fingers in ZFTA-NCOA1/2 fusions. Acta Neuropathol Commun 2021; 9:135. [PMID: 34389065 PMCID: PMC8362233 DOI: 10.1186/s40478-021-01238-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Accepted: 08/05/2021] [Indexed: 12/11/2022] Open
Abstract
The cIMPACT-NOW Update 7 has replaced the WHO nosology of “ependymoma, RELA fusion positive” by “Supratentorial-ependymoma, C11orf95-fusion positive”. This modification reinforces the idea that supratentorial-ependymomas exhibiting fusion that implicates the C11orf95 (now called ZFTA) gene with or without the RELA gene, represent the same histomolecular entity. A hot off the press molecular study has identified distinct clusters of the DNA methylation class of ZFTA fusion-positive tumors. Interestingly, clusters 2 and 4 comprised tumors of different morphologies, with various ZFTA fusions without involvement of RELA. In this paper, we present a detailed series of thirteen cases of non-RELA ZFTA-fused supratentorial tumors with extensive clinical, radiological, histopathological, immunohistochemical, genetic and epigenetic (DNA methylation profiling) characterization. Contrary to the age of onset and MRI aspects similar to RELA fusion-positive EPN, we noted significant histopathological heterogeneity (pleomorphic xanthoastrocytoma-like, astroblastoma-like, ependymoma-like, and even sarcoma-like patterns) in this cohort. Immunophenotypically, these NFκB immunonegative tumors expressed GFAP variably, but EMA constantly and L1CAM frequently. Different gene partners were fused with ZFTA: NCOA1/2, MAML2 and for the first time MN1. These tumors had epigenetic homologies within the DNA methylation class of ependymomas-RELA and were classified as satellite clusters 2 and 4. Cluster 2 (n = 9) corresponded to tumors with classic ependymal histological features (n = 4) but also had astroblastic features (n = 5). Various types of ZFTA fusions were associated with cluster 2, but as in the original report, ZFTA:MAML2 fusion was frequent. Cluster 4 was enriched with sarcoma-like tumors. Moreover, we reported a novel anatomy of three ZFTA:NCOA1/2 fusions with only 1 ZFTA zinc finger domain in the putative fusion protein, whereas all previously reported non-RELA ZFTA fusions have 4 ZFTA zinc fingers. All three cases presented a sarcoma-like morphology. This genotype/phenotype association requires further studies for confirmation. Our series is the first to extensively characterize this new subset of supratentorial ZFTA-fused ependymomas and highlights the usefulness of ZFTA FISH analysis to confirm the existence of a rearrangement without RELA abnormality.
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Lötsch D, Kirchhofer D, Englinger B, Jiang L, Okonechnikov K, Senfter D, Laemmerer A, Gabler L, Pirker C, Donson AM, Bannauer P, Korbel P, Jaunecker CN, Hübner JM, Mayr L, Madlener S, Schmook MT, Ricken G, Maaß K, Grusch M, Holzmann K, Grasl-Kraupp B, Spiegl-Kreinecker S, Hsu J, Dorfer C, Rössler K, Azizi AA, Foreman NK, Peyrl A, Haberler C, Czech T, Slavc I, Filbin MG, Pajtler KW, Kool M, Berger W, Gojo J. Targeting fibroblast growth factor receptors to combat aggressive ependymoma. Acta Neuropathol 2021; 142:339-360. [PMID: 34046693 PMCID: PMC8270873 DOI: 10.1007/s00401-021-02327-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 04/10/2021] [Accepted: 05/10/2021] [Indexed: 12/16/2022]
Abstract
Ependymomas (EPN) are central nervous system tumors comprising both aggressive and more benign molecular subtypes. However, therapy of the high-risk subtypes posterior fossa group A (PF-A) and supratentorial RELA-fusion positive (ST-RELA) is limited to gross total resection and radiotherapy, as effective systemic treatment concepts are still lacking. We have recently described fibroblast growth factor receptors 1 and 3 (FGFR1/FGFR3) as oncogenic drivers of EPN. However, the underlying molecular mechanisms and their potential as therapeutic targets have not yet been investigated in detail. Making use of transcriptomic data across 467 EPN tissues, we found that FGFR1 and FGFR3 were both widely expressed across all molecular groups. FGFR3 mRNA levels were enriched in ST-RELA showing the highest expression among EPN as well as other brain tumors. We further identified high expression levels of fibroblast growth factor 1 and 2 (FGF1, FGF2) across all EPN subtypes while FGF9 was elevated in ST-EPN. Interrogation of our EPN single-cell RNA-sequencing data revealed that FGFR3 was further enriched in cycling and progenitor-like cell populations. Corroboratively, we found FGFR3 to be predominantly expressed in radial glia cells in both mouse embryonal and human brain datasets. Moreover, we detected alternative splicing of the FGFR1/3-IIIc variant, which is known to enhance ligand affinity and FGFR signaling. Dominant-negative interruption of FGFR1/3 activation in PF-A and ST-RELA cell models demonstrated inhibition of key oncogenic pathways leading to reduced cell growth and stem cell characteristics. To explore the feasibility of therapeutically targeting FGFR, we tested a panel of FGFR inhibitors in 12 patient-derived EPN cell models revealing sensitivity in the low-micromolar to nano-molar range. Finally, we gain the first clinical evidence for the activity of the FGFR inhibitor nintedanib in the treatment of a patient with recurrent ST-RELA. Together, these preclinical and clinical data suggest FGFR inhibition as a novel and feasible approach to combat aggressive EPN.
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MESH Headings
- Animals
- Central Nervous System Neoplasms/genetics
- Central Nervous System Neoplasms/pathology
- Ependymoma/genetics
- Ependymoma/pathology
- Humans
- Mice
- Neoplasm Recurrence, Local/genetics
- Neoplasm Recurrence, Local/metabolism
- Neoplasm Recurrence, Local/pathology
- Receptor, Fibroblast Growth Factor, Type 1/genetics
- Receptor, Fibroblast Growth Factor, Type 1/metabolism
- Receptor, Fibroblast Growth Factor, Type 3/metabolism
- Receptors, Fibroblast Growth Factor/genetics
- Receptors, Fibroblast Growth Factor/metabolism
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Affiliation(s)
- Daniela Lötsch
- Department of Neurosurgery, Medical University of Vienna, Vienna, Austria
- Department of Medicine I, Institute of Cancer Research and Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
- Department of Pediatrics and Adolescent Medicine and Comprehensive Center for Pediatrics, Medical University of Vienna, Vienna, Austria
| | - Dominik Kirchhofer
- Department of Medicine I, Institute of Cancer Research and Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
- Department of Pediatrics and Adolescent Medicine and Comprehensive Center for Pediatrics, Medical University of Vienna, Vienna, Austria
| | - Bernhard Englinger
- Department of Medicine I, Institute of Cancer Research and Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
- Department of Pediatric Oncology, Dana-Farber Boston Children's Cancer and Blood Disorders Center, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, USA
| | - Li Jiang
- Department of Pediatric Oncology, Dana-Farber Boston Children's Cancer and Blood Disorders Center, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, USA
| | - Konstantin Okonechnikov
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Daniel Senfter
- Department of Pediatrics and Adolescent Medicine and Comprehensive Center for Pediatrics, Medical University of Vienna, Vienna, Austria
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Anna Laemmerer
- Department of Medicine I, Institute of Cancer Research and Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
- Department of Pediatrics and Adolescent Medicine and Comprehensive Center for Pediatrics, Medical University of Vienna, Vienna, Austria
| | - Lisa Gabler
- Department of Medicine I, Institute of Cancer Research and Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
| | - Christine Pirker
- Department of Medicine I, Institute of Cancer Research and Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
| | - Andrew M Donson
- Morgan Adams Foundation Pediatric Brain Tumor Research Program, Children's Hospital Colorado, Aurora, CO, USA
- Department of Pediatrics, University of Colorado Denver, Aurora, CO, USA
| | - Peter Bannauer
- Department of Medicine I, Institute of Cancer Research and Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
- Department of Pediatrics and Adolescent Medicine and Comprehensive Center for Pediatrics, Medical University of Vienna, Vienna, Austria
| | - Pia Korbel
- Department of Medicine I, Institute of Cancer Research and Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
- Department of Pediatrics and Adolescent Medicine and Comprehensive Center for Pediatrics, Medical University of Vienna, Vienna, Austria
| | - Carola N Jaunecker
- Department of Medicine I, Institute of Cancer Research and Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
- Department of Pediatrics and Adolescent Medicine and Comprehensive Center for Pediatrics, Medical University of Vienna, Vienna, Austria
| | - Jens-Martin Hübner
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Lisa Mayr
- Department of Pediatrics and Adolescent Medicine and Comprehensive Center for Pediatrics, Medical University of Vienna, Vienna, Austria
| | - Sibylle Madlener
- Department of Pediatrics and Adolescent Medicine and Comprehensive Center for Pediatrics, Medical University of Vienna, Vienna, Austria
| | - Maria T Schmook
- Department of Biomedical Imaging and Image-Guided Therapy, Medical University of Vienna, Vienna, Austria
| | - Gerda Ricken
- Division of Neuropathology and Neurochemistry, Department of Neurology, Medical University of Vienna, Vienna, Austria
| | - Kendra Maaß
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Michael Grusch
- Department of Medicine I, Institute of Cancer Research and Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
| | - Klaus Holzmann
- Department of Medicine I, Institute of Cancer Research and Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
| | - Bettina Grasl-Kraupp
- Department of Medicine I, Institute of Cancer Research and Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
| | - Sabine Spiegl-Kreinecker
- Department of Neurosurgery, Kepler University Hospital GmbH, Johannes Kepler University, Linz, Austria
| | - Jennifer Hsu
- Department of Medicine I, Institute of Cancer Research and Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
| | - Christian Dorfer
- Department of Neurosurgery, Medical University of Vienna, Vienna, Austria
| | - Karl Rössler
- Department of Neurosurgery, Medical University of Vienna, Vienna, Austria
| | - Amedeo A Azizi
- Department of Pediatrics and Adolescent Medicine and Comprehensive Center for Pediatrics, Medical University of Vienna, Vienna, Austria
| | - Nicholas K Foreman
- Morgan Adams Foundation Pediatric Brain Tumor Research Program, Children's Hospital Colorado, Aurora, CO, USA
- Department of Pediatrics, University of Colorado Denver, Aurora, CO, USA
| | - Andreas Peyrl
- Department of Pediatrics and Adolescent Medicine and Comprehensive Center for Pediatrics, Medical University of Vienna, Vienna, Austria
| | - Christine Haberler
- Division of Neuropathology and Neurochemistry, Department of Neurology, Medical University of Vienna, Vienna, Austria
| | - Thomas Czech
- Department of Neurosurgery, Medical University of Vienna, Vienna, Austria
| | - Irene Slavc
- Department of Pediatrics and Adolescent Medicine and Comprehensive Center for Pediatrics, Medical University of Vienna, Vienna, Austria
| | - Mariella G Filbin
- Department of Pediatric Oncology, Dana-Farber Boston Children's Cancer and Blood Disorders Center, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, USA
| | - Kristian W Pajtler
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Heidelberg, Germany
- Department of Pediatric Haematology and Oncology, Heidelberg University Hospital, Heidelberg, Germany
| | - Marcel Kool
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Heidelberg, Germany
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - Walter Berger
- Department of Medicine I, Institute of Cancer Research and Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
| | - Johannes Gojo
- Department of Medicine I, Institute of Cancer Research and Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria.
- Department of Pediatrics and Adolescent Medicine and Comprehensive Center for Pediatrics, Medical University of Vienna, Vienna, Austria.
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany.
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Heidelberg, Germany.
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